A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization.

PubMed

Li, Zhen; Bian, Xin; Yang, Xiu; Karniadakis, George Em

2016-07-28

We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.

Mimicking coarse-grained simulations without coarse-graining: enhanced sampling by damping short-range interactions.

PubMed

Wei, Dongshan; Wang, Feng

2010-08-28

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Mimicking coarse-grained simulations without coarse-graining: Enhanced sampling by damping short-range interactions

NASA Astrophysics Data System (ADS)

Wei, Dongshan; Wang, Feng

2010-08-01

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhen; Bian, Xin; Yang, Xiu

We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics basedmore » on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models are not interchangeable. If the free parameters are properly selected, the reverse CG procedure also yields an effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhen; Bian, Xin; Karniadakis, George Em, E-mail: george-karniadakis@brown.edu

We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamicsmore » based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.« less

Coarse-grained stochastic processes and kinetic Monte Carlo simulators for the diffusion of interacting particles

NASA Astrophysics Data System (ADS)

Katsoulakis, Markos A.; Vlachos, Dionisios G.

2003-11-01

We derive a hierarchy of successively coarse-grained stochastic processes and associated coarse-grained Monte Carlo (CGMC) algorithms directly from the microscopic processes as approximations in larger length scales for the case of diffusion of interacting particles on a lattice. This hierarchy of models spans length scales between microscopic and mesoscopic, satisfies a detailed balance, and gives self-consistent fluctuation mechanisms whose noise is asymptotically identical to the microscopic MC. Rigorous, detailed asymptotics justify and clarify these connections. Gradient continuous time microscopic MC and CGMC simulations are compared under far from equilibrium conditions to illustrate the validity of our theory and delineate the errors obtained by rigorous asymptotics. Information theory estimates are employed for the first time to provide rigorous error estimates between the solutions of microscopic MC and CGMC, describing the loss of information during the coarse-graining process. Simulations under periodic boundary conditions are used to verify the information theory error estimates. It is shown that coarse-graining in space leads also to coarse-graining in time by q2, where q is the level of coarse-graining, and overcomes in part the hydrodynamic slowdown. Operation counting and CGMC simulations demonstrate significant CPU savings in continuous time MC simulations that vary from q3 for short potentials to q4 for long potentials. Finally, connections of the new coarse-grained stochastic processes to stochastic mesoscopic and Cahn-Hilliard-Cook models are made.

Automated optimization of water-water interaction parameters for a coarse-grained model.

PubMed

Fogarty, Joseph C; Chiu, See-Wing; Kirby, Peter; Jakobsson, Eric; Pandit, Sagar A

2014-02-13

We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment.

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

NASA Astrophysics Data System (ADS)

Kawaguchi, Kazutomo; Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

PubMed

McCarty, J; Clark, A J; Copperman, J; Guenza, M G

2014-05-28

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora

2016-02-05

Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly modeled. In this paper, we probe the degree of coarse graining required to simultaneously retain significant atomistic details and access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using linear polyethylene as a model system, we probe how the coarse-graining scale affects the measured dynamics. Iterative Boltzmann inversion ismore » used to derive coarse-grained potentials with 2–6 methylene groups per coarse-grained bead from a fully atomistic melt simulation. We show that atomistic detail is critical to capturing large-scale dynamics. Finally, using these models we simulate polyethylene melts for times over 500 μs to study the viscoelastic properties of well-entangled polymer melts.« less

On the applicability of density dependent effective interactions in cluster-forming systems

NASA Astrophysics Data System (ADS)

Montes-Saralegui, Marta; Kahl, Gerhard; Nikoubashman, Arash

2017-02-01

We systematically studied the validity and transferability of the force-matching algorithm for computing effective pair potentials in a system of dendritic polymers, i.e., a particular class of ultrasoft colloids. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping particles to minimize the contact area with the surrounding implicit solvent. Simulations were performed for both the monomeric and coarse-grained models in the liquid phase at densities ranging from infinite dilution up to values close to the freezing point. The effective pair potentials for the coarse-grained simulations were computed from the monomeric simulations both in the zero-density limit (Φeff0) and at each investigated finite density (Φeff). Conducting the coarse-grained simulations with Φeff0 at higher densities is not appropriate as they failed at reproducing the structural properties of the monomeric simulations. In contrast, we found excellent agreement between the spatial dendrimer distributions obtained from the coarse-grained simulations with Φeff and the microscopically detailed simulations at low densities, where the macromolecules were distributed homogeneously in the system. However, the reliability of the coarse-grained simulations deteriorated significantly as the density was increased further and the cluster occupation became more polydisperse. Under these conditions, the effective pair potential of the coarse-grained model can no longer be computed by averaging over the whole system, but the local density needs to be taken into account instead.

Predictive coarse-graining

NASA Astrophysics Data System (ADS)

Schöberl, Markus; Zabaras, Nicholas; Koutsourelakis, Phaedon-Stelios

2017-03-01

We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method [1] and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extended to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo - Expectation-Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.

Predictive coarse-graining

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schöberl, Markus, E-mail: m.schoeberl@tum.de; Zabaras, Nicholas; Department of Aerospace and Mechanical Engineering, University of Notre Dame, 365 Fitzpatrick Hall, Notre Dame, IN 46556

We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extendedmore » to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo – Expectation–Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.« less

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

NASA Astrophysics Data System (ADS)

Sanyal, Tanmoy; Shell, M. Scott

2016-07-01

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

Relative entropy as a universal metric for multiscale errors

NASA Astrophysics Data System (ADS)

Chaimovich, Aviel; Shell, M. Scott

2010-06-01

We show that the relative entropy, Srel , suggests a fundamental indicator of the success of multiscale studies, in which coarse-grained (CG) models are linked to first-principles (FP) ones. We demonstrate that Srel inherently measures fluctuations in the differences between CG and FP potential energy landscapes, and develop a theory that tightly and generally links it to errors associated with coarse graining. We consider two simple case studies substantiating these results, and suggest that Srel has important ramifications for evaluating and designing coarse-grained models.

Relative entropy as a universal metric for multiscale errors.

PubMed

Chaimovich, Aviel; Shell, M Scott

2010-06-01

We show that the relative entropy, Srel, suggests a fundamental indicator of the success of multiscale studies, in which coarse-grained (CG) models are linked to first-principles (FP) ones. We demonstrate that Srel inherently measures fluctuations in the differences between CG and FP potential energy landscapes, and develop a theory that tightly and generally links it to errors associated with coarse graining. We consider two simple case studies substantiating these results, and suggest that Srel has important ramifications for evaluating and designing coarse-grained models.

Structure-based coarse-graining for inhomogeneous liquid polymer systems.

PubMed

Fukuda, Motoo; Zhang, Hedong; Ishiguro, Takahiro; Fukuzawa, Kenji; Itoh, Shintaro

2013-08-07

The iterative Boltzmann inversion (IBI) method is used to derive interaction potentials for coarse-grained (CG) systems by matching structural properties of a reference atomistic system. However, because it depends on such thermodynamic conditions as density and pressure of the reference system, the derived CG nonbonded potential is probably not applicable to inhomogeneous systems containing different density regimes. In this paper, we propose a structure-based coarse-graining scheme to devise CG nonbonded potentials that are applicable to different density bulk systems and inhomogeneous systems with interfaces. Similar to the IBI, the radial distribution function (RDF) of a reference atomistic bulk system is used for iteratively refining the CG nonbonded potential. In contrast to the IBI, however, our scheme employs an appropriately estimated initial guess and a small amount of refinement to suppress transfer of the many-body interaction effects included in the reference RDF into the CG nonbonded potential. To demonstrate the application of our approach to inhomogeneous systems, we perform coarse-graining for a liquid perfluoropolyether (PFPE) film coated on a carbon surface. The constructed CG PFPE model favorably reproduces structural and density distribution functions, not only for bulk systems, but also at the liquid-vacuum and liquid-solid interfaces, demonstrating that our CG scheme offers an easy and practical way to accurately determine nonbonded potentials for inhomogeneous systems.

Coarse graining atomistic simulations of plastically deforming amorphous solids

NASA Astrophysics Data System (ADS)

Hinkle, Adam R.; Rycroft, Chris H.; Shields, Michael D.; Falk, Michael L.

2017-05-01

The primary mode of failure in disordered solids results from the formation and persistence of highly localized regions of large plastic strains known as shear bands. Continuum-level field theories capable of predicting this mechanical response rely upon an accurate representation of the initial and evolving states of the amorphous structure. We perform molecular dynamics simulations of a metallic glass and propose a methodology for coarse graining discrete, atomistic quantities, such as the potential energies of the elemental constituents. A strain criterion is established and used to distinguish the coarse-grained degrees-of-freedom inside the emerging shear band from those of the surrounding material. A signal-to-noise ratio provides a means of evaluating the strength of the signal of the shear band as a function of the coarse graining. Finally, we investigate the effect of different coarse graining length scales by comparing a two-dimensional, numerical implementation of the effective-temperature description in the shear transformation zone (STZ) theory with direct molecular dynamics simulations. These comparisons indicate the coarse graining length scale has a lower bound, above which there is a high level of agreement between the atomistics and the STZ theory, and below which the concept of effective temperature breaks down.

Physics-based statistical learning approach to mesoscopic model selection.

PubMed

Taverniers, Søren; Haut, Terry S; Barros, Kipton; Alexander, Francis J; Lookman, Turab

2015-11-01

In materials science and many other research areas, models are frequently inferred without considering their generalization to unseen data. We apply statistical learning using cross-validation to obtain an optimally predictive coarse-grained description of a two-dimensional kinetic nearest-neighbor Ising model with Glauber dynamics (GD) based on the stochastic Ginzburg-Landau equation (sGLE). The latter is learned from GD "training" data using a log-likelihood analysis, and its predictive ability for various complexities of the model is tested on GD "test" data independent of the data used to train the model on. Using two different error metrics, we perform a detailed analysis of the error between magnetization time trajectories simulated using the learned sGLE coarse-grained description and those obtained using the GD model. We show that both for equilibrium and out-of-equilibrium GD training trajectories, the standard phenomenological description using a quartic free energy does not always yield the most predictive coarse-grained model. Moreover, increasing the amount of training data can shift the optimal model complexity to higher values. Our results are promising in that they pave the way for the use of statistical learning as a general tool for materials modeling and discovery.

An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations

NASA Astrophysics Data System (ADS)

Poursina, Mohammad; Anderson, Kurt S.

2014-08-01

This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method.

A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sinitskiy, Anton V.; Voth, Gregory A., E-mail: gavoth@uchicago.edu

2015-09-07

Computational modeling of the condensed phase based on classical statistical mechanics has been rapidly developing over the last few decades and has yielded important information on various systems containing up to millions of atoms. However, if a system of interest contains important quantum effects, well-developed classical techniques cannot be used. One way of treating finite temperature quantum systems at equilibrium has been based on Feynman’s imaginary time path integral approach and the ensuing quantum-classical isomorphism. This isomorphism is exact only in the limit of infinitely many classical quasiparticles representing each physical quantum particle. In this work, we present a reductionistmore » perspective on this problem based on the emerging methodology of coarse-graining. This perspective allows for the representations of one quantum particle with only two classical-like quasiparticles and their conjugate momenta. One of these coupled quasiparticles is the centroid particle of the quantum path integral quasiparticle distribution. Only this quasiparticle feels the potential energy function. The other quasiparticle directly provides the observable averages of quantum mechanical operators. The theory offers a simplified perspective on quantum statistical mechanics, revealing its most reductionist connection to classical statistical physics. By doing so, it can facilitate a simpler representation of certain quantum effects in complex molecular environments.« less

A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals.

PubMed

Sinitskiy, Anton V; Voth, Gregory A

2015-09-07

Computational modeling of the condensed phase based on classical statistical mechanics has been rapidly developing over the last few decades and has yielded important information on various systems containing up to millions of atoms. However, if a system of interest contains important quantum effects, well-developed classical techniques cannot be used. One way of treating finite temperature quantum systems at equilibrium has been based on Feynman's imaginary time path integral approach and the ensuing quantum-classical isomorphism. This isomorphism is exact only in the limit of infinitely many classical quasiparticles representing each physical quantum particle. In this work, we present a reductionist perspective on this problem based on the emerging methodology of coarse-graining. This perspective allows for the representations of one quantum particle with only two classical-like quasiparticles and their conjugate momenta. One of these coupled quasiparticles is the centroid particle of the quantum path integral quasiparticle distribution. Only this quasiparticle feels the potential energy function. The other quasiparticle directly provides the observable averages of quantum mechanical operators. The theory offers a simplified perspective on quantum statistical mechanics, revealing its most reductionist connection to classical statistical physics. By doing so, it can facilitate a simpler representation of certain quantum effects in complex molecular environments.

Path statistics, memory, and coarse-graining of continuous-time random walks on networks

PubMed Central

Kion-Crosby, Willow; Morozov, Alexandre V.

2015-01-01

Continuous-time random walks (CTRWs) on discrete state spaces, ranging from regular lattices to complex networks, are ubiquitous across physics, chemistry, and biology. Models with coarse-grained states (for example, those employed in studies of molecular kinetics) or spatial disorder can give rise to memory and non-exponential distributions of waiting times and first-passage statistics. However, existing methods for analyzing CTRWs on complex energy landscapes do not address these effects. Here we use statistical mechanics of the nonequilibrium path ensemble to characterize first-passage CTRWs on networks with arbitrary connectivity, energy landscape, and waiting time distributions. Our approach can be applied to calculating higher moments (beyond the mean) of path length, time, and action, as well as statistics of any conservative or non-conservative force along a path. For homogeneous networks, we derive exact relations between length and time moments, quantifying the validity of approximating a continuous-time process with its discrete-time projection. For more general models, we obtain recursion relations, reminiscent of transfer matrix and exact enumeration techniques, to efficiently calculate path statistics numerically. We have implemented our algorithm in PathMAN (Path Matrix Algorithm for Networks), a Python script that users can apply to their model of choice. We demonstrate the algorithm on a few representative examples which underscore the importance of non-exponential distributions, memory, and coarse-graining in CTRWs. PMID:26646868

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanyal, Tanmoy; Shell, M. Scott, E-mail: shell@engineering.ucsb.edu

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one atmore » which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.« less

Comparison of iterative inverse coarse-graining methods

NASA Astrophysics Data System (ADS)

Rosenberger, David; Hanke, Martin; van der Vegt, Nico F. A.

2016-10-01

Deriving potentials for coarse-grained Molecular Dynamics (MD) simulations is frequently done by solving an inverse problem. Methods like Iterative Boltzmann Inversion (IBI) or Inverse Monte Carlo (IMC) have been widely used to solve this problem. The solution obtained by application of these methods guarantees a match in the radial distribution function (RDF) between the underlying fine-grained system and the derived coarse-grained system. However, these methods often fail in reproducing thermodynamic properties. To overcome this deficiency, additional thermodynamic constraints such as pressure or Kirkwood-Buff integrals (KBI) may be added to these methods. In this communication we test the ability of these methods to converge to a known solution of the inverse problem. With this goal in mind we have studied a binary mixture of two simple Lennard-Jones (LJ) fluids, in which no actual coarse-graining is performed. We further discuss whether full convergence is actually needed to achieve thermodynamic representability.

Enhancing the Electrochemical Behavior of Pure Copper by Cyclic Potentiodynamic Passivation: A Comparison between Coarse- and Nano-Grained Pure Copper

NASA Astrophysics Data System (ADS)

Fattah-alhosseini, Arash; Imantalab, Omid; Attarzadeh, Farid Reza

2016-10-01

Electrochemical behavior of coarse- and nano-grained pure copper were modified and improved to a large extent by the application of cyclic potentiodynamic passivation. The efficacy of this method was evaluated on the basis of grain size which is of great importance in corrosion studies. In this study, the eight passes of accumulative roll bonding process at room temperature were successfully performed to produce nano-grained pure copper. Transmission electron microscopy image indicated that the average grain size reached below 100 nm after eight passes. On the basis of cyclic voltammetry and also the electrochemical tests performed after that, it was revealed that cyclic potentiodynamic passivation had a significant improving effect on the passive behavior of both coarse- and nano-grained samples. In addition, a superior behavior of nano-grained sample in comparison to coarse-grained one was distinguished by its smaller cyclic voltammogram loops, nobler free potentials, larger capacitive arcs in the Nyquist plots, and less charge carrier densities within the passive film.

Multiblob coarse-graining for mixtures of long polymers and soft colloids

NASA Astrophysics Data System (ADS)

Locatelli, Emanuele; Capone, Barbara; Likos, Christos N.

2016-11-01

Soft nanocomposites represent both a theoretical and an experimental challenge due to the high number of the microscopic constituents that strongly influence the behaviour of the systems. An effective theoretical description of such systems invokes a reduction of the degrees of freedom to be analysed, hence requiring the introduction of an efficient, quantitative, coarse-grained description. We here report on a novel coarse graining approach based on a set of transferable potentials that quantitatively reproduces properties of mixtures of linear and star-shaped homopolymeric nanocomposites. By renormalizing groups of monomers into a single effective potential between a f-functional star polymer and an homopolymer of length N0, and through a scaling argument, it will be shown how a substantial reduction of the to degrees of freedom allows for a full quantitative description of the system. Our methodology is tested upon full monomer simulations for systems of different molecular weight, proving its full predictive potential.

Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu

2015-12-28

The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF.more » We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.« less

A Hybrid Coarse-graining Approach for Lipid Bilayers at Large Length and Time Scales

PubMed Central

Ayton, Gary S.; Voth, Gregory A.

2009-01-01

A hybrid analytic-systematic (HAS) coarse-grained (CG) lipid model is developed and employed in a large-scale simulation of a liposome. The methodology is termed hybrid analyticsystematic as one component of the interaction between CG sites is variationally determined from the multiscale coarse-graining (MS-CG) methodology, while the remaining component utilizes an analytic potential. The systematic component models the in-plane center of mass interaction of the lipids as determined from an atomistic-level MD simulation of a bilayer. The analytic component is based on the well known Gay-Berne ellipsoid of revolution liquid crystal model, and is designed to model the highly anisotropic interactions at a highly coarse-grained level. The HAS CG approach is the first step in an “aggressive” CG methodology designed to model multi-component biological membranes at very large length and timescales. PMID:19281167

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

PubMed Central

Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.; de Pablo, Juan J.

2013-01-01

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridization rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering. PMID:24116642

Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations

PubMed Central

Bell, David R.; Cheng, Sara Y.; Salazar, Heber; Ren, Pengyu

2017-01-01

We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R2 = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs. stacking interactions allowed RACER to distinguish folded vs. unfolded states. In RACER, base pairing and stacking interactions each provide an approximate stability of 3–4 kcal/mol for an A-form helix. RACER was developed based on PDB structural statistics and experimental thermodynamic data. In contrast with previous work, RACER implements a novel effective vdW potential energy function, which led us to re-parameterize hydrogen bond and electrostatic potential energy functions. Further, RACER is validated and optimized using a simulated annealing protocol to generate potential energy vs. RMSD landscapes. Finally, RACER is tested using extensive equilibrium pulling simulations (0.86 ms total) on eleven RNA sequences (hairpins and duplexes). PMID:28393861

Structural properties of thiophenes investigated with simulations of a coarse-grained model

NASA Astrophysics Data System (ADS)

Luettmer-Strathmann, Jutta; Almutairi, Amani

Thiophenes have important applications in organic electronics, energy conversion, and storage. The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. In recent work, we developed a coarse-grained model for alpha-oligothiophenes in the bulk and near gold surfaces. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. In this work, we investigate structural properties of thiophenes with simulations of our coarse-grained model.

Premelting, fluctuations, and coarse-graining of water-ice interfaces.

PubMed

Limmer, David T; Chandler, David

2014-11-14

Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

Premelting, fluctuations, and coarse-graining of water-ice interfaces

NASA Astrophysics Data System (ADS)

Limmer, David T.; Chandler, David

2014-11-01

Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

Algorithms for tensor network renormalization

NASA Astrophysics Data System (ADS)

Evenbly, G.

2017-01-01

We discuss in detail algorithms for implementing tensor network renormalization (TNR) for the study of classical statistical and quantum many-body systems. First, we recall established techniques for how the partition function of a 2 D classical many-body system or the Euclidean path integral of a 1 D quantum system can be represented as a network of tensors, before describing how TNR can be implemented to efficiently contract the network via a sequence of coarse-graining transformations. The efficacy of the TNR approach is then benchmarked for the 2 D classical statistical and 1 D quantum Ising models; in particular the ability of TNR to maintain a high level of accuracy over sustained coarse-graining transformations, even at a critical point, is demonstrated.

Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM)

NASA Astrophysics Data System (ADS)

Sinitskiy, Anton V.; Voth, Gregory A.

2018-01-01

Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).

PubMed

Sinitskiy, Anton V; Voth, Gregory A

2018-01-07

Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

Role of Various Entropies in the Black Hole Information Loss Problem

NASA Astrophysics Data System (ADS)

Nieuwenhuizen, Th. M.; Volovich, I. V.

2007-09-01

We discuss the current status of the black hole information loss paradox and propose a plan for its solution based on analogies with solid state physics and the irreversibility problem. In a recent paper Hawking has argued that there is no information loss in black holes in asymptotically AdS spacetimes. We remind that there are several types of information (entropy) in statistical physics - fine grained (microscopic) and coarse grained (macroscopic) ones which behave differently under unitary evolution. We suggest that the coarse grained information of the rest of the Universe is lost while fine grained information is preserved. A possibility to develop in quantum gravity an analogue of the Bogoliubov derivation of the irreversible Boltzmann and Navier - Stokes equations from the reversible mechanical equations is discussed.

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.

2013-10-14

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridizationmore » rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering.« less

Coarse graining of atactic polystyrene and its derivatives

NASA Astrophysics Data System (ADS)

Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

2014-03-01

Capturing large length scales in polymers and soft matter while retaining atomistic properties is imperative to computational studies of dynamic systems. Here we present a new methodology developing coarse-grain model based on atomistic simulation of atactic polystyrene (PS). Similar to previous work by Fritz et al., each monomer is described by two coarse grained beads. In contrast to this earlier work where intramolecular potentials were based on Monte Carlo simulation of both isotactic and syndiotactic single PS molecule to capture stereochemistry, we obtained intramolecular interactions from a single molecular dynamics simulation of an all-atom atactic PS melts. The non-bonded interactions are obtained using the iterative Boltzmann inversion (IBI) scheme. This methodology has been extended to coarse graining of poly-(t-butyl-styrene) (PtBS). An additional coarse-grained bead is used to describe the t-butyl group. Similar to the process for PS, the intramolecular interactions are obtained from a single all atom atactic melt simulation. Starting from the non-bonded interactions for PS, we show that the IBI method for the non-bonded interactions of PtBS converges relatively fast. A generalized scheme for substituted PS is currently in development. We would like to acknowledge Prof. Kurt Kremer for helpful discussions during this work.

Geochemical evidence for the provenance of aeolian deposits in the Qaidam Basin, Tibetan Plateau

NASA Astrophysics Data System (ADS)

Du, Shisong; Wu, Yongqiu; Tan, Lihua

2018-06-01

The main purpose of this study is to analyse the material source of different grain-size components of dune sand in the Qaidam Basin. We determined the trace and rare earth element (REE) compositions and Sr-Nd isotopic compositions of the coarse (75-500 μm) and fine (<75 μm) fractions of surface sediment samples. The comparison of the immobile trace element and REE compositions, Sr-Nd isotopic compositions and multidimensional scaling (MDS) results of the dune sands with those of different types of sediments in potential source areas revealed the following information. (1) The fine- and coarse-grained fractions of dune sands in the Qaidam Basin exhibit distinctly different elemental concentrations, elemental patterns and characteristic parameters of REE. Moreover, Sr-Nd isotopic differences also exist between different grain-size fractions of aeolian sand, which means that different grain-size fractions of these dune sands have different source areas. (2) The geochemical characteristics of the coarse particles of dune sand exhibit obvious regional heterogeneity and generally record a local origin derived from local fluvial sediments and alluvial/proluvial sediments. The coarse- and fine-grained dune sand in the southern Qaidam Basin mainly came from Kunlun Mountains, whereas the coarse- and fine-grained dune sand in the northeastern Qaidam Basin mainly came from Qilian Mountains. (3) The fine-grained fractions of sediments throughout the entire Qaidam Basin may have been affected by the input of foreign materials from the Tarim Basin.

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

PubMed

Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

2016-04-20

RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Edgeworth streaming model for redshift space distortions

NASA Astrophysics Data System (ADS)

Uhlemann, Cora; Kopp, Michael; Haugg, Thomas

2015-09-01

We derive the Edgeworth streaming model (ESM) for the redshift space correlation function starting from an arbitrary distribution function for biased tracers of dark matter by considering its two-point statistics and show that it reduces to the Gaussian streaming model (GSM) when neglecting non-Gaussianities. We test the accuracy of the GSM and ESM independent of perturbation theory using the Horizon Run 2 N -body halo catalog. While the monopole of the redshift space halo correlation function is well described by the GSM, higher multipoles improve upon including the leading order non-Gaussian correction in the ESM: the GSM quadrupole breaks down on scales below 30 Mpc /h whereas the ESM stays accurate to 2% within statistical errors down to 10 Mpc /h . To predict the scale-dependent functions entering the streaming model we employ convolution Lagrangian perturbation theory (CLPT) based on the dust model and local Lagrangian bias. Since dark matter halos carry an intrinsic length scale given by their Lagrangian radius, we extend CLPT to the coarse-grained dust model and consider two different smoothing approaches operating in Eulerian and Lagrangian space, respectively. The coarse graining in Eulerian space features modified fluid dynamics different from dust while the coarse graining in Lagrangian space is performed in the initial conditions with subsequent single-streaming dust dynamics, implemented by smoothing the initial power spectrum in the spirit of the truncated Zel'dovich approximation. Finally, we compare the predictions of the different coarse-grained models for the streaming model ingredients to N -body measurements and comment on the proper choice of both the tracer distribution function and the smoothing scale. Since the perturbative methods we considered are not yet accurate enough on small scales, the GSM is sufficient when applied to perturbation theory.

Local free energies for the coarse-graining of adsorption phenomena: The interacting pair approximation

NASA Astrophysics Data System (ADS)

Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco

2018-05-01

We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr; Harmandaris, Vagelis, E-mail: harman@uoc.gr; Institute of Applied and Computational Mathematics

Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse grainingmore » mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems.« less

Consistent integration of experimental and ab initio data into molecular and coarse-grained models

NASA Astrophysics Data System (ADS)

Vlcek, Lukas

As computer simulations are increasingly used to complement or replace experiments, highly accurate descriptions of physical systems at different time and length scales are required to achieve realistic predictions. The questions of how to objectively measure model quality in relation to reference experimental or ab initio data, and how to transition seamlessly between different levels of resolution are therefore of prime interest. To address these issues, we use the concept of statistical distance to define a measure of similarity between statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the systems' measurable properties. Through systematic coarse-graining, we arrive at appropriate expressions for optimization loss functions consistently incorporating microscopic ab initio data as well as macroscopic experimental data. The design of coarse-grained and multiscale models is then based on factoring the model system partition function into terms describing the system at different resolution levels. The optimization algorithm takes advantage of thermodynamic perturbation expressions for fast exploration of the model parameter space, enabling us to scan millions of parameter combinations per hour on a single CPU. The robustness and generality of the new model optimization framework and its efficient implementation are illustrated on selected examples including aqueous solutions, magnetic systems, and metal alloys.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de; Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de

We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in moremore » efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.« less

Coarse-graining using the relative entropy and simplex-based optimization methods in VOTCA

NASA Astrophysics Data System (ADS)

Rühle, Victor; Jochum, Mara; Koschke, Konstantin; Aluru, N. R.; Kremer, Kurt; Mashayak, S. Y.; Junghans, Christoph

2014-03-01

Coarse-grained (CG) simulations are an important tool to investigate systems on larger time and length scales. Several methods for systematic coarse-graining were developed, varying in complexity and the property of interest. Thus, the question arises which method best suits a specific class of system and desired application. The Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) provides a uniform platform for coarse-graining methods and allows for their direct comparison. We present recent advances of VOTCA, namely the implementation of the relative entropy method and downhill simplex optimization for coarse-graining. The methods are illustrated by coarse-graining SPC/E bulk water and a water-methanol mixture. Both CG models reproduce the pair distributions accurately. SYM is supported by AFOSR under grant 11157642 and by NSF under grant 1264282. CJ was supported in part by the NSF PHY11-25915 at KITP. K. Koschke acknowledges funding by the Nestle Research Center.

Coarse-graining errors and numerical optimization using a relative entropy framework

NASA Astrophysics Data System (ADS)

Chaimovich, Aviel; Shell, M. Scott

2011-03-01

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, Srel, that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework.

The self-assembly of particles with isotropic interactions: Using DNA coated colloids to create designer nanomaterials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, R. B.; Dion, S.; Konigslow, K. von

Self-consistent field theory equations are presented that are suitable for use as a coarse-grained model for DNA coated colloids, polymer-grafted nanoparticles and other systems with approximately isotropic interactions. The equations are generalized for arbitrary numbers of chemically distinct colloids. The advantages and limitations of such a coarse-grained approach for DNA coated colloids are discussed, as are similarities with block copolymer self-assembly. In particular, preliminary results for three species self-assembly are presented that parallel results from a two dimensional ABC triblock copolymer phase. The possibility of incorporating crystallization, dynamics, inverse statistical mechanics and multiscale modelling techniques are discussed.

Adhesion between a rutile surface and a polyimide: a coarse grained molecular dynamics study

NASA Astrophysics Data System (ADS)

Kumar, Arun; Sudarkodi, V.; Parandekar, Priya V.; Sinha, Nishant K.; Prakash, Om; Nair, Nisanth N.; Basu, Sumit

2018-04-01

Titanium, due to its high strength to weight ratio and polyimides, due to their excellent thermal stability are being increasingly used in aerospace applications. We investigate the bonding between a (110) rutile substrate and a popular commercial polyimide, PMR-15, starting from the known atomic structure of the rutile substrate and the architecture of the polymer. First, the long PMR-15 molecule is divided into four fragments and an all-atom non-bonded forcefield governing the interaction between PMR-15 and a rutile substrate is developed. To this end, parameters of Buckingham potential for interaction between each atom in the fragments and the rutile surface are fitted, so as to ensure that the sum of non-bonded and electrostatic interaction energy between the substrate and a large number of configurations of each fragment, calculated by the quantum mechanical route and obtained from the fitted potential, is closely matched. Further, two coarse grained models of PMR-15 are developed—one for interaction between two coarse grained PMR-15 molecules and another for that between a coarse grained PMR-15 and the rutile substrate. Molecular dynamics simulations with the coarse grained models yields a traction separation law—a very useful tool for conducting continuum level finite element simulations of rutile-PMR-15 joints—governing the normal separation of a PMR-15 block from a flat rutile substrate. Moreover, detailed information about the affinity of various fragments to the substrate are also obtained. In fact, though the separation energy between rutile and PMR-15 turns out to be rather low, our analysis—with merely the molecular architecture of the polyimide as the starting point—provides a scheme for in-silico prediction of adhesion energies for new polyimide formulations.

Role of translational entropy in spatially inhomogeneous, coarse-grained models

NASA Astrophysics Data System (ADS)

Langenberg, Marcel; Jackson, Nicholas E.; de Pablo, Juan J.; Müller, Marcus

2018-03-01

Coarse-grained models of polymer and biomolecular systems have enabled the computational study of cooperative phenomena, e.g., self-assembly, by lumping multiple atomistic degrees of freedom along the backbone of a polymer, lipid, or DNA molecule into one effective coarse-grained interaction center. Such a coarse-graining strategy leaves the number of molecules unaltered. In order to treat the surrounding solvent or counterions on the same coarse-grained level of description, one can also stochastically group several of those small molecules into an effective, coarse-grained solvent bead or "fluid element." Such a procedure reduces the number of molecules, and we discuss how to compensate the concomitant loss of translational entropy by density-dependent interactions in spatially inhomogeneous systems.

Insights into DNA-mediated interparticle interactions from a coarse-grained model

NASA Astrophysics Data System (ADS)

Ding, Yajun; Mittal, Jeetain

2014-11-01

DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

Dynamics of essential collective motions in proteins: Theory

NASA Astrophysics Data System (ADS)

Stepanova, Maria

2007-11-01

A general theoretical background is introduced for characterization of conformational motions in protein molecules, and for building reduced coarse-grained models of proteins, based on the statistical analysis of their phase trajectories. Using the projection operator technique, a system of coupled generalized Langevin equations is derived for essential collective coordinates, which are generated by principal component analysis of molecular dynamic trajectories. The number of essential degrees of freedom is not limited in the theory. An explicit analytic relation is established between the generalized Langevin equation for essential collective coordinates and that for the all-atom phase trajectory projected onto the subspace of essential collective degrees of freedom. The theory introduced is applied to identify correlated dynamic domains in a macromolecule and to construct coarse-grained models representing the conformational motions in a protein through a few interacting domains embedded in a dissipative medium. A rigorous theoretical background is provided for identification of dynamic correlated domains in a macromolecule. Examples of domain identification in protein G are given and employed to interpret NMR experiments. Challenges and potential outcomes of the theory are discussed.

Coarse-graining and self-dissimilarity of complex networks

NASA Astrophysics Data System (ADS)

Itzkovitz, Shalev; Levitt, Reuven; Kashtan, Nadav; Milo, Ron; Itzkovitz, Michael; Alon, Uri

2005-01-01

Can complex engineered and biological networks be coarse-grained into smaller and more understandable versions in which each node represents an entire pattern in the original network? To address this, we define coarse-graining units as connectivity patterns which can serve as the nodes of a coarse-grained network and present algorithms to detect them. We use this approach to systematically reverse-engineer electronic circuits, forming understandable high-level maps from incomprehensible transistor wiring: first, a coarse-grained version in which each node is a gate made of several transistors is established. Then the coarse-grained network is itself coarse-grained, resulting in a high-level blueprint in which each node is a circuit module made of many gates. We apply our approach also to a mammalian protein signal-transduction network, to find a simplified coarse-grained network with three main signaling channels that resemble multi-layered perceptrons made of cross-interacting MAP-kinase cascades. We find that both biological and electronic networks are “self-dissimilar,” with different network motifs at each level. The present approach may be used to simplify a variety of directed and nondirected, natural and designed networks.

Coarse-graining errors and numerical optimization using a relative entropy framework.

PubMed

Chaimovich, Aviel; Shell, M Scott

2011-03-07

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, S(rel), that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework. © 2011 American Institute of Physics.

Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy.

PubMed

Chaimovich, Aviel; Shell, M Scott

2009-03-28

Recent efforts have attempted to understand many of liquid water's anomalous properties in terms of effective spherically-symmetric pairwise molecular interactions entailing two characteristic length scales (so-called "core-softened" potentials). In this work, we examine the extent to which such simple descriptions of water are representative of the true underlying interactions by extracting coarse-grained potential functions that are optimized to reproduce the behavior of an all-atom model. To perform this optimization, we use a novel procedure based upon minimizing the relative entropy, a quantity that measures the extent to which a coarse-grained configurational ensemble overlaps with a reference all-atom one. We show that the optimized spherically-symmetric water models exhibit notable variations with the state conditions at which they were optimized, reflecting in particular the shifting accessibility of networked hydrogen bonding interactions. Moreover, we find that water's density and diffusivity anomalies are only reproduced when the effective coarse-grained potentials are allowed to vary with state. Our results therefore suggest that no state-independent spherically-symmetric potential can fully capture the interactions responsible for water's unique behavior; rather, the particular way in which the effective interactions vary with temperature and density contributes significantly to anomalous properties.

Coarse-Grained Molecular Monte Carlo Simulations of Liquid Crystal-Nanoparticle Mixtures

NASA Astrophysics Data System (ADS)

Neufeld, Ryan; Kimaev, Grigoriy; Fu, Fred; Abukhdeir, Nasser M.

Coarse-grained intermolecular potentials have proven capable of capturing essential details of interactions between complex molecules, while substantially reducing the number of degrees of freedom of the system under study. In the domain of liquid crystals, the Gay-Berne (GB) potential has been successfully used to model the behavior of rod-like and disk-like mesogens. However, only ellipsoid-like interaction potentials can be described with GB, making it a poor fit for many real-world mesogens. In this work, the results of Monte Carlo simulations of liquid crystal domains using the Zewdie-Corner (ZC) potential are presented. The ZC potential is constructed from an orthogonal series of basis functions, allowing for potentials of essentially arbitrary shapes to be modeled. We also present simulations of mixtures of liquid crystalline mesogens with nanoparticles. Experimentally these mixtures have been observed to exhibit microphase separation and formation of long-range networks under some conditions. This highlights the need for a coarse-grained approach which can capture salient details on the molecular scale while simulating sufficiently large domains to observe these phenomena. We compare the phase behavior of our simulations with that of a recently presented continuum theory. This work was made possible by the Natural Sciences and Engineering Research Council of Canada and Compute Ontario.

Angle-resolved effective potentials for disk-shaped molecules

NASA Astrophysics Data System (ADS)

Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.

2014-12-01

We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.

Simulation study of entropy production in the one-dimensional Vlasov system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, Zongliang, E-mail: liangliang1223@gmail.com; Wang, Shaojie

2016-07-15

The coarse-grain averaged distribution function of the one-dimensional Vlasov system is obtained by numerical simulation. The entropy productions in cases of the random field, the linear Landau damping, and the bump-on-tail instability are computed with the coarse-grain averaged distribution function. The computed entropy production is converged with increasing length of coarse-grain average. When the distribution function differs slightly from a Maxwellian distribution, the converged value agrees with the result computed by using the definition of thermodynamic entropy. The length of the coarse-grain average to compute the coarse-grain averaged distribution function is discussed.

Non-Markovian closure models for large eddy simulations using the Mori-Zwanzig formalism

NASA Astrophysics Data System (ADS)

Parish, Eric J.; Duraisamy, Karthik

2017-01-01

This work uses the Mori-Zwanzig (M-Z) formalism, a concept originating from nonequilibrium statistical mechanics, as a basis for the development of coarse-grained models of turbulence. The mechanics of the generalized Langevin equation (GLE) are considered, and insight gained from the orthogonal dynamics equation is used as a starting point for model development. A class of subgrid models is considered which represent nonlocal behavior via a finite memory approximation [Stinis, arXiv:1211.4285 (2012)], the length of which is determined using a heuristic that is related to the spectral radius of the Jacobian of the resolved variables. The resulting models are intimately tied to the underlying numerical resolution and are capable of approximating non-Markovian effects. Numerical experiments on the Burgers equation demonstrate that the M-Z-based models can accurately predict the temporal evolution of the total kinetic energy and the total dissipation rate at varying mesh resolutions. The trajectory of each resolved mode in phase space is accurately predicted for cases where the coarse graining is moderate. Large eddy simulations (LESs) of homogeneous isotropic turbulence and the Taylor-Green Vortex show that the M-Z-based models are able to provide excellent predictions, accurately capturing the subgrid contribution to energy transfer. Last, LESs of fully developed channel flow demonstrate the applicability of M-Z-based models to nondecaying problems. It is notable that the form of the closure is not imposed by the modeler, but is rather derived from the mathematics of the coarse graining, highlighting the potential of M-Z-based techniques to define LES closures.

Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

D’Adamo, Giuseppe, E-mail: giuseppe.dadamo@sissa.it; Pelissetto, Andrea, E-mail: andrea.pelissetto@roma1.infn.it; Pierleoni, Carlo, E-mail: carlo.pierleoni@aquila.infn.it

2014-12-28

A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach, groups of monomers are mapped onto a single pseudoatom (a blob) and the effective blob-blob interactions are obtained by requiring the model to reproduce some large-scale structural properties in the zero-density limit. We show that an accurate parametrization of the polymer-colloid interactions is obtained by simply introducing pair potentials between blobs and colloids. For the coarse-grained (CG) model in which polymers are modelled as four-blob chains (tetramers), the pair potentials are determined by means of the iterative Boltzmannmore » inversion scheme, taking full-monomer (FM) pair correlation functions at zero-density as targets. For a larger number n of blobs, pair potentials are determined by using a simple transferability assumption based on the polymer self-similarity. We validate the model by comparing its predictions with full-monomer results for the interfacial properties of polymer solutions in the presence of a single colloid and for thermodynamic and structural properties in the homogeneous phase at finite polymer and colloid density. The tetramer model is quite accurate for q ≲ 1 (q=R{sup ^}{sub g}/R{sub c}, where R{sup ^}{sub g} is the zero-density polymer radius of gyration and R{sub c} is the colloid radius) and reasonably good also for q = 2. For q = 2, an accurate coarse-grained description is obtained by using the n = 10 blob model. We also compare our results with those obtained by using single-blob models with state-dependent potentials.« less

Dynamics in entangled polyethylene melts using coarse-grained models

NASA Astrophysics Data System (ADS)

Peters, Brandon L.; Grest, Gary S.; Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora

Polymer dynamics creates distinctive viscoelastic behavior as a result of a coupled interplay of motion on multiple length scales. Capturing the broad time and length scales of polymeric motion however, remains a challenge. Using polyethylene (PE) as a model system, we probe the effects of the degree of coarse graining on polymer dynamics. Coarse-grained (CG) potentials are derived using iterative Boltzmann inversion (iBi) with 2-6 methyl groups per CG bead from all fully atomistic melt simulations for short chains. While the iBi methods produces non-bonded potentials which give excellent agreement for the atomistic and CG pair correlation functions, the pressure P = 100-500MPa for the CG model. Correcting for potential so P 0 leads to non-bonded models with slightly smaller effective diameter and much deeper minimum. However, both the pressure and non-pressure corrected CG models give similar results for mean squared displacement (MSD) and the stress auto correlation function G(t) for PE melts above the melting point. The time rescaling factor between CG and atomistic models is found to be nearly the same for both CG models. Transferability of potential for different temperatures was tested by comparing the MSD and G(t) for potentials generated at different temperatures.

On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies

NASA Astrophysics Data System (ADS)

Degiacomi, Matteo T.

2018-05-01

Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies' subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals. While the first is determined by experimental error, the latter is based on a statistical analysis on a range of protein dimers. Here, we first propose a new expression to describe the overlap between two spheres. Then we analyze the effect of specific overlap cutoff choices on the precision and accuracy of super coarse-grained models. Finally, we propose a method to determine overlap cutoff levels on a per-case scenario, based on collected CCS data, and show that it can be applied to the characterization of the assembly topology of symmetrical homo-multimers. [Figure not available: see fulltext.

Resolving Properties of Polymers and Nanoparticle Assembly through Coarse-Grained Computational Studies.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grest, Gary S.

2017-09-01

Coupled length and time scales determine the dynamic behavior of polymers and polymer nanocomposites and underlie their unique properties. To resolve the properties over large time and length scales it is imperative to develop coarse grained models which retain the atomistic specificity. Here we probe the degree of coarse graining required to simultaneously retain significant atomistic details a nd access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using polyethylene as a model system, we probe how the coarse - graining scale affects themore » measured dynamics with different number methylene group s per coarse - grained beads. Using these models we simulate polyethylene melts for times over 500 ms to study the viscoelastic properties of well - entangled polymer melts and large nanoparticle assembly as the nanoparticles are driven close enough to form nanostructures.« less

Role of Grain Boundaries under Long-Time Radiation

NASA Astrophysics Data System (ADS)

Zhu, Yichao; Luo, Jing; Guo, Xu; Xiang, Yang; Chapman, Stephen Jonathan

2018-06-01

Materials containing a high proportion of grain boundaries offer significant potential for the development of radiation-resistant structural materials. However, a proper understanding of the connection between the radiation-induced microstructural behavior of a grain boundary and its impact at long natural time scales is still missing. In this Letter, point defect absorption at interfaces is summarized by a jump Robin-type condition at a coarse-grained level, wherein the role of interface microstructure is effectively taken into account. Then a concise formula linking the sink strength of a polycrystalline aggregate with its grain size is introduced and is well compared with experimental observation. Based on the derived model, a coarse-grained formulation incorporating the coupled evolution of grain boundaries and point defects is proposed, so as to underpin the study of long-time morphological evolution of grains induced by irradiation. Our simulation results suggest that the presence of point defect sources within a grain further accelerates its shrinking process, and radiation tends to trigger the extension of twin boundary sections.

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

NASA Astrophysics Data System (ADS)

Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

2011-10-01

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.

Parameterizing the Morse Potential for Coarse-Grained Modeling of Blood Plasma

PubMed Central

Zhang, Na; Zhang, Peng; Kang, Wei; Bluestein, Danny; Deng, Yuefan

2014-01-01

Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately. PMID:24910470

Effects of coarse-graining on the scaling behavior of long-range correlated and anti-correlated signals.

PubMed

Xu, Yinlin; Ma, Qianli D Y; Schmitt, Daniel T; Bernaola-Galván, Pedro; Ivanov, Plamen Ch

2011-11-01

We investigate how various coarse-graining (signal quantization) methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the magnitude of a signal, we consider (i) the Floor, (ii) the Symmetry and (iii) the Centro-Symmetry coarse-graining methods. We find that for anti-correlated signals coarse-graining in the magnitude leads to a crossover to random behavior at large scales, and that with increasing the width of the coarse-graining partition interval Δ, this crossover moves to intermediate and small scales. In contrast, the scaling of positively correlated signals is less affected by the coarse-graining, with no observable changes when Δ < 1, while for Δ > 1 a crossover appears at small scales and moves to intermediate and large scales with increasing Δ. For very rough coarse-graining (Δ > 3) based on the Floor and Symmetry methods, the position of the crossover stabilizes, in contrast to the Centro-Symmetry method where the crossover continuously moves across scales and leads to a random behavior at all scales; thus indicating a much stronger effect of the Centro-Symmetry compared to the Floor and the Symmetry method. For coarse-graining in time, where data points are averaged in non-overlapping time windows, we find that the scaling for both anti-correlated and positively correlated signals is practically preserved. The results of our simulations are useful for the correct interpretation of the correlation and scaling properties of symbolic sequences.

Effects of coarse-graining on the scaling behavior of long-range correlated and anti-correlated signals

PubMed Central

Xu, Yinlin; Ma, Qianli D.Y.; Schmitt, Daniel T.; Bernaola-Galván, Pedro; Ivanov, Plamen Ch.

2014-01-01

We investigate how various coarse-graining (signal quantization) methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the magnitude of a signal, we consider (i) the Floor, (ii) the Symmetry and (iii) the Centro-Symmetry coarse-graining methods. We find that for anti-correlated signals coarse-graining in the magnitude leads to a crossover to random behavior at large scales, and that with increasing the width of the coarse-graining partition interval Δ, this crossover moves to intermediate and small scales. In contrast, the scaling of positively correlated signals is less affected by the coarse-graining, with no observable changes when Δ < 1, while for Δ > 1 a crossover appears at small scales and moves to intermediate and large scales with increasing Δ. For very rough coarse-graining (Δ > 3) based on the Floor and Symmetry methods, the position of the crossover stabilizes, in contrast to the Centro-Symmetry method where the crossover continuously moves across scales and leads to a random behavior at all scales; thus indicating a much stronger effect of the Centro-Symmetry compared to the Floor and the Symmetry method. For coarse-graining in time, where data points are averaged in non-overlapping time windows, we find that the scaling for both anti-correlated and positively correlated signals is practically preserved. The results of our simulations are useful for the correct interpretation of the correlation and scaling properties of symbolic sequences. PMID:25392599

The grain-size lineup: A test of a novel eyewitness identification procedure.

PubMed

Horry, Ruth; Brewer, Neil; Weber, Nathan

2016-04-01

When making a memorial judgment, respondents can regulate their accuracy by adjusting the precision, or grain size, of their responses. In many circumstances, coarse-grained responses are less informative, but more likely to be accurate, than fine-grained responses. This study describes a novel eyewitness identification procedure, the grain-size lineup, in which participants eliminated any number of individuals from the lineup, creating a choice set of variable size. A decision was considered to be fine-grained if no more than 1 individual was left in the choice set or coarse-grained if more than 1 individual was left in the choice set. Participants (N = 384) watched 2 high-quality or low-quality videotaped mock crimes and then completed 4 standard simultaneous lineups or 4 grain-size lineups (2 target-present and 2 target-absent). There was some evidence of strategic regulation of grain size, as the most difficult lineup was associated with a greater proportion of coarse-grained responses than the other lineups. However, the grain-size lineup did not outperform the standard simultaneous lineup. Fine-grained suspect identifications were no more diagnostic than suspect identifications from standard lineups, whereas coarse-grained suspect identifications carried little probative value. Participants were generally reluctant to provide coarse-grained responses, which may have hampered the utility of the procedure. For a grain-size approach to be useful, participants may need to be trained or instructed to use the coarse-grained option effectively. (c) 2016 APA, all rights reserved).

Introduction of a Classical Level in Quantum Theory

NASA Astrophysics Data System (ADS)

Prosperi, G. M.

2016-11-01

In an old paper of our group in Milano a formalism was introduced for the continuous monitoring of a system during a certain interval of time in the framework of a somewhat generalized approach to quantum mechanics (QM). The outcome was a distribution of probability on the space of all the possible continuous histories of a set of quantities to be considered as a kind of coarse grained approximation to some ordinary quantum observables commuting or not. In fact the main aim was the introduction of a classical level in the context of QM, treating formally a set of basic quantities, to be considered as beables in the sense of Bell, as continuously taken under observation. However the effect of such assumption was a permanent modification of the Liouville-von Neumann equation for the statistical operator by the introduction of a dissipative term which is in conflict with basic conservation rules in all reasonable models we had considered. Difficulties were even encountered for a relativistic extension of the formalism. In this paper I propose a modified version of the original formalism which seems to overcome both difficulties. First I study the simple models of an harmonic oscillator and a free scalar field in which a coarse grain position and a coarse grained field respectively are treated as beables. Then I consider the more realistic case of spinor electrodynamics in which only certain coarse grained electric and magnetic fields are introduced as classical variables and no matter related quantities.

Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr; Schnell, Benoît

2014-04-07

We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining levelmore » on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.« less

Coarse-grained forms for equations describing the microscopic motion of particles in a fluid.

PubMed

Das, Shankar P; Yoshimori, Akira

2013-10-01

Exact equations of motion for the microscopically defined collective density ρ(x,t) and the momentum density ĝ(x,t) of a fluid have been obtained in the past starting from the corresponding Langevin equations representing the dynamics of the fluid particles. In the present work we average these exact equations of microscopic dynamics over the local equilibrium distribution to obtain stochastic partial differential equations for the coarse-grained densities with smooth spatial and temporal dependence. In particular, we consider Dean's exact balance equation for the microscopic density of a system of interacting Brownian particles to obtain the basic equation of the dynamic density functional theory with noise. Our analysis demonstrates that on thermal averaging the dependence of the exact equations on the bare interaction potential is converted to dependence on the corresponding thermodynamic direct correlation functions in the coarse-grained equations.

Coarse-graining of proteins based on elastic network models

NASA Astrophysics Data System (ADS)

Sinitskiy, Anton V.; Voth, Gregory A.

2013-08-01

To simulate molecular processes on biologically relevant length- and timescales, coarse-grained (CG) models of biomolecular systems with tens to even hundreds of residues per CG site are required. One possible way to build such models is explored in this article: an elastic network model (ENM) is employed to define the CG variables. Free energy surfaces are approximated by Taylor series, with the coefficients found by force-matching. CG potentials are shown to undergo renormalization due to roughness of the energy landscape and smoothing of it under coarse-graining. In the case study of hen egg-white lysozyme, the entropy factor is shown to be of critical importance for maintaining the native structure, and a relationship between the proposed ENM-mode-based CG models and traditional CG-bead-based models is discussed. The proposed approach uncovers the renormalizable character of CG models and offers new opportunities for automated and computationally efficient studies of complex free energy surfaces.

Mechanical response of two polyimides through coarse-grained molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sudarkodi, V.; Sooraj, K.; Nair, Nisanth N.; Basu, Sumit; Parandekar, Priya V.; Sinha, Nishant K.; Prakash, Om; Tsotsis, Tom

2018-03-01

Coarse-grained molecular dynamics (MD) simulations allow us to predict the mechanical responses of polymers, starting merely with a description of their molecular architectures. It is interesting to ask whether, given two competing molecular architectures, coarse-grained MD simulations can predict the differences that can be expected in their mechanical responses. We have studied two crosslinked polyimides PMR15 and HFPE52—both used in high- temperature applications—to assess whether the subtle differences in their uniaxial stress-strain responses, revealed by experiments, can be reproduced by carefully coarse-grained MD models. The coarse graining procedure for PMR15 is outlined in this work, while the coarse grain forcefields for HFPE52 are borrowed from an earlier one (Pandiyan et al 2015 Macromol. Theory Simul. 24 513-20). We show that the stress-strain responses of both these polyimides are qualitatively reproduced, and important insights into their deformation and failure mechanisms are obtained. More importantly, the differences in the molecular architecture between the polyimides carry over to the differences in the stress-strain responses in a manner that parallels the experimental results. A critical assessment of the successes and shortcomings of predicting mechanical responses through coarse-grained MD simulations has been made.

MAHLI at the Rocknest sand shadow: Science and science-enabling activities

NASA Astrophysics Data System (ADS)

Minitti, M. E.; Kah, L. C.; Yingst, R. A.; Edgett, K. S.; Anderson, R. C.; Beegle, L. W.; Carsten, J. L.; Deen, R. G.; Goetz, W.; Hardgrove, C.; Harker, D. E.; Herkenhoff, K. E.; Hurowitz, J. A.; Jandura, L.; Kennedy, M. R.; Kocurek, G.; Krezoski, G. M.; Kuhn, S. R.; Limonadi, D.; Lipkaman, L.; Madsen, M. B.; Olson, T. S.; Robinson, M. L.; Rowland, S. K.; Rubin, D. M.; Seybold, C.; Schieber, J.; Schmidt, M.; Sumner, D. Y.; Tompkins, V. V.; Van Beek, J. K.; Van Beek, T.

2013-11-01

Martian solar days 57-100, the Mars Science Laboratory Curiosity rover acquired and processed a solid (sediment) sample and analyzed its mineralogy and geochemistry with the Chemistry and Mineralogy and Sample Analysis at Mars instruments. An aeolian deposit—herein referred to as the Rocknest sand shadow—was inferred to represent a global average soil composition and selected for study to facilitate integration of analytical results with observations from earlier missions. During first-time activities, the Mars Hand Lens Imager (MAHLI) was used to support both science and engineering activities related to sample assessment, collection, and delivery. Here we report on MAHLI activities that directly supported sample analysis and provide MAHLI observations regarding the grain-scale characteristics of the Rocknest sand shadow. MAHLI imaging confirms that the Rocknest sand shadow is one of a family of bimodal aeolian accumulations on Mars—similar to the coarse-grained ripples interrogated by the Mars Exploration Rovers Spirit and Opportunity—in which a surface veneer of coarse-grained sediment stabilizes predominantly fine-grained sediment of the deposit interior. The similarity in grain size distribution of these geographically disparate deposits support the widespread occurrence of bimodal aeolian transport on Mars. We suggest that preservation of bimodal aeolian deposits may be characteristic of regions of active deflation, where winnowing of the fine-sediment fraction results in a relatively low sediment load and a preferential increase in the coarse-grained fraction of the sediment load. The compositional similarity of Martian aeolian deposits supports the potential for global redistribution of fine-grained components, combined with potential local contributions.

Cyclic hardening behavior of extruded ZK60 magnesium alloy with different grain sizes

NASA Astrophysics Data System (ADS)

Zhang, Lixin; Zhang, Wencong; Chen, Wenzhen; Wang, Wenke

2018-04-01

Montonic and fully reversed strain-controlled cyclic deformation experiments were conducted on extruded ZK60 magnesium alloy with two different grain sizes in ambient air. Results revealed that the hardening rates of the ZK60 magnesium alloy rods with fine grain and coarse grain in the monotonic deformation and the fully reversed strain-controlled cyclic deformation were opposite along the extrusion direction. Electron Backscatter Diffration analysis revealed that fine grains were more easily rotated than coarse grains under the cyclic deformation. Under the twinning and detwinning process of the cyclic deformation at a large strain amplitude, the coarse grained ZK60 magnesium alloys were more prone to tension twinning {10-12}<10-11> and more residual twins were observed. Texture hardening of coarse grained magnesium alloy was more obvious in cyclic defromation than fine-grained magnesium alloy.

New Coarse-Grained Model and Its Implementation in Simulations of Graphene Assemblies.

PubMed

Shang, Jun-Jun; Yang, Qing-Sheng; Liu, Xia

2017-08-08

Graphene is a one-atom thick layer of carbon atoms arranged in a hexagonal pattern, which makes it the strongest material in the world. The Tersoff potential is a suitable potential for simulating the mechanical behavior of the complex covalently bonded system of graphene. In this paper, we describe a new coarse-grained (CG) potential, TersoffCG, which is based on the function form of the Tersoff potential. The TersoffCG applies to a CG model of graphene that uses the same hexagonal pattern as the atomistic model. The parameters of the TersoffCG potential are determined using structural feature and potential-energy fitting between the CG model and the atomic model. The modeling process of graphene is highly simplified using the present CG model as it avoids the necessity to define bonds/angles/dihedrals connectivity. What is more, the present CG model provides a new perspective of coarse-graining scheme for crystal structures of nanomaterials. The structural changes and mechanical properties of multilayer graphene were calculated using the new potential. Furthermore, a CG model of a graphene aerogel was built in a specific form of assembly. The chemical bonding in the joints of graphene-aerogel forms automatically during the energy relaxation process. The compressive and recover test of the graphene aerogel was reproduced to study its high elasticity. Our computational examples show that the TersoffCG potential can be used for simulations of graphene and its assemblies, which have many applications in areas of environmental protection, aerospace engineering, and others.

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O 1 →4 -bonded polyglucose chains

NASA Astrophysics Data System (ADS)

Lubecka, Emilia A.; Liwo, Adam

2017-09-01

Based on the theory of the construction of coarse-grained force fields for polymer chains described in our recent work [A. K. Sieradzan et al., J. Chem. Phys. 146, 124106 (2017)], in this work effective coarse-grained potentials, to be used in the SUGRES-1P model of polysaccharides that is being developed in our laboratory, have been determined for the O ⋯O ⋯O virtual-bond angles (θ ) and for the dihedral angles for rotation about the O ⋯O virtual bonds (γ ) of 1 → 4 -linked glucosyl polysaccharides, for all possible combinations of [α ,β ]-[d,l]-glucose. The potentials of mean force corresponding to the virtual-bond angles and the virtual-bond dihedral angles were calculated from the free-energy surfaces of [α ,β ]-[d,l]-glucose pairs, determined by umbrella-sampling molecular-dynamics simulations with the AMBER12 force field, or combinations of the surfaces of two pairs sharing the overlapping residue, respectively, by integrating the respective Boltzmann factor over the dihedral angles λ for the rotation of the sugar units about the O ⋯O virtual bonds. Analytical expressions were subsequently fitted to the potentials of mean force. The virtual-bond-torsional potentials depend on both virtual-bond-dihedral angles and virtual-bond angles. The virtual-bond-angle potentials contain a single minimum at about θ =14 0° for all pairs except β -d-[α ,β ] -l-glucose, where the global minimum is shifted to θ =150° and a secondary minimum appears at θ =90°. The torsional potentials favor small negative γ angles for the α -d-glucose and extended negative angles γ for the β -d-glucose chains, as observed in the experimental structures of starch and cellulose, respectively. It was also demonstrated that the approximate expression derived based on Kubo's cluster-cumulant theory, whose coefficients depend on the identity of the disugar units comprising a trisugar unit that defines a torsional potential, fits simultaneously all torsional potentials very well, thus reducing the number of parameters significantly.

Molecular modeling of polycarbonate materials: Glass transition and mechanical properties

NASA Astrophysics Data System (ADS)

Palczynski, Karol; Wilke, Andreas; Paeschke, Manfred; Dzubiella, Joachim

2017-09-01

Linking the experimentally accessible macroscopic properties of thermoplastic polymers to their microscopic static and dynamic properties is a key requirement for targeted material design. Classical molecular dynamics simulations enable us to study the structural and dynamic behavior of molecules on microscopic scales, and statistical physics provides a framework for relating these properties to the macroscopic properties. We take a first step toward creating an automated workflow for the theoretical prediction of thermoplastic material properties by developing an expeditious method for parameterizing a simple yet surprisingly powerful coarse-grained bisphenol-A polycarbonate model which goes beyond previous coarse-grained models and successfully reproduces the thermal expansion behavior, the glass transition temperature as a function of the molecular weight, and several elastic properties.

The effective colloid interaction in the Asakura-Oosawa model. Assessment of non-pairwise terms from the virial expansion.

PubMed

Santos, Andrés; López de Haro, Mariano; Fiumara, Giacomo; Saija, Franz

2015-06-14

The relevance of neglecting three- and four-body interactions in the coarse-grained version of the Asakura-Oosawa model is examined. A mapping between the first few virial coefficients of the binary nonadditive hard-sphere mixture representative of this model and those arising from the coarse-grained (pairwise) depletion potential approximation allows for a quantitative evaluation of the effect of such interactions. This turns out to be especially important for large size ratios and large reservoir polymer packing fractions.

Development of Simultaneous Corrosion Barrier and Optimized Microstructure in FeCrAl Heat-Resistant Alloy for Energy Applications. Part II: The Optimized Creep-Resistant Microstructure

NASA Astrophysics Data System (ADS)

Pimentel, G.; Aranda, M. M.; Chao, J.; González-Carrasco, J. L.; Capdevila, C.

2015-09-01

The first part of this two-part study reported the possibility of simultaneously generating a dense, self-healing α-alumina layer by thermal oxidation and a coarse-grained microstructure with a potential goodness for high-temperature creep resistance in a FeCrAl oxide dispersion-strengthened ferritic alloy that was cold deformed after hot rolling and extrusion. In this second part, the factors affecting the formation of the coarse-grained microstructure such as strain gradients induced during the rolling process are analyzed. It is concluded that larger strain gradients lead to more refined and more isotropic grain structures.

A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide).

PubMed

Abbott, Lauren J; Stevens, Mark J

2015-12-28

A coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil-globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Kawaguchi, Kazutomo; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

PubMed Central

Gu, Junfeng; Bai, Fang; Li, Honglin; Wang, Xicheng

2012-01-01

Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled. PMID:23203075

Shock Simulations of Single-Site Coarse-Grain RDX using the Dissipative Particle Dynamics Method with Reactivity

NASA Astrophysics Data System (ADS)

Sellers, Michael; Lisal, Martin; Schweigert, Igor; Larentzos, James; Brennan, John

2015-06-01

In discrete particle simulations, when an atomistic model is coarse-grained, a trade-off is made: a boost in computational speed for a reduction in accuracy. Dissipative Particle Dynamics (DPD) methods help to recover accuracy in viscous and thermal properties, while giving back a small amount of computational speed. One of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. Today, pairing the current evolution of DPD-RX with a coarse-grained potential and its chemical decomposition reactions allows for the simulation of the shock behavior of energetic materials at a timescale faster than an atomistic counterpart. In 2007, Maillet et al. introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We have recently extended the DPD-RX method and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its tranition to hot product gases within DPD-RX will be presented. Additionally, examples of the effect of microstructure on shock behavior will be shown. Approved for public release. Distribution is unlimited.

Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.

PubMed

Li, Min; Zhang, John Zenghui; Xia, Fei

2016-04-12

Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10,000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems.

cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA.

PubMed

De Bruin, Lennart; Maddocks, John H

2018-06-14

The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.

Temperature dependence of the radiation tolerance of nanocrystalline pyrochlores A 2Ti 2O 7 (A = Gd, Ho and Lu)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wen, J.; Sun, C.; Dholabhai, P. P.

A potentially enhanced radiation resistance of nanocrystalline materials, as a consequence of the high density of interfaces and surfaces, has attracted much attention both to understand the fundamental role of these defect sinks and to develop them for high-radiation environments. Here, irradiation response of nanocrystalline A 2Ti 2O 7 (A = Gd, Ho and Lu) pyrochlore powders with grain sizes of 20–30 nm was investigated by 1-MeV Kr 2+ ion bombardment. In situ transmission electron microscopy (TEM) revealed that the critical amorphization fluence for each nanocrystalline compound at room temperature was greater than that for their coarse-grained counterparts, indicating anmore » enhanced amorphization resistance. The effect of temperature on the irradiation response of one of these compounds, nanocrystalline Lu 2Ti 2O 7, was further examined by performing ion irradiation at an elevated temperature range of 480–600 K. The critical amorphization temperature (T c) was found to be noticeably higher in nanocrystalline Lu 2Ti 2O 7 (610 K) than its coarse-grained counterpart (480 K), revealing that nanocrystalline Lu 2Ti 2O 7 is less resistant to amorphization compared to its coarse-grained phase under high temperatures. We interpret these results with the aid of atomistic simulations. Molecular statics calculations find that cation antisite defects are less energetically costly to form near surfaces than in the bulk, suggesting that the nanocrystalline form of these materials is generally less susceptible to amorphization than coarse-grained counterparts at low temperatures where defect kinetics are negligible. In contrast, at high temperatures, the annealing efficiency of antisite defects by cation interstitials is significantly reduced due to the sink properties of the surfaces in the nanocrystalline pyrochlore, which contributes to the observed higher amorphization temperature in the nano-grained phase than in coarse-grained counterpart. Altogether, these results provide new insight into the behavior of nanocrystalline materials under irradiation.« less

Temperature dependence of the radiation tolerance of nanocrystalline pyrochlores A 2Ti 2O 7 (A = Gd, Ho and Lu)

DOE PAGES

Wen, J.; Sun, C.; Dholabhai, P. P.; ...

2016-03-21

A potentially enhanced radiation resistance of nanocrystalline materials, as a consequence of the high density of interfaces and surfaces, has attracted much attention both to understand the fundamental role of these defect sinks and to develop them for high-radiation environments. Here, irradiation response of nanocrystalline A 2Ti 2O 7 (A = Gd, Ho and Lu) pyrochlore powders with grain sizes of 20–30 nm was investigated by 1-MeV Kr 2+ ion bombardment. In situ transmission electron microscopy (TEM) revealed that the critical amorphization fluence for each nanocrystalline compound at room temperature was greater than that for their coarse-grained counterparts, indicating anmore » enhanced amorphization resistance. The effect of temperature on the irradiation response of one of these compounds, nanocrystalline Lu 2Ti 2O 7, was further examined by performing ion irradiation at an elevated temperature range of 480–600 K. The critical amorphization temperature (T c) was found to be noticeably higher in nanocrystalline Lu 2Ti 2O 7 (610 K) than its coarse-grained counterpart (480 K), revealing that nanocrystalline Lu 2Ti 2O 7 is less resistant to amorphization compared to its coarse-grained phase under high temperatures. We interpret these results with the aid of atomistic simulations. Molecular statics calculations find that cation antisite defects are less energetically costly to form near surfaces than in the bulk, suggesting that the nanocrystalline form of these materials is generally less susceptible to amorphization than coarse-grained counterparts at low temperatures where defect kinetics are negligible. In contrast, at high temperatures, the annealing efficiency of antisite defects by cation interstitials is significantly reduced due to the sink properties of the surfaces in the nanocrystalline pyrochlore, which contributes to the observed higher amorphization temperature in the nano-grained phase than in coarse-grained counterpart. Altogether, these results provide new insight into the behavior of nanocrystalline materials under irradiation.« less

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

PubMed Central

Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

2011-01-01

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into “alpha helix” and “beta sheet” structures. The 5-residue polyalanine displays a substantial increase in the “beta strand” fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling. PMID:22029338

All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

PubMed Central

2017-01-01

Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.

PubMed

He, Yi; Xiao, Yi; Liwo, Adam; Scheraga, Harold A

2009-10-01

We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal alpha-helical and a minimal beta-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with alpha or alpha + beta structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. Copyright 2009 Wiley Periodicals, Inc.

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

NASA Astrophysics Data System (ADS)

Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.

2015-11-01

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase.

PubMed

Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H L

2015-11-07

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

Investigation of nanoparticle transport inside coarse-grained geological media using magnetic resonance imaging.

PubMed

Ramanan, B; Holmes, W M; Sloan, W T; Phoenix, V R

2012-01-03

Quantifying nanoparticle (NP) transport inside saturated porous geological media is imperative for understanding their fate in a range of natural and engineered water systems. While most studies focus upon finer grained systems representative of soils and aquifers, very few examine coarse-grained systems representative of riverbeds and gravel based sustainable urban drainage systems. In this study, we investigated the potential of magnetic resonance imaging (MRI) to image transport behaviors of nanoparticles (NPs) through a saturated coarse-grained system. MRI successfully imaged the transport of superparamagnetic NPs, inside a porous column composed of quartz gravel using T(2)-weighted images. A calibration protocol was then used to convert T(2)-weighted images into spatially resolved quantitative concentration maps of NPs at different time intervals. Averaged concentration profiles of NPs clearly illustrates that transport of a positively charged amine-functionalized NP within the column was slower compared to that of a negatively charged carboxyl-functionalized NP, due to electrostatic attraction between positively charged NP and negatively charged quartz grains. Concentration profiles of NPs were then compared with those of a convection-dispersion model to estimate coefficients of dispersivity and retardation. For the amine functionalized NPs (which exhibited inhibited transport), a better model fit was obtained when permanent attachment (deposition) was incorporated into the model as opposed to nonpermanent attachment (retardation). This technology can be used to further explore transport processes of NPs inside coarse-grained porous media, either by using the wide range of commercially available (super)paramagnetically tagged NPs or by using custom-made tagged NPs.

Molecular dynamics simulation of water in and around carbon nanotubes: A coarse-grained description

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pantawane, Sanwardhini; Choudhury, Niharendu, E-mail: nihcho@barc.gov.in

2016-05-23

In the present study, we intend to investigate behaviour of water in and around hydrophobic open ended carbon nanotubes (CNTs) using a coarse-grained, core-softened model potential for water. The model potential considered here for water has recently been shown to successfully reproduce dynamic, thermodynamic and structural anomalies of water. The epitome of the study is to understand the incarceration of this coarse-grained water in a single-file carbon nanotube. In order to examine the effect of fluid-water van der Waals interaction on the structure of fluid in and around the nanotube, we have simulated three different CNT-water systems with varying degreemore » of solute-water dispersion interaction. The analyses of the radial one-particle density profiles reveal varying degree of permeation and wetting of the CNT interior depending on the degree of fluid-solute attractive van der Waals interaction. A peak in the radial density profile slightly off the nanotube axis signifies a zigzag chain of water molecule around the CNT axis. The average numbers of water molecules inside the CNT have been shown to increase with the increase in fluid-water attractive dispersion interaction.« less

Highly Coarse-Grained Representations of Transmembrane Proteins

PubMed Central

2017-01-01

Numerous biomolecules and biomolecular complexes, including transmembrane proteins (TMPs), are symmetric or at least have approximate symmetries. Highly coarse-grained models of such biomolecules, aiming at capturing the essential structural and dynamical properties on resolution levels coarser than the residue scale, must preserve the underlying symmetry. However, making these models obey the correct physics is in general not straightforward, especially at the highly coarse-grained resolution where multiple (∼3–30 in the current study) amino acid residues are represented by a single coarse-grained site. In this paper, we propose a simple and fast method of coarse-graining TMPs obeying this condition. The procedure involves partitioning transmembrane domains into contiguous segments of equal length along the primary sequence. For the coarsest (lowest-resolution) mappings, it turns out to be most important to satisfy the symmetry in a coarse-grained model. As the resolution is increased to capture more detail, however, it becomes gradually more important to match modular repeats in the secondary structure (such as helix-loop repeats) instead. A set of eight TMPs of various complexity, functionality, structural topology, and internal symmetry, representing different classes of TMPs (ion channels, transporters, receptors, adhesion, and invasion proteins), has been examined. The present approach can be generalized to other systems possessing exact or approximate symmetry, allowing for reliable and fast creation of multiscale, highly coarse-grained mappings of large biomolecular assemblies. PMID:28043122

Interlaced coarse-graining for the dynamical cluster approximation

NASA Astrophysics Data System (ADS)

Haehner, Urs; Staar, Peter; Jiang, Mi; Maier, Thomas; Schulthess, Thomas

The negative sign problem remains a challenging limiting factor in quantum Monte Carlo simulations of strongly correlated fermionic many-body systems. The dynamical cluster approximation (DCA) makes this problem less severe by coarse-graining the momentum space to map the bulk lattice to a cluster embedded in a dynamical mean-field host. Here, we introduce a new form of an interlaced coarse-graining and compare it with the traditional coarse-graining. We show that it leads to more controlled results with weaker cluster shape and smoother cluster size dependence, which with increasing cluster size converge to the results obtained using the standard coarse-graining. In addition, the new coarse-graining reduces the severity of the fermionic sign problem. Therefore, it enables calculations on much larger clusters and can allow the evaluation of the exact infinite cluster size result via finite size scaling. To demonstrate this, we study the hole-doped two-dimensional Hubbard model and show that the interlaced coarse-graining in combination with the DCA+ algorithm permits the determination of the superconducting Tc on cluster sizes, for which the results can be fitted with the Kosterlitz-Thouless scaling law. This research used resources of the Oak Ridge Leadership Computing Facility (OLCF) awarded by the INCITE program, and of the Swiss National Supercomputing Center. OLCF is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725.

A multiscale model for charge inversion in electric double layers

NASA Astrophysics Data System (ADS)

Mashayak, S. Y.; Aluru, N. R.

2018-06-01

Charge inversion is a widely observed phenomenon. It is a result of the rich statistical mechanics of the molecular interactions between ions, solvent, and charged surfaces near electric double layers (EDLs). Electrostatic correlations between ions and hydration interactions between ions and water molecules play a dominant role in determining the distribution of ions in EDLs. Due to highly polar nature of water, near a surface, an inhomogeneous and anisotropic arrangement of water molecules gives rise to pronounced variations in the electrostatic and hydration energies of ions. Classical continuum theories fail to accurately describe electrostatic correlations and molecular effects of water in EDLs. In this work, we present an empirical potential based quasi-continuum theory (EQT) to accurately predict the molecular-level properties of aqueous electrolytes. In EQT, we employ rigorous statistical mechanics tools to incorporate interatomic interactions, long-range electrostatics, correlations, and orientation polarization effects at a continuum-level. Explicit consideration of atomic interactions of water molecules is both theoretically and numerically challenging. We develop a systematic coarse-graining approach to coarse-grain interactions of water molecules and electrolyte ions from a high-resolution atomistic scale to the continuum scale. To demonstrate the ability of EQT to incorporate the water orientation polarization, ion hydration, and electrostatic correlations effects, we simulate confined KCl aqueous electrolyte and show that EQT can accurately predict the distribution of ions in a thin EDL and also predict the complex phenomenon of charge inversion.

Brazing Inconel 625 Using Two Ni/(Fe)-Based Amorphous Filler Foils

NASA Astrophysics Data System (ADS)

Chen, Wen-Shiang; Shiue, Ren-Kae

2012-07-01

For MBF-51 filler, the brazed joint consists of interfacial grain boundary borides, coarse Nb6Ni16Si7, and Ni/Cr-rich matrix. In contrast, the VZ-2106 brazed joint is composed of interfacial Nb6Ni16Si7 precipitates as well as grain boundary borides, coarse Nb6Ni16Si7, and Ni/Cr/Fe-rich matrix. The maximum tensile strength of 443 MPa is obtained from the MBF-51 brazed specimen. The tensile strengths of VZ-2106 brazed joints are approximately 300 MPa. Both amorphous filler foils demonstrate potential in brazing IN-625 substrate.

The relative entropy is fundamental to adaptive resolution simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kreis, Karsten; Graduate School Materials Science in Mainz, Staudingerweg 9, 55128 Mainz; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de

Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy withmore » respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner.« less

The relative entropy is fundamental to adaptive resolution simulations

NASA Astrophysics Data System (ADS)

Kreis, Karsten; Potestio, Raffaello

2016-07-01

Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy with respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner.

A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide)

DOE PAGES

Abbott, Lauren J.; Stevens, Mark J.

2015-12-22

In this study, a coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil–globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomisticmore » simulations.« less

Magma Mixing: Magmatic Enclaves in Morne Micotrin, Dominica

NASA Astrophysics Data System (ADS)

Hickernell, S.; Frey, H. M.; Manon, M. R. F.; Waters, L. E.

2017-12-01

Magmatic enclaves in volcanic rocks provide direct evidence of magma mingling/mixing within a magma reservoir and may reinvigorate the system and trigger eruption, as documented at the Soufriere Hills in Montserrat. Lava domes on the neighboring island of Dominica also contain multiple enclave populations and may be evidence for similar magma chamber processes. The central dome of Micotrin is at the head of the Roseau Valley, which was filled with 3 km3 of pyroclastic deposits from eruptions spanning 65 - 25 ka. There appear to be two distinct types of enclaves in the crystal-rich Micotrin andesites (60 wt% SiO2), fine-grained and coarse-grained. Fine-grained mafic enclaves (52 wt% SiO2) vary in size from 1 to 15 cm in diameter, whereas the coarse-grained enclaves are generally larger and range from 3-20 cm. Fine-grained enclaves are saturated in plag (35%) + opx (35%) + cpx (20%) + oxides (10%). Average pyroxenes are 0.01 to 0.02 cm in size, whereas plagioclase averages 0.05 cm and up to 0.1 cm. The texture of the fine-grained enclaves is cumulate-like, devoid of microlites and matrix glass. Coarse-grained enclaves lack cpx and have different modal abundances and textures: plag (75%) + opx (10%) + oxides (5%) + plag microlites (10%). Plagioclase are 0.1 cm in size and orthopyroxenes average 0.05 cm. The coarse-grained enclaves are highly vesicular, a notable difference from the host as well as the fine-grained enclaves. The boundaries of both the fine- and coarse-grained enclaves are quite sharp and distinct and there do not appear to be enclave minerals disaggregated in the host rock. Temperatures were determined by two oxides. The fine-grained enclaves had two populations of magnetite, yielding 847 + 21° and 920 + 17°C. The coarse-grained enclave was 890 + 42 °C, but the oxides were extensively exsolved. Plagioclase composition in both coarse and fine-grained samples was comparable, ranging from An50 to An80. Despite compositional similarity the textures of the plagioclase are distinctive. Fine-grained enclave plagioclase has patchy, uneven zoning, whereas coarse-grained enclave plagioclase has oscillatory zoning. The presence of these enclaves indicates that there may be several different magma inputs contributing to the system that is feeding Micotrin, and the injection of these unique magmas may be eruption triggers.

Mutually unbiased coarse-grained measurements of two or more phase-space variables

NASA Astrophysics Data System (ADS)

Paul, E. C.; Walborn, S. P.; Tasca, D. S.; Rudnicki, Łukasz

2018-05-01

Mutual unbiasedness of the eigenstates of phase-space operators—such as position and momentum, or their standard coarse-grained versions—exists only in the limiting case of infinite squeezing. In Phys. Rev. Lett. 120, 040403 (2018), 10.1103/PhysRevLett.120.040403, it was shown that mutual unbiasedness can be recovered for periodic coarse graining of these two operators. Here we investigate mutual unbiasedness of coarse-grained measurements for more than two phase-space variables. We show that mutual unbiasedness can be recovered between periodic coarse graining of any two nonparallel phase-space operators. We illustrate these results through optics experiments, using the fractional Fourier transform to prepare and measure mutually unbiased phase-space variables. The differences between two and three mutually unbiased measurements is discussed. Our results contribute to bridging the gap between continuous and discrete quantum mechanics, and they could be useful in quantum-information protocols.

Emergent dynamic structures and statistical law in spherical lattice gas automata.

PubMed

Yao, Zhenwei

2017-12-01

Various lattice gas automata have been proposed in the past decades to simulate physics and address a host of problems on collective dynamics arising in diverse fields. In this work, we employ the lattice gas model defined on the sphere to investigate the curvature-driven dynamic structures and analyze the statistical behaviors in equilibrium. Under the simple propagation and collision rules, we show that the uniform collective movement of the particles on the sphere is geometrically frustrated, leading to several nonequilibrium dynamic structures not found in the planar lattice, such as the emergent bubble and vortex structures. With the accumulation of the collision effect, the system ultimately reaches equilibrium in the sense that the distribution of the coarse-grained speed approaches the two-dimensional Maxwell-Boltzmann distribution despite the population fluctuations in the coarse-grained cells. The emergent regularity in the statistical behavior of the system is rationalized by mapping our system to a generalized random walk model. This work demonstrates the capability of the spherical lattice gas automaton in revealing the lattice-guided dynamic structures and simulating the equilibrium physics. It suggests the promising possibility of using lattice gas automata defined on various curved surfaces to explore geometrically driven nonequilibrium physics.

Emergent dynamic structures and statistical law in spherical lattice gas automata

NASA Astrophysics Data System (ADS)

Yao, Zhenwei

2017-12-01

Various lattice gas automata have been proposed in the past decades to simulate physics and address a host of problems on collective dynamics arising in diverse fields. In this work, we employ the lattice gas model defined on the sphere to investigate the curvature-driven dynamic structures and analyze the statistical behaviors in equilibrium. Under the simple propagation and collision rules, we show that the uniform collective movement of the particles on the sphere is geometrically frustrated, leading to several nonequilibrium dynamic structures not found in the planar lattice, such as the emergent bubble and vortex structures. With the accumulation of the collision effect, the system ultimately reaches equilibrium in the sense that the distribution of the coarse-grained speed approaches the two-dimensional Maxwell-Boltzmann distribution despite the population fluctuations in the coarse-grained cells. The emergent regularity in the statistical behavior of the system is rationalized by mapping our system to a generalized random walk model. This work demonstrates the capability of the spherical lattice gas automaton in revealing the lattice-guided dynamic structures and simulating the equilibrium physics. It suggests the promising possibility of using lattice gas automata defined on various curved surfaces to explore geometrically driven nonequilibrium physics.

Nonlinear evolution of coarse-grained quantum systems with generalized purity constraints

NASA Astrophysics Data System (ADS)

Burić, Nikola

2010-12-01

Constrained quantum dynamics is used to propose a nonlinear dynamical equation for pure states of a generalized coarse-grained system. The relevant constraint is given either by the generalized purity or by the generalized invariant fluctuation, and the coarse-grained pure states correspond to the generalized coherent, i.e. generalized nonentangled states. Open system model of the coarse-graining is discussed. It is shown that in this model and in the weak coupling limit the constrained dynamical equations coincide with an equation for pointer states, based on Hilbert-Schmidt distance, that was previously suggested in the context of the decoherence theory.

Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules.

PubMed

Zhang, Yuwei; Cao, Zexing; Zhang, John Zenghui; Xia, Fei

2017-02-27

Construction of coarse-grained (CG) models for large biomolecules used for multiscale simulations demands a rigorous definition of CG sites for them. Several coarse-graining methods such as the simulated annealing and steepest descent (SASD) based on the essential dynamics coarse-graining (ED-CG) or the stepwise local iterative optimization (SLIO) based on the fluctuation maximization coarse-graining (FM-CG), were developed to do it. However, the practical applications of these methods such as SASD based on ED-CG are subject to limitations because they are too expensive. In this work, we extend the applicability of ED-CG by combining it with the SLIO algorithm. A comprehensive comparison of optimized results and accuracy of various algorithms based on ED-CG show that SLIO is the fastest as well as the most accurate algorithm among them. ED-CG combined with SLIO could give converged results as the number of CG sites increases, which demonstrates that it is another efficient method for coarse-graining large biomolecules. The construction of CG sites for Ras protein by using MD fluctuations demonstrates that the CG sites derived from FM-CG can reflect the fluctuation properties of secondary structures in Ras accurately.

On information, negentropy and H-theorem

NASA Astrophysics Data System (ADS)

Chakrabarti, C. G.; Sarker, N. G.

1983-09-01

The paper deals with the imprtance of the Kullback descrimination information in the statistical characterization of negentropy of non-equilibrium state and the irreversibility of a classical dynamical system. The theory based on the Kullback discrimination information as the H-function gives new insight into the interrelation between the concepts of coarse-graining and the principle of sufficiency leading to important statistical characterization of thermal equilibrium of a closed system.

Response formulae for n-point correlations in statistical mechanical systems and application to a problem of coarse graining

NASA Astrophysics Data System (ADS)

Lucarini, Valerio; Wouters, Jeroen

2017-09-01

Predicting the response of a system to perturbations is a key challenge in mathematical and natural sciences. Under suitable conditions on the nature of the system, of the perturbation, and of the observables of interest, response theories allow to construct operators describing the smooth change of the invariant measure of the system of interest as a function of the small parameter controlling the intensity of the perturbation. In particular, response theories can be developed both for stochastic and chaotic deterministic dynamical systems, where in the latter case stricter conditions imposing some degree of structural stability are required. In this paper we extend previous findings and derive general response formulae describing how n- point correlations are affected by perturbations to the vector flow. We also show how to compute the response of the spectral properties of the system to perturbations. We then apply our results to the seemingly unrelated problem of coarse graining in multiscale systems: we find explicit formulae describing the change in the terms describing the parameterisation of the neglected degrees of freedom resulting from applying perturbations to the full system. All the terms envisioned by the Mori-Zwanzig theory—the deterministic, stochastic, and non-Markovian terms—are affected at first order in the perturbation. The obtained results provide a more comprehensive understanding of the response of statistical mechanical systems to perturbations. They also contribute to the goal of constructing accurate and robust parameterisations and are of potential relevance for fields like molecular dynamics, condensed matter, and geophysical fluid dynamics. We envision possible applications of our general results to the study of the response of climate variability to anthropogenic and natural forcing and to the study of the equivalence of thermostatted statistical mechanical systems.

Comparison of corrosion behavior between coarse grained and nano/ultrafine grained alloy 690

NASA Astrophysics Data System (ADS)

Jinlong, Lv; Tongxiang, Liang; Chen, Wang; Ting, Guo

2016-01-01

The effect of grain refinement on corrosion resistance of alloy 690 was investigated. The electron work function value of coarse grained alloy 690 was higher than that of nano/ultrafine grained one. The grain refinement reduced the electron work function of alloy 690. The passive films formed on coarse grained and nano/ultrafine grained alloy 690 in borate buffer solution were studied by potentiodynamic curves and electrochemical impedance spectroscopy and X-ray photoelectron spectroscopy. The results showed that the grain refinement improved corrosion resistance of alloy 690. This was attributed to the fact that grain refinement promoted the enrichment of Cr2O3 and inhibited Cr(OH)3 in the passive film. More Cr2O3 in passive film could significantly improve the corrosion resistance of the nano/ultrafine grained alloy 690.

A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties

NASA Astrophysics Data System (ADS)

Fu, Chia-Chun; Kulkarni, Pandurang M.; Scott Shell, M.; Gary Leal, L.

2012-10-01

Coarse-graining (CG) techniques have recently attracted great interest for providing descriptions at a mesoscopic level of resolution that preserve fluid thermodynamic and transport behaviors with a reduced number of degrees of freedom and hence less computational effort. One fundamental question arises: how well and to what extent can a "bottom-up" developed mesoscale model recover the physical properties of a molecular scale system? To answer this question, we explore systematically the properties of a CG model that is developed to represent an intermediate mesoscale model between the atomistic and continuum scales. This CG model aims to reduce the computational cost relative to a full atomistic simulation, and we assess to what extent it is possible to preserve both the thermodynamic and transport properties of an underlying reference all-atom Lennard-Jones (LJ) system. In this paper, only the thermodynamic properties are considered in detail. The transport properties will be examined in subsequent work. To coarse-grain, we first use the iterative Boltzmann inversion (IBI) to determine a CG potential for a (1-ϕ)N mesoscale particle system, where ϕ is the degree of coarse-graining, so as to reproduce the radial distribution function (RDF) of an N atomic particle system. Even though the uniqueness theorem guarantees a one to one relationship between the RDF and an effective pairwise potential, we find that RDFs are insensitive to the long-range part of the IBI-determined potentials, which provides some significant flexibility in further matching other properties. We then propose a reformulation of IBI as a robust minimization procedure that enables simultaneous matching of the RDF and the fluid pressure. We find that this new method mainly changes the attractive tail region of the CG potentials, and it improves the isothermal compressibility relative to pure IBI. We also find that there are optimal interaction cutoff lengths for the CG system, as a function of ϕ, that are required to attain an adequate potential while maintaining computational speedup. To demonstrate the universality of the method, we test a range of state points for the LJ liquid as well as several LJ chain fluids.

Influence of UFG structure formation on mechanical and fatigue properties in Ti-6Al-7Nb alloy

NASA Astrophysics Data System (ADS)

Polyakova, V. V.; Anumalasetty, V. N.; Semenova, I. P.; Valiev, R. Z.

2014-08-01

Ultrafine-grained (UFG) Ti alloys have potential applications in osteosynthesis and orthopedics due to high bio-compatibility and increased weight-to- strength ratio. In current study, Ti6Al7Nb ELI alloy is processed through equal channel angular pressing-conform (ECAP-Conform) and subsequent thermomechanical processing to generate a UFG microstructure. The fatigue properties of UFG alloys are compared to coarse grained (CG) alloys. Our study demonstrates that the UFG alloys with an average grain size of ~180 nm showed 35% enhancement of fatigue endurance limit as compared to coarse-grained alloys. On the fracture surfaces of the UFG and CG samples fatigue striations and dimpled relief were observed. However, the fracture surface of the UFG sample looks smoother; fewer amounts of secondary micro-cracks and more ductile rupture were also observed, which testifies to the good crack resistance in the UFG alloy after high-cyclic fatigue tests.

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field

PubMed Central

Stark, Austin C.; Andrews, Casey T.

2013-01-01

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods – especially with regard to using them to model, for example, intracellular environments – is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields. PMID:24223529

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.

PubMed

Stark, Austin C; Andrews, Casey T; Elcock, Adrian H

2013-09-10

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.

Atomistic and Coarse-Grained Modeling of the Adsorption of Graphene Nanoflakes at the Oil-Water Interface.

PubMed

Ardham, Vikram Reddy; Leroy, Frédéric

2018-03-01

The high interfacial tension between two immiscible liquids can provide the necessary driving force for the self-assembly of nanoparticles at the interface. Particularly, the interface between water and oily liquids (hydrocarbon chains) has been exploited to prepare networks of highly interconnected graphene sheets of only a few layers thickness, which are well suited for industrial applications. Studying such complex systems through particle-based simulations could greatly enhance the understanding of the various driving forces in action and could possibly give more control over the self-assembly process. However, the interaction potentials used in particle-based simulations are typically derived by reproducing bulk properties and are therefore not suitable for describing systems dominated by interfaces. To address this issue, we introduce a methodology to derive solid-liquid interaction potentials that yield an accurate representation of the balance between interfacial interactions at atomistic and coarse-grained resolutions. Our approach is validated through its ability to lead to the adsorption of graphene nanoflakes at the interface between water and n-hexane. The development of accurate coarse-grained potentials that our approach enables will allow us to perform large-scale simulations to study the assembly of graphene nanoparticles at the interface between immiscible liquids. Our methodology is illustrated through a simulation of many graphene nanoflakes adsorbing at the interface.

Evaluation of ultrasonic array imaging algorithms for inspection of a coarse grained material

NASA Astrophysics Data System (ADS)

Van Pamel, A.; Lowe, M. J. S.; Brett, C. R.

2014-02-01

Improving the ultrasound inspection capability for coarse grain metals remains of longstanding interest to industry and the NDE research community and is expected to become increasingly important for next generation power plants. A test sample of coarse grained Inconel 625 which is representative of future power plant components has been manufactured to test the detectability of different inspection techniques. Conventional ultrasonic A, B, and C-scans showed the sample to be extraordinarily difficult to inspect due to its scattering behaviour. However, in recent years, array probes and Full Matrix Capture (FMC) imaging algorithms, which extract the maximum amount of information possible, have unlocked exciting possibilities for improvements. This article proposes a robust methodology to evaluate the detection performance of imaging algorithms, applying this to three FMC imaging algorithms; Total Focusing Method (TFM), Phase Coherent Imaging (PCI), and Decomposition of the Time Reversal Operator with Multiple Scattering (DORT MSF). The methodology considers the statistics of detection, presenting the detection performance as Probability of Detection (POD) and probability of False Alarm (PFA). The data is captured in pulse-echo mode using 64 element array probes at centre frequencies of 1MHz and 5MHz. All three algorithms are shown to perform very similarly when comparing their flaw detection capabilities on this particular case.

Quantum decimation in Hilbert space: Coarse graining without structure

NASA Astrophysics Data System (ADS)

Singh, Ashmeet; Carroll, Sean M.

2018-03-01

We present a technique to coarse grain quantum states in a finite-dimensional Hilbert space. Our method is distinguished from other approaches by not relying on structures such as a preferred factorization of Hilbert space or a preferred set of operators (local or otherwise) in an associated algebra. Rather, we use the data corresponding to a given set of states, either specified independently or constructed from a single state evolving in time. Our technique is based on principle component analysis (PCA), and the resulting coarse-grained quantum states live in a lower-dimensional Hilbert space whose basis is defined using the underlying (isometric embedding) transformation of the set of fine-grained states we wish to coarse grain. Physically, the transformation can be interpreted to be an "entanglement coarse-graining" scheme that retains most of the global, useful entanglement structure of each state, while needing fewer degrees of freedom for its reconstruction. This scheme could be useful for efficiently describing collections of states whose number is much smaller than the dimension of Hilbert space, or a single state evolving over time.

Coarse-grained Mineral Dust Deposition in Alpine Lake Sediments: Implications for Regional Drought Patterns and Land-use Changes in the Southwest USA

NASA Astrophysics Data System (ADS)

Pedraza, A.; Kingsley, C.; Marchitto, T. M., Jr.; Lora, J. M.; Pollen, A.; Vollmer, T.; Leithold, E. L.; Mitchell, J.; Tripati, A. K.; Bhattacharya, A.

2017-12-01

Mineral dust accumulation is often causally associated with aridity. However, the relation might not be as straightforward. Consideration of grain sizes and geochemical fingerprinting of the coarse grain fraction will clearly have an impact on how we interpret the sedimentary record of mineral dust in depositional environments e.g. coarse grain fractions of mineral dust would most certainly be transported over relatively short distances and as such in depositional environments, the depositional rate of coarse grains must be determined in order to reliably understand erosional patterns associated with meteorological events (such as frequency of intense wind events such as tornadoes), climatological phenomenon (such as regional droughts) as well as more recently land-use changes. In this study we separate the two size fractions of mineral dust accumulation- fine fraction (typically <4 microns) and coarse fraction (typically >25 microns using grain size analysis from well-studied cores collected from several lake sites distributed across the western southwestern and the Great Plain regions; furthermore we use trace element analysis in each size fraction to identify contributing source regions. We find evidence that the coarser-grain size fraction in the studied lake cores could be of regional origin (and not just local in orgin);. the coarser fraction also appears to be related to intense meteorological events (i.e., the occurrence of cyclones). Analysis is underway to understand the impact of land-use changes on coarse grain fraction

The Effects of Hydration on Protein of Azurin using Coarse-Grained Method and The Free-Energy Analysis

NASA Astrophysics Data System (ADS)

Fitrasari, Dian; Purqon, Acep

2017-07-01

Proteins play important roles in body metabolism. However, to reveal hydration effects, it is cost computing especially for all-atom calculation. Coarse-grained method is one of potential solution to reduce the calculation and computable in longer timescale. Furthermore, the protein of Azurin is interesting protein and potentially applicable to cancer medicine for the stability property reason. We investigate the effects of hydration on Azurin, the conformation and the stabilities. Furthermore, we analyze the free-energy of the conformation system to find the favorable structure using free energy perturbation (FEP) calculation. Our calculation results show that free energy value of azurin is -136.9 kJ/mol. It shows a good agreement with experimental results with relative error index remained at 0.07%.

Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vögele, Martin; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M.; Holm, Christian

2015-12-28

We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models aremore » able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.« less

Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

PubMed Central

Chng, Choon-Peng; Yang, Lee-Wei

2008-01-01

Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the absence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed. PMID:19812774

High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.

PubMed

Haxton, Thomas K

2015-03-10

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are accurately approximated by their average values, while retaining soft degrees of freedom (unconstrained dihedral angles) mostly responsible for conformational variability. We demonstrate that our scheme retains nearly atomistic resolution by mapping all experimental protein configurations in the Protein Data Bank onto coarse-grained configurations and then analytically backmapping those configurations back to all-atom configurations. This roundtrip mapping throws away all information associated with the eliminated (stiff) degrees of freedom except for their average values, which we use to construct optimal backmapping functions. Despite the 4:1 reduction in the number of degrees of freedom, we find that heavy atoms move only 0.051 Å on average during the roundtrip mapping, while hydrogens move 0.179 Å on average, an unprecedented combination of efficiency and accuracy among coarse-grained protein models. We discuss the advantages of such a high-resolution model for parametrizing effective interactions and accurately calculating observables through direct or multiscale simulations.

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

PubMed Central

Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.

2015-01-01

We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences. PMID:26723608

Coarse-grained molecular dynamics simulations of depletion-induced interactions for soft matter systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shendruk, Tyler N., E-mail: tyler.shendruk@physics.ox.ac.uk; Bertrand, Martin; Harden, James L.

2014-12-28

Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics (MD) simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (Weeks-Chandler-Andersen (WCA)) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer. It is found that the depletion-induced well depth for the combinatorial-WCA model is significantly deeper than the shifted-WCA model because the resulting overlap ofmore » the colloids yields extra accessible volume for depletants. For both shifted- and combinatorial-WCA simulations, the second virial coefficients and pair potentials between colloids are demonstrated to be well approximated by the Morphometric Thermodynamics (MT) model. This agreement suggests that the presence of depletants can be accurately modelled in MD simulations by implicitly including them through simple, analytical MT forms for depletion-induced interactions. Although both WCA potentials are found to be effective generic coarse-grained simulation approaches for studying depletion effects in complicated soft matter systems, combinatorial-WCA is the more efficient approach as depletion effects are enhanced at lower depletant densities. The findings indicate that for soft matter systems that are better modelled by potentials with some compressibility, predictions from hard-sphere systems could greatly underestimate the magnitude of depletion effects at a given depletant density.« less

Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

PubMed

Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

2013-10-08

We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

Glass Formation of n-Butanol: Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

NASA Astrophysics Data System (ADS)

Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

2012-04-01

Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

Coarse graining of NN inelastic interactions up to 3 GeV: Repulsive versus structural core

NASA Astrophysics Data System (ADS)

Fernández-Soler, P.; Ruiz Arriola, E.

2017-07-01

The repulsive short-distance core is one of the main paradigms of nuclear physics which even seems confirmed by QCD lattice calculations. On the other hand nuclear potentials at short distances are motivated by high energy behavior where inelasticities play an important role. We analyze NN interactions up to 3 GeV in terms of simple coarse grained complex and energy dependent interactions. We discuss two possible and conflicting scenarios which share the common feature of a vanishing wave function at the core location in the particular case of S waves. We find that the optical potential with a repulsive core exhibits a strong energy dependence whereas the optical potential with the structural core is characterized by a rather adiabatic energy dependence which allows one to treat inelasticity perturbatively. We discuss the possible implications for nuclear structure calculations of both alternatives.

Using Bayes' theorem for free energy calculations

NASA Astrophysics Data System (ADS)

Rogers, David M.

Statistical mechanics is fundamentally based on calculating the probabilities of molecular-scale events. Although Bayes' theorem has generally been recognized as providing key guiding principals for setup and analysis of statistical experiments [83], classical frequentist models still predominate in the world of computational experimentation. As a starting point for widespread application of Bayesian methods in statistical mechanics, we investigate the central quantity of free energies from this perspective. This dissertation thus reviews the basics of Bayes' view of probability theory, and the maximum entropy formulation of statistical mechanics before providing examples of its application to several advanced research areas. We first apply Bayes' theorem to a multinomial counting problem in order to determine inner shell and hard sphere solvation free energy components of Quasi-Chemical Theory [140]. We proceed to consider the general problem of free energy calculations from samples of interaction energy distributions. From there, we turn to spline-based estimation of the potential of mean force [142], and empirical modeling of observed dynamics using integrator matching. The results of this research are expected to advance the state of the art in coarse-graining methods, as they allow a systematic connection from high-resolution (atomic) to low-resolution (coarse) structure and dynamics. In total, our work on these problems constitutes a critical starting point for further application of Bayes' theorem in all areas of statistical mechanics. It is hoped that the understanding so gained will allow for improvements in comparisons between theory and experiment.

Coarse grained modeling of directed assembly to form functional nanoporous films

NASA Astrophysics Data System (ADS)

Al Khatib, Amir

A coarse-grained (CG) simulation of polyethylene glycol (PEG) and Polymethylsilsesquixane nanoparticle (PMSSQ) referred to as (NP) at different sizes and concentrations were done using the Martini coarse-grained (CG) force field. The interactions between CG PEG and CG NP were parameterized from the chemical compound of each molecule and based on Martini force field. NP particles migrates to the surface of the substrate in an agreement with the experimental output at high temperature of 800K. This demonstration of nanoparticles-polymer film to direct it to self-assemble a systematically spatial pattern using the substrate surface energy as the key gating parameter. Validation of the model comparing molecular dynamics simulations with experimental data collected from previous study. NP interaction with the substrate at low interactions energy using Lennard-Johns potential were able to direct the NP to self-assemble in a hexagonal shape up to 4 layers above the substrate. This thesis established that substrate surface energy is a key gating parameter to direct the collective behavior of functional nanoparticles to form thin nanoporous films with spatially predetermined optical/dielectric constants.

Inverse Coarse-Graining: A New Tool for Molecular Design

DTIC Science & Technology

2010-12-16

simulations. When compared with the more general multiscale coarse-graining (MS-CG) method, the EF-CG method retains the transferable part of the CG...Y.; Yan, T.; Voth, G. A., A Multiscale coarse-graining study of liquid/vacuum interface of room-temperature ionic liquids with alkyl substituents of...Energetic Room Temperature Ionic Liquid 1-Hydroxyethyl-4Amino-1, 2, 4-Triazolium Nitrate (HEATN). J. Phys. Chem. B 2008, 112, 3121-3131. 6. Liu, P

Preparation of Entangled Polymer Melts of Various Architecture for Coarse-Grained Models

DTIC Science & Technology

2011-09-01

Simulator ( LAMMPS ). This report presents a theory overview and a manual how to use the method. 15. SUBJECT TERMS Ammunition, coarse-grained model...polymer builder, LAMMPS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF PAGES 26 19a. NAME OF RESPONSIBLE PERSON...scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ). Gel is an in house written C program of coarse- grained polymer builder, and LAMMPS is

Initial Isotopic Heterogeneities in ZAGAMI: Evidence of a Complex Magmatic History

NASA Technical Reports Server (NTRS)

Nyquist, L. E.; Shih, C.-Y.; Reese, Y. D.

2006-01-01

Interpretations of Zagami s magmatic history range from complex [1,2] to relatively simple [3]. Discordant radiometric ages led to a suggestion that the ages had been reset [4]. In an attempt to identify the mechanism, Rb-Sr isochrons were individually determined for both fine-grained and coarse-grained Zagami [5]. Ages of approx.180 Ma were obtained from both lithologies, but the initial Sr-87/Sr-86 (ISr) of the fine-grained lithology was higher by 8.6+/-0.4 e-units. Recently, a much older age of approx.4 Ga has been advocated [6]. Here, we extend our earlier investigation [5]. Rb-Sr Data: In [5] we applied identical, simplified, procedures to both lithologies to test whether a grain-size dependent process such as thermally-driven subsolidus isotopic reequilibration had caused age-resetting. Minerals were separated only by density. In the present experiment, purer mineral separates were analysed with improved techniques. Combined Rb-Sr results give ages (T) = 166+/-12 Ma and 177+/-9 Ma and I(subSr) = 0.72174+/-9 and 0.72227+/-7 for the coarse-grained and fine-grained lithologies, respectively. ISr in the fine-grained sample is thus higher than in the coarse-grained sample by 7.3+/-1.6 e-units. The results for the coarse-grained lithology are in close agreement with T = 166+/-6 Ma, ISr = 0.72157+/-8 for an adjacent sample [7] and T = 178+/-4 Ma, ISr = 0.72151+/-5 [4, adjusted] for a separate sample. Thus, fine-grained Zagami appears on average to be less typical of the bulk than coarse-grained Zagami.

Plutonium isotopes offer an alternative approach to establishing chronological profiles in coarse sediments

NASA Astrophysics Data System (ADS)

Pondell, C.; Kuehl, S. A.; Canuel, E. A.

2016-12-01

There are several methodologies used to determine chronologies for sediments deposited within the past 100 years, including 210Pb and 137Cs radioisotopes and organic and inorganic contaminants. These techniques are quite effective in fine sediments, which generally have a high affinity for metals and organic compounds. However, the application of these chronological tools becomes limited in systems where coarse sediments accumulate. Englebright Lake is an impoundment in northern California where sediment accumulation is characterized by a combination of fine and coarse sediments. This combination of sediment grain size complicated chronological analysis using the more traditional 137Cs chronological approach. This study established a chronology of these sediments using 239+240Pu isotopes. While most of the 249+240Pu activity was measured in the fine grain size fraction (<63 microns), up to 25% of the plutonium activity was detected in the coarse size fractions of sediments from Englebright Lake. Profiles of 239+240Pu were similar to available 137Cs profiles, verifying the application of plutonium isotopes for determining sediment chronologies and expanding the established geochronology for Englebright Lake sediments. This study of sediment accumulation in Englebright Lake demonstrates the application of plutonium isotopes in establishing chronologies in coarse sediments and highlights the potential for plutonium to offer new insights into patterns of coarse sediment accumulation.

Insights into the deformation behavior of the CrMnFeCoNi high-entropy alloy revealed by elevated temperature nanoindentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maier-Kiener, Verena; Schuh, Benjamin; George, Easo P.

A CrMnFeCoNi high-entropy alloy was investigated by nanoindentation from room temperature to 400 °C in the nanocrystalline state and cast plus homogenized coarse-grained state. In the latter case a < 100 >-orientated grain was selected by electron back scatter diffraction for nanoindentation. It was found that hardness decreases more strongly with increasing temperature than Young’s modulus, especially for the coarse-grained state. The modulus of the nanocrystalline state was slightly higher than that of the coarse-grained one. For the coarse-grained sample a strong thermally activated deformation behavior was found up to 100–150 °C, followed by a diminishing thermally activated contribution atmore » higher testing temperatures. For the nanocrystalline state, different temperature dependent deformation mechanisms are proposed. At low temperatures, the governing processes appear to be similar to those in the coarse-grained sample, but with increasing temperature, dislocation-grain boundary interactions likely become more dominant. Finally, at 400 °C, decomposition of the nanocrystalline alloy causes a further reduction in thermal activation. Furthermore, this is rationalized by a reduction of the deformation controlling internal length scale by precipitate formation in conjunction with a diffusional contribution.« less

Sediment distribution and hydrologic conditions of the Potomac aquifer in Virginia and parts of Maryland and North Carolina

USGS Publications Warehouse

McFarland, Randolph E.

2013-01-01

Sediments of the heavily used Potomac aquifer broadly contrast across major structural features of the Atlantic Coastal Plain Physiographic Province in eastern Virginia and adjacent parts of Maryland and North Carolina. Thicknesses and relative dominance of the highly interbedded fluvial sediments vary regionally. Vertical intervals in boreholes of coarse-grained sediment commonly targeted for completion of water-supply wells are thickest and most widespread across the central and southern parts of the Virginia Coastal Plain. Designated as the Norfolk arch depositional subarea, the entire sediment thickness here functions hydraulically as a single interconnected aquifer. By contrast, coarse-grained sediment intervals are thinner and less widespread across the northern part of the Virginia Coastal Plain and into southern Maryland, designated as the Salisbury embayment depositional subarea. Fine-grained intervals that are generally avoided for completion of water-supply wells are increasingly thick and widespread northward. Fine-grained intervals collectively as thick as several hundred feet comprise two continuous confining units that hydraulically separate three vertically spaced subaquifers. The subaquifers are continuous northward but merge southward into the single undivided Potomac aquifer. Lastly, far southeastern Virginia and northeastern North Carolina are designated as the Albemarle embayment depositional subarea, where both coarse- and fine-grained intervals are of only moderate thickness. The entire sediment thickness functions hydraulically as a single interconnected aquifer. A substantial hydrologic separation from overlying aquifers is imposed by the upper Cenomanian confining unit. Potomac aquifer sediments were deposited by a fluvial depositional complex spanning the Virginia Coastal Plain approximately 100 to 145 million years ago. Westward, persistently uplifted granite and gneiss source rocks sustained a supply of coarse-grained sand and gravel. Immature, high-gradient braided streams deposited longitudinal bars and channel fills across the Norfolk arch subarea. By contrast, across the Salisbury and Albemarle embayment subareas, mature, medium- to low-gradient meandering streams deposited medium- to coarse-grained channel fills and point bars segregated from fine-grained overbank deposits. The Virginia depositional complex merged northward across the Salisbury embayment subarea with another complex in Maryland. Here, additional sediments were received from schist source rocks that underwent three cycles of initial uplift and rapid erosion followed by crustal stability and erosional leveling. Because of the predominance of coarse-grained sediments, transmissivity, hydraulic conductivity, and regional velocities of lateral flow through the Potomac aquifer are greatest across the Norfolk arch depositional subarea, but decrease progressively northward with increasingly fine-grained sediments. Confining units hydraulically separate the Potomac aquifer from overlying aquifers, as indicated by large vertical hydraulic gradients. By contrast, most of the Potomac aquifer internally functions hydraulically as a single interconnected aquifer, as indicated by uniformly small vertical gradients. Most fine-grained sediments within the aquifer do not hydraulically separate overlying and underlying coarse-grained sediments. Across the Salisbury embayment depositional subarea, however, hydraulic separation among the vertically spaced subaquifers is imposed by the intervening confining units. The Potomac aquifer is the largest and most heavily used source of groundwater in the Virginia Coastal Plain. Water-level declines as great as 200 feet create the potential for saltwater intrusion. Conventional stratigraphic correlation has been generally ineffective at accurately characterizing complexly distributed fluvial sediments that compose the Potomac aquifer. Consequently, the aquifer’s internal hydraulic connectivity and overall hydrologic function have not been well understood. Water-supply planning and development efforts have been hampered, and interpretations of regulatory criteria for allowable water-level declines have been ambiguous. An investigation undertaken during 2010–11 by the U.S. Geological Survey, in cooperation with the Virginia Department of Environmental Quality, provides a comprehensive regional description of the spatial distribution of Potomac aquifer sediments and their relation to hydrologic conditions. Altitudes and thicknesses of 2,725 vertical sediment intervals represent the spatial distribution of Potomac aquifer sediments in the Virginia Coastal Plain and adjacent parts of Maryland and North Carolina. Sediment intervals are designated as either dominantly coarse or fine grained and were determined by interpretation of geophysical logs and ancillary information from 456 boreholes. Sediment-interval and borehole summary statistical data indicate regional trends in sediment lithology and stratigraphic continuity, upon which three structurally based and hydrologically distinct sediment depositional subareas are designated. Broad patterns of sediment deposition over time are inferred from published sediment pollen-age data. Discrepancies in previously drawn hydrostratigraphic relations between southeastern Virginia and northeastern North Carolina are partly resolved based on borehole geophysical logs and a recently documented geologic map and corehole. A conceptual model theorizes the depositional history of the sediments and geologically accounts for their distribution. Documented pumping tests of the Potomac aquifer at 197 locations produced 336 values of transmissivity and 127 values of storativity. Based on effective aquifer thicknesses, 296 values of sediment hydraulic conductivity and 113 values of sediment specific storage are calculated. Vertical hydraulic gradients are calculated from 9,479 pairs of water levels measured between November 17, 1953, and October 4, 2011, in 129 closely spaced pairs of wells. Borehole sediment-interval and related data provide a means to achieve high yielding production wells in the Potomac aquifer by site-specific targeting of drilling operations toward water-bearing coarse-grained sand and gravel. Advance knowledge of the potential of different parts of the aquifer also aids in planning optimal groundwater-development areas. Depositional subareas further provide a possible context for resource management. Current (2013) regulatory limits on water-level declines are relative to top surfaces of subdivided upper, middle, and lower Potomac aquifers across the entire Virginia Coastal Plain, but have the potential to exceed the same limit relative to a single undivided Potomac aquifer. By contrast, designation of the sediments as a single aquifer in the Norfolk arch and Albemarle embayment subareas—and as a series of vertically spaced subaquifers and intervening confining units in the Salisbury embayment subarea—best reflects understanding of the Potomac aquifer and can avoid the potential for excessive water-level declines. Simulation modeling to evaluate effects of groundwater withdrawals could be designed similarly, including vertical discretization and (or) zonation of the Potomac aquifer based on depositional subareas and a geostatistical distribution of aquifer properties derived from borehole sediment-interval data. Further resource-management information needs extend beyond the developed part of the Potomac aquifer, particularly across the Northern Neck and Middle Peninsula where only the shallowest part of the aquifer is known, and include structural aspects such as faults, basement bedrock, and the Chesapeake Bay impact crater.

Characteristics of sedimentary structures in coarse-grained alluvial rivers

NASA Astrophysics Data System (ADS)

Ackerley, David; Powell, Mark

2013-04-01

The characteristics of coarse-grained alluvial surfaces have important implications for the estimation of flow resistance, entrainment thresholds and sediment transport rates in gravel-bed rivers. This area of research has, thus, demanded attention from geomorphologists, sedimentologists, and river engineers. The majority of research has focused towards understanding the characteristics and adjustments in surface grain size. Bed stability, however, is not ultimately defined by particle size but how grains are arranged within the bed surface. For example, by the organisation of particles into a variety of grain and form scale sedimentary structures and bedforms (e.g. imbrication; pebble clusters, stone nets, transverse ribs). While it is widely acknowledged sedimentary structuring must be considered within estimates of flow resistance and sediment transport, relatively little is known about the structural properties of water-worked river gravels. As a consequence, we remain woefully ignorant of this important aspect of gravel-bed river sedimentology. The aim of this poster is to present some preliminary results of a study designed to characterise the morphodynamics of sedimentary structures in coarse-grained alluvial rivers and their implications upon entrainment thresholds and sediment transport rates. The poster focuses on investigating the variability in grain and form scale sedimentary structuring across a number of field sites. Representative patches of three gravel bars on the Rivers Wharfe, Manifold and Afon Elan, UK, have been surveyed using a Leica HDS 3000 Terrestrial Laser Scanner. The resultant raw point-cloud data, recorded at a 4mm resolution, has been registered, filtered, and interpolated to produce highly detailed 2½D digital elevation models of gravel-bed surface topography. These surfaces have been analysed using a number of structural parameters including bed elevation probability distribution function statistics (standard deviation, skewness, kurtosis), semivariograms, and inclination indices. This research enhances our understanding of alluvial bed surface structures and lays the foundations for developing a more detailed understanding of their morphodynamics.

On system behaviour using complex networks of a compression algorithm

NASA Astrophysics Data System (ADS)

Walker, David M.; Correa, Debora C.; Small, Michael

2018-01-01

We construct complex networks of scalar time series using a data compression algorithm. The structure and statistics of the resulting networks can be used to help characterize complex systems, and one property, in particular, appears to be a useful discriminating statistic in surrogate data hypothesis tests. We demonstrate these ideas on systems with known dynamical behaviour and also show that our approach is capable of identifying behavioural transitions within electroencephalogram recordings as well as changes due to a bifurcation parameter of a chaotic system. The technique we propose is dependent on a coarse grained quantization of the original time series and therefore provides potential for a spatial scale-dependent characterization of the data. Finally the method is as computationally efficient as the underlying compression algorithm and provides a compression of the salient features of long time series.

Coarse-Grained and Atomistic Modeling of Polyimides

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Hinkley, Jeffrey A.

2004-01-01

A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of BPDA (3,3,4,4' - biphenyltetracarboxylic dianhydride) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energy between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarsegrained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit.

The effect of surface grinding and sandblasting on flexural strength and reliability of Y-TZP zirconia ceramic.

PubMed

Kosmac, T; Oblak, C; Jevnikar, P; Funduk, N; Marion, L

1999-11-01

This study was conducted to evaluate the effect of grinding and sandblasting on the microstructure, biaxial flexural strength and reliability of two yttria stabilized tetragonal zirconia (Y-TZP) ceramics. Two Y-TZP powders were used to produce fine grained and coarse grained microstructures. Sixty discs from each material were randomly divided into six groups of ten. For each group, a different surface treatment was applied: dry grinding, wet grinding, sandblasting, dry grinding + sandblasting, sandblasting + dry grinding and a control group. Biaxial flexural strength was determined and data were analyzed using one-way ANOVA, followed by Tukey's HSD test (p < 0.05). In addition, Weibull statistics was used to analyze the variability of flexural strength. The relative amount of transformed monoclinic zirconia, corresponding transformed zone depth (TZD) and the mean critical defect size Ccr were calculated. There was no difference in mean strength between the as sintered fine and coarse grained Y-TZP. Significant differences (p < 0.05) were found between the control group and ground fine grained material for both wet and dry grinding. Sandblasting significantly increased the strength in fine and coarse grained materials. All surface treatment procedures reduced the Weibull modulus of Y-TZP. For both materials, the highest amount of the monoclinic phase and the largest TZD was found after sandblasting. Lower amounts of the monoclinic phase were obtained after both grinding procedures, where the highest mean critical defect size Ccr was also calculated. Our results indicate that sandblasting may provide a powerful technique for strengthening Y-TZP in clinical practice. In contrast, grinding may lead to substantial strength degradation and reduced reliability of prefabricated zirconia elements, therefore, sandblasting of ground surfaces is suggested.

Cross-Correlation for Automated Stitching of Two-Dimensional Multi-Tile Electron Backscatter Diffraction Data (Preprint)

DTIC Science & Technology

2012-08-01

270 350x 650 (25, 26) 2 20 Ni-15Al- 5Cr+C,B,Zr 187 x 187 500x 44 ( 4 , 11) 0.5 40 A. Coarse grain, single phase α- titanium The coarse grained... titanium alloy serves as an instructive example because, as evident in Figure 4 (a), only one triple point and one grain boundary appear in the search...wpafb.af.mil Figure 4 . Crystal orientation maps for the first (left) and second (current) tiles of (a) coarse grained α- Titanium , (b) a 2x2 array of a

Thermodynamics of adaptive molecular resolution

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, R.

2016-11-01

A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U(1)-U(0). The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al., J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as `real' thermodynamic variables. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Rapid Configurational Fluctuations in a Model of Methylcellulose

NASA Astrophysics Data System (ADS)

Li, Xiaolan; Dorfman, Kevin

Methylcellulose is a thermoresponsive polymer that undergoes a phase transition at elevated temperature, forming fibrils of a uniform diameter. However, the gelation mechanism is still unclear, in particular at higher polymer concentrations. We have investigated a coarse-grained model for methylcellulose, proposed by Larson and coworkers, that produces collapsed toroids in dilute solution with a radius close to that in experiments. Using Brownian Dynamics simulations, we demonstrate that this model's dihedral potential generates ``flipping events'', which helps the chain to avoid kinetic traps by undergoing a sudden transition between a coiled and a collapsed state. If the dihedral potential is removed, the chains cannot escape from their collapsed configuration, whereas at high dihedral potentials, the chains cannot stabilize the collapsed state. We will present quantitative results on the effect of the dihedral potential on both chain statistics and dynamic behavior, and discuss the implication of our results on the spontaneous formation of high-aspect ratio fibrils in experiments.

In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force

NASA Astrophysics Data System (ADS)

Menichetti, Roberto; Kanekal, Kiran H.; Kremer, Kurt; Bereau, Tristan

2017-09-01

The partitioning of small molecules in cell membranes—a key parameter for pharmaceutical applications—typically relies on experimentally available bulk partitioning coefficients. Computer simulations provide a structural resolution of the insertion thermodynamics via the potential of mean force but require significant sampling at the atomistic level. Here, we introduce high-throughput coarse-grained molecular dynamics simulations to screen thermodynamic properties. This application of physics-based models in a large-scale study of small molecules establishes linear relationships between partitioning coefficients and key features of the potential of mean force. This allows us to predict the structure of the insertion from bulk experimental measurements for more than 400 000 compounds. The potential of mean force hereby becomes an easily accessible quantity—already recognized for its high predictability of certain properties, e.g., passive permeation. Further, we demonstrate how coarse graining helps reduce the size of chemical space, enabling a hierarchical approach to screening small molecules.

Accumulation of fossil fuels and metallic minerals in active and ancient rift lakes

USGS Publications Warehouse

Robbins, E.I.

1983-01-01

A study of active and ancient rift systems around the world suggests that accumulations of fossil fuels and metallic minerals are related to the interactions of processes that form rift valleys with those that take place in and around rift lakes. The deposition of the precursors of petroleum, gas, oil shale, coal, phosphate, barite, Cu-Pb-Zn sulfides, and uranium begins with erosion of uplifted areas, and the consequent input of abundant nutrients and solute loads into swamps and tectonic lakes. Hot springs and volcanism add other nutrients and solutes. The resulting high biological productivity creates oxidized/reduced interfaces, and anoxic and H2S-rich bottom waters which preserves metal-bearing organic tissues and horizons. In the depositional phases, the fine-grained lake deposits are in contact with coarse-grained beach, delta, river, talus, and alluvial fan deposits. Earthquake-induced turbidites also are common coarse-grained deposits of rift lakes. Postdepositional processes in rifts include high heat flow and a resulting concentration of the organic and metallic components that were dispersed throughout the lakebeds. Postdepositional faulting brings organic- and metal-rich sourcebeds in contact with coarse-grained host and reservoir rocks. A suite of potentially economic deposits is therefore a characteristic of rift valleys. ?? 1983.

Accumulation of fossil fuels and metallic minerals in active and ancient rift lakes

NASA Astrophysics Data System (ADS)

Robbins, Eleanora Iberall

1983-05-01

A study of active and ancient rift systems around the world suggests that accumulations of fossil fuels and metallic minerals are related to the interactions of processes that form rift valleys with those that take place in and around rift lakes. The deposition of the precursors of petroleum, gas, oil shale, coal, phosphate, barite, Cu-Pb-Zn sulfides, and uranium begins with erosion of uplifted areas, and the consequent input of abundant nutrients and solute loads into swamps and tectonic lakes. Hot springs and volcanism add other nutrients and solutes. The resulting high biological productivity creates oxidized/reduced interfaces, and anoxic and H 2S-rich bottom waters which preserves metal-bearing organic tissues and horizons. In the depositional phases, the fine-grained lake deposits are in contact with coarse-grained beach, delta, river, talus, and alluvial fan deposits. Earthquake-induced turbidites also are common coarse-grained deposits of rift lakes. Postdepositional processes in rifts include high heat flow and a resulting concentration of the organic and metallic components that were dispersed throughout the lakebeds. Postdepositional faulting brings organic- and metal-rich sourcebeds in contact with coarse-grained host and reservoir rocks. A suite of potentially economic deposits is therefore a characteristic of rift valleys.

Paramaterization of a coarse-grained model for linear alkylbenzene sulfonate surfactants and molecular dynamics studies of their self-assembly in aqueous solution

NASA Astrophysics Data System (ADS)

He, Xibing; Shinoda, Wataru; DeVane, Russell; Anderson, Kelly L.; Klein, Michael L.

2010-02-01

A coarse-grained (CG) forcefield for linear alkylbenzene sulfonates (LAS) was systematically parameterized. Thermodynamic data from experiments and structural data obtained from all-atom molecular dynamics were used as targets to parameterize CG potentials for the bonded and non-bonded interactions. The added computational efficiency permits one to employ computer simulation to probe the self-assembly of LAS aqueous solutions into different morphologies starting from a random configuration. The present CG model is shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization.

Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

PubMed Central

2015-01-01

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations. PMID:25290376

Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

PubMed

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

2014-10-16

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations.

Swash mark and grain flow

USGS Publications Warehouse

Sallenger,, Asbury H.

1981-01-01

Swash marks composed entirely of coarse sand are commonly found on coarse-sand beaches. These swash marks are 10 to 30 centimeters in width and a few millimeters to one centimeter in height. Previous observations, mostly on finer-sand beaches, indicate swash marks are seldom over a few millimeters in height and are commonly composed of material readily floated by surface tension (e.g., mica flakes and shell fragments). Swash marks composed of coarse sand have both fining seaward and fining with depth trends in grain size. Apparently, the leading margin of a wave upwash drives a highly concentrated flow of grains in which both grain size and grain velocity decrease with depth. Therefore, large grains are transported at greater velocities than are smaller grains. Thus, at the maximum advance of an upwash, a swash mark is deposited which has the observed fining seaward and fining with depth trends in grain size.

Textural and stable isotope studies of the Big Mike cupriferous volcanogenic massive sulfide deposit, Pershing County, Nevada.

USGS Publications Warehouse

Rye, R.O.; Roberts, R.J.; Snyder, W.S.; Lahusen, G.L.; Motica, J.E.

1984-01-01

The Big Mike deposit is a massive sulphide lens entirely within a carbonaceous argillite of the Palaeozoic Havallah pelagic sequence. The massive ore contains two generations of pyrite, a fine- and a coarse-grained variety; framboidal pyrite occurs in the surrounding carbonaceous argillite. Coarse grained pyrite is largely recrystallized fine-grained pyrite and is proportionately more abundant toward the margins of the lens. Chalcopyrite and sphalerite replace fine-grained pyrite and vein-fragmented coarse-grained pyrite. Quartz fills openings in the sulphide fabric. S-isotope data are related to sulphide mineralogy and textures. Isotopically light S in the early fine-grained pyrite was probably derived from framboidal biogenic pyrite. The S-isotope values of the later coarse-grained pyrite and chalcopyrite probably reflect a combination of reduced sea-water sulphate and igneous S. Combined S- and O-isotope and textural data accord with precipitation of fine-grained pyrite from a hydrothermal plume like those at the East Pacific Rise spreading centre at lat. 21oN. The primary material was recystallized and mineralized by later fluids of distinctly different S-isotope composition. -G.J.N.

Molecular Modeling of Thermosetting Polymers: Effects of Degree of Curing and Chain Length on Thermo-Mechanical Properties

DTIC Science & Technology

2012-08-01

paper, we will first briefly discuss our recent results, using coarse-grained bead - spring model , on the dependence of failure stress and failure...length of the resin strands. In the coarse-grained model used here the polymer network is treated as a bead - spring system. To create highly cross...simulations of Thermosets We have used a coarse-grained bead - spring model to study the dependence of the mechanical properties of thermosets on chain

Mechanical behavior of nanostructured and ultrafine-grained materials under shock wave loadings. experimental data and results of computer simulation

NASA Astrophysics Data System (ADS)

Skripnyak, Vladimir

2012-03-01

Features of mechanical behavior of nanostructured and ultrafine-grained metals under quasistatic and shock wave loadings are discussed. Features of mechanical behavior of nanostructured and ultrafine grained metals over a wide range of strain rates are discussed. A constitutive model for mechanical behavior of metal alloys under shock wave loading including a grain size distribution, a precipitate hardening, and physical mechanisms of shear stress relaxation is presented. Strain rate sensitivity of the yield stress of face-centered-cubic, hexagonal close-packed metal alloys depends on grain size, whereas the Hugoniot elastic limits of ultrafine-grained copper, aluminum, and titanium alloys are close to values of coarse-grained counterparts. At quasi-static loading the yield strength and the tensile strength of titanium alloys with grain size from 300 to 500 nm are twice higher than at coarse-grained counterparts. But the spall strength of the UFG titanium alloys exceeds the value of coarse-grained counterparts only for 10 percents.

Application of pinch-and-swell structure rheology gauge to determine rock paleo-rheological parameters in Taili, western Liaoning, NE China

NASA Astrophysics Data System (ADS)

Sun, Zhengquan; Zeng, Zuoxun; Wu, Linbo; Xu, Shaopeng; Yang, Shuang; Chen, Deli; Wang, Jianxiu

2017-05-01

New results, in combination with previously published ones, reveal that when the Stress Exponent of the Competent layer (SEC) ranges from 1 to 10 (1 < n < 10), Pinch-and-Swell structure Rheology Gauge (PSRG) can only be available under the condition that the Viscosity ratio between the Competent layer and its corresponding Matrix layer (VCM) is larger than 10. Therefore, we made the attempt to calculate the viscosity ratio of pinch-and-swell structure of competent layer to the related matrix and stress exponent. Based on this knowledge, we applied this gauge to calculate SECs and VCMs of eight types of pinch-and-swell structures, which are widely developed in the Taili area of the west Liaoning Province in China. Statistical analysis of the SEC resulted in intervals of four types of competent layers, that is, Medium-scale Granitic coarse-to-pegmatitic Veins, Small-scale Augen Granite aplite Veins, Small-scale Granite aplite Veins, and Small-scale Augen Quartz-K-feldspar veins, with intervals of [3.50, 4.63], [2.64, 4.29], [2.70, 3.51], and [2.50, 3.36] respectively. The preferred intervals of VCM of the five types of pinch-and-swell structures, Small-scale Augen Granite aplite Veins + Fine-grained Biotite-Hornblende-plagioclase Gneiss, Medium-scale Granitic coarse-to-pegmatitic Veins + Fine-grained Biotite-Hornblende-plagioclase Gneiss, Small-scale Augen Granite aplite Veins + medium-to-fine-grained granitic gneiss, Medium-scale Granitic coarse-to-pegmatitic Veins + medium-to-fine-grained granitic gneiss, and Small-scale Augen Granite aplite Veins + fine-grained biotite-plagioclase gneiss, are [19.98, 62.51], [15.90, 61.17], [26.72, 93.27], [22.21, 107.26], and [76.33, 309.39] respectively. The similarities between these calculated SEC statistical preferred intervals and the physical experimental results verify the validity of the PSRG. The competent layers of the pinch-and-swell structures were presented in this study as power-law flow with SEC values that increased with the thickness of the layer. Grain-size plays an important role in the rheology of pinch-and-swell structures. The results offer a case for the application of PSRG and determine the key rock rheological parameters of North China Craton for future related studies.

A method for automatic grain segmentation of multi-angle cross-polarized microscopic images of sandstone

NASA Astrophysics Data System (ADS)

Jiang, Feng; Gu, Qing; Hao, Huizhen; Li, Na; Wang, Bingqian; Hu, Xiumian

2018-06-01

Automatic grain segmentation of sandstone is to partition mineral grains into separate regions in the thin section, which is the first step for computer aided mineral identification and sandstone classification. The sandstone microscopic images contain a large number of mixed mineral grains where differences among adjacent grains, i.e., quartz, feldspar and lithic grains, are usually ambiguous, which make grain segmentation difficult. In this paper, we take advantage of multi-angle cross-polarized microscopic images and propose a method for grain segmentation with high accuracy. The method consists of two stages, in the first stage, we enhance the SLIC (Simple Linear Iterative Clustering) algorithm, named MSLIC, to make use of multi-angle images and segment the images as boundary adherent superpixels. In the second stage, we propose the region merging technique which combines the coarse merging and fine merging algorithms. The coarse merging merges the adjacent superpixels with less evident boundaries, and the fine merging merges the ambiguous superpixels using the spatial enhanced fuzzy clustering. Experiments are designed on 9 sets of multi-angle cross-polarized images taken from the three major types of sandstones. The results demonstrate both the effectiveness and potential of the proposed method, comparing to the available segmentation methods.

Effect of physicochemical factors on transport and retention of graphene oxide in saturated media.

PubMed

Chen, Chong; Shang, Jianying; Zheng, Xiaoli; Zhao, Kang; Yan, Chaorui; Sharma, Prabhakar; Liu, Kesi

2018-05-01

Fate and transport of graphene oxide (GO) have received much attention recently with the increase of GO applications. This study investigated the effect of salt concentration on the transport and retention behavior of GO particles in heterogeneous saturated porous media. Transport experiments were conducted in NaCl solutions with three concentrations (1, 20, and 50 mM) using six structurally packed columns (two homogeneous and four heterogeneous) which were made of fine and coarse grains. The results showed that GO particles had high mobility in all the homogeneous and heterogeneous columns when solution ionic strength (IS) was low. When IS was high, GO particles showed distinct transport ability in six structurally heterogeneous porous media. In homogeneous columns, decreasing ionic strength and increasing grain size increased the mobility of GO. For the column containing coarse-grained channel, the preferential flow path resulted in an early breakthrough of GO, and further larger contact area between coarse and fine grains caused a lower breakthrough peak and a stronger tailing at different IS. In the layered column, there was significant GO retention at coarse-fine grain interface where water flowed from coarse grain to fine grain. Our results indicated that the fate and transport of GO particles in the natural heterogeneous porous media was highly related to the coupled effect of medium structure and salt solution concentration. Copyright © 2018 Elsevier Ltd. All rights reserved.

Can coarse surface layers in gravel-bedded rivers be mobilized by finer gravel bedload?

NASA Astrophysics Data System (ADS)

Venditti, J. G.; Dietrich, W. E.; Nelson, P. A.; Wydzga, M. A.; Fadde, J.; Sklar, L.

2005-12-01

In response to reductions in sediment supply, gravel-bed rivers undergo a coarsening of the sediments that comprise the river's bed and, over some longer time scale, a river's grade may also be reduced as sediments are depleted from upstream reaches. Coarse, degraded river reaches are commonly observed downstream of dams across the Western United States. Following dam closure, these riverbeds become immobile under the altered flow and sediment supply regimes, leading to a reduction in the available salmon spawning and rearing habitat. Gravel augmentation to these streams is now common practice. This augmentation is typically seen as resurfacing the static coarse bed. As an alternative, we propose that the addition of appropriately finer gravels to these channels may be capable of mobilizing an otherwise immobile coarse surface layer, creating the potential to release fine material trapped beneath the surface. A series of laboratory experiments are being undertaken to test this hypothesis in a 30 m long and 0.86 m wide gravel-bedded flume channel using a constant discharge and a unimodal bed sediment with a median grain size of 8 mm and no sand present. The channel width-to-depth ratio of ~4 suppresses the development of lateral topography and allows us to focus on grain-to-grain interactions. Experiments proceed by maintaining a constant sediment feed until an equilibrium grade and transport rate are established, starving the flume of sediment for at least 24 hours, and then adding narrowly graded gravel over a period of one to two hours at a rate that is ~4x the bedload rate observed prior to terminating the sediment supply. The bed prior to sediment addition has an armor median grain size that is typically twice that of the subsurface and feed size distribution. The volume and median grain size of the resulting pulses are varied. Pulses move downstream rapidly with well-defined fronts in the form of bedload sheets and cause peaks in the sediment flux approximately equal to the supply rate. Once the pulse has passed through the flume, bedload flux rapidly drops to background values, leaving few introduced grains on the bed. When the sediment feed is the median grain size of the subsurface bed material mixture, few armor grains are mobilized, although there is some exchange between the surface and bedload. Pulses composed of the fine tail of the surface grain size distribution are capable of mobilizing all grain sizes in the armor (including the largest grains) as finer bedload fills the interstices of the coarse surface layer. This suggests that gravel augmentation using fine gravel may provide an effective means of improving bed mobility conditions. Further experiments are underway to explore the effects of repeated fine gravel addition on bed state.

A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

PubMed Central

Qin, Feng

2015-01-01

The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

Sediment transport processes in the Pearl River Estuary as revealed by grain-size end-member modeling and sediment trend analysis

NASA Astrophysics Data System (ADS)

Li, Tao; Li, Tuan-Jie

2018-04-01

The analysis of grain-size distribution enables us to decipher sediment transport processes and understand the causal relations between dynamic processes and grain-size distributions. In the present study, grain sizes were measured from surface sediments collected in the Pearl River Estuary and its adjacent coastal areas. End-member modeling analysis attempts to unmix the grain sizes into geologically meaningful populations. Six grain-size end-members were identified. Their dominant modes are 0 Φ, 1.5 Φ, 2.75 Φ, 4.5 Φ, 7 Φ, and 8 Φ, corresponding to coarse sand, medium sand, fine sand, very coarse silt, silt, and clay, respectively. The spatial distributions of the six end-members are influenced by sediment transport and depositional processes. The two coarsest end-members (coarse sand and medium sand) may reflect relict sediments deposited during the last glacial period. The fine sand end-member would be difficult to transport under fair weather conditions, and likely indicates storm deposits. The three remaining fine-grained end-members (very coarse silt, silt, and clay) are recognized as suspended particles transported by saltwater intrusion via the flood tidal current, the Guangdong Coastal Current, and riverine outflow. The grain-size trend analysis shows distinct transport patterns for the three fine-grained end-members. The landward transport of the very coarse silt end-member occurs in the eastern part of the estuary, the seaward transport of the silt end-member occurs in the western part, and the east-west transport of the clay end-member occurs in the coastal areas. The results show that grain-size end-member modeling analysis in combination with sediment trend analysis help to better understand sediment transport patterns and the associated transport mechanisms.

Piedramuelle Limestone in the building heritage of Oviedo, Spain, and adjacent towns.

NASA Astrophysics Data System (ADS)

Cardenes Van den Eynde, Victor; Mateos, Felix Javier; Valdeon, Luis; Rojo, Araceli

2017-04-01

The Piedramuelle limestone has a very important representation in the building heritage of Oviedo, historical capital of Asturias (Spain) and surrounding towns. This argillaceous limestone has been quarried since the High Middle Ages until the beginning of the XX century. The main mineralogical components are carbonates (mainly calcite and sometimes ankerite, 70-90%), quartz (5-15%), terrigenous minerals (6-15%) and iron oxides (<5%). Two different facies, with different constructive uses, can be clearly distinguished depending on the grain size: fine-grained facies and coarse-grained facies. The fine-grained facies has color ranging from red to yellow, slightly higher content in carbonates, higher terrigenous components and a micro crystalline texture. The coarse-grained facies is mainly yellow, with detrital clastic texture. The open porosity is higher for the coarse-grained facies (16-20%), while for the fine-grained facies it ranges between 5 and 15%. The fine-grained facies is more vulnerable to weathering than the coarse-grained one, and it is used in the building heritage mainly for ornamental details, while the coarse-grained one is found in the bigger blocks and ashlars of the buildings. Some of the buildings constructed with Piedramuelle limestone are the Cathedral, the Old University and the Palaces from the XVII and XVIII centuries. The ambiance and historical architecture of Oviedo and adjacent towns is closely linked with the textures and colors of this stone. Nowadays, the Piedramuelle limestone is not exploited anymore, being the quarries exhausted. This represents an issue from a conservation point of view, since there is not a suitable stone for replacement. In order to preserve and maintain the building heritage of these towns, it is very important to prospect and protect the remaining outcrops still able to supply this characteristic stone.

Force-field parameters from the SAFT-γ equation of state for use in coarse-grained molecular simulations.

PubMed

Müller, Erich A; Jackson, George

2014-01-01

A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.

Adaptive resolution simulation of an atomistic protein in MARTINI water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecularmore » dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.« less

Adaptive resolution simulation of an atomistic protein in MARTINI water.

PubMed

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J; Praprotnik, Matej

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

Coarse-grained simulations of cis- and trans-polybutadiene: A bottom-up approach

NASA Astrophysics Data System (ADS)

Lemarchand, Claire A.; Couty, Marc; Rousseau, Bernard

2017-02-01

We apply the dissipative particle dynamics strategy proposed by Hijón et al. [Faraday Discuss. 144, 301-322 (2010)] and based on an exact derivation of the generalized Langevin equation to cis- and trans-1,4-polybutadiene. We prove that it is able to reproduce not only the structural but also the dynamical properties of these polymers without any fitting parameter. A systematic study of the effect of the level of coarse-graining is done on cis-1,4-polybutadiene. We show that as the level of coarse-graining increases, the dynamical properties are better and better reproduced while the structural properties deviate more and more from those calculated in molecular dynamics (MD) simulations. We suggest two reasons for this behavior: the Markovian approximation is better satisfied as the level of coarse-graining increases, while the pair-wise approximation neglects important contributions due to the relative orientation of the beads at large levels of coarse-graining. Finally, we highlight a possible limit of the Markovian approximation: the fact that in constrained simulations, in which the centers-of-mass of the beads are kept constant, the bead rotational dynamics become extremely slow.

Coarse-grained hydrodynamics from correlation functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palmer, Bruce

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configuration from a molecular dynamics simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilbrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is applied to some simple hydrodynamic cases to determine the feasibility of applying this to realistic nanoscale systems.

Graph-based analysis of kinetics on multidimensional potential-energy surfaces.

PubMed

Okushima, T; Niiyama, T; Ikeda, K S; Shimizu, Y

2009-09-01

The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters.

Monte-Carlo simulations of a coarse-grained model for α-oligothiophenes

NASA Astrophysics Data System (ADS)

Almutairi, Amani; Luettmer-Strathmann, Jutta

The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. Oligothiophenes are small, π-conjugated molecules with applications in organic electronics that also serve as small-molecule models for polythiophenes. α-hexithiophene (6T) is a six-ring molecule, whose adsorption on noble metal surfaces has been studied extensively (see, e.g., Ref.). In this work, we develop a coarse-grained model for α-oligothiophenes. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. We perform Monte Carlo simulations to study the structure of isolated and adsorbed molecules

Modeling epidemics on adaptively evolving networks: A data-mining perspective.

PubMed

Kattis, Assimakis A; Holiday, Alexander; Stoica, Ana-Andreea; Kevrekidis, Ioannis G

2016-01-01

The exploration of epidemic dynamics on dynamically evolving ("adaptive") networks poses nontrivial challenges to the modeler, such as the determination of a small number of informative statistics of the detailed network state (that is, a few "good observables") that usefully summarize the overall (macroscopic, systems-level) behavior. Obtaining reduced, small size accurate models in terms of these few statistical observables--that is, trying to coarse-grain the full network epidemic model to a small but useful macroscopic one--is even more daunting. Here we describe a data-based approach to solving the first challenge: the detection of a few informative collective observables of the detailed epidemic dynamics. This is accomplished through Diffusion Maps (DMAPS), a recently developed data-mining technique. We illustrate the approach through simulations of a simple mathematical model of epidemics on a network: a model known to exhibit complex temporal dynamics. We discuss potential extensions of the approach, as well as possible shortcomings.

Landau-Lifshitz-Bloch equation for exchange-coupled grains

NASA Astrophysics Data System (ADS)

Vogler, Christoph; Abert, Claas; Bruckner, Florian; Suess, Dieter

2014-12-01

Heat-assisted recording is a promising technique to further increase the storage density in hard disks. Multilayer recording grains with graded Curie temperature is discussed to further assist the write process. Describing the correct magnetization dynamics of these grains, from room temperature to far above the Curie point, during a write process is required for the calculation of bit error rates. We present a coarse-grained approach based on the Landau-Lifshitz-Bloch (LLB) equation to model exchange-coupled grains with low computational effort. The required temperature-dependent material properties such as the zero-field equilibrium magnetization as well as the parallel and normal susceptibilities are obtained by atomistic Landau-Lifshitz-Gilbert simulations. Each grain is described with one magnetization vector. In order to mimic the atomistic exchange interaction between the grains a special treatment of the exchange field in the coarse-grained approach is presented. With the coarse-grained LLB model the switching probability of a recording grain consisting of two layers with graded Curie temperature is investigated in detail by calculating phase diagrams for different applied heat pulses and external magnetic fields.

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

PubMed

Shen, Lin; Hu, Hao

2014-06-10

We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

Adiabatic coarse-graining and simulations of stochastic biochemical networks

PubMed Central

Sinitsyn, N. A.; Hengartner, Nicolas; Nemenman, Ilya

2009-01-01

We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian fluctuations of the slow ones. Our approach is similar to the Born–Oppenheimer approximation in quantum mechanics and follows from the stochastic path integral representation of the cumulant generating function of reaction events. In applications with a small number of chemical reactions, it produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, interpretable representation and can be used for high-accuracy, low-complexity coarse-grained numerical simulations. As an example, we derive the coarse-grained description for a chain of biochemical reactions and show that the coarse-grained and the microscopic simulations agree, but the former is 3 orders of magnitude faster. PMID:19525397

Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.

PubMed

Henrich, Oliver; Gutiérrez Fosado, Yair Augusto; Curk, Tine; Ouldridge, Thomas E

2018-05-10

During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.

Local-feature analysis for automated coarse-graining of bulk-polymer molecular dynamics simulations.

PubMed

Xue, Y; Ludovice, P J; Grover, M A

2012-12-01

A method for automated coarse-graining of bulk polymers is presented, using the data-mining tool of local feature analysis. Most existing methods for polymer coarse-graining define superatoms based on their covalent bonding topology along the polymer backbone, but here superatoms are defined based only on their correlated motions, as observed in molecular dynamics simulations. Correlated atomic motions are identified in the simulation data using local feature analysis, between atoms in the same or in different polymer chains. Groups of highly correlated atoms constitute the superatoms in the coarse-graining scheme, and the positions of their seed coordinates are then projected forward in time. Based on only the seed positions, local feature analysis enables the full reconstruction of all atomic positions. This reconstruction suggests an iterative scheme to reduce the computation of the simulations to initialize another short molecular dynamic simulation, identify new superatoms, and again project forward in time.

Volatile elements in Allende inclusions. [Mn, Na and Cl relation to meteorite evolution

NASA Technical Reports Server (NTRS)

Grossman, L.; Ganapathy, R.

1975-01-01

New data are presented on the relatively volatile elements (Mn, Na, and Cl) in coarse- and fine-grained Ca/Al-rich inclusions of different textures and mineralogy in the Allende meteorite. It is shown that the coarse-grained inclusions condensed from the solar nebula at high temperature and contained vanishingly small quantities of volatile elements at that time. Later, volatiles were added to these during the metamorphism of the Allende parent body. The fine-grained inclusions were also affected by the addition of volatiles during this metamorphism but, unlike the coarse-grained ones, they incorporated large amounts of volatiles when they condensed from the solar nebula, accounting for their higher volatile element contents.

Thermodynamics of adaptive molecular resolution.

PubMed

Delgado-Buscalioni, R

2016-11-13

A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U (1) -U (0) The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al, J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as 'real' thermodynamic variablesThis article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Geochemistry and tectonic implications of the Early Carboniferous Keketuobie intrusion in the West Junggar foldbelt, NW China

NASA Astrophysics Data System (ADS)

Deng, Yu-Feng; Yuan, Feng; Zhou, Taofa; Hollings, Pete; Zhang, Dayu

2018-06-01

The Keketuobie intrusion is situated in the northern part of the West Junggar foldbelt at the southern margin of the Central Asian Orogeic Belt. The intrusion consists of medium- to coarse-grained gabbro, fine-grained gabbro and diorite. Igneous zircons from the medium- to coarse-grained gabbro yielded a LA-ICP-MS U-Pb age of 320.8 ± 5.7 Ma, indicating that the intrusion was emplaced in the Early Carboniferous. The intrusive contact between the medium- to coarse-grained gabbro and the fine-grained gabbro indicates they formed from distinct magma pulses. Magnetite crystals from the fine-grained gabbro have lower V2O3 but higher TiO2 and Al2O3 contents than those of the medium- to coarse-grained gabbro, suggesting that the fine-grained gabbro crystallized in a relatively higher fO2 and temperature magma than the medium- to coarse-grained gabbro. The Keketuobie intrusive rocks are characterized by enriched large ion lithophile elements and depleted high field strength elements relative to N-MORB with restricted (87Sr/86Sr)t ratios (0.70370-0.70400) and εNd(t) values (+5.85 to +6.97). The petrography and geochemistry are comparable to those of subduction-related volcanic rocks. The trace elements and isotopic compositions of the mafic intrusive rocks suggest that the primary magmas were derived from mixing of metasomatized lithospheric mantle and depleted asthenospheric melts, perhaps triggered by slab break-off. The Keketuobie intrusion is younger than adjacent ophiolite sequences, island arc volcanic rocks and porphyry deposits, but predates the post-collisional A-type granites and bimodal volcanic rocks in the district, suggesting that the Keketuobie intrusion likely formed in a syn-collisional setting.

Effects of cross-linking on partitioning of nanoparticles into a polymer brush: Coarse-grained simulations test simple approximate theories

NASA Astrophysics Data System (ADS)

Ozmaian, Masoumeh; Jasnow, David; Eskandari Nasrabad, Afshin; Zilman, Anton; Coalson, Rob D.

2018-01-01

The effect of cohesive contacts or, equivalently, dynamical cross-linking on the equilibrium morphology of a polymer brush infiltrated by nanoparticles that are attracted to the polymer strands is studied for plane-grafted brushes using coarse-grained molecular dynamics and approximate statistical mechanical models. In particular, the Alexander-de Gennes (AdG) and Strong Stretching Theory (SST) mean-field theory (MFT) models are considered. It is found that for values of the MFT cross-link strength interaction parameter beyond a certain threshold, both AdG and SST models predict that the polymer brush will be in a compact state of nearly uniform density packed next to the grafting surface over a wide range of solution phase nanoparticle concentrations. Coarse grained molecular dynamics simulations confirm this prediction, for both small nanoparticles (nanoparticle volume = monomer volume) and large nanoparticles (nanoparticle volume = 27 × monomer volume). Simulation results for these cross-linked systems are compared with analogous results for systems with no cross-linking. At the same solution phase nanoparticle concentration, strong cross-linking results in additional compression of the brush relative to the non-crosslinked analog and, at all but the lowest concentrations, to a lesser degree of infiltration by nanoparticles. For large nanoparticles, the monomer density profiles show clear oscillations moving outwards from the grafting surface, corresponding to a degree of layering of the absorbed nanoparticles in the brush as they pack against the grafting surface.

The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems.

PubMed

Koehl, Patrice; Poitevin, Frédéric; Navaza, Rafael; Delarue, Marc

2017-03-14

Understanding the dynamics of biomolecules is the key to understanding their biological activities. Computational methods ranging from all-atom molecular dynamics simulations to coarse-grained normal-mode analyses based on simplified elastic networks provide a general framework to studying these dynamics. Despite recent successes in studying very large systems with up to a 100,000,000 atoms, those methods are currently limited to studying small- to medium-sized molecular systems due to computational limitations. One solution to circumvent these limitations is to reduce the size of the system under study. In this paper, we argue that coarse-graining, the standard approach to such size reduction, must define a hierarchy of models of decreasing sizes that are consistent with each other, i.e., that each model contains the information of the dynamics of its predecessor. We propose a new method, Decimate, for generating such a hierarchy within the context of elastic networks for normal-mode analysis. This method is based on the concept of the renormalization group developed in statistical physics. We highlight the details of its implementation, with a special focus on its scalability to large systems of up to millions of atoms. We illustrate its application on two large systems, the capsid of a virus and the ribosome translation complex. We show that highly decimated representations of those systems, containing down to 1% of their original number of atoms, still capture qualitatively and quantitatively their dynamics. Decimate is available as an OpenSource resource.

Multi-scale mechanics of granular solids from grain-resolved X-ray measurements

NASA Astrophysics Data System (ADS)

Hurley, R. C.; Hall, S. A.; Wright, J. P.

2017-11-01

This work discusses an experimental technique for studying the mechanics of three-dimensional (3D) granular solids. The approach combines 3D X-ray diffraction and X-ray computed tomography to measure grain-resolved strains, kinematics and contact fabric in the bulk of a granular solid, from which continuum strains, grain stresses, interparticle forces and coarse-grained elasto-plastic moduli can be determined. We demonstrate the experimental approach and analysis of selected results on a sample of 1099 stiff, frictional grains undergoing multiple uniaxial compression cycles. We investigate the inter-particle force network, elasto-plastic moduli and associated length scales, reversibility of mechanical responses during cyclic loading, the statistics of microscopic responses and microstructure-property relationships. This work serves to highlight both the fundamental insight into granular mechanics that is furnished by combined X-ray measurements and describes future directions in the field of granular materials that can be pursued with such approaches.

Interplay between grain structure and protein adsorption on functional response of osteoblasts: ultrafine-grained versus coarse-grained substrates.

PubMed

Misra, R D K; Nune, C; Pesacreta, T C; Somani, M C; Karjalainen, L P

2013-01-01

The rapid adsorption of proteins is the starting and primary biological response that occurs when a biomedical device is implanted in the physiological system. The biological response, however, depends on the surface characteristics of the device. Considering the significant interest in nano-/ultrafine surfaces and nanostructured coatings, we describe here, the interplay between grain structure and protein adsorption (bovine serum albumin: BSA) on osteoblasts functions by comparing nanograined/ultrafine-grained (NG/UFG) and coarse-grained (CG: grain size in the micrometer range) substrates by investigating cell-substrate interactions. The protein adsorption on NG/UFG surface was beneficial in favorably modulating biological functions including cell attachment, proliferation, and viability, whereas the effect was less pronounced on protein adsorbed CG surface. Additionally, immunofluorescence studies demonstrated stronger vinculin signals associated with actin stress fibers in the outer regions of the cells and cellular extensions on protein adsorbed NG/UFG surface. The functional response followed the sequence: NG/UFG(BSA) > NG/UFG > CG(BSA) > CG. The differences in the cellular response on bare and protein adsorbed NG/UFG and CG surfaces are attributed to cumulative contribution of grain structure and degree of hydrophilicity. The study underscores the potential advantages of protein adsorption on artificial biomedical devices to enhance the bioactivity and regulate biological functions. Copyright © 2012 Wiley Periodicals, Inc.

Database Dictionary for Ethiopian National Ground-Water Database (ENGDA) Data Fields

DTIC Science & Technology

2007-01-01

Coarse Sand Fine Sand Fine-Grained Sandstone Fractured Igneous and Metamorphic Rock Gravel Karst Limestone, Dolomite Medium Sand Medium-Grained...Coarse Sand; Fine Sand; Fine-Grained Sandstone; Fractured Igneous and Metamorphic Rock; Gravel; Karst Limestone/ Dolomite ; Medium Sand; Medium...aquifer lithology (rock type; Babcock and other, 2004). - 20 - Data Type: List, 1-character code C Consolidated porous sedimentary I Fractured

Deformation in Metallic Glass: Connecting Atoms to Continua

NASA Astrophysics Data System (ADS)

Hinkle, Adam R.; Falk, Michael L.; Rycroft, Chris H.; Shields, Michael D.

Metallic glasses like other amorphous solids experience strain localization as the primary mode of failure. However, the development of continuum constitutive laws which provide a quantitative description of disorder and mechanical deformation remains an open challenge. Recent progress has shown the necessity of accurately capturing fluctuations in material structure, in particular the statistical changes in potential energy of the atomic constituents during the non-equilibrium process of applied shear. Here we directly cross-compare molecular dynamics shear simulations of a ZrCu glass with continuum shear transformation zone (STZ) theory representations. We present preliminary results for a methodology to coarse-grain detailed molecular dynamics data with the goal of initializing a continuum representation in the STZ theory. NSF Grants Awards 1107838, 1408685, and 0801471.

A methodology for evaluating detection performance of ultrasonic array imaging algorithms for coarse-grained materials.

PubMed

Van Pamel, Anton; Brett, Colin R; Lowe, Michael J S

2014-12-01

Improving the ultrasound inspection capability for coarse-grained metals remains of longstanding interest and is expected to become increasingly important for next-generation electricity power plants. Conventional ultrasonic A-, B-, and C-scans have been found to suffer from strong background noise caused by grain scattering, which can severely limit the detection of defects. However, in recent years, array probes and full matrix capture (FMC) imaging algorithms have unlocked exciting possibilities for improvements. To improve and compare these algorithms, we must rely on robust methodologies to quantify their performance. This article proposes such a methodology to evaluate the detection performance of imaging algorithms. For illustration, the methodology is applied to some example data using three FMC imaging algorithms; total focusing method (TFM), phase-coherent imaging (PCI), and decomposition of the time-reversal operator with multiple scattering filter (DORT MSF). However, it is important to note that this is solely to illustrate the methodology; this article does not attempt the broader investigation of different cases that would be needed to compare the performance of these algorithms in general. The methodology considers the statistics of detection, presenting the detection performance as probability of detection (POD) and probability of false alarm (PFA). A test sample of coarse-grained nickel super alloy, manufactured to represent materials used for future power plant components and containing some simple artificial defects, is used to illustrate the method on the candidate algorithms. The data are captured in pulse-echo mode using 64-element array probes at center frequencies of 1 and 5 MHz. In this particular case, it turns out that all three algorithms are shown to perform very similarly when comparing their flaw detection capabilities.

Generalized Quantum Theory of Bianchi IX Cosmologies

NASA Astrophysics Data System (ADS)

Craig, David; Hartle, James

2003-04-01

We apply sum-over-histories generalized quantum theory to the closed homogeneous minisuperspace Bianchi IX cosmological model. We sketch how the probabilities in decoherent sets of alternative, coarse-grained histories of this model universe are calculated. We consider in particular, the probabilities for classical evolution in a suitable coarse-graining. For a restricted class of initial conditions and coarse grainings we exhibit the approximate decoherence of alternative histories in which the universe behaves classically and those in which it does not, illustrating the prediction that these universes will evolve in an approximately classical manner with a probability near unity.

Coarse-grained Simulations of Conformational Changes in Multidrug Resistance Transporters

NASA Astrophysics Data System (ADS)

Jewel, S. M. Yead; Dutta, Prashanta; Liu, Jin

2016-11-01

The overexpression of multidrug resistance (MDR) systems on the gram negative bacteria causes serious problems for treatment of bacterial infectious diseases. The system effectively pumps the antibiotic drugs out of the bacterial cells. During the pumping process one of the MDR components, AcrB undergoes a series of large-scale conformational changes which are responsible for drug recognition, binding and expelling. All-atom simulations are unable to capture those conformational changes because of computational cost. Here, we implement a hybrid coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid, to investigate the proton-dependent conformational changes of AcrB. The simulation results in early stage ( 100 ns) of proton-dependent conformational changes agree with all-atom simulations, validating the coarse-grained model. The coarse-grained force field allows us to explore the process in microsecond simulations. Starting from the crystal structures of Access(A)/Binding(B)/Extrusion(E) monomers in AcrB, we find that deprotonation of Asp407 and Asp408 in monomer E causes a series of large-scale conformational changes from ABE to AAA in absence of drug molecules, which is consistent with experimental findings. This work is supported by NIH Grant: 1R01GM122081-01.

Mechanical Properties of a Superalloy Disk with a Dual Grain Structure

NASA Technical Reports Server (NTRS)

Gayda, John; Gabb, Timothy; Kantzos, Peter

2003-01-01

Mechanical properties from an advanced, nickel-base superalloy disk, with a dual grain structure consisting of a fine grain bore and coarse grain rim, were evaluated. The dual grain structure was produced using NASA's low cost Dual Microstructure Heat Treatment (DMHT) process. The results showed the DMHT disk to have a high strength, fatigue resistant bore comparable to a subsolvus (fine grain) heat treated disk, and a creep resistant rim comparable to a supersolvus (coarse grain) heat treated disk. Additional work on subsolvus solutioning before or after the DMHT conversion appears to be a viable avenue for further improvement in disk properties.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.

PubMed

Andrews, Casey T; Elcock, Adrian H

2014-11-11

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions-which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)-quantitatively reproduced all of the "target" MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic ( PLoS Comput. Biol. 2014 , 5 , e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP's nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

PubMed Central

2015-01-01

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins. PMID:25400526

Modeling Cell Size Regulation: From Single-Cell-Level Statistics to Molecular Mechanisms and Population-Level Effects.

PubMed

Ho, Po-Yi; Lin, Jie; Amir, Ariel

2018-05-20

Most microorganisms regulate their cell size. In this article, we review some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics that they generate. We review the biologically relevant insights obtained from these models. We then describe cell cycle regulation and its molecular implementations, protein number regulation, and population growth, all in relation to size regulation. Finally, we discuss several future directions for developing understanding beyond phenomenological models of cell size regulation.

Texture evolution during thermomechanical processing in rare earth free magnesium alloys

NASA Astrophysics Data System (ADS)

Miller, Victoria Mayne

The use of wrought magnesium alloys is highly desirable for a wide range of applications where low component weight is desirable due to the high specific strength and stiffness the alloys can achieve. However, the implementation of wrought magnesium has been hindered by the limited room temperature formability which typically results from deformation processing. This work identifies opportunities for texture modification during thermomechanical processing of conventional (rare earth free) magnesium alloys via a combination of experimental investigation and polycrystal plasticity simulations. During deformation, it is observed that a homogeneous distribution of coarse intermetallic particles efficiently weakens deformation texture at all strain levels, while a highly inhomogeneous particle distribution is only effective at high strains. The particle deformation effects are complemented by the addition of alkaline earth solute, which modifies the relative deformation mode activity. During recrystallization, grains with basal orientations recrystallize more readily than off-basal grains, despite similar levels of internal misorientation. Dislocation substructure investigations revealed that this is a result of enhanced nucleation in the basal grains due to the dominance of prismatic slip. This dissertation identifies avenues to enhance the potential formability of magnesium alloys during thermomechanical processing by minimizing the evolved texture strength. The following are the identified key aspects of microstructural control: -Maintaining a fine grain size, likely via Zener pinning, to favorably modify deformation mode activity and homogenize deformation. -Developing a coarse, homogeneously distributed population of coarse intermetallic particles to promote a diffuse deformation texture. -Minimizing the activity of prismatic slip to retard the recrystallization of grains with basal orientations, allowing the development of a more diffuse recrystallization texture.

Emergent space-time via a geometric renormalization method

NASA Astrophysics Data System (ADS)

Rastgoo, Saeed; Requardt, Manfred

2016-12-01

We present a purely geometric renormalization scheme for metric spaces (including uncolored graphs), which consists of a coarse graining and a rescaling operation on such spaces. The coarse graining is based on the concept of quasi-isometry, which yields a sequence of discrete coarse grained spaces each having a continuum limit under the rescaling operation. We provide criteria under which such sequences do converge within a superspace of metric spaces, or may constitute the basin of attraction of a common continuum limit, which hopefully may represent our space-time continuum. We discuss some of the properties of these coarse grained spaces as well as their continuum limits, such as scale invariance and metric similarity, and show that different layers of space-time can carry different distance functions while being homeomorphic. Important tools in this analysis are the Gromov-Hausdorff distance functional for general metric spaces and the growth degree of graphs or networks. The whole construction is in the spirit of the Wilsonian renormalization group (RG). Furthermore, we introduce a physically relevant notion of dimension on the spaces of interest in our analysis, which, e.g., for regular lattices reduces to the ordinary lattice dimension. We show that this dimension is stable under the proposed coarse graining procedure as long as the latter is sufficiently local, i.e., quasi-isometric, and discuss the conditions under which this dimension is an integer. We comment on the possibility that the limit space may turn out to be fractal in case the dimension is noninteger. At the end of the paper we briefly mention the possibility that our network carries a translocal far order that leads to the concept of wormhole spaces and a scale dependent dimension if the coarse graining procedure is no longer local.

Coarse-Grained Clustering Dynamics of Heterogeneously Coupled Neurons.

PubMed

Moon, Sung Joon; Cook, Katherine A; Rajendran, Karthikeyan; Kevrekidis, Ioannis G; Cisternas, Jaime; Laing, Carlo R

2015-12-01

The formation of oscillating phase clusters in a network of identical Hodgkin-Huxley neurons is studied, along with their dynamic behavior. The neurons are synaptically coupled in an all-to-all manner, yet the synaptic coupling characteristic time is heterogeneous across the connections. In a network of N neurons where this heterogeneity is characterized by a prescribed random variable, the oscillatory single-cluster state can transition-through [Formula: see text] (possibly perturbed) period-doubling and subsequent bifurcations-to a variety of multiple-cluster states. The clustering dynamic behavior is computationally studied both at the detailed and the coarse-grained levels, and a numerical approach that can enable studying the coarse-grained dynamics in a network of arbitrarily large size is suggested. Among a number of cluster states formed, double clusters, composed of nearly equal sub-network sizes are seen to be stable; interestingly, the heterogeneity parameter in each of the double-cluster components tends to be consistent with the random variable over the entire network: Given a double-cluster state, permuting the dynamical variables of the neurons can lead to a combinatorially large number of different, yet similar "fine" states that appear practically identical at the coarse-grained level. For weak heterogeneity we find that correlations rapidly develop, within each cluster, between the neuron's "identity" (its own value of the heterogeneity parameter) and its dynamical state. For single- and double-cluster states we demonstrate an effective coarse-graining approach that uses the Polynomial Chaos expansion to succinctly describe the dynamics by these quickly established "identity-state" correlations. This coarse-graining approach is utilized, within the equation-free framework, to perform efficient computations of the neuron ensemble dynamics.

Coastal dune facies, Permian Cutler Formation (White Rim Sandstone), Capitol Reef National Park area, southern Utah

NASA Astrophysics Data System (ADS)

Kamola, Diane L.; Chan, Marjorie A.

1988-04-01

The Permian Cutler Formation (White Rim Sandstone) in the Capitol Reef National Park area in southern Utah is an excellent example of a coastal dune complex subjected to periodic flooding by marine waters. Wind-ripple, grainfall and grainflow laminae compose the cross-sets deposited by eolian dunes. However, wave-reworked structures such as oscillation ripples, the occurrence of the characteristically marine trace fossils Thalassinoides and Chondrites, and interfingering marine carbonate beds of the Kaibab Formation collectively indicate marine interaction with the eolian environment. Four facies are distinguished: cross-stratified sandstone, burrowed to bioturbated sandstone, brecciated and deformed sandstone, and ripple-laminated sandstone and thin carbonate beds. One unusual aspect of the cross-stratified sandstone facies is the abundance of coarse-grained sand. Coarse-grained sand is atypical in many ancient eolian slipface deposits, but occurs here in large slipface foresets as both grainflow and wind-ripple deposits. No water-laid structures are found in these slipface deposits. Coarse-grained sand was probably transported to the Cutler shoreline by fluvial systems draining the Uncompahgre Uplift to the east, and then concentrated as coarse-grained ripples in interdune areas. Some of these coarse-grained ripples migrated up the stoss side of the dunes and accumulations of coarse-grained sand avalanched down the crest to form grainflow deposits. An extensive amount of soft-sediment deformation is indicated by the presence of convolute bedding and brecciation. These features occur near the zone of interfingering with marine carbonate beds of the Kaibab Formation. The water-saturated and moist conditions required for extensive deformation may have been controlled by the proximity of these sandstones to the shoreline, and fluctuations in the associated groundwater table.

The Femtosecond Laser Ablation on Ultrafine-Grained Copper

NASA Astrophysics Data System (ADS)

Lu, Jianxun; Wu, Xiaoyu; Ruan, Shuangchen; Guo, Dengji; Du, Chenlin; Liang, Xiong; Wu, Zhaozhi

2018-07-01

To investigate the effects of femtosecond laser ablation on the surface morphology and microstructure of ultrafine-grained copper, point, single-line scanning, and area scanning ablation of ultrafine-grained and coarse-grained copper were performed at room temperature. The ablation threshold gradually increased and materials processing became more difficult with decreasing grain size. In addition, the ablation depth and width of the channels formed by single-line scanning ablation gradually increased with increasing grain size for the same laser pulse energy. The microhardness of the ablated specimens was also evaluated as a function of laser pulse energy using area scanning ablation. The microhardness difference before and after ablation increased with decreasing grain size for the same laser pulse energy. In addition, the microhardness after ablation gradually decreased with increasing laser pulse energy for the ultrafine-grained specimens. However, for the coarse-grained copper specimens, no clear changes of the microhardness were observed after ablation with varying laser pulse energies. The grain sizes of the ultrafine-grained specimens were also surveyed as a function of laser pulse energy using electron backscattered diffraction (EBSD). The heat generated by laser ablation caused recrystallization and grain growth of the ultrafine-grained copper; moreover, the grain size gradually increased with increasing pulse energy. In contrast, no obvious changes in grain size were observed for the coarse-grained copper specimens with increasing pulse energy.

The Femtosecond Laser Ablation on Ultrafine-Grained Copper

NASA Astrophysics Data System (ADS)

Lu, Jianxun; Wu, Xiaoyu; Ruan, Shuangchen; Guo, Dengji; Du, Chenlin; Liang, Xiong; Wu, Zhaozhi

2018-05-01

To investigate the effects of femtosecond laser ablation on the surface morphology and microstructure of ultrafine-grained copper, point, single-line scanning, and area scanning ablation of ultrafine-grained and coarse-grained copper were performed at room temperature. The ablation threshold gradually increased and materials processing became more difficult with decreasing grain size. In addition, the ablation depth and width of the channels formed by single-line scanning ablation gradually increased with increasing grain size for the same laser pulse energy. The microhardness of the ablated specimens was also evaluated as a function of laser pulse energy using area scanning ablation. The microhardness difference before and after ablation increased with decreasing grain size for the same laser pulse energy. In addition, the microhardness after ablation gradually decreased with increasing laser pulse energy for the ultrafine-grained specimens. However, for the coarse-grained copper specimens, no clear changes of the microhardness were observed after ablation with varying laser pulse energies. The grain sizes of the ultrafine-grained specimens were also surveyed as a function of laser pulse energy using electron backscattered diffraction (EBSD). The heat generated by laser ablation caused recrystallization and grain growth of the ultrafine-grained copper; moreover, the grain size gradually increased with increasing pulse energy. In contrast, no obvious changes in grain size were observed for the coarse-grained copper specimens with increasing pulse energy.

Meso-scale Computational Investigation of Polyurea Microstructure and Its Role in Shockwave Attenuation/dispersion

DTIC Science & Technology

2015-07-01

grained simulations of the formation of meso-segregated microstructure and its interaction with the shockwave is analyzed in the present work. It is...help identify these phenomena and processes, meso-scale coarse-grained simulations of the formation of meso-segregated microstructure and its...of shockwave-induced hard-domain densification. Keywords: Polyurea; Meso-scale; Coarse-grained simulations ; Shockwave attenuation; shockwave

Energy landscapes and properties of biomolecules.

PubMed

Wales, David J

2005-11-09

Thermodynamic and dynamic properties of biomolecules can be calculated using a coarse-grained approach based upon sampling stationary points of the underlying potential energy surface. The superposition approximation provides an overall partition function as a sum of contributions from the local minima, and hence functions such as internal energy, entropy, free energy and the heat capacity. To obtain rates we must also sample transition states that link the local minima, and the discrete path sampling method provides a systematic means to achieve this goal. A coarse-grained picture is also helpful in locating the global minimum using the basin-hopping approach. Here we can exploit a fictitious dynamics between the basins of attraction of local minima, since the objective is to find the lowest minimum, rather than to reproduce the thermodynamics or dynamics.

Development of Coarse Grained Models for Long Chain Alkanes

NASA Astrophysics Data System (ADS)

Gyawali, Gaurav; Sternfield, Samuel; Hwang, In Chul; Rick, Steven; Kumar, Revati; Rick Group Team; Kumar Group Team

Modeling aggregation in aqueous solution is a challenge for molecular simulations as it involves long time scales, a range of length scales, and the correct balance of hydrophobic and hydrophilic interactions. We have developed a coarse-grained model fast enough for the rapid testing of molecular structures for their aggregation properties. This model, using the Stillinger-Weber potential, achieves efficiency through a reduction in the number of interaction sites and the use of short-ranged interactions. The model can be two to three orders of magnitude more efficient than conventional all atom simulations, yet through a careful parameterization process and the use of many-body interactions can be remarkably accurate. We have developed models for long chain alkanes in water that reproduce the thermodynamics and structure of water-alkane and liquid alkane systems.

Hydrogeology of the Susquehanna River valley-fill aquifer system and adjacent areas in eastern Broome and southeastern Chenango Counties, New York

USGS Publications Warehouse

Heisig, Paul M.

2012-01-01

The hydrogeology of the valley-fill aquifer system along a 32-mile reach of the Susquehanna River valley and adjacent areas was evaluated in eastern Broome and southeastern Chenango Counties, New York. The surficial geology, inferred ice-marginal positions, and distribution of stratified-drift aquifers were mapped from existing data. Ice-marginal positions, which represent pauses in the retreat of glacial ice from the region, favored the accumulation of coarse-grained deposits whereas more steady or rapid ice retreat between these positions favored deposition of fine-grained lacustrine deposits with limited coarse-grained deposits at depth. Unconfined aquifers with thick saturated coarse-grained deposits are the most favorable settings for water-resource development, and three several-mile-long sections of valley were identified (mostly in Broome County) as potentially favorable: (1) the southernmost valley section, which extends from the New York–Pennsylvania border to about 1 mile north of South Windsor, (2) the valley section that rounds the west side of the umlaufberg (an isolated bedrock hill within a valley) north of Windsor, and (3) the east–west valley section at the Broome County–Chenango County border from Nineveh to East of Bettsburg (including the lower reach of the Cornell Brook valley). Fine-grained lacustrine deposits form extensive confining units between the unconfined areas, and the water-resource potential of confined aquifers is largely untested. Recharge, or replenishment, of these aquifers is dependent not only on infiltration of precipitation directly on unconfined aquifers, but perhaps more so from precipitation that falls in adjacent upland areas. Surface runoff and shallow groundwater from the valley walls flow downslope and recharge valley aquifers. Tributary streams that drain upland areas lose flow as they enter main valleys on permeable alluvial fans. This infiltrating water also recharges valley aquifers. Current (2012) use of water resources in the area is primarily through domestic wells, most of which are completed in fractured bedrock in upland areas. A few villages in the Susquehanna River valley have supply wells that draw water from beneath alluvial fans and near the Susquehanna River, which is a large potential source of water from induced infiltration.

Effect of ultrafine grain on tensile behaviour and corrosion resistance of the duplex stainless steel.

PubMed

Jinlong, Lv; Tongxiang, Liang; Chen, Wang; Limin, Dong

2016-05-01

The ultrafine grained 2205 duplex stainless steel was obtained by cold rolling and annealing. The tensile properties were investigated at room temperature. Comparing with coarse grained stainless steel, ultrafine grained sample showed higher strength and plasticity. In addition, grain size changed deformation orientation. The strain induced α'-martensite was observed in coarse grained 2205 duplex stainless steel with large strain. However, the grain refinement inhibited the transformation of α'-martensite;nevertheless, more deformation twins improved the strength and plasticity of ultrafine grained 2205 duplex stainless steel. In addition, the grain refinement improved corrosion resistance of the 2205 duplex stainless steel in sodium chloride solution. Copyright © 2016 Elsevier B.V. All rights reserved.

Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch

NASA Astrophysics Data System (ADS)

Morelli, Marco J.; Allen, Rosalind J.; Tǎnase-Nicola, Sorin; ten Wolde, Pieter Rein

2008-01-01

In many stochastic simulations of biochemical reaction networks, it is desirable to "coarse grain" the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network that is particularly sensitive to dynamical fluctuations: a bistable genetic switch. We remove protein-DNA and/or protein-protein association-dissociation reactions from the reaction set using various coarse-graining strategies. We determine the effects on the steady-state probability distribution function and on the rate of fluctuation-driven switch flipping transitions. We find that protein-protein interactions may be safely eliminated from the reaction set, but protein-DNA interactions may not. We also find that it is important to use the chemical master equation rather than macroscopic rate equations to compute effective propensity functions for the coarse-grained reactions.

Model reduction for agent-based social simulation: coarse-graining a civil violence model.

PubMed

Zou, Yu; Fonoberov, Vladimir A; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G

2012-06-01

Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

Model reduction for agent-based social simulation: Coarse-graining a civil violence model

NASA Astrophysics Data System (ADS)

Zou, Yu; Fonoberov, Vladimir A.; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G.

2012-06-01

Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

Communication: Is a coarse-grained model for water sufficient to compute Kapitza conductance on non-polar surfaces?

PubMed

Ardham, Vikram Reddy; Leroy, Frédéric

2017-10-21

Coarse-grained models have increasingly been used in large-scale particle-based simulations. However, due to their lack of degrees of freedom, it is a priori unlikely that they straightforwardly represent thermal properties with the same accuracy as their atomistic counterparts. We take a first step in addressing the impact of liquid coarse-graining on interfacial heat conduction by showing that an atomistic and a coarse-grained model of water may yield similar values of the Kapitza conductance on few-layer graphene with interactions ranging from hydrophobic to mildly hydrophilic. By design the water models employed yield similar liquid layer structures on the graphene surfaces. Moreover, they share common vibration properties close to the surfaces and thus couple with the vibrations of graphene in a similar way. These common properties explain why they yield similar Kapitza conductance values despite their bulk thermal conductivity differing by more than a factor of two.

Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten

NASA Astrophysics Data System (ADS)

Wachtel, Artur; Rao, Riccardo; Esposito, Massimiliano

2018-04-01

Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Our results lay the foundations for systematic studies of the thermodynamics of large-scale biochemical reaction networks. Moreover, we identify the conditions under which a relation between one-way fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux–force relation. As a further consequence we show that, in contrast to common belief, the second law of thermodynamics does not require the currents and the forces of biochemical reaction networks to be always aligned.

The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Zhen; Voth, Gregory A., E-mail: gavoth@uchicago.edu

It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operatormore » are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model.« less

A unified data representation theory for network visualization, ordering and coarse-graining

PubMed Central

Kovács, István A.; Mizsei, Réka; Csermely, Péter

2015-01-01

Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form. PMID:26348923

Extension of coarse-grained UNRES force field to treat carbon nanotubes.

PubMed

Sieradzan, Adam K; Mozolewska, Magdalena A

2018-04-26

Carbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer simulations are very useful for such studies. Classical all-atom force fields limit simulation time scale and size of the systems significantly. Therefore, in this work, we implemented CNTs into the coarse-grained UNited RESidue (UNRES) force field. A CNT is represented as a rigid infinite-length cylinder which interacts with a protein through the Kihara potential. Energy conservation in microcanonical coarse-grained molecular dynamics simulations and temperature conservation in canonical simulations with UNRES containing the CNT component have been verified. Subsequently, studies of three proteins, bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTs, were performed to examine the influence of CNTs on the structure and dynamics of these proteins. It was found that nanotubes bind to these proteins and influence their structure. Our results show that the UNRES force field can be used for further studies of CNT-protein systems with 3-4 order of magnitude larger timescale than using regular all-atom force fields. Graphical abstract Bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTsᅟ.

Direct construction of mesoscopic models from microscopic simulations

NASA Astrophysics Data System (ADS)

Lei, Huan; Caswell, Bruce; Karniadakis, George Em

2010-02-01

Starting from microscopic molecular-dynamics (MD) simulations of constrained Lennard-Jones (LJ) clusters (with constant radius of gyration Rg ), we construct two mesoscopic models [Langevin dynamics and dissipative particle dynamics (DPD)] by coarse graining the LJ clusters into single particles. Both static and dynamic properties of the coarse-grained models are investigated and compared with the MD results. The effective mean force field is computed as a function of the intercluster distance, and the corresponding potential scales linearly with the number of particles per cluster and the temperature. We verify that the mean force field can reproduce the equation of state of the atomistic systems within a wide density range but the radial distribution function only within the dilute and the semidilute regime. The friction force coefficients for both models are computed directly from the time-correlation function of the random force field of the microscopic system. For high density or a large cluster size the friction force is overestimated and the diffusivity underestimated due to the omission of many-body effects as a result of the assumed pairwise form of the coarse-grained force field. When the many-body effect is not as pronounced (e.g., smaller Rg or semidilute system), the DPD model can reproduce the dynamic properties of the MD system.

Computationally Guided Design of Polymer Electrolytes for Battery Applications

NASA Astrophysics Data System (ADS)

Wang, Zhen-Gang; Webb, Michael; Savoie, Brett; Miller, Thomas

We develop an efficient computational framework for guiding the design of polymer electrolytes for Li battery applications. Short-times molecular dynamics (MD) simulations are employed to identify key structural and dynamic features in the solvation and motion of Li ions, such as the structure of the solvation shells, the spatial distribution of solvation sites, and the polymer segmental mobility. Comparative studies on six polyester-based polymers and polyethylene oxide (PEO) yield good agreement with experimental data on the ion conductivities, and reveal significant differences in the ion diffusion mechanism between PEO and the polyesters. The molecular insights from the MD simulations are used to build a chemically specific coarse-grained model in the spirit of the dynamic bond percolation model of Druger, Ratner and Nitzan. We apply this coarse-grained model to characterize Li ion diffusion in several existing and yet-to-be synthesized polyethers that differ by oxygen content and backbone stiffness. Good agreement is obtained between the predictions of the coarse-grained model and long-timescale atomistic MD simulations, thus providing validation of the model. Our study predicts higher Li ion diffusivity in poly(trimethylene oxide-alt-ethylene oxide) than in PEO. These results demonstrate the potential of this computational framework for rapid screening of new polymer electrolytes based on ion diffusivity.

Distributions of experimental protein structures on coarse-grained free energy landscapes

PubMed Central

Liu, Jie; Jernigan, Robert L.

2015-01-01

Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available structures in sets of related proteins, it is now possible to directly visualize the clusters of conformations and their conformational transitions through the use of principal component analysis. The most striking observation about the distributions of the structures along the principal components is their highly non-uniform distributions. In this work, we use principal component analysis of experimental structures of 50 diverse proteins to extract the most important directions of their motions, sample structures along these directions, and estimate their free energy landscapes by combining knowledge-based potentials and entropy computed from elastic network models. When these resulting motions are visualized upon their coarse-grained free energy landscapes, the basis for conformational pathways becomes readily apparent. Using three well-studied proteins, T4 lysozyme, serum albumin, and sarco-endoplasmic reticular Ca2+ adenosine triphosphatase (SERCA), as examples, we show that such free energy landscapes of conformational changes provide meaningful insights into the functional dynamics and suggest transition pathways between different conformational states. As a further example, we also show that Monte Carlo simulations on the coarse-grained landscape of HIV-1 protease can directly yield pathways for force-driven conformational changes. PMID:26723638

Impact evaluation of the industrial activities in the Bay of Bakar (Adriatic Sea, Croatia): recent benthic foraminifera and heavy metals.

PubMed

Popadić, Adriana; Vidović, Jelena; Cosović, Vlasta; Medaković, Davorin; Dolenec, Matej; Felja, Igor

2013-11-15

The Bay of Bakar is one of the most heavily polluted bays at the Eastern Adriatic. Three major industrial companies potentially endanger the bay. The concentration of major, minor and trace elements in surface sediments from thirteen stations was discussed in relation to the sediment type and foraminiferal assemblages. The distribution of major elements in the bay is influenced by geological nature of surroundings. Heavy metal distribution depends on pollution sources and on amount of mud fraction: fine-grained sediments are enriched by them in comparison with coarse-grained ones. Different sediment quality criteria complicate the pollution assessment in the bay. Heavy metal concentrations generally fall into allowed depositional values for marine environments; only area in front of the coke plant and the City of Bakar harbor is heavily polluted. Stress-tolerant foraminiferal species dominate at stations with higher concentrations of heavy metals and coarse-grained sediments consist of larger number of epifaunal taxa. Copyright © 2013 Elsevier Ltd. All rights reserved.

BioVEC: a program for biomolecule visualization with ellipsoidal coarse-graining.

PubMed

Abrahamsson, Erik; Plotkin, Steven S

2009-09-01

Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which may be output from molecular dynamics simulations that include orientation output in either quaternion or ANISOU format, and can render frames of the trajectory in several common image formats for subsequent concatenation into a movie file. The BioVEC program is written in C++, uses the OpenGL API for rendering, and is open source. It is lightweight, allows for user-defined settings for and texture, and runs on either Windows or Linux platforms.

Multiple time-scales and the developmental dynamics of social systems.

PubMed

Flack, Jessica C

2012-07-05

To build a theory of social complexity, we need to understand how aggregate social properties arise from individual interaction rules. Here, I review a body of work on the developmental dynamics of pigtailed macaque social organization and conflict management that provides insight into the mechanistic causes of multi-scale social systems. In this model system coarse-grained, statistical representations of collective dynamics are more predictive of the future state of the system than the constantly in-flux behavioural patterns at the individual level. The data suggest that individuals can perceive and use these representations for strategical decision-making. As an interaction history accumulates the coarse-grained representations consolidate. This constrains individual behaviour and provides the foundations for new levels of organization. The time-scales on which these representations change impact whether the consolidating higher-levels can be modified by individuals and collectively. The time-scales appear to be a function of the 'coarseness' of the representations and the character of the collective dynamics over which they are averages. The data suggest that an advantage of multiple timescales is that they allow social systems to balance tradeoffs between predictability and adaptability. I briefly discuss the implications of these findings for cognition, social niche construction and the evolution of new levels of organization in biological systems.

Optimal reproduction in salmon spawning substrates linked to grain size and fish length

NASA Astrophysics Data System (ADS)

Riebe, Clifford S.; Sklar, Leonard S.; Overstreet, Brandon T.; Wooster, John K.

2014-02-01

Millions of dollars are spent annually on revitalizing salmon spawning in riverbeds where redd building by female salmon is inhibited by sediment that is too big for fish to move. Yet the conditions necessary for productive spawning remain unclear. There is no gauge for quantifying how grain size influences the reproductive potential of coarse-bedded rivers. Hence, managers lack a quantitative basis for optimizing spawning habitat restoration for reproductive value. To overcome this limitation, we studied spawning by Chinook, sockeye, and pink salmon (Oncorhynchus tshawytscha, O. nerka, and O. gorbuscha) in creeks and rivers of California and the Pacific Northwest. Our analysis shows that coarse substrates have been substantially undervalued as spawning habitat in previous work. We present a field-calibrated approach for estimating the number of redds and eggs a substrate can accommodate from measurements of grain size and fish length. Bigger fish can move larger sediment and thus use more riverbed area for spawning. They also tend to have higher fecundity, and so can deposit more eggs per redd. However, because redd area increases with fish length, the number of eggs a substrate can accommodate is maximized for moderate-sized fish. This previously unrecognized tradeoff raises the possibility that differences in grain size help regulate river-to-river differences in salmon size. Thus, population diversity and species resilience may be linked to lithologic, geomorphic, and climatic factors that determine grain size in rivers. Our approach provides a tool for managing grain-size distributions in support of optimal reproductive potential and species resilience.

Effect of bimodal harmonic structure design on the deformation behaviour and mechanical properties of Co-Cr-Mo alloy.

PubMed

Vajpai, Sanjay Kumar; Sawangrat, Choncharoen; Yamaguchi, Osamu; Ciuca, Octav Paul; Ameyama, Kei

2016-01-01

In the present work, Co-Cr-Mo alloy compacts with a unique bimodal microstructural design, harmonic structure design, were successfully prepared via a powder metallurgy route consisting of controlled mechanical milling of pre-alloyed powders followed by spark plasma sintering. The harmonic structured Co-Cr-Mo alloy with bimodal grain size distribution exhibited relatively higher strength together with higher ductility as compared to the coarse-grained specimens. The harmonic Co-Cr-Mo alloy exhibited a very complex deformation behavior wherein it was found that the higher strength and the high retained ductility are derived from fine-grained shell and coarse-grained core regions, respectively. Finally, it was observed that the peculiar spatial/topological arrangement of stronger fine-grained and ductile coarse-grained regions in the harmonic structure promotes uniformity of strain distribution, leading to improved mechanical properties by suppressing the localized plastic deformation during straining. Copyright © 2015 Elsevier B.V. All rights reserved.

Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association

PubMed Central

2016-01-01

Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein–lipid and protein–protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining a good collective variable to describe the binding and unbinding transitions, and upon criteria for assessing the convergence of the simulation toward representative equilibrium sampling. As examples, we calculate protein–lipid binding PMFs for ANT/cardiolipin and Kir2.2/PIP2, using umbrella sampling on a distance coordinate. These highlight the importance of replica exchange between windows for convergence. The use of two independent sets of simulations, initiated from bound and unbound states, provide strong evidence for simulation convergence. For a model protein–protein interaction within a membrane, center-of-mass distance is shown to be a poor collective variable for describing transmembrane helix–helix dimerization. Instead, we employ an alternative intermolecular distance matrix RMS (DRMS) coordinate to obtain converged PMFs for the association of the glycophorin transmembrane domain. While the coarse-grained force field gives a reasonable Kd for dimerization, the majority of the bound population is revealed to be in a near-native conformation. Thus, the combination of a refined reaction coordinate with improved sampling reveals previously unnoticed complexities of the dimerization free energy landscape. We propose the use of replica-exchange umbrella sampling starting from different initial conditions as a robust approach for calculation of the binding energies in membrane simulations. PMID:27807980

Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association.

PubMed

Domański, Jan; Hedger, George; Best, Robert B; Stansfeld, Phillip J; Sansom, Mark S P

2017-04-20

Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein-lipid and protein-protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining a good collective variable to describe the binding and unbinding transitions, and upon criteria for assessing the convergence of the simulation toward representative equilibrium sampling. As examples, we calculate protein-lipid binding PMFs for ANT/cardiolipin and Kir2.2/PIP 2 , using umbrella sampling on a distance coordinate. These highlight the importance of replica exchange between windows for convergence. The use of two independent sets of simulations, initiated from bound and unbound states, provide strong evidence for simulation convergence. For a model protein-protein interaction within a membrane, center-of-mass distance is shown to be a poor collective variable for describing transmembrane helix-helix dimerization. Instead, we employ an alternative intermolecular distance matrix RMS (D RMS ) coordinate to obtain converged PMFs for the association of the glycophorin transmembrane domain. While the coarse-grained force field gives a reasonable K d for dimerization, the majority of the bound population is revealed to be in a near-native conformation. Thus, the combination of a refined reaction coordinate with improved sampling reveals previously unnoticed complexities of the dimerization free energy landscape. We propose the use of replica-exchange umbrella sampling starting from different initial conditions as a robust approach for calculation of the binding energies in membrane simulations.

A field study of large-scale oscillation ripples in a very coarse-grained, high-energy marine environment

USGS Publications Warehouse

Hirschaut, D.W.; Dingler, J.R.

1982-01-01

Monastery Beach, Carmel, California is a pocket beach that sits within 200 m of the head of Carmel Submarine Canyon. Coarse to very coarse sand covers both the beach and adjacent shelf; in the latter area incoming waves have shaped the sand into large oscillation ripples. The accessibility of this area and a variable wave climate produce a unique opportunity to study large-scale coarse-grained ripples in a high-energy environment. These ripples, which only occur in very coarse sand, form under the intense, wave-generated currents that exist during storm conditions. Once formed, these ripples do not significantly change under lower energy waves. On three separate occasions scuba divers measured ripples and collected sand samples from ripple crests near fixed reference stakes along three transects. Ripple wavelength and grain size decreased with an increase in water depth. Sediment sorting was best closest to the surf zone and poorest at the rim of Carmel Canyon. Cobbles and gravel observed in ripple troughs represent lag deposits. Carmel Canyon refracts waves approaching Monastery Beach such that wave energy is focused towards the northern and southern portions of the beach, leaving the central part of the beach lower in energy. This energy distribution causes spatial variations in the ripples and grain sizes with the shortest wavelengths and smallest grain sizes being in the central part of the shelf.

A comparative computational study of coarse-grained and all-atom water models in shock Hugoniot states

NASA Astrophysics Data System (ADS)

Min, Sa Hoon; Berkowitz, Max L.

2018-04-01

We performed molecular dynamics simulations to study how well some of the water models used in simulations describe shocked states. Water in our simulations was described using three different models. One was an often-used all-atom TIP4P/2005 model, while the other two were coarse-grained models used with the MARTINI force field: non-polarizable and polarizable MARTINI water. The all-atom model provided results in good agreement with Hugoniot curves (for data on pressure versus specific volume or, equivalently, on shock wave velocity versus "piston" velocity) describing shocked states in the whole range of pressures (up to 11 GPa) under study. If simulations of shocked states of water using coarse-grained models were performed for short time periods, we observed that data obtained for shocked states at low pressure were fairly accurate compared to experimental Hugoniot curves. Polarizable MARTINI water still provided a good description of Hugoniot curves for pressures up to 11 GPa, while the results for the non-polarizable MARTINI water substantially deviated from the Hugoniot curves. We also calculated the temperature of the Hugoniot states and observed that for TIP4P/2005 water, they were consistent with those from theoretical calculations, while both coarse-grained models predicted much higher temperatures. These high temperatures for MARTINI water can be explained by the loss of degrees of freedom due to coarse-graining procedure.

Multiscale equation-free algorithms for molecular dynamics

NASA Astrophysics Data System (ADS)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

Microscopic derivation of particle-based coarse-grained dynamics: Exact expression for memory function

NASA Astrophysics Data System (ADS)

Izvekov, Sergei

2017-03-01

We consider the generalized Langevin equations of motion describing exactly the particle-based coarse-grained dynamics in the classical microscopic ensemble that were derived recently within the Mori-Zwanzig formalism based on new projection operators [S. Izvekov, J. Chem. Phys. 138(13), 134106 (2013)]. The fundamental difference between the new family of projection operators and the standard Zwanzig projection operator used in the past to derive the coarse-grained equations of motion is that the new operators average out the explicit irrelevant trajectories leading to the possibility of solving the projected dynamics exactly. We clarify the definition of the projection operators and revisit the formalism to compute the projected dynamics exactly for the microscopic system in equilibrium. The resulting expression for the projected force is in the form of a "generalized additive fluctuating force" describing the departure of the generalized microscopic force associated with the coarse-grained coordinate from its projection. Starting with this key expression, we formulate a new exact formula for the memory function in terms of microscopic and coarse-grained conservative forces. We conclude by studying two independent limiting cases of practical importance: the Markov limit (vanishing correlations of projected force) and the limit of weak dependence of the memory function on the particle momenta. We present computationally affordable expressions which can be efficiently evaluated from standard molecular dynamics simulations.

Application of ground-penetrating-radar methods in hydrogeologic studies

USGS Publications Warehouse

Beres, Milan; Haeni, F.P.

1991-01-01

A ground-penetrating-radar system was used to study selected stratified-drift deposits in Connecticut. Ground-penetrating radar is a surface-geophysical method that depends on the emission, transmission, reflection, and reception of an electromagnetic pulse and can produce continuous high-resolution profiles of the subsurface rapidly and efficiently. Traverse locations on land included a well field in the town of Mansfield, a sand and gravel pit and a farm overlying a potential aquifer in the town of Coventry, and Haddam Meadows State Park in the town of Haddam. Traverse locations on water included the Willimantic River in Coventry and Mansfield Hollow Lake in Mansfield. The penetration depth of the radar signal ranged from about 20 feet in fine-grained glaciolacustrine sediments to about 70 feet in coarse sand and gravel. Some land records in coarse-grained sediments show a distinct, continuous reflection from the water table about 5 to 11 feet below land surface. Parallel reflectors on the records are interpreted as fine-grained sediments. Hummocky or chaotic reflectors are interpreted as cross-bedded or coarse-grained sediments. Other features observed on some of the radar records include the till and bedrock surface. Records collected on water had distinct water-bottom multiples (more than one reflection) and diffraction patterns from boulders. The interpretation of the radar records, which required little or no processing, was verified by using lithologic logs from test holes located along some of the land traverses and near the water traverses.

Conditional maximum-entropy method for selecting prior distributions in Bayesian statistics

NASA Astrophysics Data System (ADS)

Abe, Sumiyoshi

2014-11-01

The conditional maximum-entropy method (abbreviated here as C-MaxEnt) is formulated for selecting prior probability distributions in Bayesian statistics for parameter estimation. This method is inspired by a statistical-mechanical approach to systems governed by dynamics with largely separated time scales and is based on three key concepts: conjugate pairs of variables, dimensionless integration measures with coarse-graining factors and partial maximization of the joint entropy. The method enables one to calculate a prior purely from a likelihood in a simple way. It is shown, in particular, how it not only yields Jeffreys's rules but also reveals new structures hidden behind them.

Viscoplastic Creep Response and Microstructure of As-Fabricated Microscale Sn-3.0Ag-0.5Cu Solder Interconnects

NASA Astrophysics Data System (ADS)

Cuddalorepatta, Gayatri; Williams, Maureen; Dasgupta, Abhijit

2010-10-01

The viscoplastic behavior of as-fabricated, undamaged, microscale Sn-3.0 Ag-0.5Cu (SAC305) Pb-free solder is investigated and compared with that of eutectic Sn-37Pb solder and near-eutectic Sn-3.8Ag-0.7Cu (SAC387) solder from prior studies. Creep measurements of microscale SAC305 solder shear specimens show significant piece-to-piece variability under identical loading. Orientation imaging microscopy reveals that these specimens contain only a few, highly anisotropic Sn grains across the entire joint. For the studied loads, the coarse-grained Sn microstructure has a more significant impact on the scatter in primary creep compared to that in the secondary creep. The observed lack of statistical homogeneity (microstructure) and joint-dependent mechanical behavior of microscale SAC305 joints are consistent with those observed for functional microelectronics interconnects. Compared with SAC305 joints, microscale Sn-37Pb shear specimens exhibit more homogenous behavior and microstructure with a large number of small Sn (and Pb) grains. Creep damage in the Pb-free joint is predominantly concentrated at highly misoriented Sn grain boundaries. The coarse-grained Sn microstructure recrystallizes into new grains with high misorientation angles under creep loading. In spite of the observed joint-dependent behavior, as-fabricated SAC305 is significantly more creep resistant than Sn-37Pb solder and slightly less creep resistant than near-eutectic SAC387 solder. Average model constants for primary and secondary creep of SAC305 are presented. Since the viscoplastic measurements are averaged over a wide range of grain configurations, the creep model constants represent the effective continuum behavior in an average sense. The average secondary creep behavior suggests that the dominant creep mechanism is dislocation climb assisted by dislocation pipe diffusion.

The anterior hippocampus supports a coarse, global environmental representation and the posterior hippocampus supports fine-grained, local environmental representations.

PubMed

Evensmoen, Hallvard Røe; Lehn, Hanne; Xu, Jian; Witter, Menno P; Nadel, Lynn; Håberg, Asta K

2013-11-01

Representing an environment globally, in a coarse way, and locally, in a fine-grained way, are two fundamental aspects of how our brain interprets the world that surrounds us. The neural correlates of these representations have not been explicated in humans. In this study we used fMRI to investigate these correlates and to explore a possible functional segregation in the hippocampus and parietal cortex. We hypothesized that processing a coarse, global environmental representation engages anterior parts of these regions, whereas processing fine-grained, local environmental information engages posterior parts. Participants learned a virtual environment and then had to find their way during fMRI. After scanning, we assessed strategies used and representations stored. Activation in the hippocampal head (anterior) was related to the multiple distance and global direction judgments and to the use of a coarse, global environmental representation during navigation. Activation in the hippocampal tail (posterior) was related to both local and global direction judgments and to using strategies like number of turns. A structural shape analysis showed that the use of a coarse, global environmental representation was related to larger right hippocampal head volume and smaller right hippocampal tail volume. In the inferior parietal cortex, a similar functional segregation was observed, with global routes represented anteriorly and fine-grained route information such as number of turns represented posteriorly. In conclusion, moving from the anterior to the posterior hippocampus and inferior parietal cortex reflects a shift from processing coarse global environmental representations to processing fine-grained, local environmental representations.

RACER a Coarse-Grained RNA Model for Capturing Folding Free Energy in Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Cheng, Sara; Bell, David; Ren, Pengyu

RACER is a coarse-grained RNA model that can be used in molecular dynamics simulations to predict native structures and sequence-specific variation of free energy of various RNA structures. RACER is capable of accurate prediction of native structures of duplexes and hairpins (average RMSD of 4.15 angstroms), and RACER can capture sequence-specific variation of free energy in excellent agreement with experimentally measured stabilities (r-squared =0.98). The RACER model implements a new effective non-bonded potential and re-parameterization of hydrogen bond and Debye-Huckel potentials. Insights from the RACER model include the importance of treating pairing and stacking interactions separately in order to distinguish folded an unfolded states and identification of hydrogen-bonding, base stacking, and electrostatic interactions as essential driving forces for RNA folding. Future applications of the RACER model include predicting free energy landscapes of more complex RNA structures and use of RACER for multiscale simulations.

Enterprise Management Network Architecture Distributed Knowledge Base Support

DTIC Science & Technology

1990-11-01

Advantages Potentially, this makes a distributed system more powerful than a conventional, centralized one in two ways: " First, it can be more reliable...does not completely apply [35]. The grain size of the processors measures the individual problem-solving power of the agents. In this definition...problem-solving power amounts to the conceptual size of a single action taken by an agent visible to the other agents in the system. If the grain is coarse

Analytical mesoscale modeling of aeolian sand transport

NASA Astrophysics Data System (ADS)

Lämmel, Marc; Kroy, Klaus

2017-11-01

The mesoscale structure of aeolian sand transport determines a variety of natural phenomena studied in planetary and Earth science. We analyze it theoretically beyond the mean-field level, based on the grain-scale transport kinetics and splash statistics. A coarse-grained analytical model is proposed and verified by numerical simulations resolving individual grain trajectories. The predicted height-resolved sand flux and other important characteristics of the aeolian transport layer agree remarkably well with a comprehensive compilation of field and wind-tunnel data, suggesting that the model robustly captures the essential mesoscale physics. By comparing the predicted saturation length with field data for the minimum sand-dune size, we elucidate the importance of intermittent turbulent wind fluctuations for field measurements and reconcile conflicting previous models for this most enigmatic emergent aeolian scale.

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

Geophysical characterization of areas prone to quick-clay landslides using radio-magnetotelluric and seismic methods

NASA Astrophysics Data System (ADS)

Wang, Shunguo; Malehmir, Alireza; Bastani, Mehrdad

2016-05-01

Landslides attributed to quick clays have not only considerable influences on surface geomorphology, they have caused delays in transportation systems, environmental problems and human fatalities, especially in Scandinavia and North America. If the subsurface distributions of quick clays are known, potential damages can be mitigated and the triggers of landslides can better be studied and understood. For this purpose, new radio-magnetotelluric (RMT) and seismic data were acquired in an area near the Göta River in southwest Sweden that contains quick clays and associated landslides. High-resolution data along 4 new lines, in total 3.8 km long, were acquired and merged with earlier acquired data from the site. Velocity and resistivity models derived from first breaks and RMT data were used to delineate subsurface geology, in particular the bedrock surface and coarse-grained materials that overlay the bedrock. The latter often are found underlying quick clays at the site. Comparably high-resistivity and sometimes high-velocity regions within marine clays are attributed to a combination of leached salt from marine clays or potential quick clays and coarse-grained materials. The resistivity and tomographic velocity models suggest a much larger role of the coarse-grained materials at the site than previously thought, but they also suggest two different scenarios for triggering quick-clay landslides at the site. These scenarios are related to the erosion of the riverbank, increased pore-pressure and surface topography when close to the river and human activity when away from the river and where bowl-shaped bedrock surrounds the sediments.

Archie's Saturation Exponent for Natural Gas Hydrate in Coarse-Grained Reservoirs

NASA Astrophysics Data System (ADS)

Cook, Ann E.; Waite, William F.

2018-03-01

Accurately quantifying the amount of naturally occurring gas hydrate in marine and permafrost environments is important for assessing its resource potential and understanding the role of gas hydrate in the global carbon cycle. Electrical resistivity well logs are often used to calculate gas hydrate saturations, Sh, using Archie's equation. Archie's equation, in turn, relies on an empirical saturation parameter, n. Though n = 1.9 has been measured for ice-bearing sands and is widely used within the hydrate community, it is highly questionable if this n value is appropriate for hydrate-bearing sands. In this work, we calibrate n for hydrate-bearing sands from the Canadian permafrost gas hydrate research well, Mallik 5L-38, by establishing an independent downhole Sh profile based on compressional-wave velocity log data. Using the independently determined Sh profile and colocated electrical resistivity and bulk density logs, Archie's saturation equation is solved for n, and uncertainty is tracked throughout the iterative process. In addition to the Mallik 5L-38 well, we also apply this method to two marine, coarse-grained reservoirs from the northern Gulf of Mexico Gas Hydrate Joint Industry Project: Walker Ridge 313-H and Green Canyon 955-H. All locations yield similar results, each suggesting n ≈ 2.5 ± 0.5. Thus, for the coarse-grained hydrate bearing (Sh > 0.4) of greatest interest as potential energy resources, we suggest that n = 2.5 ± 0.5 should be applied in Archie's equation for either marine or permafrost gas hydrate settings if independent estimates of n are not available.

A coarse-grained simulation for the folding of molybdenum disulphide

NASA Astrophysics Data System (ADS)

Wang, Cui-Xia; Zhang, Chao; Jiang, Jin-Wu; Rabczuk, Timon

2016-01-01

We investigate the folding of molybdenum disulphide (MoS2) using coarse-grained (CG) simulations, in which all the parameters are determined analytically from the Stillinger-Weber atomic potential. Owing to its simplicity, the CG model can be used to derive analytic predictions for the relaxed configuration of the folded MoS2 and the resonant frequency for the breathing-like oscillation. We disclose two interesting phenomena for the breathing-like oscillation in the folded MoS2. First, the breathing-like oscillation is self-actuated, since this oscillation can be actuated by intrinsic thermal vibrations without any external actuation force. Second, the resonant frequency of the breathing-like oscillation is insensitive to the adsorption effect. These two features enable practical applications of the folded MoS2 based nanoresonators, where stable resonant oscillations are desirable.

Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Ishioka, T.; Yamada, H.; Miyakawa, T.; Morikawa, R.; Akanuma, S.; Yamagishi, A.; Takasu, M.

2016-12-01

Proteins, which incorporate charged and hydrophobic amino acid residues, are useful as a material of nanotechnology. Among these proteins, IPMDH (3-isopropylmalate dehydrogenase), which has thermal stability, has potential as a material of nanofiber. In this study, we performed coarse-grained molecular dynamics simulation of IPMDH using MARTINI force fields, and we investigated the orientation for the binding of IPMDH. In simulation, we analyzed wild type of IPMDH and the mutated IPMDH proteins, where 13, 20, 27, 332, 335 and 338th amino acid residues are replaced by lysine residues which have positive charge and by glutamic acid residues which have negative charge. Since the binding of mutated IPMDH is advantageous compared with the binding of wild type for one orientation, we suggest that the Coulomb interaction for the binding of IPMDH is important.

Protein-Protein Interactions of Azurin Complex by Coarse-Grained Simulations with a Gō-Like Model

NASA Astrophysics Data System (ADS)

Rusmerryani, Micke; Takasu, Masako; Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

Proteins usually perform their biological functions by forming a complex with other proteins. It is very important to study the protein-protein interactions since these interactions are crucial in many processes of a living organism. In this study, we develop a coarse grained model to simulate protein complex in liquid system. We carry out molecular dynamics simulations with topology-based potential interactions to simulate dynamical properties of Pseudomonas Aeruginosa azurin complex systems. Azurin is known to play an essential role as an anticancer agent and bind many important intracellular molecules. Some physical properties are monitored during simulation time to get a better understanding of the influence of protein-protein interactions to the azurin complex dynamics. These studies will provide valuable insights for further investigation on protein-protein interactions in more realistic system.

Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

PubMed Central

Ayton, Gary S.; Lyman, Edward

2014-01-01

An overall multiscale simulation strategy for large scale coarse-grain simulations of membrane protein systems is presented. The protein is modeled as a heterogeneous elastic network, while the lipids are modeled using the hybrid analytic-systematic (HAS) methodology, where in both cases atomistic level information obtained from molecular dynamics simulation is used to parameterize the model. A feature of this approach is that from the outset liposome length scales are employed in the simulation (i.e., on the order of ½ a million lipids plus protein). A route to develop highly coarse-grained models from molecular-scale information is proposed and results for N-BAR domain protein remodeling of a liposome are presented. PMID:20158037

C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

DOE PAGES

de Oliveira, Tiago E.; Netz, Paulo A.; Kremer, Kurt; ...

2016-05-03

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. In addition, we observe much faster convergence within C–IBI compared to IBI. To validate the robustness, we apply C–IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.

Moving beyond Watson-Crick models of coarse grained DNA dynamics.

PubMed

Linak, Margaret C; Tourdot, Richard; Dorfman, Kevin D

2011-11-28

DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

NASA Astrophysics Data System (ADS)

Zeman, Johannes; Uhlig, Frank; Smiatek, Jens; Holm, Christian

2017-12-01

We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range. In situations where an explicit treatment of electronic polarizability might be crucial, we expect the force field to be an improvement over non-polarizable models, while still profiting from the reduction of computational cost due to the coarse-grained representation.

Coarse-grained hydrodynamics from correlation functions

NASA Astrophysics Data System (ADS)

Palmer, Bruce

2018-02-01

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is demonstrated on a discrete particle simulation of diffusion with a spatially dependent diffusion coefficient. Correlation functions are calculated from the particle simulation and the spatially varying diffusion coefficient is recovered using a fitting procedure.

A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: Theory and application to microfilaments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Tong; Gu, YuanTong, E-mail: yuantong.gu@qut.edu.au

As all-atom molecular dynamics method is limited by its enormous computational cost, various coarse-grained strategies have been developed to extend the length scale of soft matters in the modeling of mechanical behaviors. However, the classical thermostat algorithm in highly coarse-grained molecular dynamics method would underestimate the thermodynamic behaviors of soft matters (e.g. microfilaments in cells), which can weaken the ability of materials to overcome local energy traps in granular modeling. Based on all-atom molecular dynamics modeling of microfilament fragments (G-actin clusters), a new stochastic thermostat algorithm is developed to retain the representation of thermodynamic properties of microfilaments at extra coarse-grainedmore » level. The accuracy of this stochastic thermostat algorithm is validated by all-atom MD simulation. This new stochastic thermostat algorithm provides an efficient way to investigate the thermomechanical properties of large-scale soft matters.« less

Continuous modeling of a grain boundary in MgO and its disclination induced grain-boundary migration mechanism

NASA Astrophysics Data System (ADS)

Cordier, P.; Sun, X.; Taupin, V.; Fressengeas, C.

2016-12-01

Grain boundaries (GBs) are thin material layers where the lattice rotates from one orientation to the next one within a few nanometers. Because they treat these layers as infinitely thin interfaces, large-scale polycrystalline representations fail to describe their structure. Conversely, atomistic representations provide a detailed description of the GBs, but their character remains discrete and not prone to coarse-graining procedures. Continuum descriptions based on kinematic and crystal defect fields defined at interatomic scale are appealing because they can provide smooth and thorough descriptions of GBs, recovering in some sense the atomistic description and potentially serving as a basis for coarse-grained polycrystalline representations. In this work, a crossover between atomistic description and continuous representation of a MgO tilt boundary in polycrystals is set-up to model the periodic arrays of structural units by using dislocation and disclination dipole arrays along GBs. The strain, rotation, curvature, disclination and dislocation density fields are determined in the boundary area by using the discrete atomic positions generated by molecular dynamics simulations. Then, this continuous disclination/dislocation model is used as part of the initial conditions in elasto-plastic continuum mechanics simulations to investigate the shear-coupled boundary migration of tilt boundaries. The present study leads to better understanding of the structure and mechanical architecture of grain boundaries.

Advanced Polymer Network Structures

DTIC Science & Technology

2016-02-01

double networks in a single step was identified from coarse-grained molecular dynamics simulations of polymer solvents bearing rigid side chains dissolved...in a polymer network. Coarse-grained molecular dynamics simulations also explored the mechanical behavior of traditional double networks and...DRI), polymer networks, polymer gels, molecular dynamics simulations , double networks 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF

Effects of Particle Size on the Shear Behavior of Coarse Grained Soils Reinforced with Geogrid.

PubMed

Kim, Daehyeon; Ha, Sungwoo

2014-02-07

In order to design civil structures that are supported by soils, the shear strength parameters of soils are required. Due to the large particle size of coarse-grained soils, large direct shear tests should be performed. In this study, large direct shear tests on three types of coarse grained soils (4.5 mm, 7.9 mm, and 15.9 mm) were performed to evaluate the effects of particle size on the shear behavior of coarse grained soils with/without geogrid reinforcements. Based on the direct shear test results, it was found that, in the case of no-reinforcement, the larger the maximum particle size became, the larger the friction angle was. Compared with the no-reinforcement case, the cases reinforced with either soft geogrid or stiff geogrid have smaller friction angles. The cohesion of the soil reinforced with stiff geogrid was larger than that of the soil reinforced with soft geogrid. The difference in the shear strength occurs because the case with a stiff geogrid has more soil to geogrid contact area, leading to the reduction in interlocking between soil particles.

Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

NASA Astrophysics Data System (ADS)

Patrone, Paul N.; Rosch, Thomas W.; Phelan, Frederick R.

2016-04-01

Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.

Temporal acceleration of spatially distributed kinetic Monte Carlo simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatterjee, Abhijit; Vlachos, Dionisios G.

The computational intensity of kinetic Monte Carlo (KMC) simulation is a major impediment in simulating large length and time scales. In recent work, an approximate method for KMC simulation of spatially uniform systems, termed the binomial {tau}-leap method, was introduced [A. Chatterjee, D.G. Vlachos, M.A. Katsoulakis, Binomial distribution based {tau}-leap accelerated stochastic simulation, J. Chem. Phys. 122 (2005) 024112], where molecular bundles instead of individual processes are executed over coarse-grained time increments. This temporal coarse-graining can lead to significant computational savings but its generalization to spatially lattice KMC simulation has not been realized yet. Here we extend the binomial {tau}-leapmore » method to lattice KMC simulations by combining it with spatially adaptive coarse-graining. Absolute stability and computational speed-up analyses for spatial systems along with simulations provide insights into the conditions where accuracy and substantial acceleration of the new spatio-temporal coarse-graining method are ensured. Model systems demonstrate that the r-time increment criterion of Chatterjee et al. obeys the absolute stability limit for values of r up to near 1.« less

Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule.

PubMed

Mandal, Taraknath; Marson, Ryan L; Larson, Ronald G

2016-10-04

We describe a systematic coarse-graining method to study crystallization and predict possible polymorphs of small organic molecules. In this method, a coarse-grained (CG) force field is obtained by inverse-Boltzmann iteration from the radial distribution function of atomistic simulations of the known crystal. With the force field obtained by this method, we show that CG simulations of the drug phenytoin predict growth of a crystalline slab from a melt of phenytoin, allowing determination of the fastest-growing surface, as well as giving the correct lattice parameters and crystal morphology. By applying meta-dynamics to the coarse-grained model, a new crystalline form of phenytoin (monoclinic, space group P2 1 ) was predicted which is different from the experimentally known crystal structure (orthorhombic, space group Pna2 1 ). Atomistic simulations and quantum calculations then showed the polymorph to be meta-stable at ambient temperature and pressure, and thermodynamically more stable than the conventional orthorhombic crystal at high pressure. The results suggest an efficient route to study crystal growth of small organic molecules that could also be useful for identification of possible polymorphs as well.

Hierarchical coarse-graining model for photosystem II including electron and excitation-energy transfer processes.

PubMed

Matsuoka, Takeshi; Tanaka, Shigenori; Ebina, Kuniyoshi

2014-03-01

We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achieve a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Quantitative comparison of alternative methods for coarse-graining biological networks

PubMed Central

Bowman, Gregory R.; Meng, Luming; Huang, Xuhui

2013-01-01

Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesian model comparison to determine which of these coarse-graining methods provides the models that are most faithful to the original set of states. We find that the Bayesian agglomerative clustering engine and the hierarchical Nyström expansion graph (HNEG) typically provide the best performance. Surprisingly, the original Perron cluster cluster analysis (PCCA) method often provides the next best results, outperforming the newer PCCA+ method and the most probable paths algorithm. We also show that the differences between the models are qualitatively significant, rather than being minor shifts in the boundaries between states. The performance of the methods correlates well with the entropy of the resulting coarse-grainings, suggesting that finding states with more similar populations (i.e., avoiding low population states that may just be noise) gives better results. PMID:24089717

Path-space variational inference for non-equilibrium coarse-grained systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harmandaris, Vagelis, E-mail: harman@uoc.gr; Institute of Applied and Computational Mathematics; Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr

In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirelymore » data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.« less

Coarse-Grained Molecular Dynamics Simulation of Ionic Polymer Networks

DTIC Science & Technology

2008-07-01

AFRL-RX-WP-TP-2009-4198 COARSE-GRAINED MOLECULAR DYNAMICS SIMULATION OF IONIC POLYMER NETWORKS (Postprint) T.E. Dirama, V. Varshney, K.L...GRAINED MOLECULAR DYNAMICS SIMULATION OF IONIC POLYMER NETWORKS (Postprint) 5a. CONTRACT NUMBER FA8650-05-D-5807-0052 5b. GRANT NUMBER 5c...We studied two types of networks which differ only by one containing ionic pairs that amount to 7% of the total number of bonds present. The stress

Influence of heat treatment on microstructure and hot crack susceptibility of laser-drilled turbine blades made from Rene 80

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osterle, W.; Krause, S.; Moelders, T.

2008-11-15

Turbine components from conventionally cast nickel-base alloy Rene 80 show different hot cracking susceptibilities depending on their heat treatment conditions leading to slightly different microstructures. Electron probe micro-analysis, focused ion beam technique and analytical transmission electron microscopy were applied to reveal and identify grain boundary precipitates and the {gamma}-{gamma}'-microstructure. The distribution of borides along grain boundaries was evaluated statistically by quantitative metallography. The following features could be correlated with an increase of cracking susceptibility: i) Increasing grain size, ii) increasing fraction of grain boundaries with densely spaced borides, iii) lack of secondary {gamma}'-particles in matrix channels between the coarse cuboidalmore » {gamma}'-precipitates. The latter feature seems to be responsible for linking-up of cracked grain boundary precipitates which occurred as an additional cracking mechanism after one heat treatment, whereas decohesion at the boride-matrix-interface in the heat affected zone of laser-drilled holes was observed for both heat treatments.« less

Effect of aggregate graining compositions on skid resistance of Exposed Aggregate Concrete pavement

NASA Astrophysics Data System (ADS)

Wasilewska, Marta; Gardziejczyk, Wladysław; Gierasimiuk, Pawel

2018-05-01

The paper presents the evaluation of skid resistance of EAC (Exposed Aggregate Concrete) pavements which differ in aggregate graining compositions. The tests were carried out on concrete mixes with a maximum aggregate size of 8 mm. Three types of coarse aggregates were selected depending on their resistance to polishing which was determined on the basis of the PSV (Polished Stone Value). Basalt (PSV 48), gabbro (PSV 50) and trachybasalt (PSV 52) aggregates were chosen. For each type of aggregate three graining compositions were designed, which differed in the content of coarse aggregate > 4mm. Their content for each series was as follows: A - 38%, B - 50% and C - 68%. Evaluation of the skid resistance has been performed using the FAP (Friction After Polishing) test equipment also known as the Wehner/Schulze machine. Laboratory method enables to compare the skid resistance of different types of wearing course under specified conditions simulating polishing processes. In addition, macrotexture measurements were made on the surface of each specimen using the Elatexure laser profile. Analysis of variance showed that at significance level α = 0.05, aggregate graining compositions as well as the PSV have a significant influence on the obtained values of the friction coefficient μm of the tested EAC pavements. The highest values of the μm have been obtained for EAC with the lowest amount of coarse aggregates (compositions A). In these cases the resistance to polishing of the aggregate does not significantly affect the friction coefficients. This is related to the large areas of cement mortar between the exposed coarse grains. Based on the analysis of microscope images, it was observed that the coarse aggregates were not sufficiently exposed. It has been proved that PSV significantly affected the coefficient of friction in the case of compositions B and C. This is caused by large areas of exposed coarse aggregate. The best parameters were achieved for the EAC pavements with graining composition B and C and trachybasalt aggregate.

First Principles Dynamics and Coarse-Grained Characterization of Photoisomerization in Complex Environments

ERIC Educational Resources Information Center

Virshup, Aaron Michael

2009-01-01

Photoisomerization of conjugated systems is a common pathway for photomechanical energy conversion in biological chromophores. Such reactions are mediated by conical intersections (CIs)--points of degeneracy between different potential energy surfaces, which efficiently funnel population between electronic states. There are many examples of a…

Spall Fracture Patterns for the Heterophase Cu-Al-Ni Alloy in Ultrafine- and Coarse-Grained States Exposed to a Nanosecond Relativistic High-Current Electron Beam

NASA Astrophysics Data System (ADS)

Dudarev, E. F.; Markov, A. B.; Mayer, A. E.; Bakach, G. P.; Tabachenko, A. N.; Kashin, O. A.; Pochivalova, G. P.; Skosyrskii, A. B.; Kitsanov, S. A.; Zhorovkov, M. F.; Yakovlev, E. V.

2013-05-01

A comparative study of spall fracture patterns for the heterophase Cu - 8.45% Al - 5.06% Ni alloy (аt.%) in ultrafine- and coarse-grained states under shock-wave loading using the "SINUS-7" electron accelerator is carried out. For electron energy of 1.4 MeV, pulse duration of 50 ns, and power density of 1.6·1010 W/cm2, the shock wave amplitude was 8 GPa and the strain rate was ~2·105 s-1. It is established that the thickness of the spalled layer increased for both grained structures, and the degree of plastic strain decreased with increasing target thickness. Based on experimental data obtained and results of theoretical calculations, it is demonstrated that the spall strength of ultrafine- and coarse-grained structures is ~3 GPa. The data on the grained structure at different distances from the spall surface and spall fraction patterns and mechanism are presented.

Embrittlement of Intercritically Reheated Coarse Grain Heat-Affected Zone of ASTM4130 Steel

NASA Astrophysics Data System (ADS)

Li, Liying; Han, Tao; Han, Bin

2018-04-01

In this investigation, a thermal welding simulation technique was used to investigate the microstructures and mechanical properties of the intercritically reheated coarse grain heat-affected zone (IR CGHAZ) of ASTM4130 steel. The effect of post weld heat treatment (PWHT) on the toughness of IR CGHAZ was also analyzed. The toughness of IR CGHAZ was measured by means of Charpy impact, and it is found that IR CGHAZ has the lowest toughness which is much lower than that of the base metal regardless of whether PWHT is applied or not. The as-welded IR CGHAZ is mainly composed of ferrite, martensite, and many blocky M-A constituents distributing along grain boundaries and subgrain boundaries in a near-connected network. Also, the prior austenite grains are still as coarse as those in the coarse grain heat-affected zone (CGHAZ). The presence of the blocky M-A constituents and the coarsened austenite grains result in the toughness deterioration of the as-welded IR CGHAZ. Most of the blocky M-A constituents are decomposed to granular bainite due to the effect of the PWHT. However, PWHT cannot refine the prior austenite grains. Thus, the low toughness of IR CGHAZ after PWHT can be attributed to two factors, i.e., the coarsened austenite grains, and the presence of the remaining M-A constituents and granular bainite, which are located at grain boundaries and subgrain boundaries in a near-connected network. The absorbed energy of the IR CGHAZ was increased by about 3.75 times, which means that the PWHT can effectively improve the toughness but it cannot be recovered to the level of base metal.

Microstructure and nanohardness distribution in a polycrystalline Zn deformed by high strain rate impact

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dirras, G., E-mail: dirras@univ-paris13.fr; Ouarem, A.; Couque, H.

2011-05-15

Polycrystalline Zn with an average grain size of about 300 {mu}m was deformed by direct impact Hopkinson pressure bar at a velocity of 29 m/s. An inhomogeneous grain structure was found consisting of a center region having large average grain size of 20 {mu}m surrounded by a fine-grained rim with an average grain size of 6 {mu}m. Transmission electron microscopy investigations showed a significant dislocation density in the large-grained area while in the fine-grained rim the dislocation density was negligible. Most probably, the higher strain yielded recrystallization in the outer ring while in the center only recovery occurred. The hardeningmore » effect of dislocations overwhelms the smaller grain size strengthening in the center part resulting in higher nanohardness in this region than in the outer ring. - Graphical Abstract: (a): EBSD micrograph showing the initial microstructure of polycrystalline Zn that was subsequently submitted to high strain rate impact. (b): an inhomogeneous grain size refinement was obtained which consists of a central coarse-grained area, surrounded by a fine-grained recrystallized rim. The black arrow points to the disc center. Research Highlights: {yields} A polycrystalline Zn specimen was submitted to high strain rate impact loading. {yields} Inhomogeneous grain refinement occurred due to strain gradient in impacted sample. {yields} A fine-grained recrystallized rim surrounded the coarse-grained center of specimen. {yields} The coarse-grained center exhibited higher hardness than the fine-grained rim. {yields} The higher hardness of the center was caused by the higher dislocation density.« less

Finding equilibrium in the spatiotemporal chaos of the complex Ginzburg-Landau equation

NASA Astrophysics Data System (ADS)

Ballard, Christopher C.; Esty, C. Clark; Egolf, David A.

2016-11-01

Equilibrium statistical mechanics allows the prediction of collective behaviors of large numbers of interacting objects from just a few system-wide properties; however, a similar theory does not exist for far-from-equilibrium systems exhibiting complex spatial and temporal behavior. We propose a method for predicting behaviors in a broad class of such systems and apply these ideas to an archetypal example, the spatiotemporal chaotic 1D complex Ginzburg-Landau equation in the defect chaos regime. Building on the ideas of Ruelle and of Cross and Hohenberg that a spatiotemporal chaotic system can be considered a collection of weakly interacting dynamical units of a characteristic size, the chaotic length scale, we identify underlying, mesoscale, chaotic units and effective interaction potentials between them. We find that the resulting equilibrium Takahashi model accurately predicts distributions of particle numbers. These results suggest the intriguing possibility that a class of far-from-equilibrium systems may be well described at coarse-grained scales by the well-established theory of equilibrium statistical mechanics.

Finding equilibrium in the spatiotemporal chaos of the complex Ginzburg-Landau equation.

PubMed

Ballard, Christopher C; Esty, C Clark; Egolf, David A

2016-11-01

Equilibrium statistical mechanics allows the prediction of collective behaviors of large numbers of interacting objects from just a few system-wide properties; however, a similar theory does not exist for far-from-equilibrium systems exhibiting complex spatial and temporal behavior. We propose a method for predicting behaviors in a broad class of such systems and apply these ideas to an archetypal example, the spatiotemporal chaotic 1D complex Ginzburg-Landau equation in the defect chaos regime. Building on the ideas of Ruelle and of Cross and Hohenberg that a spatiotemporal chaotic system can be considered a collection of weakly interacting dynamical units of a characteristic size, the chaotic length scale, we identify underlying, mesoscale, chaotic units and effective interaction potentials between them. We find that the resulting equilibrium Takahashi model accurately predicts distributions of particle numbers. These results suggest the intriguing possibility that a class of far-from-equilibrium systems may be well described at coarse-grained scales by the well-established theory of equilibrium statistical mechanics.

Evolution of twinning in extruded AZ31 alloy with bimodal grain structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcés, G., E-mail: ggarces@cenim.csic.es

2017-04-15

Twinning in extruded AZ31 alloy with a bimodal grain structure is studied under compression along the extrusion direction. This study has combined in-situ measurements during the compression tests by Synchrotron Radiation Diffraction and Acoustic Emission techniques and the evaluation of the microstructure and texture in post-mortem compression samples deformed at different strains. The microstructure of the alloy is characterized by the coexistence of large areas of fine dynamic recrystallized grains and coarse non-recrystallized grains elongated along extrusion direction. Twinning occurs initially in large elongated grains before the macroscopic yield stress which is controlled by the twinning in equiaxed dynamically recrystallizedmore » grains. - Highlights: • The AZ31 extruded at low temperature exhibits a bimodal grains structure. • Twinning takes place before macroscopic yielding in coarse non-DRXed grains. • DRXed grains controls the beginning of plasticity in magnesium alloys with bimodal grain structure.« less

Study of the Micro-Nonuniformity of the Plastic Deformation of Steel

NASA Technical Reports Server (NTRS)

Chechulin, B. B.

1957-01-01

The plastic flow during deformation of real polycrystalline metals has specific characteristics which distinguish the plastic deformation of metals from the deformation of ordinary isotropic bodies. One of these characteristics is the marked micro-nonuniformity of the plastic deformation of metals. P.O. Pashkov demonstrated the presence of a considerable micro-nonuniformity of the plastic deformation of coarse-grained steel wit medium or low carbon content. Analogous results in the case of tension of coarse-grained aluminum were obtained by W. Boas, who paid particular attention to the role of the grain boundaries in plastic flow. The nonuniformit of the plastic deformation in microvolumes was also recorded by T.N. Gudkova and others, on the alloy KhN80T. N.F. Lashko pointed out the nonuniformity of the plastic deformation for a series of pure polycrystalline metals and one-phase alloys. In his later reports, P.O. Pashkov arrives at he conclusion that the nonuniformity of the distribution of the deformation along the individual grains has a significant effect on the strength and plastic characteristics of polycrystalline metals in the process of plastic flow. However, until now there has not existed any systematic investigation of the general rules of the microscopic nonuniformit of plastic deformation even though the real polycrystalline metals are extremely simple with regard to structure. In the present report, an attempt is made to study the micrononuniformity of the flow of polycrystalline metals by the method of statistical analysis of the variation of the frequency diagrams of the nonuniformity of the grains in the process of plastic deformation.

Nonideal detonation regimes in low density explosives

NASA Astrophysics Data System (ADS)

Ershov, A. P.; Kashkarov, A. O.; Pruuel, E. R.; Satonkina, N. P.; Sil'vestrov, V. V.; Yunoshev, A. S.; Plastinin, A. V.

2016-02-01

Measurements using Velocity Interferometer System for Any Reflector (VISAR) were performed for three high explosives at densities slightly above the natural loose-packed densities. The velocity histories at the explosive/window interface demonstrate that the grain size of the explosives plays an important role. Fine-grained materials produced rather smooth records with reduced von Neumann spike amplitudes. For commercial coarse-grained specimens, the chemical spike (if detectable) was more pronounced. This difference can be explained as a manifestation of partial burn up. In fine-grained explosives, which are more sensitive, the reaction can proceed partly within the compression front, which leads to a lower initial shock amplitude. The reaction zone was shorter in fine-grained materials because of higher density of hot spots. The noise level was generally higher for the coarse-grained explosives, which is a natural stochastic effect of the highly non-uniform flow of the heterogeneous medium. These results correlate with our previous data of electrical conductivity diagnostics. Instead of the classical Zel'dovich-von Neumann-Döring profiles, violent oscillations around the Chapman-Jouguet level were observed in about half of the shots using coarse-grained materials. We suggest that these unusual records may point to a different detonation wave propagation mechanism.

Microstructures and performance of CaO-based ceramic cores with different particle size distributions for investment casting

NASA Astrophysics Data System (ADS)

Zhou, P. P.; Wu, G. Q.; Tao, Y.; Cheng, X.; Zhao, J. Q.; Nan, H.

2018-02-01

A series of calcium-based ceramic cores for casting titanium alloy were prepared by mixing different amounts of coarse and fine powders through injection molding. The effects of particle size on the microstructures and properties of the ceramic cores were investigated using quantitative and statistical analysis methods. It is found that the shrinkage and room-temperature strength of the ceramic cores were enhanced as increasing the contents of fine particles. Moreover, the creep resistance of the ceramic cores increased initially and then decreased. The increase in the fine particle content of the cores reduced the number and mean diameter of pores after sintering. The grain boundary density decreased firstly and then increased. The flexural strength of the ceramic cores at room temperature decreased with increasing porosity of ceramic cores, whereas the creep resistance increased with decreasing grain boundary density. A core exhibiting the optimal property was obtained when mixing 65 wt% of coarse powders (75-150 μm) and 35 wt% of fine powders (25-48 μm).

Dynamics in entangled polyethylene melts [Multi time scale dynamics in entangled polyethylene melts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salerno, K. Michael; Agrawal, Anupriya; Peters, Brandon L.

Polymer dynamics creates distinctive viscoelastic behavior as a result of a coupled interplay of motion at the atomic length scale and motion of the entire macromolecule. Capturing the broad time and length scales of polymeric motion however, remains a challenge. Using linear polyethylene as a model system, we probe the effects of the degree of coarse graining on polymer dynamics. Coarse-grained (CG) potentials are derived using iterative Boltzmann inversion with λ methylene groups per CG bead (denoted CGλ) with λ = 2,3,4 and 6 from a fully-atomistic polyethylene melt simulation. By rescaling time in the CG models by a factormore » α, the chain mobility for the atomistic and CG models match. We show that independent of the degree of coarse graining, all measured static and dynamic properties are essentially the same once the dynamic scaling factor α and a non-crossing constraint for the CG6 model are included. The speedup of the CG4 model is about 3 times that of the CG3 model and is comparable to that of the CG6 model. Furthermore, using these CG models we were able to reach times of over 500 μs, allowing us to measure a number of quantities, including the stress relaxation function, plateau modulus and shear viscosity, and compare directly to experiment.« less

Dynamics in entangled polyethylene melts [Multi time scale dynamics in entangled polyethylene melts

DOE PAGES

Salerno, K. Michael; Agrawal, Anupriya; Peters, Brandon L.; ...

2016-10-10

Polymer dynamics creates distinctive viscoelastic behavior as a result of a coupled interplay of motion at the atomic length scale and motion of the entire macromolecule. Capturing the broad time and length scales of polymeric motion however, remains a challenge. Using linear polyethylene as a model system, we probe the effects of the degree of coarse graining on polymer dynamics. Coarse-grained (CG) potentials are derived using iterative Boltzmann inversion with λ methylene groups per CG bead (denoted CGλ) with λ = 2,3,4 and 6 from a fully-atomistic polyethylene melt simulation. By rescaling time in the CG models by a factormore » α, the chain mobility for the atomistic and CG models match. We show that independent of the degree of coarse graining, all measured static and dynamic properties are essentially the same once the dynamic scaling factor α and a non-crossing constraint for the CG6 model are included. The speedup of the CG4 model is about 3 times that of the CG3 model and is comparable to that of the CG6 model. Furthermore, using these CG models we were able to reach times of over 500 μs, allowing us to measure a number of quantities, including the stress relaxation function, plateau modulus and shear viscosity, and compare directly to experiment.« less

Effects of debris-flow composition on runout and erosion

NASA Astrophysics Data System (ADS)

Haas, T. D.; Kleinhans, M. G.

2016-12-01

Predicting debris-flow runout is of major importance for hazard mitigation. Apart from topography and volume, runout depends on debris-flow composition (i.e., particle-size distribution and water content), but how is poorly understood. Moreover, debris flows can grow greatly in size by entrainment of bed material, enhancing their volume and thereby runout and hazardous impact. Debris-flow erosion rates also depend on debris-flow composition, but the relation between the two is largely unexplored. Composition thus strongly affects the dynamics of debris flows. We experimentally investigate the effects of composition on debris-flow runout and erosion. We find a clear optimum in the relations of runout with coarse-material fraction and clay fraction. Increasing coarse material concentration leads to larger runout. However, excess coarse material results in a large accumulation of coarse debris at the flow front and enhances diffusivity, increasing frontal friction and decreasing runout. Increasing clay content initially enhances runout, but too much clay leads to very viscous flows, reducing runout. We further find that debris-flow runout depends at least as much on composition as on topography. In general, erosion depth increases with basal shear stress in our experiments, while there is no correlation with grain collisional stress. There are substantial differences in the scour caused by different types of debris flows. Mean and maximum erosion depths generally become larger with increasing water fraction and grain size and decrease with increasing clay content. However, the erodibility of the very coarse-grained experimental debris flows is unrelated to basal shear stress. This relates to the relatively large influence of grain-collisional stress to the total bed stress in these flows (30-50%). The relative effect of grain-collisional stress is low in the other experimental debris flows (<5%) causing erosion to be largely controlled by basal shear stress. These results show that the erosive behaviour of debris flows may change from basal-shear stress dominated to grain-collisional stress dominated in increasingly coarse-grained debris flows. In short, this study improves our understanding of the effects of debris-flow composition on runout and erosion.

Diagrammatic analysis of correlations in polymer fluids: Cluster diagrams via Edwards' field theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morse, David C.

2006-10-15

Edwards' functional integral approach to the statistical mechanics of polymer liquids is amenable to a diagrammatic analysis in which free energies and correlation functions are expanded as infinite sums of Feynman diagrams. This analysis is shown to lead naturally to a perturbative cluster expansion that is closely related to the Mayer cluster expansion developed for molecular liquids by Chandler and co-workers. Expansion of the functional integral representation of the grand-canonical partition function yields a perturbation theory in which all quantities of interest are expressed as functionals of a monomer-monomer pair potential, as functionals of intramolecular correlation functions of non-interacting molecules,more » and as functions of molecular activities. In different variants of the theory, the pair potential may be either a bare or a screened potential. A series of topological reductions yields a renormalized diagrammatic expansion in which collective correlation functions are instead expressed diagrammatically as functionals of the true single-molecule correlation functions in the interacting fluid, and as functions of molecular number density. Similar renormalized expansions are also obtained for a collective Ornstein-Zernicke direct correlation function, and for intramolecular correlation functions. A concise discussion is given of the corresponding Mayer cluster expansion, and of the relationship between the Mayer and perturbative cluster expansions for liquids of flexible molecules. The application of the perturbative cluster expansion to coarse-grained models of dense multi-component polymer liquids is discussed, and a justification is given for the use of a loop expansion. As an example, the formalism is used to derive a new expression for the wave-number dependent direct correlation function and recover known expressions for the intramolecular two-point correlation function to first-order in a renormalized loop expansion for coarse-grained models of binary homopolymer blends and diblock copolymer melts.« less

Lubrication by Diamond and Diamondlike Carbon Coatings

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1997-01-01

Regardless of environment (ultrahigh vacuum, humid air, dry nitrogen, or water), ion-beam-deposited diamondlike carbon (DLC) and nitrogen-ion-implanted, chemical-vapor-deposited (CVD) diamond films had low steady-state coefficients of friction (less than 0.1) and low wear rates (less than or equal to 10(exp -6)cu mm/N(dot)m). These films can be used as effective wear-resistant, self-lubricating coatings regardless of environment. On the other hand, as-deposited, fine-grain CVD diamond films; polished, coarse-grain CVD diamond films; and polished and then fluorinated, coarse-grain CVD diamond films can be used as effective wear-resistant, self-lubricating coatings in humid air, in dry nitrogen, and in water, but they had a high coefficient of friction and a high wear rate in ultrahigh vacuum. The polished, coarse-grain CVD diamond film revealed an extremely low wear rate, far less than 10(exp 10) cu mm/N(dot)m, in water.

Design of Energetic Ionic Liquids (Preprint)

DTIC Science & Technology

2008-05-07

mesoscale-level simulations of bulk ionic liquids based upon multiscale coarse graining techniques. 15. SUBJECT TERMS 16. SECURITY...simulations utilizing polarizable force fields, and mesoscale-level simulations of bulk ionic liquids based upon multiscale coarse graining...Simulations of the Energetic Ionic Liquid 1-hydroxyethyl-4-amino-1, 2, 4- triazolium Nitrate (HEATN): Molecular dynamics (MD) simulations have been

Time evolution as refining, coarse graining and entangling

NASA Astrophysics Data System (ADS)

Dittrich, Bianca; Steinhaus, Sebastian

2014-12-01

We argue that refining, coarse graining and entangling operators can be obtained from time evolution operators. This applies in particular to geometric theories, such as spin foams. We point out that this provides a construction principle for the physical vacuum in quantum gravity theories and more generally allows construction of a (cylindrically) consistent continuum limit of the theory.

Subsurface Optical Microscopy of Coarse Grain Spinels. Phase 1

DTIC Science & Technology

2013-12-01

A 456 nm LED line bar illuminated in figure 15 and a Xenon fiber optic bar illuminator is shown for figure 16. The optical in situ or subsurface ... imaging of coarse grain spinels and AlONs is optically more complex than expected. An overhead view of the side illumination field is shown in figure 20

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

PubMed

Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto

2015-12-08

Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.

Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations

PubMed Central

2015-01-01

Many commonly used coarse-grained models for proteins are based on simplified interaction sites and consequently may suffer from significant limitations, such as the inability to properly model protein secondary structure without the addition of restraints. Recent work on a benzene fluid (LettieriS.; ZuckermanD. M.J. Comput. Chem.2012, 33, 268−27522120971) suggested an alternative strategy of tabulating and smoothing fully atomistic orientation-dependent interactions among rigid molecules or fragments. Here we report our initial efforts to apply this approach to the polar and covalent interactions intrinsic to polypeptides. We divide proteins into nearly rigid fragments, construct distance and orientation-dependent tables of the atomistic interaction energies between those fragments, and apply potential energy smoothing techniques to those tables. The amount of smoothing can be adjusted to give coarse-grained models that range from the underlying atomistic force field all the way to a bead-like coarse-grained model. For a moderate amount of smoothing, the method is able to preserve about 70–90% of the α-helical structure while providing a factor of 3–10 improvement in sampling per unit computation time (depending on how sampling is measured). For a greater amount of smoothing, multiple folding–unfolding transitions of the peptide were observed, along with a factor of 10–100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations. For a β hairpin, secondary structure is also preserved, albeit for a narrower range of the smoothing parameter and, consequently, for a more modest improvement in sampling. We have also applied the new method in a “resolution exchange” setting, in which each replica runs a Monte Carlo simulation with a different degree of smoothing. We obtain exchange rates that compare favorably to our previous efforts at resolution exchange (LymanE.; ZuckermanD. M.J. Chem. Theory Comput.2006, 2, 656−666). PMID:25400525

Coarse-grained component concurrency in Earth system modeling: parallelizing atmospheric radiative transfer in the GFDL AM3 model using the Flexible Modeling System coupling framework

NASA Astrophysics Data System (ADS)

Balaji, V.; Benson, Rusty; Wyman, Bruce; Held, Isaac

2016-10-01

Climate models represent a large variety of processes on a variety of timescales and space scales, a canonical example of multi-physics multi-scale modeling. Current hardware trends, such as Graphical Processing Units (GPUs) and Many Integrated Core (MIC) chips, are based on, at best, marginal increases in clock speed, coupled with vast increases in concurrency, particularly at the fine grain. Multi-physics codes face particular challenges in achieving fine-grained concurrency, as different physics and dynamics components have different computational profiles, and universal solutions are hard to come by. We propose here one approach for multi-physics codes. These codes are typically structured as components interacting via software frameworks. The component structure of a typical Earth system model consists of a hierarchical and recursive tree of components, each representing a different climate process or dynamical system. This recursive structure generally encompasses a modest level of concurrency at the highest level (e.g., atmosphere and ocean on different processor sets) with serial organization underneath. We propose to extend concurrency much further by running more and more lower- and higher-level components in parallel with each other. Each component can further be parallelized on the fine grain, potentially offering a major increase in the scalability of Earth system models. We present here first results from this approach, called coarse-grained component concurrency, or CCC. Within the Geophysical Fluid Dynamics Laboratory (GFDL) Flexible Modeling System (FMS), the atmospheric radiative transfer component has been configured to run in parallel with a composite component consisting of every other atmospheric component, including the atmospheric dynamics and all other atmospheric physics components. We will explore the algorithmic challenges involved in such an approach, and present results from such simulations. Plans to achieve even greater levels of coarse-grained concurrency by extending this approach within other components, such as the ocean, will be discussed.

Corrosion Behavior of Pure Copper Surrounded by Hank's Physiological Electrolyte at 310 K (37 °C) as a Potential Biomaterial for Contraception: An Analogy Drawn Between Micro- and Nano-grained Copper

NASA Astrophysics Data System (ADS)

Fattah-alhosseini, Arash; Imantalab, Omid; Vafaeian, Saeed; Ansari, Ghazaleh

2017-08-01

This work aims to evaluate the corrosion behavior of pure copper from the microstructural viewpoint for a biomedical application, namely intrauterine devices. For this purpose, Tafel polarization and electrochemical impedance spectroscopy (EIS) techniques were used to evaluate the corrosion behavior of annealed pure copper (with the average grain size of 45 ± 1 µm) and nano-grained microstructure in physiological electrolyte of Hank at 310 K (37 °C). Pure copper in nanoscale grain size, typically an average of 90 ± 5 nm, was successfully made by eight-cycle accumulative roll bonding process at room temperature. On the basis of Tafel polarization results, it was revealed that nano-grained sample had lower corrosion current density and more noble corrosion potential for prolonged exposure in Hank's physiological solution at 310 K (37 °C). In addition, the EIS results showed that the nano-grained sample had more corrosion resistance compared to the coarse-grained one for long-time immersion.

Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu

This work investigates the promise of a “bottom-up” extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstratemore » that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative “structure” within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.« less

Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures.

PubMed

Dunn, Nicholas J H; Noid, W G

2016-05-28

This work investigates the promise of a "bottom-up" extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstrate that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative "structure" within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.

Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model.

PubMed

Jämbeck, Joakim P M; Eriksson, Emma S E; Laaksonen, Aatto; Lyubartsev, Alexander P; Eriksson, Leif A

2014-01-14

Liposomes are proposed as drug delivery systems and can in principle be designed so as to cohere with specific tissue types or local environments. However, little detail is known about the exact mechanisms for drug delivery and the distributions of drug molecules inside the lipid carrier. In the current work, a coarse-grained (CG) liposome model is developed, consisting of over 2500 lipids, with varying degrees of drug loading. For the drug molecule, we chose hypericin, a natural compound proposed for use in photodynamic therapy, for which a CG model was derived and benchmarked against corresponding atomistic membrane bilayer model simulations. Liposomes with 21-84 hypericin molecules were generated and subjected to 10 microsecond simulations. Distribution of the hypericins, their orientations within the lipid bilayer, and the potential of mean force for transferring a hypericin molecule from the interior aqueous "droplet" through the liposome bilayer are reported herein.

Development of Simultaneous Corrosion Barrier and Optimized Microstructure in FeCrAl Heat-Resistant Alloy for Energy Applications. Part 1: The Protective Scale

NASA Astrophysics Data System (ADS)

Pimentel, G.; Aranda, M. M.; Chao, J.; González-Carrasco, J. L.; Capdevila, C.

2015-09-01

Coarse-grained Fe-based oxide dispersion-strengthened (ODS) steels are a class of advanced materials for combined cycle gas turbine systems to deal with operating temperatures and pressures of around 1100°C and 15-30 bar in aggressive environments, which would increase biomass energy conversion efficiencies up to 45% and above. This two-part paper reports the possibility of the development of simultaneous corrosion barrier and optimized microstructure in a FeCrAl heat-resistant alloy for energy applications. The first part reports the mechanism of generating a dense, self-healing α-alumina layer by thermal oxidation, during a heat treatment that leads to a coarse-grained microstructure with a potential value for high-temperature creep resistance in a FeCrAl ODS ferritic alloy, which will be described in more detail in the second part.

Coarse-Grained Simulation of Solvated Cellulose Ib Microfibril

NASA Astrophysics Data System (ADS)

Fan, Bingxin; Maranas, Janna; Zhong, Linghao; Zhen Zhao Collaboration

2013-03-01

We construct a coarse-grained (CG) model of cellulose microfibrils in water. The force field is derived from atomistic simulation of a 40 glucose-unit-long microfibril by requiring consistency between the chain configuration, intermolecular packing and hydrogen bonding of the two levels of modeling. Intermolecular interactions such as hydrogen bonding are added sequentially until the force field holds the microfibril crystal structure. This stepwise process enables us to evaluate the importance of each potential and provides insight to ordered and disordered regions. We simulate cellulose microfibrils with 100 to 400 residues, comparable to the smallest observed microfibrils. Microfibrils longer than 100nm would form a bending region along their longitudinal direction. Multiple bends are observed in the microfibril containing 400 residues. Although the cause is not clear, the bending regions may provide us insights about the periodicity and the behavior of the disordered regions in the microfibril.

Development of DPD coarse-grained models: From bulk to interfacial properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solano Canchaya, José G.; Dequidt, Alain, E-mail: alain.dequidt@univ-bpclermont.fr; Goujon, Florent

2016-08-07

A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG andmore » atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve.« less

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

PubMed

Boudard, Mélanie; Bernauer, Julie; Barth, Dominique; Cohen, Johanne; Denise, Alain

2015-01-01

Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.

Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics

PubMed Central

Parker, David; Bryant, Zev; Delp, Scott L.

2010-01-01

Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at www.simtk.org. PMID:20428469

Only pick the right grains: Modelling the bias due to subjective grain-size interval selection for chronometric and fingerprinting approaches.

NASA Astrophysics Data System (ADS)

Dietze, Michael; Fuchs, Margret; Kreutzer, Sebastian

2016-04-01

Many modern approaches of radiometric dating or geochemical fingerprinting rely on sampling sedimentary deposits. A key assumption of most concepts is that the extracted grain-size fraction of the sampled sediment adequately represents the actual process to be dated or the source area to be fingerprinted. However, these assumptions are not always well constrained. Rather, they have to align with arbitrary, method-determined size intervals, such as "coarse grain" or "fine grain" with partly even different definitions. Such arbitrary intervals violate principal process-based concepts of sediment transport and can thus introduce significant bias to the analysis outcome (i.e., a deviation of the measured from the true value). We present a flexible numerical framework (numOlum) for the statistical programming language R that allows quantifying the bias due to any given analysis size interval for different types of sediment deposits. This framework is applied to synthetic samples from the realms of luminescence dating and geochemical fingerprinting, i.e. a virtual reworked loess section. We show independent validation data from artificially dosed and subsequently mixed grain-size proportions and we present a statistical approach (end-member modelling analysis, EMMA) that allows accounting for the effect of measuring the compound dosimetric history or geochemical composition of a sample. EMMA separates polymodal grain-size distributions into the underlying transport process-related distributions and their contribution to each sample. These underlying distributions can then be used to adjust grain-size preparation intervals to minimise the incorporation of "undesired" grain-size fractions.

Precipitation Kinetics of M23C6 Carbides in the Super304H Austenitic Heat-Resistant Steel

NASA Astrophysics Data System (ADS)

Zhou, Qingwen; Ping, Shaobo; Meng, Xiaobo; Wang, Ruikun; Gao, Yan

2017-12-01

The precipitation kinetics of M23C6 carbides in Super304H and TP304H steels were investigated using the selective-etching method, SEM backscattered electron images and Image-Pro-Plus 6.0 software. Precipitation-temperature-time (PTT) diagrams of M23C6 carbides in the as-received Super304H (fine grains), coarsened Super304H (coarse grains) and TP304H (coarse grains) steels all show the typical C-shaped character with nose temperature range from 800 to 850 °C. Compared with the TP304H steel, the same trend is found of the PTT curve of M23C6 carbides for both kinds of Super304H steels, but their start lines move to the right and finish lines to the left. The preferential formation of Nb(C,N) phase at grain boundaries in the Super304H steels inhibited the nucleation of M23C6 carbides in the early stage of precipitation, causing the right shift of the start line of PTT curve. The main reason for the left shift of the finish line of the two Super304H steels was the quicker growing and coarsening rate of M23C6 in the later precipitation stage due to their higher C content than in TP304H. For the difference in PPT curves between the two grain sizes of the Super304H steel, the lower diffusion rate of atoms in the coarse-grained Super304H steel may explain its righter finish line than the fine-grained counterpart, while the reason for its lefter start line is due to the higher solute segregation along coarse-grained boundaries.

Luminescence and Radiocarbon dating of roman time harbour sediments from Cologne - A comparison of different methods

NASA Astrophysics Data System (ADS)

Lauer, Tobias; Frechen, Manfred; Fuchs, Magret C.; Trier, Marcus; Tsukamoto, Sumiko

2010-05-01

Optically stimulated luminescence (OSL) dating was applied to fluvial and colluvial deposits which were taken from a roman time harbour basin in Cologne. Hence, independent age control was given by roman artefacts (coins, bricks) of known age and by three radiocarbon data. For one sample (well sorted fluvial sand), a single aliquot regenerative (SAR) protocol was applied to coarse grain quartz. A large number of equivalent doses (80) were collected and after De-measurements, different statistical approaches were tested. The results show, that calculating the age by using the Mean or Median of all accepted De-values yields OSL ages of 3.5 ± 0.3 ka and 2.8 ± 0.3 ka, respectively, what would be significantly too old. The application of the Leading Edge Method (Lepper & McKeever 2002), the statistical approach after Fuchs & Lang (2001) or the Minimum Age Method (MAM3) after Galbraith et al. (1999) yield OSL age estimates of 2.0 ± 0.1 ka, 2.1 ± 0.1 ka and 1.7 ± 0.6 ka, respectively. Those ages fit very well to the 14C-ages and are in better agreement with the known archaeological background. For the colluvial sample, the quartz OSL signal was effected by feldspar impurities. For this sample, different methodological approaches were tested to see which one has the best potential to minimize the feldspar contribution. Therefore the post-IR blue stimulated quartz luminescence was recorded. The quartz signal was measured using continuous wave (CW) and pulsed OSL (POSL). For the CW measurements, it was tested if a prior IR-bleach @ 50°C or @ 225°C has better potential for minimizing the feldspar signal. In this case, an IR-bleach @ 225°C (Buylaert et al. in press) was the most effective way to obtain a higher purity of the quartz OSL signal. Buylaert, J.P., Murray, A.S., Thomsen, K.J., Jain, M.: The effect of preheating on the IRSL signal from feldspar. In press. - Radiat. Meas., special issue, LED08. Fuchs, M. & Lang, A. (2001): OSL dating of coarse-grain fluvial quartz using single-aliquot protocols on sediments from NE Peloponnese, Greece. - Quaternary Science Reviews, 20: 783-787. Galbraith, R. F., Roberts, R. G., Laslett, G. M., Yoshida, H. & Olley, J. M. (1999): Optical dating of single and multiple grains of quartz from Jinmium Rock Shelter, northern Australia: Part 1, experimental design and statistical models. - Archaeometry, 41: 339-364. Lepper, K. & McKeever, S.W.S. (2002): An objective methodology for dose distribution analysis. Radiation Protection Dosimetry. - Solid State Dosimetry, 101: 349-352.

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores

PubMed Central

Yoo, Jejoong; Jackson, Meyer B.; Cui, Qiang

2013-01-01

To establish the validity of continuum mechanics models quantitatively for the analysis of membrane remodeling processes, we compare the shape and energies of the membrane fusion pore predicted by coarse-grained (MARTINI) and continuum mechanics models. The results at these distinct levels of resolution give surprisingly consistent descriptions for the shape of the fusion pore, and the deviation between the continuum and coarse-grained models becomes notable only when the radius of curvature approaches the thickness of a monolayer. Although slow relaxation beyond microseconds is observed in different perturbative simulations, the key structural features (e.g., dimension and shape of the fusion pore near the pore center) are consistent among independent simulations. These observations provide solid support for the use of coarse-grained and continuum models in the analysis of membrane remodeling. The combined coarse-grained and continuum analysis confirms the recent prediction of continuum models that the fusion pore is a metastable structure and that its optimal shape is neither toroidal nor catenoidal. Moreover, our results help reveal a new, to our knowledge, bowing feature in which the bilayers close to the pore axis separate more from one another than those at greater distances from the pore axis; bowing helps reduce the curvature and therefore stabilizes the fusion pore structure. The spread of the bilayer deformations over distances of hundreds of nanometers and the substantial reduction in energy of fusion pore formation provided by this spread indicate that membrane fusion can be enhanced by allowing a larger area of membrane to participate and be deformed. PMID:23442963

Gradients estimation from random points with volumetric tensor in turbulence

NASA Astrophysics Data System (ADS)

Watanabe, Tomoaki; Nagata, Koji

2017-12-01

We present an estimation method of fully-resolved/coarse-grained gradients from randomly distributed points in turbulence. The method is based on a linear approximation of spatial gradients expressed with the volumetric tensor, which is a 3 × 3 matrix determined by a geometric distribution of the points. The coarse grained gradient can be considered as a low pass filtered gradient, whose cutoff is estimated with the eigenvalues of the volumetric tensor. The present method, the volumetric tensor approximation, is tested for velocity and passive scalar gradients in incompressible planar jet and mixing layer. Comparison with a finite difference approximation on a Cartesian grid shows that the volumetric tensor approximation computes the coarse grained gradients fairly well at a moderate computational cost under various conditions of spatial distributions of points. We also show that imposing the solenoidal condition improves the accuracy of the present method for solenoidal vectors, such as a velocity vector in incompressible flows, especially when the number of the points is not large. The volumetric tensor approximation with 4 points poorly estimates the gradient because of anisotropic distribution of the points. Increasing the number of points from 4 significantly improves the accuracy. Although the coarse grained gradient changes with the cutoff length, the volumetric tensor approximation yields the coarse grained gradient whose magnitude is close to the one obtained by the finite difference. We also show that the velocity gradient estimated with the present method well captures the turbulence characteristics such as local flow topology, amplification of enstrophy and strain, and energy transfer across scales.

Sediment delivery after a wildfire

USGS Publications Warehouse

Reneau, Steven L.; Katzman, D.; Kuyumjian, G.A.; Lavine, A.; Malmon, D.V.

2007-01-01

We use a record of sedimentation a small reservoir within the Cerro Grande burn area, New Mexico, to document postfire delivery of ash, other fine-grained sediment carried in suspension within floods, and coarse-grained sediment transported as bedload over a five-year period. Ash content of sediment layers is estimated using fallout 137Cs as a tracer, and ash concentrations are shown to rapidly decrease through a series of moderate-intensity convective storms in the first rainy season after the fire. Over 90% of the ash was delivered to the reservoir in the first year, and ash concentrations in suspended sediment were negligible after the second year. Delivery of the remainder of the fine sediment also declined rapidly after the first year despite the occurrence of higher-intensity storms in the second year. Fine sediment loads after five years remained significantly above prefire averages. Deposition of coarse-grained sediment was irregular in time and was associated with transport by snowmelt runoff of sediment stored along the upstream channel during short-duration summer floods. Coarse sediment delivery in the first four years was strongly correlated with snowmelt volume, suggesting a transport-limited system with abundant available sediment. Transport rates of coarse sediment declined in the fifth year, consistent with a transition to a more stable channel as the accessible sediment supply was depleted and the channel bed coarsened. Maximum impacts from ash and other fine-grained sediment therefore occurred soon after the fire, whereas the downstream impacts from coarse-grained sediment were attenuated by the more gradual process of bedload sediment transport. ?? 2007 Geological Society of America.

Coarse-graining to the meso and continuum scales with molecular-dynamics-like models

NASA Astrophysics Data System (ADS)

Plimpton, Steve

Many engineering-scale problems that industry or the national labs try to address with particle-based simulations occur at length and time scales well beyond the most optimistic hopes of traditional coarse-graining methods for molecular dynamics (MD), which typically start at the atomic scale and build upward. However classical MD can be viewed as an engine for simulating particles at literally any length or time scale, depending on the models used for individual particles and their interactions. To illustrate I'll highlight several coarse-grained (CG) materials models, some of which are likely familiar to molecular-scale modelers, but others probably not. These include models for water droplet freezing on surfaces, dissipative particle dynamics (DPD) models of explosives where particles have internal state, CG models of nano or colloidal particles in solution, models for aspherical particles, Peridynamics models for fracture, and models of granular materials at the scale of industrial processing. All of these can be implemented as MD-style models for either soft or hard materials; in fact they are all part of our LAMMPS MD package, added either by our group or contributed by collaborators. Unlike most all-atom MD simulations, CG simulations at these scales often involve highly non-uniform particle densities. So I'll also discuss a load-balancing method we've implemented for these kinds of models, which can improve parallel efficiencies. From the physics point-of-view, these models may be viewed as non-traditional or ad hoc. But because they are MD-style simulations, there's an opportunity for physicists to add statistical mechanics rigor to individual models. Or, in keeping with a theme of this session, to devise methods that more accurately bridge models from one scale to the next.

Graph coarse-graining reveals differences in the module-level structure of functional brain networks.

PubMed

Kujala, Rainer; Glerean, Enrico; Pan, Raj Kumar; Jääskeläinen, Iiro P; Sams, Mikko; Saramäki, Jari

2016-11-01

Networks have become a standard tool for analyzing functional magnetic resonance imaging (fMRI) data. In this approach, brain areas and their functional connections are mapped to the nodes and links of a network. Even though this mapping reduces the complexity of the underlying data, it remains challenging to understand the structure of the resulting networks due to the large number of nodes and links. One solution is to partition networks into modules and then investigate the modules' composition and relationship with brain functioning. While this approach works well for single networks, understanding differences between two networks by comparing their partitions is difficult and alternative approaches are thus necessary. To this end, we present a coarse-graining framework that uses a single set of data-driven modules as a frame of reference, enabling one to zoom out from the node- and link-level details. As a result, differences in the module-level connectivity can be understood in a transparent, statistically verifiable manner. We demonstrate the feasibility of the method by applying it to networks constructed from fMRI data recorded from 13 healthy subjects during rest and movie viewing. While independently partitioning the rest and movie networks is shown to yield little insight, the coarse-graining framework enables one to pinpoint differences in the module-level structure, such as the increased number of intra-module links within the visual cortex during movie viewing. In addition to quantifying differences due to external stimuli, the approach could also be applied in clinical settings, such as comparing patients with healthy controls. © 2016 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

The nature of turbulence in a triangular lattice gas automaton

NASA Astrophysics Data System (ADS)

Duong-Van, Minh; Feit, M. D.; Keller, P.; Pound, M.

1986-12-01

Power spectra calculated from the coarse-graining of a simple lattice gas automaton, and those of time averaging other stochastic times series that we have investigated, have exponents in the range -1.6 to -2, consistent with observation of fully developed turbulence. This power spectrum is a natural consequence of coarse-graining; the exponent -2 represents the continuum limit.

High capacitance of coarse-grained carbide derived carbon electrodes

DOE PAGES

Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; ...

2016-01-01

Here, we report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. We synthesized 70–250 μm sized particles with high surface area and a narrow pore size distribution, using a titanium carbide (TiC) precursor. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. Moreover, the material showcased capacitance above 100 F g -1 at sweep rates as high as 250 mV s -1 in organic electrolyte. 250–1000 micron thick dense CDCmore » films with up to 80 mg cm -2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.« less

Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration

PubMed Central

Miller, Thomas F.

2017-01-01

We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency. PMID:28328943

High capacitance of coarse-grained carbide derived carbon electrodes

NASA Astrophysics Data System (ADS)

Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury

2016-02-01

We report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. Using a titanium carbide (TiC) precursor, we synthesized 70-250 μm sized particles with high surface area and a narrow pore size distribution. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. The material showcased capacitance above 100 F g-1 at sweep rates as high as 250 mV s-1 in organic electrolyte. 250-1000 micron thick dense CDC films with up to 80 mg cm-2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.

Oil-water interfaces with surfactants: A systematic approach to determine coarse-grained model parameters

NASA Astrophysics Data System (ADS)

Vu, Tuan V.; Papavassiliou, Dimitrios V.

2018-05-01

In order to investigate the interfacial region between oil and water with the presence of surfactants using coarse-grained computations, both the interaction between different components of the system and the number of surfactant molecules present at the interface play an important role. However, in many prior studies, the amount of surfactants used was chosen rather arbitrarily. In this work, a systematic approach to develop coarse-grained models for anionic surfactants (such as sodium dodecyl sulfate) and nonionic surfactants (such as octaethylene glycol monododecyl ether) in oil-water interfaces is presented. The key is to place the theoretically calculated number of surfactant molecules on the interface at the critical micelle concentration. Based on this approach, the molecular description of surfactants and the effects of various interaction parameters on the interfacial tension are investigated. The results indicate that the interfacial tension is affected mostly by the head-water and tail-oil interaction. Even though the procedure presented herein is used with dissipative particle dynamics models, it can be applied for other coarse-grained methods to obtain the appropriate set of parameters (or force fields) to describe the surfactant behavior on the oil-water interface.

Variational Approach to Monte Carlo Renormalization Group

NASA Astrophysics Data System (ADS)

Wu, Yantao; Car, Roberto

2017-12-01

We present a Monte Carlo method for computing the renormalized coupling constants and the critical exponents within renormalization theory. The scheme, which derives from a variational principle, overcomes critical slowing down, by means of a bias potential that renders the coarse grained variables uncorrelated. The two-dimensional Ising model is used to illustrate the method.

Sticking properties of ice grains

NASA Astrophysics Data System (ADS)

Jongmanns, M.; Kumm, M.; Wurm, G.; Wolf, D. E.; Teiser, J.

2017-06-01

We study the size dependence of pull-off forces of water ice in laboratory experiments and numerical simulations. To determine the pull-off force in our laboratory experiments, we use a liquid nitrogen cooled centrifuge. Depending on its rotation frequency, spherical ice grains detach due to the centrifugal force which is related to the adhesive properties. Numerical simulations are conducted by means of molecular dynamics simulations of hexagonal ice using a standard coarse-grained water potential. The pull-off force of a single contact between two spherical ice grains is measured due to strain controlled simulations. Both, the experimental study and the simulations reveal a dependence between the pull-off force and the (reduced) particle radii, which differ significantly from the linear dependence of common contact theories.

Entropic elasticity based coarse-grained model of lipid membranes

NASA Astrophysics Data System (ADS)

Feng, Shuo; Hu, Yucai; Liang, Haiyi

2018-04-01

Various models for lipid bilayer membranes have been presented to investigate their morphologies. Among them, the aggressive coarse-grained models, where the membrane is represented by a single layer of particles, are computationally efficient and of practical importance for simulating membrane dynamics at the microscopic scale. In these models, soft potentials between particle pairs are used to maintain the fluidity of membranes, but the underlying mechanism of the softening requires further clarification. We have analyzed the membrane area decrease due to thermal fluctuations, and the results demonstrate that the intraparticle part of entropic elasticity is responsible for the softening of the potential. Based on the stretching response of the membrane, a bottom-up model is developed with an entropic effect explicitly involved. The model reproduces several essential properties of the lipid membrane, including the fluid state and a plateau in the stretching curve. In addition, the area compressibility modulus, bending rigidity, and spontaneous curvature display linear dependence on model parameters. As a demonstration, we have investigated the closure and morphology evolution of membrane systems driven by spontaneous curvature, and vesicle shapes observed experimentally are faithfully reproduced.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Na; Zhang, Peng; Kang, Wei

Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters aremore » systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately.« less

Tensile fracture of coarse-Grained cast austenitic manganese steels

NASA Astrophysics Data System (ADS)

Rittel, D.; Roman, I.

1988-09-01

Tensile fracture of coarse-grained (0.25 to 1 mm) cast austenitic manganese (Hadfield) steels has been investigated. Numerous surface discontinuities nucleate in coarse slip bands, on the heavily deformed surface of tensile specimens. These discontinuities do not propagate radially and final fracture results from central specimen cracking at higher strains. On the microscopic scale, bulk voids nucleate during the entire plastic deformation and they do not coalesce by shear localization (e.g., void-sheet) mechanism. Close voids coalesce by internal necking, whereas distant voids are bridged by means of small voids which nucleate at later stages of the plastic deformation. The high toughness of Hadfield steels is due to their high strain-hardening capacity which stabilizes the plastic deformation, and avoids shear localization and loss of load-bearing capacity. The observed dependence of measured mechanical properties on the specimen’s geometry results from the development of a surface layer which charac-terizes the deformation of this coarse-grained material.

Mechanical Behavior of Nanostructured and Ultrafine Grained Materials under Shock Wave Loadings. Experimental Data and Results of Computer Simulation.

NASA Astrophysics Data System (ADS)

Skripnyak, Vladimir

2011-06-01

Features of mechanical behavior of nanostructured (NS) and ultrafine grained (UFG) metal and ceramic materials under quasistatic and shock wave loadings are discussed in this report. Multilevel models developed within the approach of computational mechanics of materials were used for simulation mechanical behavior of UFG and NS metals and ceramics. Comparisons of simulation results with experimental data are presented. Models of mechanical behavior of nanostructured metal alloys takes into account a several structural factors influencing on the mechanical behavior of materials (type of a crystal lattice, density of dislocations, a size of dislocation substructures, concentration and size of phase precipitation, and distribution of grains sizes). Results show the strain rate sensitivity of the yield stress of UFG and polycrystalline alloys is various in a range from 103 up to 106 1/s. But the difference of the Hugoniot elastic limits of a UFG and coarse-grained alloys may be not considerable. The spall strength, the yield stress of UFG and NS alloys are depend not only on grains size, but a number of factors such as a distribution of grains sizes, a concentration and sizes of voids and cracks, a concentration and sizes of phase precipitation. Some titanium alloys with grain sizes from 300 to 500 nm have the quasi-static yield strength and the tensile strength twice higher than that of coarse grained counterparts. But the spall strength of the UFG titanium alloys is only 10 percents above than that of coarse grained alloys. At the same time it was found the spall strength of the bulk UFG aluminium and magnesium alloys with precipitation strengthening is essentially higher in comparison of coarse-grained counterparts. The considerable decreasing of the strain before failure of UFG alloys was predicted at high strain rates. The Hugoniot elastic limits of oxide nanoceramics depend not only on the porosity, but also on sizes and volume distribution of voids.

Structure and phase composition of ultrafine-grained TiNb alloy after high-temperature annealings

NASA Astrophysics Data System (ADS)

Eroshenko, Anna Yu.; Glukhov, Ivan A.; Mairambekova, Aikol; Tolmachev, Alexey I.; Sharkeev, Yurii P.

2017-12-01

The paper presents the experimental data observed in the microstructure and phase composition of ultrafine-grained Ti-40 mass % Nb (Ti40Nb) alloy after high-temperature annealings. The ultrafine-grained Ti40Nb alloy is produced by severe plastic deformation (SPD). This method includes multiple abc-pressing and multi-pass rolling followed by further pre-recrystallizing annealing which, in its turn, enhances the formation of ultrafine-grained structures with mean size of 0.28 µm involving stable β- and α-phase and metastable nanosized ω-phase in the alloy. It is shown that annealing at 500°C preserves the ultrafine-grained structure and phase composition. In cases of annealing at 800°C the ultrafine-grained state transforms into the coarse-grained state. The stable β-phase and the nanosized metastable ω-phase have been identified in the coarse-grained structure.

Influence of grain size distribution on the mechanical behavior of light alloys in wide range of strain rates

NASA Astrophysics Data System (ADS)

Skripnyak, Vladimir A.; Skripnyak, Natalia V.; Skripnyak, Evgeniya G.; Skripnyak, Vladimir V.

2017-01-01

Inelastic deformation and damage at the mesoscale level of ultrafine grained (UFG) light alloys with distribution of grain size were investigated in wide loading conditions by experimental and computer simulation methods. The computational multiscale models of representative volume element (RVE) with the unimodal and bimodal grain size distributions were developed using the data of structure researches aluminum and magnesium UFG alloys. The critical fracture stress of UFG alloys on mesoscale level depends on relative volumes of coarse grains. Microcracks nucleation at quasi-static and dynamic loading is associated with strain localization in UFG partial volumes with bimodal grain size distribution. Microcracks arise in the vicinity of coarse and ultrafine grains boundaries. It is revealed that the occurrence of bimodal grain size distributions causes the increasing of UFG alloys ductility, but decreasing of the tensile strength.

Coarse-grained molecular dynamics simulations for giant protein-DNA complexes

NASA Astrophysics Data System (ADS)

Takada, Shoji

Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and the fluctuation matching algorithm. CG molecular dynamics methods enable us to simulate much longer time scale motions of much larger molecular systems than fully atomistic models. After broad sampling of structures with CG models, we can easily reconstruct atomistic models, from which one can continue conventional molecular dynamics simulations if desired. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.

Recent Advances in Transferable Coarse-Grained Modeling of Proteins

PubMed Central

Kar, Parimal; Feig, Michael

2017-01-01

Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems are employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are not transferable with respect to different systems and different environments. In this review, we discuss those CG protein models that are transferable and that retain chemical specificity. We restrict ourselves to CG models of soluble proteins only. We also briefly review recent progress made in the multi-scale hybrid all-atom/coarse-grained simulations of proteins. PMID:25443957

Stochastic thermodynamics of fluctuating density fields: Non-equilibrium free energy differences under coarse-graining

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leonard, T.; Lander, B.; Seifert, U.

2013-11-28

We discuss the stochastic thermodynamics of systems that are described by a time-dependent density field, for example, simple liquids and colloidal suspensions. For a time-dependent change of external parameters, we show that the Jarzynski relation connecting work with the change of free energy holds if the time evolution of the density follows the Kawasaki-Dean equation. Specifically, we study the work distributions for the compression and expansion of a two-dimensional colloidal model suspension implementing a practical coarse-graining scheme of the microscopic particle positions. We demonstrate that even if coarse-grained dynamics and density functional do not match, the fluctuation relations for themore » work still hold albeit for a different, apparent, change of free energy.« less

Intermittent particle distribution in synthetic free-surface turbulent flows.

PubMed

Ducasse, Lauris; Pumir, Alain

2008-06-01

Tracer particles on the surface of a turbulent flow have a very intermittent distribution. This preferential concentration effect is studied in a two-dimensional synthetic compressible flow, both in the inertial (self-similar) and in the dissipative (smooth) range of scales, as a function of the compressibility C . The second moment of the concentration coarse grained over a scale r , n_{r};{2} , behaves as a power law in both the inertial and the dissipative ranges of scale, with two different exponents. The shapes of the probability distribution functions of the coarse-grained density n_{r} vary as a function of scale r and of compressibility C through the combination C/r;{kappa} (kappa approximately 0.5) , corresponding to the compressibility, coarse grained over a domain of scale r , averaged over Lagrangian trajectories.

Initial stage corrosion of nanocrystalline copper particles and thin films

NASA Astrophysics Data System (ADS)

Tao, Weimin

1997-12-01

Corrosion behavior is an important issue in nanocrystalline materials research and development. A very fine grain size is expected to have significant effects on the corrosion resistance of these novel materials. However, both the macroscopic corrosion properties and the corresponding structure evolution during corrosion have not been fully studied. Under such circumstances, conducting fundamental research in this area is important and necessary. In this study, high purity nanocrystalline and coarse-grained copper were selected as our sample material, sodium nitrite aqueous solution at room temperature and air at a high temperature were employed as corrosive environments. The weight loss testing and electrochemical methods were used to obtain the macroscopic corrosion properties, whereas the high resolution transmission electron microscope was employed for the structure analysis. The weight loss tests indicate that the corrosion rate of nanocrystalline copper is about 5 times higher than that of coarse-grained copper at the initial stage of corrosion. The electrochemical measurements show that the corrosion potential of the nanocrystalline copper has a 230 mV negative shift in comparison with that of the coarse-grained copper. The nanocrystalline copper also exhibits a significantly higher exchange current density than the coarse-grained copper. High resolution TEM revealed that the surface structure changes at the initial stage of corrosion. It was found that the first copper oxide layer formed on the surface of nanocrystalline copper thin film contains a large density of high angle grain boundaries, whereas that formed on the surface of coarse-grained copper shows highly oriented oxide nuclei and appears to show a strong tendency for forming low angle grain boundaries. A correlation between the macroscopic corrosion properties and the structure characteristics is proposed for the nanocrystalline copper based on the concept of the "apparent" exchange current density associated with mass transport of ions in the oxide layer. A hypothesis is developed that the high corrosion rate of the nanocrystalline copper is closely associated with the structure of the copper oxide layer. Therefore, a high "apparent" exchange current density for the nanocrystalline copper is associated with the high angle grain boundary structure in the initial oxide layer. Additional structure analysis was also carried out: (a) High resolution TEM imaging has provided a cross sectional view of the epitaxial interface between nanocrystalline copper and copper (I) oxide and explicitly discloses the presence of interface defects such as misfit dislocations. Based on this observation, a mechanism was proposed to explain the Cu/Cusb2O interface misfit accommodation. This appears to be the first time this interface has been directly examined. (b) A nanocrystalline analogue to a cross-section of Gwathmey's copper single crystal sphere was revealed by high resolution TEM imaging. A partially oxidized nanocrystalline copper particle is used to examine the variation of the Cu/Cusb2O orientation relationship with respect to changes in surface orientation. A new orientation relationship, Cu (011) //Cusb2O (11), ˜ Cu(011)//Cusb2O(111), was found for the oxidation of nanocrystalline copper.

Wear-Resistant, Self-Lubricating Surfaces of Diamond Coatings

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1995-01-01

In humid air and dry nitrogen, as-deposited, fine-grain diamond films and polished, coarse-grain diamond films have low steady-state coefficients of friction (less than 0.1) and low wear rates (less than or equal to 10(exp -6) mm(exp 3)/N-m). In an ultrahigh vacuum (10(exp -7) Pa), however, they have high steady-state coefficients of friction (greater than 0.6) and high wear rates (greater than or equal to 10(exp -4) mm(exp 3)/N-m). Therefore, the use of as-deposited, fine-grain and polished, coarse-grain diamond films as wear-resistant, self-lubricating coatings must be limited to normal air or gaseous environments such as dry nitrogen. On the other hand, carbon-ion-implanted, fine-grain diamond films and nitrogen-ion-implanted, coarse-grain diamond films have low steady-state coefficients of friction (less than 0.1) and low wear rates (less than or equal to 10(exp -6) mm(exp 3)/N-m) in all three environments. These films can be effectively used as wear-resistant, self-lubricating coatings in an ultrahigh vacuum as well as in normal air and dry nitrogen.

Study on the effect of temperature rise on grain refining during fabrication of nanocrystalline copper under explosive loading

NASA Astrophysics Data System (ADS)

Wang, Jinxiang; Yang, Rui; Jiang, Li; Wang, Xiaoxu; Zhou, Nan

2013-11-01

Nanocrystalline (NC) copper was fabricated by severe plastic deformation of coarse-grained copper at a high strain rate under explosive loading. The feasibility of grain refinement under different explosive loading and the influence of overall temperature rise on grain refinement under impact compression were studied in this paper. The calculation model for the macroscopic temperature rise was established according to the adiabatic shock compression theory. The calculation model for coarse-grained copper was established by the Voronoi method and the microscopic temperature rise resulted from severe plastic deformation of grains was calculated by ANSYS/ls-dyna finite element software. The results show that it is feasible to fabricate NC copper by explosively dynamic deformation of coarse-grained copper and the average grain size of the NC copper can be controlled between 200˜400 nm. The whole temperature rise would increase with the increasing explosive thickness. Ammonium nitrate fuel oil explosive was adopted and five different thicknesses of the explosive, which are 20 mm, 25 mm, 30 mm, 35 mm, 45 mm, respectively, with the same diameter using 20 mm to the fly plate were adopted. The maximum macro and micro temperature rise is up to 532.4 K, 143.4 K, respectively, which has no great effect on grain refinement due to the whole temperature rise that is lower than grain growth temperature according to the high pressure melting theory.

The relative influence of geographic location and reach-scale habitat on benthic invertebrate assemblages in six ecoregions

USGS Publications Warehouse

Munn, M.D.; Waite, I.R.; Larsen, D.P.; Herlihy, A.T.

2009-01-01

The objective of this study was to determine the relative influence of reach-specific habitat variables and geographic location on benthic invertebrate assemblages within six ecoregions across the Western USA. This study included 417 sites from six ecoregions. A total of 301 taxa were collected with the highest richness associated with ecoregions dominated by streams with coarse substrate (19-29 taxa per site). Lowest richness (seven to eight taxa per site) was associated with ecoregions dominated by fine-grain substrate. Principle component analysis (PCA) on reach-scale habitat separated the six ecoregions into those in high-gradient mountainous areas (Coast Range, Cascades, and Southern Rockies) and those in lower-gradient ecoregions (Central Great Plains and Central California Valley). Nonmetric multidimensional scaling (NMS) models performed best in ecoregions dominated by coarse-grain substrate and high taxa richness, along with coarse-grain substrates sites combined from multiple ecoregions regardless of location. In contrast, ecoregions or site combinations dominated by fine-grain substrate had poor model performance (high stress). Four NMS models showed that geographic location (i.e. latitude and longitude) was important for: (1) all ecoregions combined, (2) all sites dominated by coarse-grain sub strate combined, (3) Cascades Ecoregion, and (4) Columbia Ecoregion. Local factors (i.e. substrate or water temperature) seem to be overriding factors controlling invertebrate composition across the West, regardless of geographic location. ?? The Author(s) 2008.

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

PubMed Central

Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.

2008-01-01

The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325

Automated array assembly task development of low-cost polysilicon solar cells

NASA Technical Reports Server (NTRS)

Jones, G. T.

1980-01-01

Development of low cost, large area polysilicon solar cells was conducted in this program. Three types of polysilicon materialk were investigated. A theoretical and experimenal comparison between single crystal silicon and polysilicon solar cell efficiency was performed. Significant electrical performance differences were observed between types of wafer material, i.e. fine grain and coarse grain polysilicon and single crystal silicon. Efficiency degradation due to grain boundaries in fin grain and coarse grain polysilicon was shown to be small. It was demonstrated that 10 percent efficient polysilicon solar cells can be produced with spray on n+ dopants. This result fulfills an important goal of this project, which is the production of batch quantity of 10 percent efficient polysilicon solar cells.

Numerical and experimental investigation of DNAPL removal mechanisms in a layered porous medium by means of soil vapor extraction.

PubMed

Yoon, Hongkyu; Oostrom, Mart; Wietsma, Thomas W; Werth, Charles J; Valocchi, Albert J

2009-10-13

The purpose of this work is to identify the mechanisms that govern the removal of carbon tetrachloride (CT) during soil vapor extraction (SVE) by comparing numerical and analytical model simulations with a detailed data set from a well-defined intermediate-scale flow cell experiment. The flow cell was packed with a fine-grained sand layer embedded in a coarse-grained sand matrix. A total of 499 mL CT was injected at the top of the flow cell and allowed to redistribute in the variably saturated system. A dual-energy gamma radiation system was used to determine the initial NAPL saturation profile in the fine-grained sand layer. Gas concentrations at the outlet of the flow cell and 15 sampling ports inside the flow cell were measured during subsequent CT removal using SVE. Results show that CT mass was removed quickly in coarse-grained sand, followed by a slow removal from the fine-grained sand layer. Consequently, effluent gas concentrations decreased quickly at first, and then started to decrease gradually, resulting in long-term tailing. The long-term tailing was mainly due to diffusion from the fine-grained sand layer to the coarse-grained sand zone. An analytical solution for a one-dimensional advection and a first-order mass transfer model matched the tailing well with two fitting parameters. Given detailed knowledge of the permeability field and initial CT distribution, we were also able to predict the effluent concentration tailing and gas concentration profiles at sampling ports using a numerical simulator assuming equilibrium CT evaporation. The numerical model predictions were accurate within the uncertainty of independently measured or literature derived parameters. This study demonstrates that proper numerical modeling of CT removal through SVE can be achieved using equilibrium evaporation of NAPL if detailed fine-scale knowledge of the CT distribution and physical heterogeneity is incorporated into the model. However, CT removal could also be fit by a first-order mass transfer analytical model, potentially leading to an erroneous conclusion that the long-term tailing in the experiment was kinetically controlled due to rate-limited NAPL evaporation.

Coarse-grained modeling of polyethylene melts: Effect on dynamics

DOE PAGES

Peters, Brandon L.; Salerno, K. Michael; Agrawal, Anupriya; ...

2017-05-23

The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with three to six methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully atomistic melt simulations and the transferability of CG potentials across temperatures. While IBI produces nonbonded pair potentials thatmore » give excellent agreement between the atomistic and CG pair correlation functions, the resulting pressure for the CG models is large compared with the pressure of the atomistic system. We find that correcting the potential to match the reference pressure leads to nonbonded interactions with much deeper minima and slightly smaller effective bead diameter. However, simulations with potentials generated by IBI and pressure-corrected IBI result in similar mean-square displacements (MSDs) and stress autocorrelation functions G( t) for PE melts. While the time rescaling factor required to match CG and atomistic models is the same for pressure- and non-pressure-corrected CG models, it strongly depends on temperature. Furthermore, transferability was investigated by comparing the MSDs and stress autocorrelation functions for potentials developed at different temperatures.« less

Coarse-grained modeling of polyethylene melts: Effect on dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, Brandon L.; Salerno, K. Michael; Agrawal, Anupriya

The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with three to six methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully atomistic melt simulations and the transferability of CG potentials across temperatures. While IBI produces nonbonded pair potentials thatmore » give excellent agreement between the atomistic and CG pair correlation functions, the resulting pressure for the CG models is large compared with the pressure of the atomistic system. We find that correcting the potential to match the reference pressure leads to nonbonded interactions with much deeper minima and slightly smaller effective bead diameter. However, simulations with potentials generated by IBI and pressure-corrected IBI result in similar mean-square displacements (MSDs) and stress autocorrelation functions G( t) for PE melts. While the time rescaling factor required to match CG and atomistic models is the same for pressure- and non-pressure-corrected CG models, it strongly depends on temperature. Furthermore, transferability was investigated by comparing the MSDs and stress autocorrelation functions for potentials developed at different temperatures.« less

Identifying grain-size dependent errors on global forest area estimates and carbon studies

Treesearch

Daolan Zheng; Linda S. Heath; Mark J. Ducey

2008-01-01

Satellite-derived coarse-resolution data are typically used for conducting global analyses. But the forest areas estimated from coarse-resolution maps (e.g., 1 km) inevitably differ from a corresponding fine-resolution map (such as a 30-m map) that would be closer to ground truth. A better understanding of changes in grain size on area estimation will improve our...

JPRS Report, Latin America.

DTIC Science & Technology

1987-07-21

to Democracy 10 Agreements Reached H $600 Million Foreign Exchange Loss From Coarse Grain Drop (Bruno Quintana; AMBITO FINANCIERO , 26 May 87...FROM COARSE GRAIN DROP Buenos Aires AMBITO FINANCIERO in Spanish 26 May 87 p 22 [Article by Bruno Quintana, director of the Studies Department of the... Estado ) President Carlos Bechelli said yesterday. In an interview with the specialized daily EL CRONISTA COMERCIAL, Bechelli said that gas

Measuring Crack Length in Coarse Grain Ceramics

NASA Technical Reports Server (NTRS)

Salem, Jonathan A.; Ghosn, Louis J.

2010-01-01

Due to a coarse grain structure, crack lengths in precracked spinel specimens could not be measured optically, so the crack lengths and fracture toughness were estimated by strain gage measurements. An expression was developed via finite element analysis to correlate the measured strain with crack length in four-point flexure. The fracture toughness estimated by the strain gaged samples and another standardized method were in agreement.

Temporal pattern and memory in sediment transport in an experimental step-pool channel

NASA Astrophysics Data System (ADS)

Saletti, Matteo; Molnar, Peter; Zimmermann, André; Hassan, Marwan A.; Church, Michael; Burlando, Paolo

2015-04-01

In this work we study the complex dynamics of sediment transport and bed morphology in steep streams, using a dataset of experiments performed in a steep flume with natural sediment. High-resolution (1 sec) time series of sediment transport were measured for individual size classes at the outlet of the flume for different combinations of sediment input rates, discharges, and flume slopes. The data show that the relation between instantaneous discharge and sediment transport exhibits large variability on different levels. After dividing the time series into segments of constant water discharge, we quantify the statistical properties of transport rates by fitting the data with a Generalized Extreme Value distribution, whose 3 parameters are related to the average sediment flux. We analyze separately extreme events of transport rate in terms of their fractional composition; if only events of high magnitude are considered, coarse grains become the predominant component of the total sediment yield. We quantify the memory in grain size dependent sediment transport with variance scaling and autocorrelation analyses; more specifically, we study how the variance changes with different aggregation scales and how the autocorrelation coefficient changes with different time lags. Our results show that there is a tendency to an infinite memory regime in transport rate signals, which is limited by the intermittency of the largest fractions. Moreover, the structure of memory is both grain size-dependent and magnitude-dependent: temporal autocorrelation is stronger for small grain size fractions and when the average sediment transport rate is large. The short-term memory in coarse grain transport increases with temporal aggregation and this reveals the importance of the sampling frequency of bedload transport rates in natural streams, especially for large fractions.

The parent body controls on cosmic spherule texture: Evidence from the oxygen isotopic compositions of large micrometeorites

NASA Astrophysics Data System (ADS)

van Ginneken, M.; Gattacceca, J.; Rochette, P.; Sonzogni, C.; Alexandre, A.; Vidal, V.; Genge, M. J.

2017-09-01

High-precision oxygen isotopic compositions of eighteen large cosmic spherules (>500 μm diameter) from the Atacama Desert, Chile, were determined using IR-laser fluorination - Isotope Ratio Mass spectrometry. The four discrete isotopic groups defined in a previous study on cosmic spherules from the Transantarctic Mountains (Suavet et al., 2010) were identified, confirming their global distribution. Approximately 50% of the studied cosmic spherules are related to carbonaceous chondrites, 38% to ordinary chondrites and 12% to unknown parent bodies. Approximately 90% of barred olivine (BO) cosmic spherules show oxygen isotopic compositions suggesting they are related to carbonaceous chondrites. Similarly, ∼90% porphyritic olivine (Po) cosmic spherules are related to ordinary chondrites and none can be unambiguously related to carbonaceous chondrites. Other textures are related to all potential parent bodies. The data suggests that the textures of cosmic spherules are mainly controlled by the nature of the precursor rather than by the atmospheric entry parameters. We propose that the Po texture may essentially be formed from a coarse-grained precursor having an ordinary chondritic mineralogy and chemistry. Coarse-grained precursors related to carbonaceous chondrites (i.e. chondrules) are likely to either survive atmospheric entry heating or form V-type cosmic spherules. Due to the limited number of submicron nucleation sites after total melting, ordinary chondrite-related coarse-grained precursors that suffer higher peak temperatures will preferentially form cryptocrystalline (Cc) textures instead of BO textures. Conversely, the BO textures would be mostly related to the fine-grained matrices of carbonaceous chondrites due to the wide range of melting temperatures of their constituent mineral phases, allowing the preservation of submicron nucleation sites. Independently of the nature of the precursors, increasing peak temperatures form glassy textures.

raaSAFT: A framework enabling coarse-grained molecular dynamics simulations based on the SAFT- γ Mie force field

NASA Astrophysics Data System (ADS)

Ervik, Åsmund; Serratos, Guadalupe Jiménez; Müller, Erich A.

2017-03-01

We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology makes use of the SAFT- γ Mie force field, so the resulting coarse grained pair potentials are both closely linked to and consistent with the macroscopic thermodynamic properties of the simulated fluid. In raaSAFT both homonuclear and heteronuclear models are implemented for a wide range of compounds spanning from linear alkanes, to more complicated fluids such as water and alcohols, all the way up to nonionic surfactants and models of asphaltenes and resins. Adding new compounds as well as new features is made straightforward by the modularity of the code. To demonstrate the ease-of-use of raaSAFT, we give a detailed walkthrough of how to simulate liquid-liquid equilibrium of a hydrocarbon with water. We describe in detail how both homonuclear and heteronuclear compounds are implemented. To demonstrate the performance and versatility of raaSAFT, we simulate a large polymer-solvent mixture with 300 polystyrene molecules dissolved in 42 700 molecules of heptane, reproducing the experimentally observed temperature-dependent solubility of polystyrene. For this case we obtain a speedup of more than three orders of magnitude as compared to atomistically-detailed simulations.

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses.

PubMed

Ahmed, Aqeel; Villinger, Saskia; Gohlke, Holger

2010-12-01

A large-scale comparison of essential dynamics (ED) modes from molecular dynamic simulations and normal modes from coarse-grained normal mode methods (CGNM) was performed on a dataset of 335 proteins. As CGNM methods, the elastic network model (ENM) and the rigid cluster normal mode analysis (RCNMA) were used. Low-frequency normal modes from ENM correlate very well with ED modes in terms of directions of motions and relative amplitudes of motions. Notably, a similar performance was found if normal modes from RCNMA were used, despite a higher level of coarse graining. On average, the space spanned by the first quarter of ENM modes describes 84% of the space spanned by the five ED modes. Furthermore, no prominent differences for ED and CGNM modes among different protein structure classes (CATH classification) were found. This demonstrates the general potential of CGNM approaches for describing intrinsic motions of proteins with little computational cost. For selected cases, CGNM modes were found to be more robust among proteins that have the same topology or are of the same homologous superfamily than ED modes. In view of recent evidence regarding evolutionary conservation of vibrational dynamics, this suggests that ED modes, in some cases, might not be representative of the underlying dynamics that are characteristic of a whole family, probably due to insufficient sampling of some of the family members by MD. Copyright © 2010 Wiley-Liss, Inc.

Coarse-Grain Molecular Dynamics Simulations To Investigate the Bulk Viscosity and Critical Micelle Concentration of the Ionic Surfactant Sodium Dodecyl Sulfate (SDS) in Aqueous Solution.

PubMed

Ruiz-Morales, Yosadara; Romero-Martínez, Ascención

2018-04-12

The first critical micelle concentration (CMC) of the ionic surfactant sodium dodecyl sulfate (SDS) in diluted aqueous solution has been determined at room temperature from the investigation of the bulk viscosity, at several concentrations of SDS, by means of coarse-grain molecular dynamics simulations. The coarse-grained model molecules at the mesoscale level are adopted. The bulk viscosity of SDS was calculated at several millimolar concentrations of SDS in water using the MARTINI force field by means of NVT shear Mesocite molecular dynamics. The definition of each bead in the MARTINI force field is established, as well as their radius, volume, and mass. The effect of the size of the simulation box on the obtained CMC has been investigated, as well as the effect of the number of SDS molecules, in the simulations, on the formation of aggregates. The CMC, which was obtained from a graph of the calculated viscosities versus concentration, is in good agreement with the reported experimental data and does not depend on the size of the box used in the simulation. The formation of a spherical micelle-like aggregate is observed, where the dodecyl sulfate tails point inward and the heads point outward the aggregation micelle, in accordance with experimental observations. The advantage of using coarse-grain molecular dynamics is the possibility of treating explicitly charged beads, applying a shear flow for viscosity calculation, and processing much larger spatial and temporal scales than atomistic molecular dynamics can. Furthermore, the CMC of SDS obtained with the coarse-grained model is in much better agreement with the experimental value than the value obtained with atomistic simulations.

Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer.

PubMed

Pluhackova, Kristyna; Wassenaar, Tsjerk A; Kirsch, Sonja; Böckmann, Rainer A

2015-03-26

A molecular description of the lipid-protein interactions underlying the adsorption of proteins to membranes is crucial for understanding, for example, the specificity of adsorption or the binding strength of a protein to a bilayer, or for characterizing protein-induced changes of membrane properties. In this paper, we extend an automated in silico assay (DAFT) for binding studies and apply it to characterize the adsorption of the model fusion peptides E and K to a mixed phospholipid/cholesterol membrane using coarse-grained molecular dynamics simulations. In addition, we couple the coarse-grained protocol to reverse transformation to atomistic resolution, thereby allowing to study molecular interactions with high detail. The experimentally observed differential binding of the peptides E and K to membranes, as well as the increased binding affinity of helical over unstructered peptides, could be well reproduced using the polarizable Martini coarse-grained (CG) force field. Binding to neutral membranes is shown to be dominated by initial binding of the positively charged N-terminus to the phospholipid headgroup region, followed by membrane surface-aligned insertion of the peptide at the interface between the hydrophobic core of the membrane and its polar headgroup region. Both coarse-grained and atomistic simulations confirm a before hypothesized snorkeling of lysine side chains for the membrane-bound state of the peptide K. Cholesterol was found to be enriched in peptide vicinity, which is probably of importance for the mechanism of membrane fusion. The applied sequential multiscale method, using coarse-grained simulations for the slow adsorption process of peptides to membranes followed by backward transformation to atomistic detail and subsequent atomistic simulations of the preformed peptide-lipid complexes, is shown to be a versatile approach to study the interactions of peptides or proteins with biomembranes.

Coarse-grained incompressible magnetohydrodynamics: Analyzing the turbulent cascades

DOE PAGES

Aluie, Hussein

2017-02-21

Here, we formulate a coarse-graining approach to the dynamics of magnetohydrodynamic (MHD) fluids at a continuum of length-scales. In this methodology, effective equations are derived for the observable velocity and magnetic fields spatially-averaged at an arbitrary scale of resolution. The microscopic equations for the bare velocity and magnetic fields are renormalized by coarse-graining to yield macroscopic effective equations that contain both a subscale stress and a subscale electromotive force (EMF) generated by nonlinear interaction of eliminated fields and plasma motions. At large coarse-graining length-scales, the direct dissipation of invariants by microscopic mechanisms (such as molecular viscosity and Spitzer resistivity) ismore » shown to be negligible. The balance at large scales is dominated instead by the subscale nonlinear terms, which can transfer invariants across scales, and are interpreted in terms of work concepts for energy and in terms of topological flux-linkage for the two helicities. An important application of this approach is to MHD turbulence, where the coarse-graining length ℓ lies in the inertial cascade range. We show that in the case of sufficiently rough velocity and/or magnetic fields, the nonlinear inter-scale transfer need not vanish and can persist to arbitrarily small scales. Although closed expressions are not available for subscale stress and subscale EMF, we derive rigorous upper bounds on the effective dissipation they produce in terms of scaling exponents of the velocity and magnetic fields. These bounds provide exact constraints on phenomenological theories of MHD turbulence in order to allow the nonlinear cascade of energy and cross-helicity. On the other hand, we show that the forward cascade of magnetic helicity to asymptotically small scales is impossible unless 3rd-order moments of either velocity or magnetic field become infinite.« less

A constraint-logic based implementation of the coarse-grained approach to data acquisition scheduling of the International Ultraviolet Explorer orbiting observatory

NASA Technical Reports Server (NTRS)

Mccollum, Bruce; Graves, Mark

1994-01-01

The International Ultraviolet Explorer (IUE) satellite observatory has been in operation continuously since 1978. It typically carries out several thousand observations per year for over a hundred different science projects. These observations, which can occur in one of four different data-taking modes, fall under several satellite-related constraints and many other constraints which derive from the science goals of the projects being undertaken. One strategy which has made the scheduling problem tractable has been that of 'coarse-graining' the time into discrete blocks of equal size (8 hours), each of which is devoted to a single science program, and each of which is sufficiently long for several observations to be carried out. We call it 'coarse-graining' because the schedule is done at a 'coarse' level which ignores fine structure; i.e., no attempt is made to plan the sequence of observations occurring within each time block. We have incorporated the IUE's coarse-grained approach in new software which examines the science needs of the observations and produces a limited set of alternative schedules which meet all of the instrument and science-related constraints. With this algorithm, the IUE can still be scheduled by a single person using a standard workstation, as it has been. We believe that this software could could be adapted to a more complex mission while retaining the IUE's high flexibility and efficiency and scientific return of future satellite missions.

Major, trace and REE geochemistry of recent sediments from lower Catumbela River (Angola)

NASA Astrophysics Data System (ADS)

Vinha, Manuela; Silva, M. G.; Cabral Pinto, Marina M. S.; Carvalho, Paula Cristina S.

2016-03-01

The mineralogy, texture, major, trace and rare earth elements, from recent sediment samples collected in the lower Catumbela River, were analysed in this study to characterize and discuss the factors controlling its geochemistry and provide data that can be used as tracers of Catumbela River inputs to the Angolan continental shelf. The sediments are mainly sands and silty-sands, but sandy-silt also occurs and the mineralogy is composed of quartz, feldspar, phyllosilicates, magnetite, ilmenite and also carbonates when the river crosses limestones and marls in the downstream sector. The hydraulic sorting originates magnetite-ilmenite and REE-enriched minerals placers. The mineralogy of the sediments is controlled by the source rocks and the degree of chemical weathering is lower than erosion. The texture is mainly controlled by location. There is enrichment in all the analysed trace elements in the fine grained, clay minerals and Fe-oxy-hydroxides rich sediments, compared to the coarse grained and quartz plus feldspar rich ones. The coarse grained sediments (without the placers) are impoverished in ΣREE when compared with UCC and NASC compositions, while the fine grained sediments have ΣREE contents similar to UCC and NASC. The placers have ΣREE contents up to 959.59 mg/kg. The source composition is the dominant factor controlling the REE geochemistry of the analysed sediments as there is no difference in the (La/Yb)N, (La/Sm)N and (Gd/Yb)N ratios in coarse and fine grained sediments. The sorting of magnetite, ilmenite, zircon, throrite, thorianite, rutile and titanite explain the HREE/LREE enriched patterns of the coarse grained sediments.

Learning To Fold Proteins Using Energy Landscape Theory

PubMed Central

Schafer, N.P.; Kim, B.L.; Zheng, W.; Wolynes, P.G.

2014-01-01

This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy landscape theory of protein folding. We also present a review of the results of the AMH/AMC/AMW/AWSEM family of coarse-grained molecular dynamics protein folding models to illustrate the points covered in the first part of the article. Accurate coarse-grained structure prediction models can be used to investigate a wide range of conceptual and mechanistic issues outside of protein structure prediction; specifically, the paper concludes by reviewing how AWSEM has in recent years been able to elucidate questions related to the unusual kinetic behavior of artificially designed proteins, multidomain protein misfolding, and the initial stages of protein aggregation. PMID:25308991

Short-range, overpressure-driven methane migration in coarse-grained gas hydrate reservoirs

DOE PAGES

Nole, Michael; Daigle, Hugh; Cook, Ann E.; ...

2016-08-31

Two methane migration mechanisms have been proposed for coarse-grained gas hydrate reservoirs: short-range diffusive gas migration and long-range advective fluid transport from depth. Herein we demonstrate that short-range fluid flow due to overpressure in marine sediments is a significant additional methane transport mechanism that allows hydrate to precipitate in large quantities in thick, coarse-grained hydrate reservoirs. Two-dimensional simulations demonstrate that this migration mechanism, short-range advective transport, can supply significant amounts of dissolved gas and is unencumbered by limitations of the other two end-member mechanisms. Here, short-range advective migration can increase the amount of methane delivered to sands as compared tomore » the slow process of diffusion, yet it is not necessarily limited by effective porosity reduction as is typical of updip advection from a deep source.« less

Short-range, overpressure-driven methane migration in coarse-grained gas hydrate reservoirs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nole, Michael; Daigle, Hugh; Cook, Ann E.

Two methane migration mechanisms have been proposed for coarse-grained gas hydrate reservoirs: short-range diffusive gas migration and long-range advective fluid transport from depth. Herein we demonstrate that short-range fluid flow due to overpressure in marine sediments is a significant additional methane transport mechanism that allows hydrate to precipitate in large quantities in thick, coarse-grained hydrate reservoirs. Two-dimensional simulations demonstrate that this migration mechanism, short-range advective transport, can supply significant amounts of dissolved gas and is unencumbered by limitations of the other two end-member mechanisms. Here, short-range advective migration can increase the amount of methane delivered to sands as compared tomore » the slow process of diffusion, yet it is not necessarily limited by effective porosity reduction as is typical of updip advection from a deep source.« less

Optimization of droplets for UV-NIL using coarse-grain simulation of resist flow

NASA Astrophysics Data System (ADS)

Sirotkin, Vadim; Svintsov, Alexander; Zaitsev, Sergey

2009-03-01

A mathematical model and numerical method are described, which make it possible to simulate ultraviolet ("step and flash") nanoimprint lithography (UV-NIL) process adequately even using standard Personal Computers. The model is derived from 3D Navier-Stokes equations with the understanding that the resist motion is largely directed along the substrate surface and characterized by ultra-low values of the Reynolds number. By the numerical approximation of the model, a special finite difference method is applied (a coarse-grain method). A coarse-grain modeling tool for detailed analysis of resist spreading in UV-NIL at the structure-scale level is tested. The obtained results demonstrate the high ability of the tool to calculate optimal dispensing for given stamp design and process parameters. This dispensing provides uniform filled areas and a homogeneous residual layer thickness in UV-NIL.

Scalable parallel communications

NASA Technical Reports Server (NTRS)

Maly, K.; Khanna, S.; Overstreet, C. M.; Mukkamala, R.; Zubair, M.; Sekhar, Y. S.; Foudriat, E. C.

1992-01-01

Coarse-grain parallelism in networking (that is, the use of multiple protocol processors running replicated software sending over several physical channels) can be used to provide gigabit communications for a single application. Since parallel network performance is highly dependent on real issues such as hardware properties (e.g., memory speeds and cache hit rates), operating system overhead (e.g., interrupt handling), and protocol performance (e.g., effect of timeouts), we have performed detailed simulations studies of both a bus-based multiprocessor workstation node (based on the Sun Galaxy MP multiprocessor) and a distributed-memory parallel computer node (based on the Touchstone DELTA) to evaluate the behavior of coarse-grain parallelism. Our results indicate: (1) coarse-grain parallelism can deliver multiple 100 Mbps with currently available hardware platforms and existing networking protocols (such as Transmission Control Protocol/Internet Protocol (TCP/IP) and parallel Fiber Distributed Data Interface (FDDI) rings); (2) scale-up is near linear in n, the number of protocol processors, and channels (for small n and up to a few hundred Mbps); and (3) since these results are based on existing hardware without specialized devices (except perhaps for some simple modifications of the FDDI boards), this is a low cost solution to providing multiple 100 Mbps on current machines. In addition, from both the performance analysis and the properties of these architectures, we conclude: (1) multiple processors providing identical services and the use of space division multiplexing for the physical channels can provide better reliability than monolithic approaches (it also provides graceful degradation and low-cost load balancing); (2) coarse-grain parallelism supports running several transport protocols in parallel to provide different types of service (for example, one TCP handles small messages for many users, other TCP's running in parallel provide high bandwidth service to a single application); and (3) coarse grain parallelism will be able to incorporate many future improvements from related work (e.g., reduced data movement, fast TCP, fine-grain parallelism) also with near linear speed-ups.

A matter of scale: apparent niche differentiation of diploid and tetraploid plants may depend on extent and grain of analysis.

PubMed

Kirchheimer, Bernhard; Schinkel, Christoph C F; Dellinger, Agnes S; Klatt, Simone; Moser, Dietmar; Winkler, Manuela; Lenoir, Jonathan; Caccianiga, Marco; Guisan, Antoine; Nieto-Lugilde, Diego; Svenning, Jens-Christian; Thuiller, Wilfried; Vittoz, Pascal; Willner, Wolfgang; Zimmermann, Niklaus E; Hörandl, Elvira; Dullinger, Stefan

2016-03-22

Emerging polyploids may depend on environmental niche shifts for successful establishment. Using the alpine plant Ranunculus kuepferi as a model system, we explore the niche shift hypothesis at different spatial resolutions and in contrasting parts of the species range. European Alps. We sampled 12 individuals from each of 102 populations of R. kuepferi across the Alps, determined their ploidy levels, derived coarse-grain (100 × 100 m) environmental descriptors for all sampling sites by downscaling WorldClim maps, and calculated fine-scale environmental descriptors (2 × 2 m) from indicator values of the vegetation accompanying the sampled individuals. Both coarse and fine-scale variables were further computed for 8239 vegetation plots from across the Alps. Subsequently, we compared niche optima and breadths of diploid and tetraploid cytotypes by combining principal components analysis and kernel smoothing procedures. Comparisons were done separately for coarse and fine-grain data sets and for sympatric, allopatric and the total set of populations. All comparisons indicate that the niches of the two cytotypes differ in optima and/or breadths, but results vary in important details. The whole-range analysis suggests differentiation along the temperature gradient to be most important. However, sympatric comparisons indicate that this climatic shift was not a direct response to competition with diploid ancestors. Moreover, fine-grained analyses demonstrate niche contraction of tetraploids, especially in the sympatric range, that goes undetected with coarse-grained data. Although the niche optima of the two cytotypes differ, separation along ecological gradients was probably less decisive for polyploid establishment than a shift towards facultative apomixis, a particularly effective strategy to avoid minority cytotype exclusion. In addition, our results suggest that coarse-grained analyses overestimate niche breadths of widely distributed taxa. Niche comparison analyses should hence be conducted at environmental data resolutions appropriate for the organism and question under study.

Measurement of Heavy Ion Irradiation Induced In-Plane Strain in Patterned Face-Centered-Cubic Metal Films: An in Situ Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, K. Y.; Chen, Y.; Li, J.

Nanocrystalline Ag, Cu, and Ni thin films and their coarse grained counterparts are patterned in this paper using focused ion beam and then irradiated by Kr ions within an electron microscope at room temperature. Irradiation induced in-plane strain of the films is measured by tracking the location of nanosized holes. The magnitude of the strain in all specimens is linearly dose-dependent and the strain rates of nanocrystalline metals are significantly greater as compared to that of the coarse grained metals. Finally, real-time microscopic observation suggests that substantial grain boundary migration and grain rotation are responsible for the significant in-plane strain.

Measurement of Heavy Ion Irradiation Induced In-Plane Strain in Patterned Face-Centered-Cubic Metal Films: An in Situ Study

DOE PAGES

Yu, K. Y.; Chen, Y.; Li, J.; ...

2016-11-28

Nanocrystalline Ag, Cu, and Ni thin films and their coarse grained counterparts are patterned in this paper using focused ion beam and then irradiated by Kr ions within an electron microscope at room temperature. Irradiation induced in-plane strain of the films is measured by tracking the location of nanosized holes. The magnitude of the strain in all specimens is linearly dose-dependent and the strain rates of nanocrystalline metals are significantly greater as compared to that of the coarse grained metals. Finally, real-time microscopic observation suggests that substantial grain boundary migration and grain rotation are responsible for the significant in-plane strain.

Structure and Relaxation in Solutions of Monoclonal Antibodies.

PubMed

Wang, Gang; Varga, Zsigmond; Hofmann, Jennifer; Zarraga, Isidro E; Swan, James W

2018-03-22

Reversible self-association of therapeutic antibodies is a key factor in high protein solution viscosities. In the present work, a coarse-grained computational model accounting for electrostatic, dispersion, and long-ranged hydrodynamic interactions of two model monoclonal antibodies is applied to understand the nature of self-association, predicting the solution microstructure and resulting transport properties of the solution. For the proteins investigated, the structure factor across a range of solution conditions shows quantitative agreement with neutron-scattering experiments. We observe a homogeneous, dynamical association of the antibodies with no evidence of phase separation. Calculations of self-diffusivity and viscosity from coarse-grained dynamic simulations show the appropriate trends with concentration but, respectively, over- and under-predict the experimentally measured values. By adding constraints to the self-associated clusters that rigidify them under flow, prediction of the transport properties is significantly improved with respect to experimental measurements. We hypothesize that these rigidity constraints are associated with missing degrees of freedom in the coarse-grained model resulting from patchy and heterogeneous interactions among coarse-grained domains. These results demonstrate how structural anisotropy and anisotropy of interactions generated by features at the 2-5 nm length scale in antibodies are sufficient to recover the dynamics and rheological properties of these important macromolecular solutions.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.

PubMed

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

Orthographic and phonological contributions to reading development: tracking developmental trajectories using masked priming.

PubMed

Ziegler, Johannes C; Bertrand, Daisy; Lété, Bernard; Grainger, Jonathan

2014-04-01

The present study used a variant of masked priming to track the development of 2 marker effects of orthographic and phonological processing from Grade 1 through Grade 5 in a cross-sectional study. Pseudohomophone (PsH) priming served as a marker for phonological processing, whereas transposed-letter (TL) priming was a marker for coarse-grained orthographic processing. The results revealed a clear developmental picture. First, the PsH priming effect was significant and remained stable across development, suggesting that phonology not only plays an important role in early reading development but continues to exert a robust influence throughout reading development. This finding challenges the view that more advanced readers should rely less on phonological information than younger readers. Second, the TL priming effect increased monotonically with grade level and reading age, which suggests greater reliance on coarse-grained orthographic coding as children become better readers. Thus, TL priming effects seem to be a good marker effect for children's ability to use coarse-grained orthographic coding to speed up direct lexical access in alphabetic languages. The results were predicted by the dual-route model of orthographic processing, which suggests that direct orthographic access is achieved through coarse-grained orthographic coding that tolerates some degree of flexibility in letter order. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

NASA Astrophysics Data System (ADS)

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

The role of atomic level steric effects and attractive forces in protein folding.

PubMed

Lammert, Heiko; Wolynes, Peter G; Onuchic, José N

2012-02-01

Protein folding into tertiary structures is controlled by an interplay of attractive contact interactions and steric effects. We investigate the balance between these contributions using structure-based models using an all-atom representation of the structure combined with a coarse-grained contact potential. Tertiary contact interactions between atoms are collected into a single broad attractive well between the C(β) atoms between each residue pair in a native contact. Through the width of these contact potentials we control their tolerance for deviations from the ideal structure and the spatial range of attractive interactions. In the compact native state dominant packing constraints limit the effects of a coarse-grained contact potential. During folding, however, the broad attractive potentials allow an early collapse that starts before the native local structure is completely adopted. As a consequence the folding transition is broadened and the free energy barrier is decreased. Eventually two-state folding behavior is lost completely for systems with very broad attractive potentials. The stabilization of native-like residue interactions in non-perfect geometries early in the folding process frequently leads to structural traps. Global mirror images are a notable example. These traps are penalized by the details of the repulsive interactions only after further collapse. Successful folding to the native state requires simultaneous guidance from both attractive and repulsive interactions. Copyright © 2011 Wiley Periodicals, Inc.

Impact of the nanostructuration on the corrosion resistance and hardness of irradiated 316 austenitic stainless steels

NASA Astrophysics Data System (ADS)

Hug, E.; Prasath Babu, R.; Monnet, I.; Etienne, A.; Moisy, F.; Pralong, V.; Enikeev, N.; Abramova, M.; Sauvage, X.; Radiguet, B.

2017-01-01

The influence of grain size and irradiation defects on the mechanical behavior and the corrosion resistance of a 316 stainless steel have been investigated. Nanostructured samples were obtained by severe plastic deformation using high pressure torsion. Both coarse grain and nanostructured samples were irradiated with 10 MeV 56Fe5+ ions. Microstructures were characterized using transmission electron microscopy and atom probe tomography. Surface mechanical properties were evaluated thanks to hardness measurements and the corrosion resistance was studied in chloride environment. Nanostructuration by high pressure torsion followed by annealing leads to enrichment in chromium at grain boundaries. However, irradiation of nanostructured samples implies a chromium depletion of the same order than depicted in coarse grain specimens but without metallurgical damage like segregated dislocation loops or clusters. Potentiodynamic polarization tests highlight a definitive deterioration of the corrosion resistance of coarse grain steel with irradiation. Downsizing the grain to a few hundred of nanometers enhances the corrosion resistance of irradiated samples, despite the fact that the hardness of nanocrystalline austenitic steel is only weakly affected by irradiation. These new experimental results are discussed in the basis of couplings between mechanical and electrical properties of the passivated layer thanks to impedance spectroscopy measurements, hardness properties of the surfaces and local microstructure evolutions.

Study on the Toughness of X100 Pipeline Steel Heat Affected Zone

NASA Astrophysics Data System (ADS)

Li, Xueda; Shang, Chengjia; Ma, Xiaoping; Subramanian, S. V.

Microstructure-property correlation of heat affected zone (HAZ) in X100 longitudinal submerged arc welding (LSAW) real weld joint was studied in this paper. Coarse grained (CG) HAZ and intercritically reheated coarse grained (ICCG) HAZ were characterized by optical microscope (OM), electron backscattered diffraction (EBSD). The microstructure of CGHAZ is mostly composed of granular bainite with low density of high angle boundaries (HAB). Prior austenite grain size is 80μm. In ICCGHAZ, coarse prior austenite grains were decorated by coarse necklacing martensite-austenite (M-A) constituents. Different layers were observed within M-A constituent, which may be martensite and austenite layers. Charpy absorbed energy of two different HAZ regions (ICCGHAZ containing and non-containing regions) was recorded using instrumental Charpy impact test machine. The results showed that the existence of ICCGHAZ resulted in the sharp drop of Charpy absorbed energy from 180J to 50J, while the existence of only CGHAZ could still lead to good toughness. The fracture surface was 60% brittle in the absence of ICCGHAZ, and 100% brittle in the presence of ICCGHAZ in the impact tested samples. The underlying reason is the microstructure of ICCGHAZ consisted of granular bainite and upper bainite with necklace-type M-A constituent along the grain boundaries. Cleavage fracture initiated from M-A constituent, either through cracking of M-A or debonding from the matrix, was observed at the fracture surface of ICCGHAZ. The presence of necklace type M-A constituent in ICCGHAZ notably increases the susceptibility of cleavage microcrack nucleation. Furthermore, the study of secondary microcracks beneath the CGHAZ and the ICCGHAZ through EBSD suggested that the fracture mechanism changes from nucleation-controlled in the CGHAZ to propagation-controlled in the ICCGHAZ because of the presence of necklace-type M-A constituent in the ICCGHAZ region. Both fracture mechanism contribute to the poor toughness of the sample contained ICCGHAZ. In conclusion, big prior austenite grains with low density of HAB plus coarse necklacing M-A products along grain boundary is the dominant factor resulting in low toughness.

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

PubMed

Riniker, Sereina; van Gunsteren, Wilfred F

2011-02-28

The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostatic interactions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and all-atom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectric permittivity were chosen as primary target properties. The model properties are compared with those obtained from experiment, from clusters of simple-point-charge water molecules of appropriate size in the liquid phase, and for other CG water models if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine-grained atomistic water models.

Probing Sub-atomistic Free-Volume Imperfections in Dry-Milled Nanoarsenicals with PAL Spectroscopy.

PubMed

Shpotyuk, Oleh; Ingram, Adam; Bujňáková, Zdenka; Baláž, Peter; Shpotyuk, Yaroslav

2016-12-01

Structural transformations caused by coarse-grained powdering and fine-grained mechanochemical milling in a dry mode were probed in high-temperature modification of tetra-arsenic tetra-sulfide known as β-As4S4. In respect to X-ray diffraction analysis, the characteristic sizes of β-As4S4 crystallites in these coarse- and fine-grained powdered pellets were 90 and 40 nm, respectively. Positron annihilation lifetime spectroscopy was employed to characterize transformations occurred in free-volume structure of these nanoarsenicals. Experimentally measured positron lifetime spectra were parameterized in respect to three- or two-term fitting procedures and respectively compared with those accumulated for single crystalline realgar α-As4S4 polymorph. The effect of coarse-grained powdering was found to result in generation of large amount of positron and positronium Ps trapping sites inside arsenicals in addition to existing ones. In fine-grained powdered β-As4S4 pellets, the positron trapping sites with characteristic free volumes close to bi- and tri-atomic vacancies were evidently dominated. These defects were supposed to originate from grain boundary regions and interfacial free volumes near aggregated β-As4S4 crystallites. Thus, the cumulative production of different positron traps with lifetimes close to defect-related lifetimes in realgar α-As4S4 polymorph was detected in fine-grained milled samples.

High Temperature Fatigue Crack Growth Behavior of Alloy 10

NASA Technical Reports Server (NTRS)

Gayda, John

2001-01-01

Methods to improve the high temperature, dwell crack growth resistance of Alloy 10, a high strength, nickel-base disk alloy, were studied. Two approaches, heat treat variations and composition modifications, were investigated. Under the heat treat approach, solution temperature, cooling rates, and stabilization, were studied. It was found that higher solution temperatures, which promote coarser grain sizes, coupled with a 1550 F stabilization treatment were found to significantly reduce dwell crack growth rates at 1300 F Changes in the niobium and tantalum content were found to have a much smaller impact on crack growth behavior. Lowering the niobium:tantalum ratio did improve crack growth resistance and this effect was most pronounced for coarse grain microstructures. Based on these findings, a coarse grain microstructure for Alloy 10 appears to be the best option for improving dwell crack growth resistance, especially in the rim of a disk where temperatures can reach or exceed 1300 T. Further, the use of advanced processing technologies, which can produce a coarse grain rim and fine grain bore, would be the preferred option for Alloy 10 to obtain the optimal balance between tensile, creep, and crack growth requirements for small gas turbine engines.

Sedimentary and petrofacies analyses of the Amasiri Sandstone, southern Benue Trough, Nigeria: Implications for depositional environment and tectonic provenance

NASA Astrophysics Data System (ADS)

Okoro, A. U.; Igwe, E. O.; Nwajide, C. S.

2016-11-01

This study was undertaken to determine the depositional environment, provenance and tectonic setting for the Turonian Amasiri Sandstone, southern Benue Trough, Nigeria, using lithofacies analysis and re-appraisal of petrography of the sandstones. Local stratigraphy and field relationships show a thick succession of shales alternating with elongate/parallel sandstone ridges extending eastwards from Akpoha to Amasiri through Itigidi and Ugep to Apiapum areas. Lithofacies analysis reveals 9 lithofacies suggestive of storm (mass flow) and tidal shelf processes. These include dark grey to black laminated shale/silty mudstones, bioturbated mudstones, coquinoid limestones, very fine-grained bioturbated sandstones with shell hash/debris in places and limestone rip-up clasts, massive and chaotic sandy conglomerate with rip - up clasts, fine to medium-grained, parallel laminated sandstone, hummocky cross-stratified, massive, medium to coarse-grained sandstones, medium to very coarse-grained, planar cross-bedded sandstone, with clay-draped foresets and Ophiomorpha burrows, and coarse-grained trough cross-bedded sandstone. Petrofacies analysis identifies the sandstones as feldspathic and arkosic arenites. Ternary plot of framework mineralogy indicates derivation from an uplifted continental block related to the nearby Oban Massif and Cameroon Basement Complex.

The influence of high heat input and inclusions control for rare earth on welding in low alloy high strength steel

NASA Astrophysics Data System (ADS)

Chu, Rensheng; Mu, Shukun; Liu, Jingang; Li, Zhanjun

2017-09-01

In the current paper, it is analyzed for the influence of high heat input and inclusions control for rare earth on welding in low alloy high strength steel. It is observed for the structure for different heat input of the coarse-grained area. It is finest for the coarse grain with the high heat input of 200 kJ / cm and the coarse grain area with 400 kJ / cm is the largest. The performance with the heat input of 200 kJ / cm for -20 °C V-shaped notch oscillatory power is better than the heat input of 400 kJ / cm. The grain structure is the ferrite and bainite for different holding time. The grain structure for 5s holding time has a grain size of 82.9 μm with heat input of 200 kJ/cm and grain size of 97.9 μm for 10s holding time. For the inclusions for HSLA steel with adding rare earth, they are Al2O3-CaS inclusions in the Al2O3-CaS-CaO ternary phase diagram. At the same time, it can not be found for low melting calcium aluminate inclusions compared to the inclusions for the HSLA steel without rare earth. Most of the size for the inclusions is between 1 ~ 10μm. The overall grain structure is smaller and the welding performance is more excellent for adding rare earth.

Forging of Advanced Disk Alloy LSHR

NASA Technical Reports Server (NTRS)

Gabb, Timothy P.; Gayda, John; Falsey, John

2005-01-01

The powder metallurgy disk alloy LSHR was designed with a relatively low gamma precipitate solvus temperature and high refractory element content to allow versatile heat treatment processing combined with high tensile, creep and fatigue properties. Grain size can be chiefly controlled through proper selection of solution heat treatment temperatures relative to the gamma precipitate solvus temperature. However, forging process conditions can also significantly influence solution heat treatment-grain size response. Therefore, it is necessary to understand the relationships between forging process conditions and the eventual grain size of solution heat treated material. A series of forging experiments were performed with subsequent subsolvus and supersolvus heat treatments, in search of suitable forging conditions for producing uniform fine grain and coarse grain microstructures. Subsolvus, supersolvus, and combined subsolvus plus supersolvus heat treatments were then applied. Forging and subsequent heat treatment conditions were identified allowing uniform fine and coarse grain microstructures.

An ellipsoid-chain model for conjugated polymer solutions

NASA Astrophysics Data System (ADS)

Lee, Cheng K.; Hua, Chi C.; Chen, Show A.

2012-02-01

We propose an ellipsoid-chain model which may be routinely parameterized to capture large-scale properties of semiflexible, amphiphilic conjugated polymers in various solvent media. The model naturally utilizes the defect locations as pivotal centers connecting adjacent ellipsoids (each currently representing ten monomer units), and a variant umbrella-sampling scheme is employed to construct the potentials of mean force (PMF) for specific solvent media using atomistic dynamics data and simplex optimization. The performances, both efficacy and efficiency, of the model are thoroughly evaluated by comparing the simulation results on long, single-chain (i.e., 300-mer) structures with those from two existing, finer-grained models for a standard conjugated polymer (i.e., poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene) or MEH-PPV) in two distinct solvents (i.e., chloroform or toluene) as well as a hybrid, binary-solvent medium (i.e., chloroform/toluene = 1:1 in number density). The coarse-grained Monte Carlo (CGMC) simulation of the ellipsoid-chain model is shown to be the most efficient—about 300 times faster than the coarse-grained molecular dynamics (CGMD) simulation of the finest CG model that employs explicit solvents—in capturing elementary single-chain structures for both single-solvent media, and is a few times faster than the coarse-grained Langevin dynamics (CGLD) simulation of another implicit-solvent polymer model with a slightly greater coarse-graining level than in the CGMD simulation. For the binary-solvent system considered, however, both of the two implicit-solvent schemes (i.e., CGMC and CGLD) fail to capture the effects of conspicuous concentration fluctuations near the polymer-solvent interface, arising from a pronounced coupling between the solvent molecules and different parts of the polymer. Essential physical implications are elaborated on the success as well as the failure of the two implicit-solvent CG schemes under varying solvent conditions. Within the ellipsoid-chain model, the impact of synthesized defects on local segmental ordering as well as bulk chain conformation is also scrutinized, and essential consequences in practical applications discussed. In future perspectives, we remark on strategy that takes advantage of the coordination among various CG models and simulation schemes to warrant computational efficiency and accuracy, with the anticipated capability of simulating larger-scale, many-chain aggregate systems.

Multiscale Simulations of Protein Landscapes: Using Coarse Grained Models as Reference Potentials to Full Explicit Models

PubMed Central

Messer, Benjamin M.; Roca, Maite; Chu, Zhen T.; Vicatos, Spyridon; Kilshtain, Alexandra Vardi; Warshel, Arieh

2009-01-01

Evaluating the free energy landscape of proteins and the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of simplified coarse grained (CG) folding models offers an effective way of sampling the landscape but such a treatment, however, may not give the correct description of the effect of the actual protein residues. A general way around this problem that has been put forward in our early work (Fan et al, Theor Chem Acc (1999) 103:77-80) uses the CG model as a reference potential for free energy calculations of different properties of the explicit model. This method is refined and extended here, focusing on improving the electrostatic treatment and on demonstrating key applications. This application includes: evaluation of changes of folding energy upon mutations, calculations of transition states binding free energies (which are crucial for rational enzyme design), evaluation of catalytic landscape and simulation of the time dependent responses to pH changes. Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed. PMID:20052756

Homopolyrotaxanes and Homopolyrotaxane Networks of PEO

NASA Technical Reports Server (NTRS)

Pugh, Coleen; Mattice, Wayne

2005-01-01

In order to identify the optimum size of macrocrown ether for threading, we first investigated the size and shape of simple crown ethers in the melt at 373 K, and their extent of threading with PEO in the melt using coarse-grained Monte Carlo simulations on the 2nnd (second nearest neighbor diamond) lattice, which is a high coordination lattice whose coarse-grained chains can be reverse mapped into fully atomistic models in continuous space.

A highly coarse-grained model to simulate entangled polymer melts.

PubMed

Zhu, You-Liang; Liu, Hong; Lu, Zhong-Yuan

2012-04-14

We introduce a highly coarse-grained model to simulate the entangled polymer melts. In this model, a polymer chain is taken as a single coarse-grained particle, and the creation and annihilation of entanglements are regarded as stochastic events in proper time intervals according to certain rules and possibilities. We build the relationship between the probability of appearance of an entanglement between any pair of neighboring chains at a given time interval and the rate of variation of entanglements which describes the concurrence of birth and death of entanglements. The probability of disappearance of entanglements is tuned to keep the total entanglement number around the target value. This useful model can reflect many characteristics of entanglements and macroscopic properties of polymer melts. As an illustration, we apply this model to simulate the polyethylene melt of C(1000)H(2002) at 450 K and further validate this model by comparing to experimental data and other simulation results.

Systematic coarse-grained modeling of complexation between small interfering RNA and polycations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, Zonghui; Luijten, Erik, E-mail: luijten@northwestern.edu; Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208

All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed bindingmore » patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.« less

A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments

NASA Astrophysics Data System (ADS)

Weik, Florian; Kesselheim, Stefan; Holm, Christian

2016-11-01

We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.

Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach

NASA Astrophysics Data System (ADS)

He, Yi; Liwo, Adam; Scheraga, Harold A.

2015-12-01

Coarse-grained models are useful tools to investigate the structural and thermodynamic properties of biomolecules. They are obtained by merging several atoms into one interaction site. Such simplified models try to capture as much as possible information of the original biomolecular system in all-atom representation but the resulting parameters of these coarse-grained force fields still need further optimization. In this paper, a force field optimization method, which is based on maximum-likelihood fitting of the simulated to the experimental conformational ensembles and least-squares fitting of the simulated to the experimental heat-capacity curves, is applied to optimize the Nucleic Acid united-RESidue 2-point (NARES-2P) model for coarse-grained simulations of nucleic acids recently developed in our laboratory. The optimized NARES-2P force field reproduces the structural and thermodynamic data of small DNA molecules much better than the original force field.

Formation of incoherent deformation twin boundaries in a coarse-grained Al-7Mg alloy

NASA Astrophysics Data System (ADS)

Jin, S. B.; Zhang, K.; Bjørge, R.; Tao, N. R.; Marthinsen, K.; Lu, K.; Li, Y. J.

2015-08-01

Deformation twinning has rarely been observed in coarse grained Al and its alloys except under some extreme conditions such as ultrahigh deformation strain or strain rates. Here, we report that a significant amount of Σ3 deformation twins could be generated in a coarse-grained Al-7 Mg alloy by dynamic plastic deformation (DPD). A systematic investigation of the Σ3 boundaries shows that they are Σ3{112} type incoherent twin boundaries (ITBs). These ITBs have formed by gradual evolution from copious low-angle deformation bands through <111>-twist Σ boundaries by lattice rotation. These findings provide an approach to generate deformation twin boundaries in high stacking fault energy metallic alloys. It is suggested that high solution content of Mg in the alloy and the special deformation mode of DPD played an important role in formation of the Σ and ITBs.

A Coarse-Grained Protein Model in a Water-like Solvent

NASA Astrophysics Data System (ADS)

Sharma, Sumit; Kumar, Sanat K.; Buldyrev, Sergey V.; Debenedetti, Pablo G.; Rossky, Peter J.; Stanley, H. Eugene

2013-05-01

Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein (``H-P'') model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the ``Jagla-philic'' monomers to the solvent, while maintaining a ``hydrophobic'' core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.

Folding and stability of helical bundle proteins from coarse-grained models.

PubMed

Kapoor, Abhijeet; Travesset, Alex

2013-07-01

We develop a coarse-grained model where solvent is considered implicitly, electrostatics are included as short-range interactions, and side-chains are coarse-grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side-chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics. Copyright © 2013 Wiley Periodicals, Inc.

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

PubMed

May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

2014-02-01

To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure. We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR-pMHC complex and the MP1-p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of >500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein-protein interaction strength. The python analysis framework and data files are available for download at http://www.ibi.vu.nl/downloads/bioinformatics-2013-btt675.tgz.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chremos, Alexandros, E-mail: achremos@imperial.ac.uk; Nikoubashman, Arash, E-mail: arashn@princeton.edu; Panagiotopoulos, Athanassios Z.

In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric–isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is importantmore » from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.« less

Computational Calculation Of The Ionization Energies Of The Human Prion Protein By The Coarse-grain Method

NASA Astrophysics Data System (ADS)

Lyu, Justin; Andrianarijaona, V. M.

2016-05-01

The causes of the misfolding of prion protein -i.e. the transformation of PrPC to PrPSc - have not been clearly elucidated. Many studies have focused on identifying possible chemical conditions, such as pH, temperature and chemical denaturation, that may trigger the pathological transformation of prion proteins (Weiwei Tao, Gwonchan Yoon, Penghui Cao, `` β-sheet-like formation during the mechanical unfolding of prion protein'', The Journal of Chemical Physics, 2015, 143, 125101). Here, we attempt to calculate the ionization energies of the prion protein, which will be able to shed light onto the possible causes of the misfolding. We plan on using the coarse-grain method which allows for a more feasible calculation time by means of approximation. We believe that by being able to approximate the ionization potential, particularly that of the regions known to form stable β-strands of the PrPSc form, the possible sources of denaturation, be it chemical or mechanical, may be narrowed down.

Development of a Coarse-grained Model of Polypeptoids for Studying Self-assembly in Solution

NASA Astrophysics Data System (ADS)

Du, Pu; Rick, Steven; Kumar, Revati

Polypeptoid, a class of highly tunable biomimetic analogues of peptides, are used as a prototypical model system to study self-assembly. The focus of this work is to glean insight into the effect of electrostatic and other non-covalent secondary interactions on the self-assembly of sequence-defined polypeptoids, with different charged and uncharged side groups, in solution that will complement experiments. Atomistic (AA) molecular dynamics simulation can provide a complete description of self-assembly of polypeptoid systems. However, the long simulation length and time scales needed for these processes require the development of a computationally cheaper alternative, namely coarse-grained (CG) models. A CG model for studying polypeptoid micellar interactions is being developed, parameterized on atomistic simulations, using a hybridized approach involving the OPLS-UA force filed and the Stillinger-Weber (SW) potential form. The development of the model as well as the results from the simulations on the self-assembly as function of polypeptoid chemical structure and sequences will be presented.

On the Reduction of Molecular Degrees of Freedom in Computer Simulations

NASA Astrophysics Data System (ADS)

Lyubartsev, Alexander P.; Laaksonen, Aatto

Molecular simulations, based on atomistic force fields are a standard theoretical tool in materials, polymers and biosciences. While various methods, with quantum chemistry incorporated, have been developed for condensed phase simulations during the last decade, there is another line of development with the purpose to bridge the time and length scales based on coarse-graining. This is expected to lead to some very interesting breakthroughs in the near future. In this lecture we will first give some background to common atomistic force fields. After that, we review a few common simple techniques for reducing the number of motional degrees of freedom to speed up the simulations. Finally, we present a powerful method for reducing uninteresting degrees of freedom. This is done by solving the Inverse Problem to obtain the interaction potentials. More precisely, we make use of the radial distribution functions, and by using the method of Inverse Monte Carlo [Lyubartsev & Laaksonen, Phys. Rev. E. 52, 3730 (1995)], we can construct effective potentials which are consistent with the original RDFs. This makes it possible to simulate much larger system than would have been possible by using atomistic force fields. We present many examples: How to simulate aqueous electrolyte solutions without any water molecules but still having the hydration structure around the ions - at the speed of a primitive electrolyte model calculation. We demonstrate how a coarse-grained model can be constructed for a double-helix DNA and how it can be used. It is accurate enough to reproduce the experimental results for ion condensation around DNA for several different counterions. We also show how we can construct site-site potentials for large-scale atomistic classical simulations of arbitrary liquids from smaller scale ab initio simulations. This methodology allows us to start from a simulation with the electrons and atomic nuclei, to construct a set of atomistic effective interaction potentials, and to use them in classical simulations. As a next step we can construct a new set of potentials beyond the atomistic description and carry out mesoscopic simulations, for example by using Dissipative Particle Dynamics. In this way we can tie together three different levels of description. The Dissipative Particle Dynamics method appears as a very promising tool to use with our coarse-grained potentials.

Granular avalanches on the Moon: Mass-wasting conditions, processes, and features

NASA Astrophysics Data System (ADS)

Kokelaar, B. P.; Bahia, R. S.; Joy, K. H.; Viroulet, S.; Gray, J. M. N. T.

2017-09-01

Seven lunar crater sites of granular avalanches are studied utilizing high-resolution images (0.42-1.3 m/pixel) from the Lunar Reconnaissance Orbiter Camera; one, in Kepler crater, is examined in detail. All the sites are slopes of debris extensively aggraded by frictional freezing at their dynamic angle of repose, four in craters formed in basaltic mare and three in the anorthositic highlands. Diverse styles of mass wasting occur, and three types of dry-debris flow deposit are recognized: (1) multiple channel-and-lobe type, with coarse-grained levees and lobate terminations that impound finer debris, (2) single-surge polylobate type, with subparallel arrays of lobes and fingers with segregated coarse-grained margins, and (3) multiple-ribbon type, with tracks reflecting reworked substrate, minor levees, and no coarse terminations. The latter type results from propagation of granular erosion-deposition waves down slopes dominantly of fine regolith, and it is the first recognized natural example. Dimensions, architectures, and granular segregation styles of the two coarse-grained deposit types are like those formed in natural and experimental avalanches on Earth, although the timescale of motion differs due to the reduced gravity. Influences of reduced gravity and fine-grained regolith on dynamics of granular flow and deposition appear slight, but we distinguish, for the first time, extensive remobilization of coarse talus by inundation with finer debris. The (few) sites show no clear difference attributable to the contrasting mare basalt and highland megaregolith host rocks and their fragmentation. This lunar study offers a benchmarking of deposit types that can be attributed to formation without influence of liquid or gas.

Conformational Temperature-Dependent Behavior of a Histone H2AX: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials

DTIC Science & Technology

2012-03-19

A, Black ME, Baker D, Stoddard BL (2005) Computational thermostabilization of an enzyme . Science 308: 857. 7. Liang HK, Huang CM, Ko MT, Hwang JK...2005) Amino acid coupling patterns in thermophilic proteins. Proteins 59: 58. 8. Das R, Gerstein M (2000) The stability of thermophilic proteins: a study

Educational Brief: Using Space for a Better Foundation on Earth Mechanics of Granular Materials

NASA Technical Reports Server (NTRS)

Dooling, Dave (Editor)

2002-01-01

Soils are three-phase composite materials that consist of soil, solid particles, and voids filled with water and/or air. Based on the particle-size distribution, they are generally classified as fine-grained (clays and plastic silts) and coarse-grained soils (nonplastic silts, sand, and gravel). Soil's resistance to external loadings is mainly derived from friction between particles and cohesion. Friction resistance is due to particles' surface-to-surface friction, interlocking, crushing, rearrangement, and dilation (or expansion) during shearing. Cohesion can be due to chemical cementation between particles, electrostatic and electromagnetic forces, and soil-water reaction and equilibrium. The basic factor responsible for the strength of coarse-grained soils is friction. Cohesion can be ignored. This educational brief focuses on measuring shear strength of sands (typical example of coarse-grained soils) where, for the same material, packing density is a main factor to be considered when one asks about the shear strength value. As the external load is applied, the soil's resistance is attained through shearing resistance, which causes the soil volume to increase (expand) or decrease (compress) depending on the initial packing density.

Sedimentary differentiation of aeolian grains at the White Sands National Monument, New Mexico, USA

NASA Astrophysics Data System (ADS)

Fenton, Lori K.; Bishop, Janice L.; King, Sara; Lafuente, Barbara; Horgan, Briony; Bustos, David; Sarrazin, Philippe

2017-06-01

Gypsum (CaSO4·2H2O) has been identified as a major component of part of Olympia Undae in the northern polar region of Mars, along with the mafic minerals more typical of Martian dune fields. The source and age of the gypsum is disputed, with the proposed explanations having vastly different implications for Mars' geological history. Furthermore, the transport of low density gypsum grains relative to and concurrently with denser grains has yet to be investigated in an aeolian setting. To address this knowledge gap, we performed a field study at White Sands National Monument (WSNM) in New Mexico, USA. Although gypsum dominates the bulk of the dune field, a dolomite-rich [CaMg(CO3)2] transport pathway along the northern border of WSNM provides a suitable analog site to study the transport of gypsum grains relative to the somewhat harder and denser carbonate grains. We collected samples along the stoss slope of a dune and on two coarse-grained ripples at the upwind margin of the dune field where minerals other than gypsum were most common. For comparison, additional samples were taken along the stoss slope of a dune outside the dolomite transport pathway, in the center of the dune field. Visible and near-infrared (VNIR), X-ray powder diffraction (XRD), and Raman analyses of different sample size fractions reveal that dolomite is only prevalent in grains larger than ∼1 mm. Other minerals, most notably calcite, are also present in smaller quantities among the coarse grains. The abundance of these coarse grains, relative to gypsum grains of the same size, drops off sharply at the upwind margin of the dune field. In contrast, gypsum dominated the finer fraction (<∼1 mm) at all sample sites, displaying no spatial variation. Estimates of sediment fluxes indicate that, although mineralogical differentiation of wind-transported grains occurs gradually in creep, the process is much more rapid when winds are strong enough to saltate the ⩾1 mm grains. The observed grain segregation is consistent with the WSNM dune field formative friction velocity (0.39 m/s) proposed by Jerolmack et al. (2011): winds significantly weaker than this value would not lift the large grains into differentiation-inducing saltation, whereas the observed differentiated trend would be obliterated by significantly stronger winds. When applied to Olympia Undae, a similar sediment flux analysis suggests that the strongest winds modeled by the Mars Climate Database (MCD) are consistent with the observed concentration of gypsum at dune crests. Density-driven differentiation in transport should not influence sediment fluxes of finer grains (<1 mm) as strongly on Earth, suggesting that the high ratio of fine gypsum grains to other minerals at WSNM is caused by a relatively high production and/or abrasion rate of gypsum sand. The observed preferential transport of coarse-grained gypsum in the dune field conceals a broader range of coarse-grained minerals present on Alkali Flat, contributing to the problem that mineralogy determined through both remote sensing of dune fields and analysis of dune foresets does not fully represent that of the source regions. Unlike quartz, the concentration of gypsum in WSNM occurs not because it is more resistant to weathering and erosion than other minerals, but rather because it is more readily produced (in the case of finer grains) and transported (in the case of coarser grains) than other minerals present in the region.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de; Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial chargesmore » within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.« less

Molecular Simulation Studies of Covalently and Ionically Grafted Nanoparticles

NASA Astrophysics Data System (ADS)

Hong, Bingbing

Solvent-free covalently- or ionically-grafted nanoparticles (CGNs and IGNs) are a new class of organic-inorganic hybrid composite materials exhibiting fluid-like behaviors around room temperature. With similar structures to prior systems, e.g. nanocomposites, neutral or charged colloids, ionic liquids, etc, CGNs and IGNs inherit the functionality of inorganic nanopariticles, the facile processibility of polymers, as well as conductivity and nonvolatility from their constituent materials. In spite of the extensive prior experimental research having covered synthesis and measurements of thermal and dynamic properties, little progress in understanding of these new materials at the molecular level has been achieved, because of the lack of simulation work in this new area. Atomistic and coarse-grained molecular dynamics simulations have been performed in this thesis to investigate the thermodynamics, structure, and dynamics of these systems and to seek predictive methods predictable for their properties. Starting from poly(ethylene oxide) oligomers (PEO) melts, we established atomistic models based on united-atom representations of methylene. The Green-Kubo and Einstein-Helfand formulas were used to calculate the transport properties. The simulations generate densities, viscosities, diffusivities, in good agreement with experimental data. The chain-length dependence of the transport properties suggests that neither Rouse nor reptation models are applicable in the short-chain regime investigated. Coupled with thermodynamic integration methods, the models give good predictions of pressure-composition-density relations for CO 2 + PEO oligomers. Water effects on the Henry's constant of CO 2 in PEO have also been investigated. The dependence of the calculated Henry's constants on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. CGNs are modeled by the inclusion of solid-sphere nanoparticles into the atomistic oligomers. The calculated viscosities from Green-Kubo relationships and temperature extrapolation are of the same order of magnitude as experimental values, but show a smaller activation energy relative to real CGNs systems. Grafted systems have higher viscosities, smaller diffusion coefficients, and slower chain dynamics than the ungrafted counterparts - nanocomposites - at high temperatures. At lower temperatures, grafted systems exhibit faster dynamics for both nanoparticles and chains relative to ungrafted systems, because of lower aggregation of nanoparticles and enhanced correlations between nanoparticles and chains. This agrees with the experimental observation that the new materials have liquid-like behavior in the absence of a solvent. To lower the simulated temperatures into the experimental range, we established a coarse-grained CGNs model by matching structural distribution functions to atomistic simulation data. In contrast with linear polymer systems, for which coarse-graining always accelerate dynamics, coarse-graining of grafted nanoparticles can either accelerate or slowdown the core motions, depending on the length of the grafted chains. This can be qualitatively predicted by a simple transition-state theory. Similar atomistic models to CGNs were developed for IGNs, with ammonium counterions described by an explicit-hydrogen way; these were in turn compared with "generic" coarse-grained IGNs. The elimination of chemical details in the coarse-grained models does not bring in qualitative changes to the radial distribution functions and diffusion of atomistic IGNs, but saves considerable simulation resources and make simulations near room temperatures affordable. The chain counterions in both atomistic and coarse-grained models are mobile, moving from site to site and from nanoparticle to nanoparticle. At the same temperature and the same core volume fractions, the nanoparticle diffusivities in coarse-grained IGNs are slower by a factor ten than the cores of CGNs. The coarse-grained IGNs models are later used to investigate the system dynamics through analysis of the dependence on temperature and structural parameters of the transport properties (self-diffusion coefficients, viscosities and conductivities). Further, migration kinetics of oligomeric counterions is analyzed in a manner analogous to unimer exchange between micellar aggregates. The counterion migrations follow the "double-core" mechanism and are kinetically controlled by neighboring-core collisions. (Abstract shortened by UMI.)

Terrestrial Analogs for Clay Minerals at Yellowknife Bay, Gale Crater, Mars

NASA Technical Reports Server (NTRS)

Treiman, Allan H; Morris, Richard V.; Bristow, Thomas; Ming, Douglas W.; Achillies, Cherie; Bish, David L.; Blake, David; Vaniman, David; Chipera, Steve

2013-01-01

Sediments of the Sheepbed unit, Gale Crater, were analyzed by the CheMin X-ray diffraction instrument on the Curiosity Rover. The sediments consist of typical basalt minerals (Fe-forsterite, augite, pigeonite, plagioclase), as well as Fe oxide/hydroxides, Fesulfides, amorphous material, and a phyllosilicate. The phyllosilicate has a broad 001 peak at approx 1.0 nm, consistent with a poorly ordered smectite. However, in the absence of diagnostic tests possible on Earth, its identity is not clear. The position of the 06L diffraction band is generally used to distinguish dioctahedral from trioctahedral smectite, but it is beyond CheMin's range of 2 Theta. The measured position of the 02L diffraction band (approx 22.5deg 2 Theta by CheMin), implies that the smectite is trioctahedral. The exact position and shape of the 02L band is determined by the cations in the 'M' sites of the smectite; to constrain those cations, we sought analogs among terrestrial smectites, emphasizing those developed from basaltic precursors. A potential analog for the Sheepbed smectite is 'griffithite,' a variety of trioctahedral smectite in altered basalt of the Topanga formation, Griffith Park, Los Angeles. 'Griffithite' has an 02L diffraction band that is close in position and shape to that of the Sheepbed smectite, although 'griffithite' has a very sharp 001 peak, indicating a high degree of layer ordering not seen in the Sheepbed smectite. A typical chemical formula for 'griffithite,' determined by electron microprobe, is (Ca0.59 Na0.03) (Mg4.28 Fe1.83) (Si6.64 Al1.36) O20 (OH)4, normalized to Si+Al=8. This formula is consistent with a fully trioctahedral Fe-Mg smectite with Ca and Na as interlayer cations. In the Topanga basalt, four types of 'griffithite' are present: fine-grained, filling cracks and vesicles; coarse-grained, filling vesicles; coarse-grained, replacing olivine phenocrysts; and coarse-grained, replacing glassy mesostasis. The fine-grained 'griffithite' formed first, and the last three varieties may be contemporaneous. One sample shows agate (alpha- quartz) that was precipitated between the episodes of deposition of the fine-grained and coarse-grained 'griffithite.' 'Griffithite' is not unique as a possible terrestrial analog - some clay minerals from the Doushantou formation, China, have similar 02L diffraction bands, and many basalts contain smectites in vesicles and as replacements after olivine. Similar trioctahedral smectites occur also in the nakhlite martian meteorites - as veinlets and replacements of olivine. By understanding the formation of these terrestrial clays, we hope to constrain the nature and mechanism of formation of the Sheepbed clay mineral.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived frommore » fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.« less

A Coarse-grained Model of Stratum Corneum Lipids: Free Fatty Acids and Ceramide NS

PubMed Central

Moore, Timothy C.; Iacovella, Christopher R.; Hartkamp, Remco; Bunge, Annette L.; McCabe, Clare

2017-01-01

Ceramide (CER)-based biological membranes are used both experimentally and in simulations as simplified model systems of the skin barrier. Molecular dynamics studies have generally focused on simulating preassembled structures using atomistically detailed models of CERs, which limit the system sizes and timescales that can practically be probed, rendering them ineffective for studying particular phenomena, including self-assembly into bilayer and lamellar superstructures. Here, we report on the development of a coarse-grained (CG) model for CER NS, the most abundant CER in human stratum corneum. Multistate iterative Boltzmann inversion is used to derive the intermolecular pair potentials, resulting in a force field that is applicable over a range of state points and suitable for studying ceramide self-assembly. The chosen CG mapping, which includes explicit interaction sites for hydroxyl groups, captures the directional nature of hydrogen bonding and allows for accurate predictions of several key structural properties of CER NS bilayers. Simulated wetting experiments allow the hydrophobicity of CG beads to be accurately tuned to match atomistic wetting behavior, which affects the whole system since inaccurate hydrophobic character is found to unphysically alter the lipid packing in hydrated lamellar states. We find that CER NS can self-assemble into multilamellar structures, enabling the study of lipid systems more representative of the multilamellar lipid structures present in the skin barrier. The coarse-grained force field derived herein represents an important step in using molecular dynamics to study the human skin barrier, which gives a resolution not available through experiment alone. PMID:27564869

Hybrid continuum-coarse-grained modeling of erythrocytes

NASA Astrophysics Data System (ADS)

Lyu, Jinming; Chen, Paul G.; Boedec, Gwenn; Leonetti, Marc; Jaeger, Marc

2018-06-01

The red blood cell (RBC) membrane is a composite structure, consisting of a phospholipid bilayer and an underlying membrane-associated cytoskeleton. Both continuum and particle-based coarse-grained RBC models make use of a set of vertices connected by edges to represent the RBC membrane, which can be seen as a triangular surface mesh for the former and a spring network for the latter. Here, we present a modeling approach combining an existing continuum vesicle model with a coarse-grained model for the cytoskeleton. Compared to other two-component approaches, our method relies on only one mesh, representing the cytoskeleton, whose velocity in the tangential direction of the membrane may be different from that of the lipid bilayer. The finitely extensible nonlinear elastic (FENE) spring force law in combination with a repulsive force defined as a power function (POW), called FENE-POW, is used to describe the elastic properties of the RBC membrane. The mechanical interaction between the lipid bilayer and the cytoskeleton is explicitly computed and incorporated into the vesicle model. Our model includes the fundamental mechanical properties of the RBC membrane, namely fluidity and bending rigidity of the lipid bilayer, and shear elasticity of the cytoskeleton while maintaining surface-area and volume conservation constraint. We present three simulation examples to demonstrate the effectiveness of this hybrid continuum-coarse-grained model for the study of RBCs in fluid flows.

Effect of Composition and Deformation on Coarse-Grained Austenite Transformation in Nb-Mo Microalloyed Steels

NASA Astrophysics Data System (ADS)

Isasti, N.; Jorge-Badiola, D.; Taheri, M. L.; López, B.; Uranga, P.

2011-12-01

Thermomechanical processing of microalloyed steels containing niobium can be performed to obtain deformed austenite prior to transformation. Accelerated cooling can be employed to refine the final microstructure and, consequently, to improve both strength and toughness. This general rule is fulfilled if the transformation occurs on a quite homogeneous austenite microstructure. Nevertheless, the presence of coarse austenite grains before transformation in different industrial processes is a usual source of concern, and regarding toughness, the coarsest high-angle boundary units would determine its final value. Sets of deformation dilatometry tests were carried out using three 0.06 pct Nb microalloyed steels to evaluate the effect of Mo alloying additions (0, 0.16, and 0.31 pct Mo) on final transformation from both recrystallized and unrecrystallized coarse-grained austenite. Continuous cooling transformation (CCT) diagrams were created, and detailed microstructural characterization was achieved through the use of optical microscopy (OM), field emission gun scanning electron microscopy (FEGSEM), and electron backscattered diffraction (EBSD). The resultant microstructures ranged from polygonal ferrite (PF) and pearlite (P) at slow cooling ranges to bainitic ferrite (BF) accompanied by martensite (M) for fast cooling rates. Plastic deformation of the parent austenite accelerated both ferrite and bainite transformation, moving the CCT curves to higher temperatures and shorter times. However, an increase in the final heterogeneity was observed when BF packets were formed, creating coarse high-angle grain boundary units.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lei, Huan; Baker, Nathan A.; Li, Xiantao

We present a data-driven approach to determine the memory kernel and random noise of the generalized Langevin equation. To facilitate practical implementations, we parameterize the kernel function in the Laplace domain by a rational function, with coefficients directly linked to the equilibrium statistics of the coarse-grain variables. Further, we show that such an approximation can be constructed to arbitrarily high order. Within these approximations, the generalized Langevin dynamics can be embedded in an extended stochastic model without memory. We demonstrate how to introduce the stochastic noise so that the fluctuation-dissipation theorem is exactly satisfied.

A note on coarse-grained gravity-flow deposits within proterozoic lacustrine sedimentary rocks, Transvaal sequence, South Africa

NASA Astrophysics Data System (ADS)

Eriksson, P. G.

A widely developed, thin, coarse-matrix conglomerate occurs within early Proterozoic lacustrine mudrocks in the Transvaal Sequence, South Africa. The poorly sorted tabular chert clasts, alternation of a planar clast fabric with disorientated zones, plus normal and inverse grading in the former rock type suggest deposition by density-modified grain-flow and high density turbidity currents. The lower fan-delta slope palæenvironment inferred for the conglomerate is consistent with the lacustrine interpretation for the enclosing mudrock facies. This intracratonic setting contrasts with the marine environment generally associated with density-modified grain-flow deposits.

Testing short-range migration of microbial methane as a hydrate formation mechanism: Results from Andaman Sea and Kumano Basin drill sites and global implications

NASA Astrophysics Data System (ADS)

Malinverno, Alberto; Goldberg, David S.

2015-07-01

Methane gas hydrates in marine sediments often concentrate in coarse-grained layers surrounded by fine-grained marine muds that are hydrate-free. Methane in these hydrate deposits is typically microbial, and must have migrated from its source as the coarse-grained sediments contain little or no organic matter. In "long-range" migration, fluid flow through permeable layers transports methane from deeper sources into the gas hydrate stability zone (GHSZ). In "short-range" migration, microbial methane is generated within the GHSZ in fine-grained sediments, where small pore sizes inhibit hydrate formation. Dissolved methane can then diffuse into adjacent sand layers, where pore size does not restrict hydrate formation and hydrates can accumulate. Short-range migration has been used to explain hydrate accumulations in sand layers observed in drill sites on the northern Cascadia margin and in the Gulf of Mexico. Here we test the feasibility of short-range migration in two additional locations, where gas hydrates have been found in coarse-grained volcanic ash layers (Site NGHP-01-17, Andaman Sea, Indian Ocean) and turbidite sand beds (Site IODP-C0002, Kumano forearc basin, Nankai Trough, western Pacific). We apply reaction-transport modeling to calculate dissolved methane concentration and gas hydrate amounts resulting from microbial methane generated within the GHSZ. Model results show that short-range migration of microbial methane can explain the overall amounts of methane hydrate observed at the two sites. Short-range migration has been shown to be feasible in diverse margin environments and is likely to be a widespread methane transport mechanism in gas hydrate systems. It only requires a small amount of organic carbon and sediment sequences consisting of thin coarse-grained layers that can concentrate microbial methane generated within thick fine-grained sediment beds; these conditions are common along continental margins around the globe.

Investigating the influence of lithologic heterogeneity on gas hydrate formation and methane recycling at the base of the gas hydrate stability zone in channelized systems

NASA Astrophysics Data System (ADS)

Daigle, H.; Nole, M.; Cook, A.; Malinverno, A.

2017-12-01

In marine environments, gas hydrate preferentially accumulates in coarse-grained sediments. At the meso- to micro-scale, however, hydrate distribution in these coarse-grained units is often heterogeneous. We employ a methane hydrate reservoir simulator coupling heat and mass transfer as well as capillary effects to investigate how capillary controls on methane solubility affect gas and hydrate accumulations in reservoirs characterized by graded bedding and alternating sequences of coarse-grained sands and fine-grained silt and clay. Simulations bury a channelized reservoir unit encased in homogeneous, fine-grained material characterized by small pores (150 nm) and low permeability ( 1 md in the absence of hydrate). Pore sizes within each reservoir bed between vary between coarse sand and fine silt. Sands have a median pore size of 35 microns and a lognormal pore size distribution. We also investigate how the amount of labile organic carbon (LOC) affects hydrate growth due to microbial methanogenesis within the sediments. In a diffusion-dominated system, methane movies into reservoir layers along spatial gradients in dissolved methane concentration. Hydrate grows in such a way as to minimize these concentration gradients by accumulating slower in finer-grained reservoir layers and faster in coarser-grained layers. Channelized, fining-upwards sediment bodies accumulate hydrate first along their outer surfaces and thence inward from top to bottom. If LOC is present in thin beds within the channel, higher saturations of hydrate will be distributed more homogeneously throughout the unit. When buried beneath the GHSZ, gas recycling can occur only if enough hydrate is present to form a connected gas phase upon dissociation. Simulations indicate that this is difficult to achieve for diffusion-dominated systems, especially those with thick GHSZs and/or small amounts of LOC. However, capillary-driven fracturing behavior may be more prevalent in settings with thick GHSZs.

Investigating the influence of lithologic heterogeneity on gas hydrate formation and methane recycling at the base of the gas hydrate stability zone in channelized systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daigle, Hugh; Nole, Michael; Cook, Ann

In marine environments, gas hydrate preferentially accumulates in coarse-grained sediments. At the meso- to micro-scale, however, hydrate distribution in these coarse-grained units is often heterogeneous. We employ a methane hydrate reservoir simulator coupling heat and mass transfer as well as capillary effects to investigate how capillary controls on methane solubility affect gas and hydrate accumulations in reservoirs characterized by graded bedding and alternating sequences of coarse-grained sands and fine-grained silt and clay. Simulations bury a channelized reservoir unit encased in homogeneous, fine-grained material characterized by small pores (150 nm) and low permeability (~1 md in the absence of hydrate). Poremore » sizes within each reservoir bed between vary between coarse sand and fine silt. Sands have a median pore size of 35 microns and a lognormal pore size distribution. We also investigate how the amount of labile organic carbon (LOC) affects hydrate growth due to microbial methanogenesis within the sediments. In a diffusion-dominated system, methane movies into reservoir layers along spatial gradients in dissolved methane concentration. Hydrate grows in such a way as to minimize these concentration gradients by accumulating slower in finer-grained reservoir layers and faster in coarser-grained layers. Channelized, fining-upwards sediment bodies accumulate hydrate first along their outer surfaces and thence inward from top to bottom. If LOC is present in thin beds within the channel, higher saturations of hydrate will be distributed more homogeneously throughout the unit. When buried beneath the GHSZ, gas recycling can occur only if enough hydrate is present to form a connected gas phase upon dissociation. Simulations indicate that this is difficult to achieve for diffusion-dominated systems, especially those with thick GHSZs and/or small amounts of LOC. However, capillary-driven fracturing behavior may be more prevalent in settings with thick GHSZs.« less

Statistical physics approaches to Alzheimer's disease

NASA Astrophysics Data System (ADS)

Peng, Shouyong

Alzheimer's disease (AD) is the most common cause of late life dementia. In the brain of an AD patient, neurons are lost and spatial neuronal organizations (microcolumns) are disrupted. An adequate quantitative analysis of microcolumns requires that we automate the neuron recognition stage in the analysis of microscopic images of human brain tissue. We propose a recognition method based on statistical physics. Specifically, Monte Carlo simulations of an inhomogeneous Potts model are applied for image segmentation. Unlike most traditional methods, this method improves the recognition of overlapped neurons, and thus improves the overall recognition percentage. Although the exact causes of AD are unknown, as experimental advances have revealed the molecular origin of AD, they have continued to support the amyloid cascade hypothesis, which states that early stages of aggregation of amyloid beta (Abeta) peptides lead to neurodegeneration and death. X-ray diffraction studies reveal the common cross-beta structural features of the final stable aggregates-amyloid fibrils. Solid-state NMR studies also reveal structural features for some well-ordered fibrils. But currently there is no feasible experimental technique that can reveal the exact structure or the precise dynamics of assembly and thus help us understand the aggregation mechanism. Computer simulation offers a way to understand the aggregation mechanism on the molecular level. Because traditional all-atom continuous molecular dynamics simulations are not fast enough to investigate the whole aggregation process, we apply coarse-grained models and discrete molecular dynamics methods to increase the simulation speed. First we use a coarse-grained two-bead (two beads per amino acid) model. Simulations show that peptides can aggregate into multilayer beta-sheet structures, which agree with X-ray diffraction experiments. To better represent the secondary structure transition happening during aggregation, we refine the model to four beads per amino acid. Typical essential interactions, such as backbone hydrogen bond, hydrophobic and electrostatic interactions, are incorporated into our model. We study the aggregation of Abeta16-22, a peptide that can aggregate into a well-ordered fibrillar structure in experiments. Our results show that randomly-oriented monomers can aggregate into fibrillar subunits, which agree not only with X-ray diffraction experiments but also with solid-state NMR studies. Our findings demonstrate that coarse-grained models and discrete molecular dynamics simulations can help researchers understand the aggregation mechanism of amyloid peptides.

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul

2015-01-21

The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, whichmore » is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.« less

Coarse graining flow of spin foam intertwiners

NASA Astrophysics Data System (ADS)

Dittrich, Bianca; Schnetter, Erik; Seth, Cameron J.; Steinhaus, Sebastian

2016-12-01

Simplicity constraints play a crucial role in the construction of spin foam models, yet their effective behavior on larger scales is scarcely explored. In this article we introduce intertwiner and spin net models for the quantum group SU (2 )k×SU (2 )k, which implement the simplicity constraints analogous to four-dimensional Euclidean spin foam models, namely the Barrett-Crane (BC) and the Engle-Pereira-Rovelli-Livine/Freidel-Krasnov (EPRL/FK) model. These models are numerically coarse grained via tensor network renormalization, allowing us to trace the flow of simplicity constraints to larger scales. In order to perform these simulations we have substantially adapted tensor network algorithms, which we discuss in detail as they can be of use in other contexts. The BC and the EPRL/FK model behave very differently under coarse graining: While the unique BC intertwiner model is a fixed point and therefore constitutes a two-dimensional topological phase, BC spin net models flow away from the initial simplicity constraints and converge to several different topological phases. Most of these phases correspond to decoupling spin foam vertices; however we find also a new phase in which this is not the case, and in which a nontrivial version of the simplicity constraints holds. The coarse graining flow of the BC spin net models indicates furthermore that the transitions between these phases are not of second order. The EPRL/FK model by contrast reveals a far more intricate and complex dynamics. We observe an immediate flow away from the original simplicity constraints; however, with the truncation employed here, the models generically do not converge to a fixed point. The results show that the imposition of simplicity constraints can indeed lead to interesting and also very complex dynamics. Thus we need to further develop coarse graining tools to efficiently study the large scale behavior of spin foam models, in particular for the EPRL/FK model.

Mechanical Behaviour of Light Metal Alloys at High Strain Rates. Computer Simulation on Mesoscale Levels

NASA Astrophysics Data System (ADS)

Skripnyak, Vladimir; Skripnyak, Evgeniya; Meyer, Lothar W.; Herzig, Norman; Skripnyak, Nataliya

2012-02-01

Researches of the last years have allowed to establish that the laws of deformation and fracture of bulk ultrafine-grained and coarse-grained materials are various both in static and in dynamic loading conditions. Development of adequate constitutive equations for the description of mechanical behavior of bulk ultrafine-grained materials at intensive dynamic influences is complicated in consequence of insufficient knowledge about general rules of inelastic deformation and nucleation and growth of cracks. Multi-scale computational model was used for the investigation of deformation and fracture of bulk structured aluminum and magnesium alloys under stress pulse loadings on mesoscale level. The increment of plastic deformation is defined by the sum of the increments caused by a nucleation and gliding of dislocations, the twinning, meso-blocks movement, and grain boundary sliding. The model takes into account the influence on mechanical properties of alloys an average grains size, grain sizes distribution of and concentration of precipitates. It was obtained the nucleation and gliding of dislocations caused the high attenuation rate of the elastic precursor of ultrafine-grained alloys than in coarse grained counterparts.

Nontoxic chemical process for in situ permeability enhancement and accelerated decontamination of fine-grain subsurface sediments

DOEpatents

Kansa, E.J.; Wijesinghe, A.M.; Viani, B.E.

1997-01-14

The remediation of heterogeneous subsurfaces is extremely time consuming and expensive with current and developing technologies. Although such technologies can adequately remove contaminants in the high hydraulic conductivity, coarse-grained sediments, they cannot access the contaminated low hydraulic conductivity fine-grained sediments. The slow bleed of contaminants from the fine-grained sediments is the primary reason why subsurface remediation is so time-consuming and expensive. This invention addresses the problem of remediating contaminated fine-grained sediments. It is intended that, in the future, a heterogeneous site be treated by a hybrid process that first remediates the high hydraulic conductivity, coarse-grained sediments, to be followed by the process, described in this invention, to treat the contaminated low hydraulic conductivity fine-grained sediments. The invention uses cationic flocculants and organic solvents to collapse the swelling negative double layer surrounding water saturated clay particles, causing a flocculated, cracked clay structure. The modification of the clay fabric in fine-grained sediments dramatically increases the hydraulic conductivity of previously very tight clays many orders of magnitude. 8 figs.

Nontoxic chemical process for in situ permeability enhancement and accelerated decontamination of fine-grain subsurface sediments

DOEpatents

Kansa, Edward J.; Wijesinghe, Ananda M.; Viani, Brian E.

1997-01-01

The remediation of heterogeneous subsurfaces is extremely time consuming and expensive with current and developing technologies. Although such technologies can adequately remove contaminants in the high hydraulic conductivity, coarse-grained sediments, they cannot access the contaminated low hydraulic conductivity fine-grained sediments. The slow bleed of contaminants from the fine-grained sediments is the primary reason why subsurface remediation is so time-consuming and expensive. This invention addresses the problem of remediating contaminated fine-grained sediments. It is intended that, in the future, a heterogeneous site be treated by a hybrid process that first remediates the high hydraulic conductivity, coarse-grained sediments, to be followed by the process, described in this invention, to treat the contaminated low hydraulic conductivity fine-grained sediments. The invention uses cationic flocculents and organic solvents to collapse the swelling negative double layer surrounding water saturated clay particles, causing a flocculated, cracked clay structure. The modification of the clay fabric in fine-grained sediments dramatically increases the hydraulic conductivity of previously very tight clays many orders of magnitude.

Linking basin-scale and pore-scale gas hydrate distribution patterns in diffusion-dominated marine hydrate systems: DIFFUSION-DRIVEN HYDRATE GROWTH IN SANDS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nole, Michael; Daigle, Hugh; Cook, Ann E.

The goal of this study is to computationally determine the potential distribution patterns of diffusion-driven methane hydrate accumulations in coarse-grained marine sediments. Diffusion of dissolved methane in marine gas hydrate systems has been proposed as a potential transport mechanism through which large concentrations of hydrate can preferentially accumulate in coarse-grained sediments over geologic time. Using one-dimensional compositional reservoir simulations, we examine hydrate distribution patterns at the scale of individual sand layers (1 to 20 m thick) that are deposited between microbially active fine-grained material buried through the gas hydrate stability zone (GHSZ). We then extrapolate to two- dimensional and basin-scalemore » three-dimensional simulations, where we model dipping sands and multilayered systems. We find that properties of a sand layer including pore size distribution, layer thickness, dip, and proximity to other layers in multilayered systems all exert control on diffusive methane fluxes toward and within a sand, which in turn impact the distribution of hydrate throughout a sand unit. In all of these simulations, we incorporate data on physical properties and sand layer geometries from the Terrebonne Basin gas hydrate system in the Gulf of Mexico. We demonstrate that diffusion can generate high hydrate saturations (upward of 90%) at the edges of thin sands at shallow depths within the GHSZ, but that it is ineffective at producing high hydrate saturations throughout thick (greater than 10 m) sands buried deep within the GHSZ. As a result, we find that hydrate in fine-grained material can preserve high hydrate saturations in nearby thin sands with burial.« less

Linking basin-scale and pore-scale gas hydrate distribution patterns in diffusion-dominated marine hydrate systems: DIFFUSION-DRIVEN HYDRATE GROWTH IN SANDS

DOE PAGES

Nole, Michael; Daigle, Hugh; Cook, Ann E.; ...

2017-02-01

The goal of this study is to computationally determine the potential distribution patterns of diffusion-driven methane hydrate accumulations in coarse-grained marine sediments. Diffusion of dissolved methane in marine gas hydrate systems has been proposed as a potential transport mechanism through which large concentrations of hydrate can preferentially accumulate in coarse-grained sediments over geologic time. Using one-dimensional compositional reservoir simulations, we examine hydrate distribution patterns at the scale of individual sand layers (1 to 20 m thick) that are deposited between microbially active fine-grained material buried through the gas hydrate stability zone (GHSZ). We then extrapolate to two- dimensional and basin-scalemore » three-dimensional simulations, where we model dipping sands and multilayered systems. We find that properties of a sand layer including pore size distribution, layer thickness, dip, and proximity to other layers in multilayered systems all exert control on diffusive methane fluxes toward and within a sand, which in turn impact the distribution of hydrate throughout a sand unit. In all of these simulations, we incorporate data on physical properties and sand layer geometries from the Terrebonne Basin gas hydrate system in the Gulf of Mexico. We demonstrate that diffusion can generate high hydrate saturations (upward of 90%) at the edges of thin sands at shallow depths within the GHSZ, but that it is ineffective at producing high hydrate saturations throughout thick (greater than 10 m) sands buried deep within the GHSZ. As a result, we find that hydrate in fine-grained material can preserve high hydrate saturations in nearby thin sands with burial.« less

Crystallographic Analysis of Fatigue Crack Initiation Behavior in Coarse-Grained Magnesium Alloy Under Tension-Tension Loading Cycles

NASA Astrophysics Data System (ADS)

Tamada, Kazuhiro; Kakiuchi, Toshifumi; Uematsu, Yoshihiko

2017-07-01

Plane bending fatigue tests are conducted to investigate fatigue crack initiation mechanisms in coarse-grained magnesium alloy, AZ31, under the stress ratios R = -1 and 0.1. The initial crystallographic structures are analyzed by an electron backscatter diffraction method. The slip or twin operation during fatigue tests is identified from the line angle analyses based on Euler angles of the grains. Under the stress ratio R = -1, relatively thick tension twin bands are formed in coarse grains. Subsequently, compression twin or secondary pyramidal slip operates within the tension twin band, resulting in the fatigue crack initiation. On the other hand, under R = 0.1 with tension-tension loading cycles, twin bands are formed on the specimen surface, but the angles of those bands do not correspond to tension twins. Misorientation analyses of c-axes in the matrix grain and twin band reveal that double twins are activated. Under R = 0.1, fatigue crack initiates along the double twin boundaries. The different manners of fatigue crack initiation at R = -1 and 0.1 are related to the asymmetricity of twining under tension and compression loadings. The fatigue strengths under different stress ratios cannot be estimated by the modified Goodman diagram due to the effect of stress ratio on crack initiation mechanisms.

The Effect of Solution Heat Treatment on an Advanced Nickel-Base Disk Alloy

NASA Technical Reports Server (NTRS)

Gayda, J.; Gabb, T. P.; Kantzos, P. T.

2004-01-01

Five heat treat options for an advanced nickel-base disk alloy, LSHR, have been investigated. These included two conventional solution heat treat cycles, subsolvus/oil quench and supersolvus/fan cool, which yield fine grain and coarse grain microstructure disks respectively, as well as three advanced dual microstructure heat treat (DMHT) options. The DMHT options produce disks with a fine grain bore and a coarse grain rim. Based on an overall evaluation of the mechanical property data, it was evident that the three DMHT options achieved a desirable balance of properties in comparison to the conventional solution heat treatments for the LSHR alloy. However, one of the DMHT options, SUB/DMHT, produced the best set of properties, largely based on dwell crack growth data. Further evaluation of the SUB/DMHT option in spin pit experiments on a generic disk shape demonstrated the advantages and reliability of a dual grain structure at the component level.

Trace element distribution in mineral separates of the Allende inclusions and their genetic implications

NASA Technical Reports Server (NTRS)

Nagasawa, H.; Blanchard, D. P.; Jacobs, J. W.; Brannon, J. C.; Philpotts, J. A.; Onuma, N.

1977-01-01

Concentrations of the rare earth elements (REE), Sc, Co, Fe, Zn, Ir, Na, and Cr were determined for mineral separates of the coarseand fine-grained types (group I and II) of the Allende inclusions. These data in combination with other data suggest that the minerals in the coarse-grained inclusions (group I) crystallized in a closed system with respect to refractory elements although a totally molten stage is precluded. The data also indicate that fine-grained (group II) inclusions were formed by condensation from a super-cooled nebular gas; REE-rich clinopyroxene and spinel were formed earlier than REE-poor sodalite and nepheline. In addition, pre-existing Mg isotope anomalies in the coarse-grained inclusions must have been erased during the heating stage.

Grain-scale modeling and splash parametrization for aeolian sand transport.

PubMed

Lämmel, Marc; Dzikowski, Kamil; Kroy, Klaus; Oger, Luc; Valance, Alexandre

2017-02-01

The collision of a spherical grain with a granular bed is commonly parametrized by the splash function, which provides the velocity of the rebounding grain and the velocity distribution and number of ejected grains. Starting from elementary geometric considerations and physical principles, like momentum conservation and energy dissipation in inelastic pair collisions, we derive a rebound parametrization for the collision of a spherical grain with a granular bed. Combined with a recently proposed energy-splitting model [Ho et al., Phys. Rev. E 85, 052301 (2012)PLEEE81539-375510.1103/PhysRevE.85.052301] that predicts how the impact energy is distributed among the bed grains, this yields a coarse-grained but complete characterization of the splash as a function of the impact velocity and the impactor-bed grain-size ratio. The predicted mean values of the rebound angle, total and vertical restitution, ejection speed, and number of ejected grains are in excellent agreement with experimental literature data and with our own discrete-element computer simulations. We extract a set of analytical asymptotic relations for shallow impact geometries, which can readily be used in coarse-grained analytical modeling or computer simulations of geophysical particle-laden flows.

Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

NASA Astrophysics Data System (ADS)

Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

2017-01-01

This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.

In situ studies on radiation tolerance of nanotwinned Cu

DOE PAGES

Chen, Y.; Li, J.; Yu, K. Y.; ...

2016-03-31

We investigate the radiation response of nanotwinned Cu by using in situ Kr ion irradiation technique inside a transmission electron microscope. In comparison with coarse grained Cu, nanotwinned Cu exhibits smaller defect size and lower defect density. In situ studies also show that twin boundaries effectively remove a large number of defect clusters. The life time of defect clusters in nanotwinned Cu is very different from that in its coarse grained counterpart. This study provides further evidence on twin-boundary enabled radiation tolerance in nanotwinned metals.

Dual Microstructure Heat Treatment of a Nickel-Base Disk Alloy Assessed

NASA Technical Reports Server (NTRS)

Gayda, John

2002-01-01

Gas turbine engines for future subsonic aircraft will require nickel-base disk alloys that can be used at temperatures in excess of 1300 F. Smaller turbine engines, with higher rotational speeds, also require disk alloys with high strength. To address these challenges, NASA funded a series of disk programs in the 1990's. Under these initiatives, Honeywell and Allison focused their attention on Alloy 10, a high-strength, nickel-base disk alloy developed by Honeywell for application in the small turbine engines used in regional jet aircraft. Since tensile, creep, and fatigue properties are strongly influenced by alloy grain size, the effect of heat treatment on grain size and the attendant properties were studied in detail. It was observed that a fine grain microstructure offered the best tensile and fatigue properties, whereas a coarse grain microstructure offered the best creep resistance at high temperatures. Therefore, a disk with a dual microstructure, consisting of a fine-grained bore and a coarse-grained rim, should have a high potential for optimal performance. Under NASA's Ultra-Safe Propulsion Project and Ultra-Efficient Engine Technology (UEET) Program, a disk program was initiated at the NASA Glenn Research Center to assess the feasibility of using Alloy 10 to produce a dual-microstructure disk. The objectives of this program were twofold. First, existing dual-microstructure heat treatment (DMHT) technology would be applied and refined as necessary for Alloy 10 to yield the desired grain structure in full-scale forgings appropriate for use in regional gas turbine engines. Second, key mechanical properties from the bore and rim of a DMHT Alloy 10 disk would be measured and compared with conventional heat treatments to assess the benefits of DMHT technology. At Wyman Gordon and Honeywell, an active-cooling DMHT process was used to convert four full-scale Alloy 10 disks to a dual-grain microstructure. The resulting microstructures are illustrated in the photomicrographs. The fine grain size in the bore can be contrasted with the coarse grain size in the rim. Testing (at NASA Glenn) of coupons machined from these disks showed that the DMHT approach did indeed produce a high-strength, fatigue resistant bore and a creep-resistant rim. This combination of properties was previously unobtainable using conventional heat treatments, which produced disks with a uniform grain size. Future plans are in place to spin test a DMHT disk under the Ultra Safe Propulsion Project to assess the viability of this technology at the component level. This testing will include measurements of disk growth at a high temperature as well as the determination of burst speed at an intermediate temperature.

Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts

NASA Astrophysics Data System (ADS)

Li, Zhen; Lee, Hee Sun; Darve, Eric; Karniadakis, George Em

2017-01-01

Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions. We compare two different methods for the practical implementation of the non-Markovian interactions in GLE and DPD systems. More specifically, a direct evaluation of the non-Markovian (NM) terms is performed in LE-NM and DPD-NM models, which requires the storage of historical information that significantly increases computational complexity. Alternatively, we use a few auxiliary variables in LE-AUX and DPD-AUX models to replace the non-Markovian dynamics with a Markovian dynamics in a higher dimensional space, leading to a much reduced memory footprint and computational cost. In our numerical benchmarks, the GLE and non-Markovian DPD models are constructed from molecular dynamics (MD) simulations of star-polymer melts. Results show that a Markovian dynamics with auxiliary variables successfully generates equivalent non-Markovian dynamics consistent with the reference MD system, while maintaining a tractable computational cost. Also, transient subdiffusion of the star-polymers observed in the MD system can be reproduced by the coarse-grained models. The non-interacting particle models, LE-NM/AUX, are computationally much cheaper than the interacting particle models, DPD-NM/AUX. However, the pairwise models with momentum conservation are more appropriate for correctly reproducing the long-time hydrodynamics characterised by an algebraic decay in the velocity autocorrelation function.

Can Wet Rocky Granular Flows Become Debris Flows Due to Fine Sediment Production by Abrasion?

NASA Astrophysics Data System (ADS)

Arabnia, O.; Sklar, L. S.; Bianchi, G.; Mclaughlin, M. K.

2015-12-01

Debris flows are rapid mass movements in which elevated pore pressures are sustained by a viscous fluid matrix with high concentrations of fine sediments. Debris flows may form from coarse-grained wet granular flows as fine sediments are entrained from hillslope and channel material. Here we investigate whether abrasion of the rocks within a granular flow can produce sufficient fine sediments to create debris flows. To test this hypothesis experimentally, we used a set of 4 rotating drums ranging from 0.2 to 4.0 m diameter. Each drum has vanes along the boundary ensure shearing within the flow. Shear rate was varied by changing drum rotational velocity to maintain a constant Froude Number across drums. Initial runs used angular clasts of granodiorite with a tensile strength of 7.6 MPa, with well-sorted coarse particle size distributions linearly scaled with drum radius. The fluid was initially clear water, which rapidly acquired fine-grained wear products. After each 250 m tangential distance, we measured the particle size distributions, and then returned all water and sediment to the drums for subsequent runs. We calculate particle wear rates using statistics of size and mass distributions, and by fitting the Sternberg equation to the rate of mass loss from the size fraction > 2mm. Abundant fine sediments were produced in the experiments, but very little change in the median grain size was detected. This appears to be due to clast rounding, as evidenced by a decrease in the number of stable equilibrium resting points. We find that the growth in the fine sediment concentration in the fluid scales with unit drum power. This relationship can be used to estimate fine sediment production rates in the field. We explore this approach at Inyo Creek, a steep catchment in the Sierra Nevada, California. There, a significant debris flow occurred in July 2013, which originated as a coarse-grained wet granular flow. We use surveys to estimate flow depth and velocity where super-elevation occurred, to calculate a unit power of 4.5 KW/m2. From this we predict that 14% of the coarse mass is converted to fine sediment by abrasion per km. At that rate, the increase in fines concentration may have been sufficient to cause a wet granular flow to evolve into a debris flow within the first 1 km of its > 4km travel distance.

Mid and Late Devonian arenites deposited by sheet-flood, braided streams and rivers in the northern Barrier Ranges, far western New South Wales, Australia

NASA Astrophysics Data System (ADS)

Neef, G.; Bottrill, R. S.; Cohen, D. R.

1996-05-01

Extensive and well exposed, fine-grained fluvial sandstone and less common pebbly coarse-grained fluvial sandstone of Devonian age, crop out in the northern Barrier Ranges of far west New South Wales, Australia. These strata were deposited largely on low-gradient alluvial fans in a basin and range landscape and contain common sedimentary structures (especially streaming lineations and tabular cross-beds). Around 400 of these sedimentary structures were measured to determine the palaeoflow trends of the sheet floods, streams or rivers which deposited the sandstone. The strata are mapped as the Mid Devonian Coco Range Sandstone and the Late Devonian Nundooka Sandstone, which together are around 2.7 km thick. They were deposited at the western margin of the large Emsian to Early Carboniferous Darling Basin. The Coco Range Sandstone is Emsian to Eifelian in age (based on fragments) of fossil fish) and it is separated from the Frasnian-Famennian (Late Devonian) Nundooka Sandstone by the north-trending Nundooka Creek Fault. The eastern boundary of the Nundooka Sandstone is formed by the Western Boundary Fault. Eastward of this fault is the north-trending and 40 km wide Bancannia Trough, which contains gently folded Late Silurian to Early Carboniferous strata up to 7.5 km thick. Most of the Coco Range Sandstone and all of the Nundooka Sandstone are non-graded, fine and very fine-grained, light brown sub-litharenites which are considered to have been deposited mainly on low-gradient alluvial fans. Sedimentary successions of 1.75 to 5.25 m thickness in the fine-grained arenite usually commence with Sm (massive or slumped) → Sh (laminated arenite) or St (trough cross-beds) → Sp (tabular cross-bedded sandstone). An erosional surface commonly underlies the sedimentary successions and they are interpreted to be the result of deposition from decelerating sheet floods. Units composed of tabular cross-bedded strata several metres thick are rarely channelised and are interpreted to represent deposition within braided streams flowing upon the fans or deposited at the margin of sheet floods. In the Coco Range Sandstone there are two sheet-like coarse pebbly arenite units (The Valley Tank and Copi Dam Members) which together total 200 m in thickness. Unimodal palaeocurrent trends and heavy mineral suites from within the coarse-grained arenite indicate a derivation from the south near Broken Hill. Sedimentary structures within the coarse-grained arenite indicate a Platte River style of deposition upon distal braid plains, whereas local interdigitation of coarse-grained arenite with fine arenite strata shows that deposition was essentially continuous (i.e. the coarse arenite do not overlie unconformities) and the two lithotypes represent interdigitation of alluvial fans and braid plain deposition. The northward progradation of the coarse arenite units was probably due to a sudden retardation of basement downwarping.

Fractal dimension analysis for robust ultrasonic non-destructive evaluation (NDE) of coarse grained materials

NASA Astrophysics Data System (ADS)

Li, Minghui; Hayward, Gordon

2018-04-01

Over the recent decades, there has been a growing demand on reliable and robust non-destructive evaluation (NDE) of structures and components made from coarse grained materials such as alloys, stainless steels, carbon-reinforced composites and concrete; however, when inspected using ultrasound, the flaw echoes are usually contaminated by high-level, time-invariant, and correlated grain noise originating from the microstructure and grain boundaries, leading to pretty low signal-to-noise ratio (SNR) and the flaw information being obscured or completely hidden by the grain noise. In this paper, the fractal dimension analysis of the A-scan echoes is investigated as a measure of complexity of the time series to distinguish the echoes originating from the real defects and the grain noise, and then the normalized fractal dimension coefficients are applied to the amplitudes as the weighting factor to enhance the SNR and defect detection. Experiments on industrial samples of the mild steel and the stainless steel are conducted and the results confirm the great benefits of the method.

Microstructures and rheology of a calcite-shale thrust fault

NASA Astrophysics Data System (ADS)

Wells, Rachel K.; Newman, Julie; Wojtal, Steven

2014-08-01

A thin (˜2 cm) layer of extensively sheared fault rock decorates the ˜15 km displacement Copper Creek thrust at an exposure near Knoxville, TN (USA). In these ultrafine-grained (<0.3 μm) fault rocks, interpenetrating calcite grains form an interconnected network around shale clasts. One cm below the fault rock layer, sedimentary laminations in non-penetratively deformed footwall shale are cut by calcite veins, small faults, and stylolites. A 350 μm thick calcite vein separates the fault rocks and footwall shale. The vein is composed of layers of (1) coarse calcite grains (>5 μm) that exhibit a lattice preferred orientation (LPO) with pores at twin-twin and twin-grain boundary intersections, and (2) ultrafine-grained (0.3 μm) calcite that exhibits interpenetrating grain boundaries, four-grain junctions and lacks a LPO. Coarse calcite layers crosscut ultrafine-grained layers indicating intermittent vein formation during shearing. Calcite in the fault rock layer is derived from vein calcite and grain-size reduction of calcite took place by plasticity-induced fracture. The ultrafine-grained calcite deformed primarily by diffusion-accommodated grain boundary sliding and formed an interconnected network around shale clasts within the shear zone. The interconnected network of ultrafine-grained calcite indicates that calcite, not shale, was the weak phase in this fault zone.

Microstructural Evolution at Micro/Meso-Scale in an Ultrafine-Grained Pure Aluminum Processed by Equal-Channel Angular Pressing with Subsequent Annealing Treatment.

PubMed

Xu, Jie; Li, Jianwei; Zhu, Xiaocheng; Fan, Guohua; Shan, Debin; Guo, Bin

2015-11-04

Micro-forming with ultrafine-grained (UFG) materials is a promising direction for the fabrication of micro-electro-mechanical systems (MEMS) components due to the improved formability, good surface quality, and excellent mechanical properties it provides. In this paper, micro-compression tests were performed using UFG pure aluminum processed by equal-channel angular pressing (ECAP) with subsequent annealing treatment. Microstructural evolution was investigated by electron back-scattered diffraction (EBSD) and transmission electron microscopy (TEM). The results show that microstructural evolutions during compression tests at the micro/meso-scale in UFG pure Al are absolutely different from the coarse-grained (CG) materials. A lot of low-angle grain boundaries (LAGBs) and recrystallized fine grains are formed inside of the original large grains in CG pure aluminum after micro-compression. By contrast, ultrafine grains are kept with few sub-grain boundaries inside the grains in UFG pure aluminum, which are similar to the original microstructure before micro-compression. The surface roughness and coordinated deformation ability can be signmicrostructure; micro/meso-forming; ultrafine grains; ECAP; aluminumificantly improved with UFG pure aluminum, which demonstrates that the UFG materials have a strong potential application in micro/meso-forming.

46 CFR 148.315 - Sulfur.

Code of Federal Regulations, 2011 CFR

2011-10-01

... lump or coarse grain powder sulfur only. Fine-grained powder (“flowers of sulfur”) may not be... completed, sulfur dust must be removed from the vessel's decks, bulkheads, and overheads. Cargo residues and...

46 CFR 148.315 - Sulfur.

Code of Federal Regulations, 2013 CFR

2013-10-01

... lump or coarse grain powder sulfur only. Fine-grained powder (“flowers of sulfur”) may not be... completed, sulfur dust must be removed from the vessel's decks, bulkheads, and overheads. Cargo residues and...

46 CFR 148.315 - Sulfur.

Code of Federal Regulations, 2012 CFR

2012-10-01

... lump or coarse grain powder sulfur only. Fine-grained powder (“flowers of sulfur”) may not be... completed, sulfur dust must be removed from the vessel's decks, bulkheads, and overheads. Cargo residues and...

46 CFR 148.315 - Sulfur.

Code of Federal Regulations, 2014 CFR

2014-10-01

... lump or coarse grain powder sulfur only. Fine-grained powder (“flowers of sulfur”) may not be... completed, sulfur dust must be removed from the vessel's decks, bulkheads, and overheads. Cargo residues and...

Generalized quantum theory of recollapsing homogeneous cosmologies

NASA Astrophysics Data System (ADS)

Craig, David; Hartle, James B.

2004-06-01

A sum-over-histories generalized quantum theory is developed for homogeneous minisuperspace type A Bianchi cosmological models, focusing on the particular example of the classically recollapsing Bianchi type-IX universe. The decoherence functional for such universes is exhibited. We show how the probabilities of decoherent sets of alternative, coarse-grained histories of these model universes can be calculated. We consider in particular the probabilities for classical evolution defined by a suitable coarse graining. For a restricted class of initial conditions and coarse grainings we exhibit the approximate decoherence of alternative histories in which the universe behaves classically and those in which it does not. For these situations we show that the probability is near unity for the universe to recontract classically if it expands classically. We also determine the relative probabilities of quasiclassical trajectories for initial states of WKB form, recovering for such states a precise form of the familiar heuristic “JṡdΣ” rule of quantum cosmology, as well as a generalization of this rule to generic initial states.

Packing of sidechains in low-resolution models for proteins.

PubMed

Keskin, O; Bahar, I

1998-01-01

Atomic level rotamer libraries for sidechains in proteins have been proposed by several groups. Conformations of side groups in coarse-grained models, on the other hand, have not yet been analyzed, although low resolution approaches are the only efficient way to explore global structural features. A residue-specific backbone-dependent library for sidechain isomers, compatible with a coarse-grained model, is proposed. The isomeric states are utilized in packing sidechains of known backbone structures. Sidechain positions are predicted with a root-mean-square deviation (r.m.s.d.) of 2.40 A with respect to crystal structure for 50 test proteins. The rmsd for core residues is 1.60 A and decreases to 1.35 A when conformational correlations and directional effects in inter-residue couplings are considered. An automated method for assigning sidechain positions in coarse-grained model proteins is proposed and made available on the internet; the method accounts satisfactorily for sidechain packing, particularly in the core.

Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments

NASA Astrophysics Data System (ADS)

Wang, Wujie; Nocka, Laura M.; Wiemann, Brianne Z.; Hinckley, Daniel M.; Mukerji, Ishita; Starr, Francis W.

2016-03-01

Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior.

Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes

PubMed Central

Das, Payel; Matysiak, Silvina; Clementi, Cecilia

2005-01-01

Coarse-grained models have been extremely valuable in promoting our understanding of protein folding. However, the quantitative accuracy of existing simplified models is strongly hindered either from the complete removal of frustration (as in the widely used Gō-like models) or from the compromise with the minimal frustration principle and/or realistic protein geometry (as in the simple on-lattice models). We present a coarse-grained model that “naturally” incorporates sequence details and energetic frustration into an overall minimally frustrated folding landscape. The model is coupled with an optimization procedure to design the parameters of the protein Hamiltonian to fold into a desired native structure. The application to the study of src-Src homology 3 domain shows that this coarse-grained model contains the main physical-chemical ingredients that are responsible for shaping the folding landscape of this protein. The results illustrate the importance of nonnative interactions and energetic heterogeneity for a quantitative characterization of folding mechanisms. PMID:16006532

A coarse grain model for protein-surface interactions

NASA Astrophysics Data System (ADS)

Wei, Shuai; Knotts, Thomas A.

2013-09-01

The interaction of proteins with surfaces is important in numerous applications in many fields—such as biotechnology, proteomics, sensors, and medicine—but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.

Validating the simulation of large-scale parallel applications using statistical characteristics

DOE PAGES

Zhang, Deli; Wilke, Jeremiah; Hendry, Gilbert; ...

2016-03-01

Simulation is a widely adopted method to analyze and predict the performance of large-scale parallel applications. Validating the hardware model is highly important for complex simulations with a large number of parameters. Common practice involves calculating the percent error between the projected and the real execution time of a benchmark program. However, in a high-dimensional parameter space, this coarse-grained approach often suffers from parameter insensitivity, which may not be known a priori. Moreover, the traditional approach cannot be applied to the validation of software models, such as application skeletons used in online simulations. In this work, we present a methodologymore » and a toolset for validating both hardware and software models by quantitatively comparing fine-grained statistical characteristics obtained from execution traces. Although statistical information has been used in tasks like performance optimization, this is the first attempt to apply it to simulation validation. Lastly, our experimental results show that the proposed evaluation approach offers significant improvement in fidelity when compared to evaluation using total execution time, and the proposed metrics serve as reliable criteria that progress toward automating the simulation tuning process.« less

Influence of Grain Size Distribution on the Mechanical Behavior of Light Alloys in Wide Range of Strain Rates

NASA Astrophysics Data System (ADS)

Skripnyak, Vladimir A.; Skripnyak, Natalia V.; Skripnyak, Evgeniya G.; Skripnyak, Vladimir V.

2015-06-01

Inelastic deformation and damage at the mesoscale level of ultrafine grained (UFG) Al 1560 aluminum and Ma2-1 magnesium alloys with distribution of grain size were investigated in wide loading conditions by experimental and computer simulation methods. The computational multiscale models of representative volume element (RVE) with the unimodal and bimodal grain size distributions were developed using the data of structure researches aluminum and magnesium UFG alloys. The critical fracture stress of UFG alloys on mesoscale level depends on relative volumes of coarse grains. Microcracks nucleation at quasi-static and dynamic loading is associated with strain localization in UFG partial volumes with bimodal grain size distribution. Microcracks arise in the vicinity of coarse and ultrafine grains boundaries. It is revealed that the occurrence of bimodal grain size distributions causes the increasing of UFG alloys ductility, but decreasing of the tensile strength. The increasing of fine precipitations concentration not only causes the hardening but increasing of ductility of UFG alloys with bimodal grain size distribution. This research carried out in 2014-2015 was supported by grant from ``The Tomsk State University Academic D.I. Mendeleev Fund Program''.

Effect of Bimodal Grain Size Distribution on Scatter in Toughness

NASA Astrophysics Data System (ADS)

Chakrabarti, Debalay; Strangwood, Martin; Davis, Claire

2009-04-01

Blunt-notch tests were performed at -160 °C to investigate the effect of a bimodal ferrite grain size distribution in steel on cleavage fracture toughness, by comparing local fracture stress values for heat-treated microstructures with uniformly fine, uniformly coarse, and bimodal grain structures. An analysis of fracture stress values indicates that bimodality can have a significant effect on toughness by generating high scatter in the fracture test results. Local cleavage fracture values were related to grain size distributions and it was shown that the largest grains in the microstructure, with an area percent greater than approximately 4 pct, gave rise to cleavage initiation. In the case of the bimodal grain size distribution, the large grains from both the “fine grain” and “coarse grain” population initiate cleavage; this spread in grain size values resulted in higher scatter in the fracture stress than in the unimodal distributions. The notch-bend test results have been used to explain the difference in scatter in the Charpy energies for the unimodal and bimodal ferrite grain size distributions of thermomechanically controlled rolled (TMCR) steel, in which the bimodal distribution showed higher scatter in the Charpy impact transition (IT) region.

Cellular response of preosteoblasts to nanograined/ultrafine-grained structures.

PubMed

Misra, R D K; Thein-Han, W W; Pesacreta, T C; Hasenstein, K H; Somani, M C; Karjalainen, L P

2009-06-01

Metallic materials with submicron- to nanometer-sized grains provide surfaces that are different from conventional polycrystalline materials because of the large proportion of grain boundaries with high free energy. In the study described here, the combination of cellular and molecular biology, materials science and engineering advances our understanding of cell-substrate interactions, especially the cellular activity between preosteoblasts and nanostructured metallic surfaces. Experiments on the effect of nano-/ultrafine grains have shown that cell attachment, proliferation, viability, morphology and spread are favorably modulated and significantly different from conventional coarse-grained structures. Additionally, immunofluorescence studies demonstrated stronger vinculin signals associated with actin stress fibers in the outer regions of the cells and cellular extensions on nanograined/ultrafine-grained substrate. These observations suggest enhanced cell-substrate interaction and activity. The differences in the cellular response on nanograined/ultrafine-grained and coarse-grained substrates are attributed to grain size and degree of hydrophilicity. The outcomes of the study are expected to reduce challenges to engineer bulk nanostructured materials with specific physical and surface properties for medical devices with improved cellular attachment and response. The data lay the foundation for a new branch of nanostructured materials for biomedical applications.

Multiple time-scales and the developmental dynamics of social systems

PubMed Central

Flack, Jessica C.

2012-01-01

To build a theory of social complexity, we need to understand how aggregate social properties arise from individual interaction rules. Here, I review a body of work on the developmental dynamics of pigtailed macaque social organization and conflict management that provides insight into the mechanistic causes of multi-scale social systems. In this model system coarse-grained, statistical representations of collective dynamics are more predictive of the future state of the system than the constantly in-flux behavioural patterns at the individual level. The data suggest that individuals can perceive and use these representations for strategical decision-making. As an interaction history accumulates the coarse-grained representations consolidate. This constrains individual behaviour and provides the foundations for new levels of organization. The time-scales on which these representations change impact whether the consolidating higher-levels can be modified by individuals and collectively. The time-scales appear to be a function of the ‘coarseness’ of the representations and the character of the collective dynamics over which they are averages. The data suggest that an advantage of multiple timescales is that they allow social systems to balance tradeoffs between predictability and adaptability. I briefly discuss the implications of these findings for cognition, social niche construction and the evolution of new levels of organization in biological systems. PMID:22641819

Refined generalized multiscale entropy analysis for physiological signals

NASA Astrophysics Data System (ADS)

Liu, Yunxiao; Lin, Youfang; Wang, Jing; Shang, Pengjian

2018-01-01

Multiscale entropy analysis has become a prevalent complexity measurement and been successfully applied in various fields. However, it only takes into account the information of mean values (first moment) in coarse-graining procedure. Then generalized multiscale entropy (MSEn) considering higher moments to coarse-grain a time series was proposed and MSEσ2 has been implemented. However, the MSEσ2 sometimes may yield an imprecise estimation of entropy or undefined entropy, and reduce statistical reliability of sample entropy estimation as scale factor increases. For this purpose, we developed the refined model, RMSEσ2, to improve MSEσ2. Simulations on both white noise and 1 / f noise show that RMSEσ2 provides higher entropy reliability and reduces the occurrence of undefined entropy, especially suitable for short time series. Besides, we discuss the effect on RMSEσ2 analysis from outliers, data loss and other concepts in signal processing. We apply the proposed model to evaluate the complexity of heartbeat interval time series derived from healthy young and elderly subjects, patients with congestive heart failure and patients with atrial fibrillation respectively, compared to several popular complexity metrics. The results demonstrate that RMSEσ2 measured complexity (a) decreases with aging and diseases, and (b) gives significant discrimination between different physiological/pathological states, which may facilitate clinical application.

Fast and reliable prediction of domain-peptide binding affinity using coarse-grained structure models.

PubMed

Tian, Feifei; Tan, Rui; Guo, Tailin; Zhou, Peng; Yang, Li

2013-07-01

Domain-peptide recognition and interaction are fundamentally important for eukaryotic signaling and regulatory networks. It is thus essential to quantitatively infer the binding stability and specificity of such interaction based upon large-scale but low-accurate complex structure models which could be readily obtained from sophisticated molecular modeling procedure. In the present study, a new method is described for the fast and reliable prediction of domain-peptide binding affinity with coarse-grained structure models. This method is designed to tolerate strong random noises involved in domain-peptide complex structures and uses statistical modeling approach to eliminate systematic bias associated with a group of investigated samples. As a paradigm, this method was employed to model and predict the binding behavior of various peptides to four evolutionarily unrelated peptide-recognition domains (PRDs), i.e. human amph SH3, human nherf PDZ, yeast syh GYF and yeast bmh 14-3-3, and moreover, we explored the molecular mechanism and biological implication underlying the binding of cognate and noncognate peptide ligands to their domain receptors. It is expected that the newly proposed method could be further used to perform genome-wide inference of domain-peptide binding at three-dimensional structure level. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Distinguishing styles of explosive eruptions at Erebus, Redoubt and Taupo volcanoes using multivariate analysis of ash morphometrics

NASA Astrophysics Data System (ADS)

Avery, Meredith R.; Panter, Kurt S.; Gorsevski, Pece V.

2017-02-01

The style and dynamics of volcanic eruptions control the level and type of hazards posed for local populations and can have a temporary long-range impact on climate if eruptions are extremely energetic. The purpose of this study is to provide a statistical approach to ash morphometrics in order to provide a means by which to evaluate diverse eruption styles and mechanisms of fragmentation. The methodology presented can be applied to tephra deposits worldwide and may aid volcanic hazard mitigation by better defining a volcano's history of explosive behavior. Ash-sized grains were collected from tephra deposits on Mount Erebus, Antarctica (< 10 ka, phonolitic unit SC4), Mount Redoubt, Alaska (2009, andesitic events 2-4 & 9-18), and the Taupo volcano, New Zealand (1.8 ka, rhyolitic unit 3D). Coarse ash from each deposit was carefully hand-sieved to 1 mm diameter and display diverse morphologies that vary from grains that are moderately vesicular and more rectangular (blocky) to highly vesiculated (spongy) grains that vary from angular to sub-rounded. A total of 264 grains were imaged by scanning electron microscopy. Morphometric properties were determined using image processing software and then evaluated by several statistical methods. Discriminant analysis of all parameters was found to be the best at differentiating the tephra deposits and allowing for interpretation of eruptive styles in conjunction with field observations. A linear array of data forming a positive slope in factor space, which explains > 99% of the total data variance, is interpreted to represent a continuum between fragmentations involving water-magma interaction ("wet") to grains that were formed predominately by magmatic ("dry") fragmentation mechanisms. The Taupo Hatepe ash, which was deposited from a phreatoplinian eruption column, has the highest factor values in the array, which signifies, in part, more rectangular/blocky morphologies with smooth grain edges. Factor values for the 2009 Redoubt eruption (events 2-4) are nearly as high as Hatepe ash and based on this we suggest that it was produced, in part, by phreatomagmatic fragmentation. This is supported by field observations that document melting and eruption through glacial ice during the early phases of the 2009 activity. Redoubt ash grains from later stages of the same eruption (events 9-18) show a significant shift to lower values in factor space (more irregular/vesiculated grains) and are interpreted to be a consequence of 'dryer' conditions. Coarse ash data from Mount Erebus are completely separated from Taupo and Redoubt grains in factor space due primarily to the difference in mean gray value, which is a proxy for vesicle density and size. The vesicle characteristics (larger and deeper) are consistent with documented strombolian-style activity and the scatter in grain shape data support fragmentation by a mixture of wet and dry processes as has previously been proposed based on deposit characteristics and resemblance to tephra produced by current activity.

Programmable Potentials: Approximate N-body potentials from coarse-level logic.

PubMed

Thakur, Gunjan S; Mohr, Ryan; Mezić, Igor

2016-09-27

This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the "coefficients" of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out.

Programmable Potentials: Approximate N-body potentials from coarse-level logic

NASA Astrophysics Data System (ADS)

Thakur, Gunjan S.; Mohr, Ryan; Mezić, Igor

2016-09-01

This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the “coefficients” of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out.

Programmable Potentials: Approximate N-body potentials from coarse-level logic

PubMed Central

Thakur, Gunjan S.; Mohr, Ryan; Mezić, Igor

2016-01-01

This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the “coefficients” of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out. PMID:27671683

Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method.

PubMed

Ardham, Vikram Reddy; Deichmann, Gregor; van der Vegt, Nico F A; Leroy, Frédéric

2015-12-28

We address the question of how reducing the number of degrees of freedom modifies the interfacial thermodynamic properties of heterogeneous solid-liquid systems. We consider the example of n-hexane interacting with multi-layer graphene which we model both with fully atomistic and coarse-grained (CG) models. The CG models are obtained by means of the conditional reversible work (CRW) method. The interfacial thermodynamics of these models is characterized by the solid-liquid work of adhesion WSL calculated by means of the dry-surface methodology through molecular dynamics simulations. We find that the CRW potentials lead to values of WSL that are larger than the atomistic ones. Clear understanding of the relationship between the structure of n-hexane in the vicinity of the surface and WSL is elucidated through a detailed study of the energy and entropy components of WSL. We highlight the crucial role played by the solid-liquid energy fluctuations. Our approach suggests that CG potentials should be designed in such a way that they preserve the range of solid-liquid interaction energies, but also their fluctuations in order to preserve the reference atomistic value of WSL. Our study thus opens perspectives into deriving CG interaction potentials that preserve the thermodynamics of solid-liquid contacts and will find application in studies that intend to address materials driven by interfaces.

Microstructural effects on the room and elevated temperature low cycle fatigue behavior of Waspaloy. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Lerch, B. A.

1982-01-01

Longitudinal specimens of Waspaloy containing either coarse grains with small gamma or fine grains with large gamma were tested in air at a frequency of 0.33 Hz or 0.50 Hz. The coarse grained structures exhibited planar slip on (III) planes and precipitate shearing at all temperatures. Cracks initiated by a Stage 1 mechanism and propagated by a striation forming mechanism. At 700 C and 800 C, cleavage and intergranular cracking were observed. Testing at 500 C, 700 C, and 800 C caused precipitation of grain boundary carbides. At 700 C, carbides precipitated on slip bands. The fine grained structures exhibited planar slip on (111) planes. Dislocations looped the large gamma precipitates. This structure led to stress saturation and propagation was observed. Increasing temperatures resulted in increased specimen oxidation for both heat treatments. Slip band and grain boundary oxidation were observed. At 800 C, oxidized grain boundaries were cracked by intersecting slip bands which resulted in intergranular failure. The fine specimens had crack initiation later in the fatigue life, but with more rapid propagation crack propagation.

Holocene water mass history off NE Greenland - A first high-resolution sediment record from the western Fram Strait

NASA Astrophysics Data System (ADS)

Zehnich, Marc; Palme, Tina; Spielhagen, Robert F.; Hass, H. Christian; Bauch, Henning A.

2017-04-01

While the Holocene history of the eastern Fram Strait seems well investigated, no high-resolution paleoenvironmental records were available from the western Fram Strait so far. A new sedimentary record, obtained during expedition PS93.1 (2015) of RV Polarstern on the outermost NE Greenland shelf, allows for the first time to reconstruct Holocene changes in near-surface salinities, temperature, stratification and water masses (polar waters vs. Atlantic Water), potentially related to variations of the freshwater and sea ice export from the Arctic Ocean. The 260 cm long sedimentary record from site PS93/025 (80.5°N, 8.5°W) was investigated for sediment composition, foraminifer contents, grain size variations (sortable silt) and the isotopic composition of planktic foraminifers. Radiocarbon datings reveal an age of 10.2 cal-ka for the core base and continuous sedimentation throughout most of the Holocene. The sediments are generally very fine-grained (<2% sand). The grain size record reveals a fining-upwards trend and sediments from <6.5 cal-ka consist of <0.5% coarse fraction. A comparison of foraminifer and coarse fraction abundances shows strong similarities. Apparently the contribution of coarse terrestrial material from iceberg transport was extremely low throughout the last 10.2 cal-ka. Foraminifer abundances (both planktic and benthic) are high in Early Holocene sediments until ca. 7 cal-ka and decrease rapidly thereafter. This is interpreted to reflect a relatively strong advection of Atlantic Water to the NW Fram Strait, which correlates well with similar findings on the eastern side of the Arctic Gateway. Sortable silt grain sizes are high (27-32 µm) in the older part of the record and gradually decrease between 7 cal-ka and 4 cal-ka. After ca. 4 cal-ka, sortable silt shows values of 20-22 µm and little variation. Considering also the grain-size distribution curves, we propose a decline of bottom current velocities on the outer NE Greenland shelf after 7 cal-ka, related to a decrease of Atlantic Water advection. These preliminary results reveal a strong coupling of Holocene environments on both sides of the Fram Strait.

Environmental factors controlling the seasonal variability in particle size distribution of modern Saharan dust deposited off Cape Blanc

NASA Astrophysics Data System (ADS)

Friese, Carmen A.; van der Does, Michèlle; Merkel, Ute; Iversen, Morten H.; Fischer, Gerhard; Stuut, Jan-Berend W.

2016-09-01

The particle sizes of Saharan dust in marine sediment core records have been used frequently as a proxy for trade-wind speed. However, there are still large uncertainties with respect to the seasonality of the particle sizes of deposited Saharan dust off northwestern Africa and the factors influencing this seasonality. We investigated a three-year time-series of grain-size data from two sediment-trap moorings off Cape Blanc, Mauritania and compared them to observed wind-speed and precipitation as well as satellite images. Our results indicate a clear seasonality in the grain-size distributions: during summer the modal grain sizes were generally larger and the sorting was generally less pronounced compared to the winter season. Gravitational settling was the major deposition process during winter. We conclude that the following two mechanisms control the modal grain size of the collected dust during summer: (1) wet deposition causes increased deposition fluxes resulting in coarser modal grain sizes and (2) the development of cold fronts favors the emission and transport of coarse particles off Cape Blanc. Individual dust-storm events throughout the year could be recognized in the traps as anomalously coarse-grained samples. During winter and spring, intense cyclonic dust-storm events in the dust-source region explained the enhanced emission and transport of a larger component of coarse particles off Cape Blanc. The outcome of our study provides important implications for climate modellers and paleo-climatologists.

Spatio-temporal Evolution of Velocity Structure, Concentration and Grain-size Stratification within Experimental Particulate Gravity Flows: Potential Input Parameters for Numerical Models

NASA Astrophysics Data System (ADS)

McCaffrey, W.; Choux, C.; Baas, J.; Haughton, P.

2001-12-01

Little is known about the combined spatio-temporal evolution of velocity structure, concentration and grain size stratification within particulate gravity currents. Yet these data are of primary importance for numerical model validation, prior to application to natural flows, such as pyroclastic density currents and turbidity currents. A comprehensive study was carried out on a series of experimental particulate gravity flows of 5% by volume initial concentration. The sediment analogue was polydisperse silica flour (mean grain size ~8 microns). A uniform 30 liter suspension was prepared in an overhead reservoir, then allowed to drain (in about one minute) into an flume 10 m long and 0.3 m wide, water-filled to a depth of 0.3 m. Each flow was siphoned continuously for 52 s at 5 different heights (spaced evenly from 0.6 to 4.6 cm) with samples collected at a frequency of 0.25Hz, generating 325 samples for grain-size and concentration analysis. Simultaneously, six 4-MHz UDVP (Ultrasonic Doppler Velocity Profiling) probes recorded the horizontal component of flow velocity. All but the highest probe were positioned at the same height as the siphons. The sampling location was shifted 1.32m down-current for each of five nominally identical flows, yielding sample locations at 1.32, 2.64, 3.96, 5.28 and 6.60m from the inlet point. These data can be combined to give both the temporal and spatial evolution of a single idealised flow. The concentration data can be used to defined the structure of the flow. The flow first propagated as a jet, then became stratified. The length of the head increased with increasing distance from the reservoir (although the head propagation velocity was uniform). The maximum concentration was located at the base of the flow towards the rear of the head. Grain-size analysis showed that the head was enriched in coarse particles even at the most distal sampling location. Distinct flow stratification developed at a distance between 1.3 m and 2.6 m from the reservoir. In the body of the current, the suspended sediment was normally graded, whereas the tail exhibited inverse grading. This inverse grading may be linked to coarse particles in the head being swept upwards and backwards, then falling back into the body of the current. Alternatively, body turbulence may inhibit the settling of coarse particles. Turbulence may also explain the presence of coarse particles in the flow's head, with turbulence intensity apparently correlated with the flow competence.

Determination of canal leakage potential using continuous resistivity profiling techniques, Interstate and Tri-State Canals, western Nebraska and eastern Wyoming, 2004

USGS Publications Warehouse

Ball, Lyndsay B.; Kress, Wade H.; Steele, Gregory V.; Cannia, James C.; Andersen, Michael J.

2006-01-01

In the North Platte River Basin, a ground-water model is being developed to evaluate the effectiveness of using water leakage from selected irrigation canal systems to enhance ground-water recharge. The U.S. Geological Survey, in cooperation with the North Platte Natural Resources District, used land-based capacitively coupled and water-borne direct-current continuous resistivity profiling techniques to map the lithology of the upper 8 meters and to interpret the relative canal leakage potential of 110 kilometers of the Interstate and Tri-State Canals in western Nebraska and eastern Wyoming. Lithologic descriptions from 25 test holes were used to evaluate the effectiveness of both techniques for indicating relative grain size. An interpretive color scale was developed that symbolizes contrasting resistivity features indicative of different grain-size categories. The color scale was applied to the vertically averaged resistivity and used to classify areas of the canals as having either high, moderate, or low canal leakage potential. When results were compared with the lithologic descriptions, both land-based and water-borne continuous resistivity profiling techniques were determined to be effective at differentiating coarse-grained from fine-grained sediment. Both techniques were useful for producing independent, similar interpretations of canal leakage potential.

Coarse-Grained Molecular Dynamics Simulations of Membrane-Trehalose Interactions.

PubMed

Kapla, Jon; Stevensson, Baltzar; Maliniak, Arnold

2016-09-15

It is well established that trehalose (TRH) affects the physical properties of lipid bilayers and stabilizes biological membranes. We present molecular dynamics (MD) computer simulations to investigate the interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH. Both atomistic and coarse-grained (CG) interaction models were employed, and the coarse graining of DMPC leads to a reduction in the acyl chain length corresponding to a 1,2-dilauroyl-sn-glycero-3-phosphocholine lipid (DLPC). Several modifications of the Martini interaction model, used for CG simulations, were implemented, resulting in different potentials of mean force (PMFs) for DMPC bilayer-TRH interactions. These PMFs were subsequently used in a simple two-site analytical model for the description of sugar binding at the membrane interface. In contrast to that in atomistic MD simulations, the binding in the CG model was not in agreement with the two-site model. Our interpretation is that the interaction balance, involving water, TRH, and lipids, in the CG systems needs further tuning of the force-field parameters. The area per lipid is only weakly affected by TRH concentration, whereas the compressibility modulus related to the fluctuations of the membrane increases with an increase in TRH content. In agreement with experimental findings, the bending modulus is not affected by the inclusion of TRH. The important aspects of lipid bilayer interactions with biomolecules are membrane curvature generation and sensing. In the present investigation, membrane curvature is generated by artificial buckling of the bilayer in one dimension. It turns out that TRH prefers the regions with the highest curvature, which enables the most favorable situation for lipid-sugar interactions.

Electrolytes in a nanometer slab-confinement: Ion-specific structure and solvation forces

NASA Astrophysics Data System (ADS)

Kalcher, Immanuel; Schulz, Julius C. F.; Dzubiella, Joachim

2010-10-01

We study the liquid structure and solvation forces of dense monovalent electrolytes (LiCl, NaCl, CsCl, and NaI) in a nanometer slab-confinement by explicit-water molecular dynamics (MD) simulations, implicit-water Monte Carlo (MC) simulations, and modified Poisson-Boltzmann (PB) theories. In order to consistently coarse-grain and to account for specific hydration effects in the implicit methods, realistic ion-ion and ion-surface pair potentials have been derived from infinite-dilution MD simulations. The electrolyte structure calculated from MC simulations is in good agreement with the corresponding MD simulations, thereby validating the coarse-graining approach. The agreement improves if a realistic, MD-derived dielectric constant is employed, which partially corrects for (water-mediated) many-body effects. Further analysis of the ionic structure and solvation pressure demonstrates that nonlocal extensions to PB (NPB) perform well for a wide parameter range when compared to MC simulations, whereas all local extensions mostly fail. A Barker-Henderson mapping of the ions onto a charged, asymmetric, and nonadditive binary hard-sphere mixture shows that the strength of structural correlations is strongly related to the magnitude and sign of the salt-specific nonadditivity. Furthermore, a grand canonical NPB analysis shows that the Donnan effect is dominated by steric correlations, whereas solvation forces and overcharging effects are mainly governed by ion-surface interactions. However, steric corrections to solvation forces are strongly repulsive for high concentrations and low surface charges, while overcharging can also be triggered by steric interactions in strongly correlated systems. Generally, we find that ion-surface and ion-ion correlations are strongly coupled and that coarse-grained methods should include both, the latter nonlocally and nonadditive (as given by our specific ionic diameters), when studying electrolytes in highly inhomogeneous situations.

Bottled SAFT: A Web App Providing SAFT-γ Mie Force Field Parameters for Thousands of Molecular Fluids.

PubMed

Ervik, Åsmund; Mejía, Andrés; Müller, Erich A

2016-09-26

Coarse-grained molecular simulation has become a popular tool for modeling simple and complex fluids alike. The defining aspects of a coarse grained model are the force field parameters, which must be determined for each particular fluid. Because the number of molecular fluids of interest in nature and in engineering processes is immense, constructing force field parameter tables by individually fitting to experimental data is a futile task. A step toward solving this challenge was taken recently by Mejía et al., who proposed a correlation that provides SAFT-γ Mie force field parameters for a fluid provided one knows the critical temperature, the acentric factor and a liquid density, all relatively accessible properties. Building on this, we have applied the correlation to more than 6000 fluids, and constructed a web application, called "Bottled SAFT", which makes this data set easily searchable by CAS number, name or chemical formula. Alternatively, the application allows the user to calculate parameters for components not present in the database. Once the intermolecular potential has been found through Bottled SAFT, code snippets are provided for simulating the desired substance using the "raaSAFT" framework, which leverages established molecular dynamics codes to run the simulations. The code underlying the web application is written in Python using the Flask microframework; this allows us to provide a modern high-performance web app while also making use of the scientific libraries available in Python. Bottled SAFT aims at taking the complexity out of obtaining force field parameters for a wide range of molecular fluids, and facilitates setting up and running coarse-grained molecular simulations. The web application is freely available at http://www.bottledsaft.org . The underlying source code is available on Bitbucket under a permissive license.

Exploring the Ability of a Coarse-grained Potential to Describe the Stress-strain Response of Glassy Polystyrene

DTIC Science & Technology

2012-10-01

using the open-source code Large-scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) (http://lammps.sandia.gov) (23). The commercial...parameters are proprietary and cannot be ported to the LAMMPS 4 simulation code. In our molecular dynamics simulations at the atomistic resolution, we...IBI iterative Boltzmann inversion LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator MAPS Materials Processes and Simulations MS

Mechanism of ultra low friction of multilayer graphene studied by coarse-grained molecular simulation.

PubMed

Washizu, Hitoshi; Kajita, Seiji; Tohyama, Mamoru; Ohmori, Toshihide; Nishino, Noriaki; Teranishi, Hiroshi; Suzuki, Atsushi

2012-01-01

Coarse-grained Metropolis Monte Carlo Brownian Dynamics simulations are used to clarify the ultralow friction mechanism of a transfer film of multilayered graphene sheets. Each circular graphene sheet consists of 400 to 1,000,000 atoms confined between the upper and lower sliders and are allowed to move in 3 translational and 1 rotational directions due to thermal motion at 300 K. The sheet-sheet interaction energy is calculated by the sum of the pair potential of the sp2 carbons. The sliding simulations are done by moving the upper slider at a constant velocity. In the monolayer case, the friction force shows a stick-slip like curve and the average of the force is high. In the multilayer case, the friction force does not show any oscillation and the average of the force is very low. This is because the entire transfer film has an internal degree of freedom in the multilayer case and the lowest sheet of the layer is able to follow the equipotential surface of the lower slider.

Slip-spring model of entangled rod-coil block copolymers

NASA Astrophysics Data System (ADS)

Wang, Muzhou; Likhtman, Alexei E.; Olsen, Bradley D.

2015-03-01

Understanding the dynamics of rod-coil block copolymers is important for optimal design of functional nanostructured materials for organic electronics and biomaterials. Recently, we proposed a reptation theory of entangled rod-coil block copolymers, predicting the relaxation mechanisms of activated reptation and arm retraction that slow rod-coil dynamics relative to coil and rod homopolymers, respectively. In this work, we introduce a coarse-grained slip-spring model of rod-coil block copolymers to further explore these mechanisms. First, parameters of the coarse-grained model are tuned to match previous molecular dynamics simulation results for coils, rods, and block copolymers. For activated reptation, rod-coil copolymers are shown to disfavor configurations where the rod occupies curved portions of the entanglement tube of randomly varying curvature created by the coil ends. The effect of these barriers on diffusion is quantitatively captured by considering one-dimensional motion along an entanglement tube with a rough free energy potential. Finally, we analyze the crossover between the two mechanisms. The resulting dynamics from both mechanisms acting in combination is faster than from each one individually.

Interplay Between Hydrophobic Effect and Dipole Interactions in Peptide Aggregation

NASA Astrophysics Data System (ADS)

Ganesan, Sai; Matysiak, Silvina

In the past decade, the development of various coarse-grained models for proteins have provided key insights into the driving forces in folding and aggregation.We recently developed a low resolution Water Explicit Polarizable PROtein coarse-grained Model by adding oppositely charged dummy particles inside protein backbone beads.With this model,we were able to achieve significant α/ β secondary structure content,without any added bias.We now extend the model to study peptide aggregation at hydrophobic-hydrophilic interface using elastin-like octapeptides (GV)4 as a model system.A condensation-ordering mechanism of aggregation is observed in water.Our results suggest that backbone interpeptide dipolar interactions,not hydrophobicity,plays a more significant role in fibril-like peptide aggregation.We observe a cooperative effect in hydrogen bonding or dipolar interactions, with increase in aggregate size in water and interface.Based on this cooperative effect, we provide a potential explanation for the observed nucleus size in peptide aggregation pathways.Without dipolar particles,peptide aggregation is not observed at the hydrophilic-hydrophobic interface.Thus,the presence of dipoles,not hydrophobicity plays a key role in aggregation observed at hydrophobic interfaces.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models.

PubMed

Li, Min; Zhang, John Z H

2017-02-14

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

Coarse-Grained Molecular Models of Water: A Review

PubMed Central

Hadley, Kevin R.; McCabe, Clare

2012-01-01

Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regards to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. Finally, how the models are parameterized depends on their application, so, while some are fitted to experimental properties such as surface tension and density, others are fitted to radial distribution functions extracted from atomistic simulations. PMID:22904601

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models

NASA Astrophysics Data System (ADS)

Li, Min; Zhang, John Z. H.

2017-02-01

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.

PubMed

Poblete, Simón; Bottaro, Sandro; Bussi, Giovanni

2018-02-28

We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the $\\mathcal {E}$SCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-based model. This results in a representation able to describe planar canonical and non-canonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the CG representation.

DNA nanotechnology: understanding and optimisation through simulation

NASA Astrophysics Data System (ADS)

Ouldridge, Thomas E.

2015-01-01

DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article, I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended 'overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.

Microphase separation and the formation of ion conductivity channels in poly(ionic liquid)s: A coarse-grained molecular dynamics study

NASA Astrophysics Data System (ADS)

Weyman, Alexander; Bier, Markus; Holm, Christian; Smiatek, Jens

2018-05-01

We study generic properties of poly(ionic liquid)s (PILs) via coarse-grained molecular dynamics simulations in bulk solution and under confinement. The influence of different side chain lengths on the spatial properties of the PIL systems and on the ionic transport mechanism is investigated in detail. Our results reveal the formation of apolar and polar nanodomains with increasing side chain length in good agreement with previous results for molecular ionic liquids. The ion transport numbers are unaffected by the occurrence of these domains, and the corresponding values highlight the potential role of PILs as single-ion conductors in electrochemical devices. In contrast to bulk behavior, a pronounced formation of ion conductivity channels in confined systems is initiated in close vicinity to the boundaries. We observe higher ion conductivities in these channels for increasing PIL side chain lengths in comparison with bulk values and provide an explanation for this effect. The appearance of these domains points to an improved application of PILs in modern polymer electrolyte batteries.

Application-specific coarse-grained reconfigurable array: architecture and design methodology

NASA Astrophysics Data System (ADS)

Zhou, Li; Liu, Dongpei; Zhang, Jianfeng; Liu, Hengzhu

2015-06-01

Coarse-grained reconfigurable arrays (CGRAs) have shown potential for application in embedded systems in recent years. Numerous reconfigurable processing elements (PEs) in CGRAs provide flexibility while maintaining high performance by exploring different levels of parallelism. However, a difference remains between the CGRA and the application-specific integrated circuit (ASIC). Some application domains, such as software-defined radios (SDRs), require flexibility with performance demand increases. More effective CGRA architectures are expected to be developed. Customisation of a CGRA according to its application can improve performance and efficiency. This study proposes an application-specific CGRA architecture template composed of generic PEs (GPEs) and special PEs (SPEs). The hardware of the SPE can be customised to accelerate specific computational patterns. An automatic design methodology that includes pattern identification and application-specific function unit generation is also presented. A mapping algorithm based on ant colony optimisation is provided. Experimental results on the SDR target domain show that compared with other ordinary and application-specific reconfigurable architectures, the CGRA generated by the proposed method performs more efficiently for given applications.

Temporal variability and memory in sediment transport in an experimental step-pool channel

NASA Astrophysics Data System (ADS)

Saletti, Matteo; Molnar, Peter; Zimmermann, André; Hassan, Marwan A.; Church, Michael

2015-11-01

Temporal dynamics of sediment transport in steep channels using two experiments performed in a steep flume (8%) with natural sediment composed of 12 grain sizes are studied. High-resolution (1 s) time series of sediment transport were measured for individual grain-size classes at the outlet of the flume for different combinations of sediment input rates and flow discharges. Our aim in this paper is to quantify (a) the relation of discharge and sediment transport and (b) the nature and strength of memory in grain-size-dependent transport. None of the simple statistical descriptors of sediment transport (mean, extreme values, and quantiles) display a clear relation with water discharge, in fact a large variability between discharge and sediment transport is observed. Instantaneous transport rates have probability density functions with heavy tails. Bed load bursts have a coarser grain-size distribution than that of the entire experiment. We quantify the strength and nature of memory in sediment transport rates by estimating the Hurst exponent and the autocorrelation coefficient of the time series for different grain sizes. Our results show the presence of the Hurst phenomenon in transport rates, indicating long-term memory which is grain-size dependent. The short-term memory in coarse grain transport increases with temporal aggregation and this reveals the importance of the sampling duration of bed load transport rates in natural streams, especially for large fractions.

Ultrafine-grained titanium for medical implants

DOEpatents

Zhu, Yuntian T.; Lowe, Terry C.; Valiev, Ruslan Z.; Stolyarov, Vladimir V.; Latysh, Vladimir V.; Raab, Georgy J.

2002-01-01

We disclose ultrafine-grained titanium. A coarse-grained titanium billet is subjected to multiple extrusions through a preheated equal channel angular extrusion (ECAE) die, with billet rotation between subsequent extrusions. The resulting billet is cold processed by cold rolling and/or cold extrusion, with optional annealing. The resulting ultrafine-grained titanium has greatly improved mechanical properties and is used to make medical implants.

Reservoir sedimentology of the Big Injun sandstone in Granny Creek field, West Virginia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zou, Xiangdong; Donaldson, K.; Donaldson, A.C.

1992-01-01

Big Injun sandstones of Granny Creek oil field (WV) are interpreted as fluvial-deltaic deposits from core and geophysical log data. The reservoir consists of two distinctive lithologies throughout the field; fine-grained sandstones overlain by pebbly and coarse-grained sandstones. Lower fine-grained sandstones were deposited in westward prograding river-mouth bars, where distal, marine-dominant proximal, and fluvial-dominant proximal bar subfacies are recognized. Principal pay is marine-influenced proximal bar, where porosity ranges from 13 to 23% and permeability, up to 24 md. Thin marine transgressive shales and their laterally equivalent low-permeability sandstones bound time-rock sequences generally less than 10 meters thick. Where field mapped,more » width of prograding bar sequence is approximately 2.7 km (dip trend), measured from truncated eastern edge (pre-coarse-grained member erosional surface) to distal western margin. Dip-trending elongate lobes occur within marine-influenced proximal mouth-bar area, representing thickest part of tidally influenced preserved bar. Upper coarse-grained part of reservoir consists of pebbly sandstones of channel fill from bedload streams. Laterally persistent low permeability cemented interval in lower part commonly caps underlying pay zone and probably serves as seal to vertical oil migration. Southwest paleoflow trends based on thickness maps of unit portent emergence of West Virginia dome, which influences erosion patterns of pre-Greenbrier unconformity for this combination oil trap.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Enciso, Marta, E-mail: m.enciso@latrobe.edu.au; Schütte, Christof, E-mail: schuette@zib.de; Zuse Institute Berlin, Berlin

We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to describe the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse-grained model can account for these details.

Extrapolation to Nonequilibrium from Coarse-Grained Response Theory

NASA Astrophysics Data System (ADS)

Basu, Urna; Helden, Laurent; Krüger, Matthias

2018-05-01

Nonlinear response theory, in contrast to linear cases, involves (dynamical) details, and this makes application to many-body systems challenging. From the microscopic starting point we obtain an exact response theory for a small number of coarse-grained degrees of freedom. With it, an extrapolation scheme uses near-equilibrium measurements to predict far-from-equilibrium properties (here, second order responses). Because it does not involve system details, this approach can be applied to many-body systems. It is illustrated in a four-state model and in the near critical Ising model.

Structural Changes in Lipid Vesicles Generated by the Shock Blast Waves: Coarse-Grained Molecular Dynamics Simulation

DTIC Science & Technology

2013-11-01

duration, or shock-pulse shape. Used in this computational study is a coarse-grained model of the lipid vesicle as a simplified model of a cell...Figures iv List of Tables iv 1. Introduction 1 2. Model and Methods 3 3. Results and Discussion 6 3.1 Simulation of the Blast Waves with Low Peak...realistic detail but to focus on a simple model of the major constituent of a cell membrane, the phospholipid bilayer. In this work, we studied the

A Bayesian framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems

NASA Astrophysics Data System (ADS)

Farrell, Kathryn; Oden, J. Tinsley; Faghihi, Danial

2015-08-01

A general adaptive modeling algorithm for selection and validation of coarse-grained models of atomistic systems is presented. A Bayesian framework is developed to address uncertainties in parameters, data, and model selection. Algorithms for computing output sensitivities to parameter variances, model evidence and posterior model plausibilities for given data, and for computing what are referred to as Occam Categories in reference to a rough measure of model simplicity, make up components of the overall approach. Computational results are provided for representative applications.

Sands at Gusev Crater, Mars

NASA Astrophysics Data System (ADS)

Cabrol, Nathalie A.; Herkenhoff, Kenneth; Knoll, Andrew H.; Farmer, Jack; Arvidson, Raymond; Grin, Edmond; Li, Ronxing; Fenton, Lori; Cohen, Barbara; Bell, James F.; Aileen Yingst, R.

2014-05-01

Processes, environments, and the energy associated with the transport and deposition of sand at Gusev Crater are characterized at the microscopic scale through the comparison of statistical moments for particle size and shape distributions. Bivariate and factor analyses define distinct textural groups at 51 sites along the traverse completed by the Spirit rover as it crossed the plains and went into the Columbia Hills. Fine-to-medium sand is ubiquitous in ripples and wind drifts. Most distributions show excess fine material, consistent with a predominance of wind erosion over the last 3.8 billion years. Negative skewness at West Valley is explained by the removal of fine sand during active erosion, or alternatively, by excess accumulation of coarse sand from a local source. The coarse to very coarse sand particles of ripple armors in the basaltic plains have a unique combination of size and shape. Their distribution display significant changes in their statistical moments within the ~400 m that separate the Columbia Memorial Station from Bonneville Crater. Results are consistent with aeolian and/or impact deposition, while the elongated and rounded shape of the grains forming the ripples, as well as their direction of origin, could point to Ma'adim Vallis as a possible source. For smaller particles on the traverse, our findings confirm that aeolian processes have dominated over impact and other processes to produce sands with the observed size and shape patterns across a spectrum of geologic (e.g., ripples and plains soils) and aerographic settings (e.g., wind shadows).

Sands at Gusev Crater, Mars

USGS Publications Warehouse

Cabrol, Nathalie A.; Herkenhoff, Kenneth E.; Knoll, Andrew H.; Farmer, Jack D.; Arvidson, Raymond E.; Grin, E.A.; Li, Ron; Fenton, Lori; Cohen, B.; Bell, J.F.; Yingst, R. Aileen

2014-01-01

Processes, environments, and the energy associated with the transport and deposition of sand at Gusev Crater are characterized at the microscopic scale through the comparison of statistical moments for particle size and shape distributions. Bivariate and factor analyses define distinct textural groups at 51 sites along the traverse completed by the Spirit rover as it crossed the plains and went into the Columbia Hills. Fine-to-medium sand is ubiquitous in ripples and wind drifts. Most distributions show excess fine material, consistent with a predominance of wind erosion over the last 3.8 billion years. Negative skewness at West Valley is explained by the removal of fine sand during active erosion, or alternatively, by excess accumulation of coarse sand from a local source. The coarse to very coarse sand particles of ripple armors in the basaltic plains have a unique combination of size and shape. Their distribution display significant changes in their statistical moments within the ~400 m that separate the Columbia Memorial Station from Bonneville Crater. Results are consistent with aeolian and/or impact deposition, while the elongated and rounded shape of the grains forming the ripples, as well as their direction of origin, could point to Ma'adim Vallis as a possible source. For smaller particles on the traverse, our findings confirm that aeolian processes have dominated over impact and other processes to produce sands with the observed size and shape patterns across a spectrum of geologic (e.g., ripples and plains soils) and aerographic settings (e.g., wind shadows).

Unconstrained Structure Formation in Coarse-Grained Protein Simulations

NASA Astrophysics Data System (ADS)

Bereau, Tristan

The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid model. The lipid force field was systematically tuned to reproduce the structural and mechanical properties of phosphatidylcholine bilayers. The two models were cross-parametrized against atomistic potential of mean force curves for the insertion of single amino acid side chains into a bilayer. Coarse-grained transmembrane protein simulations were then compared with experiments and atomistic simulations to validate the force field. The transferability of the two models across amino acid sequences and lipid species permits the investigation of a wide variety of scenarios, while the absence of explicit solvent allows for studies of large-scale phenomena.

Data-driven parameterization of the generalized Langevin equation

DOE PAGES

Lei, Huan; Baker, Nathan A.; Li, Xiantao

2016-11-29

We present a data-driven approach to determine the memory kernel and random noise of the generalized Langevin equation. To facilitate practical implementations, we parameterize the kernel function in the Laplace domain by a rational function, with coefficients directly linked to the equilibrium statistics of the coarse-grain variables. Further, we show that such an approximation can be constructed to arbitrarily high order. Within these approximations, the generalized Langevin dynamics can be embedded in an extended stochastic model without memory. We demonstrate how to introduce the stochastic noise so that the fluctuation-dissipation theorem is exactly satisfied.

The Lithological Constraint To Gas Hydrate Formation: Evidence OF Grain Size Of Sediments From IODP 311 On CASCADIA Margin

NASA Astrophysics Data System (ADS)

Wang, J.

2006-12-01

A total of 614 sediment samples at intervals of about 1.5 m from all 5 sites of the Integrated Ocean Drilling Program (IODP) Expedition 311 on Cascadia Margin were analyzed using a Beckman Coulter LS-230 Particle Analyzer. The grain-size data were then plotted in depth and compared with other proxies of gas hydrate- occurrence such as soupy/mousse-like structures in sediments, gas hydrate concentration (Sh) derived from LWD data using Archie's relation, IR core images (infrared image) and the recovered samples of gas hydrate¨Cbearing sediments. A good relationship between the distribution of coarse grains in size of 31-63¦Ìm and 63-125¦Ìm sediments and the potential occurrence of gas hydrate was found across the entire gas hydrate stability zone. The depth distribution of grain size from the Site U1326 shows clear excursions at depths of 5-8, 21-26, 50- 123, 132-140, 167-180, 195-206 and 220-240 mbsf, which coincide with the potential occurrence of gas hydrate suggested by soupy/mousse-like structures, logging-derived gas hydrate concentrations (Sh) and the recovered samples of the gas hydrate¨Cbearing sand layers. The lithology of sediments significantly affects the formation of gas hydrate. Gas hydrate forms preferentially within relatively coarse grain-size sediments above 31 ¦Ìm. Key words: grain size of sediments, constraint, occurrence of gas hydrate, IODP 311 IODP Expedition 311 Scientists: Michael Riedel (Co-chief Scientist), Timothy S. Collett (Co-chief Scientist), Mitchell Malone (Expedition Project Manager/Staff Scientist), Gilles Gu¨¨rin, Fumio Akiba, Marie-Madeleine Blanc-Valleron, Michelle Ellis, Yoshitaka Hashimoto, Verena Heuer, Yosuke Higashi, Melanie Holland, Peter D. Jackson, Masanori Kaneko, Miriam Kastner, Ji-Hoon Kim, Hiroko Kitajima, Philip E. Long, Alberto Malinverno, Greg Myers, Leena D. Palekar, John Pohlman, Peter Schultheiss, Barbara Teichert, Marta E. Torres, Anne M. Tr¨¦hu, Jiasheng Wang, Ulrich G. Wortmann, Hideyoshi Yoshioka. Acknowledgement: This study was supported by the IODP/JOI Alliance, IODP-China 863 Project (grant 2004AA615030) and NSFC Project (grant 40472063).

Effects of microstructural variation on Charpy impact properties in heavy-section Mn-Mo-Ni low alloy steel for reactor pressure vessel

NASA Astrophysics Data System (ADS)

Hong, Seokmin; Song, Jaemin; Kim, Min-Chul; Choi, Kwon-Jae; Lee, Bong-Sang

2016-03-01

The effects of microstructural changes in heavy-section Mn-Mo-Ni low alloy steel on Charpy impact properties were investigated using a 210 mm thick reactor pressure vessel. Specimens were sampled from 5 different positions at intervals of 1/4 thickness from the inner surface to the outer surface. A detailed microstructural analysis of impact-fractured specimens showed that coarse carbides along the lath boundaries acted as fracture initiation sites, and cleavage cracks deviated at prior-austenite grain boundaries and bainite lath boundaries. Upper shelf energy was higher and energy transition temperature was lower at the surface positon, where fine bainitic microstructure with homogeneously distributed fine carbides were present. Toward the center, coarse upper bainite and precipitation of coarse inter-lath carbides were observed, which deteriorated impact properties. At the 1/4T position, the Charpy impact properties were worse than those at other positions owing to the combination of elongated-coarse inter-lath carbides and large effective grain size.

The theory of granular packings for coarse soils

NASA Astrophysics Data System (ADS)

Yanqui, Calixtro

2013-06-01

Coarse soils are substances made of grains of different shape, size and orientation. In this paper, new massive-measurable grain indexes are defined to develop a simple and systematic theory for the ideal packing of grains. First, a linear relationship between an assemblage of monodisperse spheres and an assemblage of polydisperse grains is deduced. Then, a general formula for the porosity of linearly ordered packings of spheres in contact is settled down by the appropriated choosing of eight neighboring spheres located at the vertices of the unit parallelepiped. The porosity of axisymmetric packings of grains, related to sand piles and axisymmetric compression tests, is proposed to be determined averaging the respective linear parameters. Since they can be tested experimentally, porosities of the densest state and the loosest state of a granular soil can be used to verify the accuracy of the present theory. Diagrams for these extreme quantities show a good agreement between the theoretical lines and the experimental data, no matter the dependency on the protocols and mineral composition.

Fabrication of MEMS components using ultrafine-grained aluminium alloys

NASA Astrophysics Data System (ADS)

Qiao, Xiao Guang; Gao, Nong; Moktadir, Zakaria; Kraft, Michael; Starink, Marco J.

2010-04-01

A novel process for the fabrication of a microelectromechanical systems (MEMS) metallic component with features smaller than 10 µm and high thermal conductivity was investigated. This may be applied to new or improved microscale components, such as (micro-) heat exchangers. In the first stage of processing, equal channel angular pressing (ECAP) was employed to refine the grain size of commercial purity aluminium (Al-1050) to the ultrafine-grained (UFG) material. Embossing was conducted using a micro silicon mould fabricated by deep reactive ion etching (DRIE). Both cold embossing and hot embossing were performed on the coarse-grained and UFG Al-1050. Cold embossing on UFG Al-1050 led to a partially transferred pattern from the micro silicon mould and high failure rate of the mould. Hot embossing on UFG Al-1050 provided a smooth embossed surface with a fully transferred pattern and a low failure rate of the mould, while hot embossing on the coarse-grained Al-1050 resulted in a rougher surface with shear bands.

Burst Testing and Analysis of Superalloy Disks With a Dual Grain Microstructure

NASA Technical Reports Server (NTRS)

Gayda, John; Kantzos, Pete

2006-01-01

Elastic-plastic finite element analyses of room temperature burst tests on four superalloy disks were conducted and reported in this paper. Two alloys, Rene 104 (General Electric Aircraft Engines) and Alloy 10 (Honeywell Engines & Systems), were studied. For both alloys an advanced dual microstructure disk, fine grain bore and coarse grain rim, were analyzed and compared with conventional disks with uniform microstructures, coarse grain for Rene 104 and fine grain for Alloy 10. The analysis and experimental data were in good agreement up to burst. At burst, the analysis underestimated the speed and growth of the Rene 104 disks, but overestimated the speed and growth of the Alloy 10 disks. Fractography revealed that the Alloy 10 disks displayed significant surface microcracking and coalescence in comparison to Rene 104 disks. This phenomenon may help explain the differences between the Alloy 10 disks and the Rene 104 disks, as well as the observed deviations between analytical and experimental data at burst.

Translocation Thermodynamics of Linear and Cyclic Nonaarginine into Model DPPC Bilayer via Coarse-Grained Molecular Dynamics Simulation: Implications of Pore Formation and Nonadditivity

PubMed Central

2015-01-01

Structural mechanisms and underlying thermodynamic determinants of efficient internalization of charged cationic peptides (cell-penetrating peptides, CPPs) such as TAT, polyarginine, and their variants, into cells, cellular constructs, and model membrane/lipid bilayers (large and giant unilamellar or multilamelar vesicles) continue to garner significant attention. Two widely held views on the translocation mechanism center on endocytotic and nonendocytotic (diffusive) processes. Espousing the view of a purely diffusive internalization process (supported by recent experimental evidence, [Säälik, P.; et al. J. Controlled Release2011, 153, 117–125]), we consider the underlying free energetics of the translocation of a nonaarginine peptide (Arg9) into a model DPPC bilayer. In the case of the Arg9 cationic peptide, recent experiments indicate a higher internalization efficiency of the cyclic structure (cyclic Arg9) relative to the linear conformer. Furthermore, recent all-atom resolution molecular dynamics simulations of cyclic Arg9 [Huang, K.; et al. Biophys. J., 2013, 104, 412–420] suggested a critical stabilizing role of water- and lipid-constituted pores that form within the bilayer as the charged Arg9 translocates deep into the bilayer center. Herein, we use umbrella sampling molecular dynamics simulations with coarse-grained Martini lipids, polarizable coarse-grained water, and peptide to explore the dependence of translocation free energetics on peptide structure and conformation via calculation of potentials of mean force along preselected reaction paths allowing and preventing membrane deformations that lead to pore formation. Within the context of the coarse-grained force fields we employ, we observe significant barriers for Arg9 translocation from bulk aqueous solution to bilayer center. Moreover, we do not find free-energy minima in the headgroup–water interfacial region, as observed in simulations using all-atom force fields. The pore-forming paths systematically predict lower free-energy barriers (ca. 90 kJ/mol lower) than the non pore-forming paths, again consistent with all-atom force field simulations. The current force field suggests no preference for the more compact or covalently cyclic structures upon entering the bilayer. Decomposition of the PMF into the system’s components indicates that the dominant stabilizing contribution along the pore-forming path originates from the membrane as both layers of it deformed due to the formation of pore. Furthermore, our analysis revealed that although there is significant entropic stabilization arising from the enhanced configurational entropy exposing more states as the peptide moves through the bilayer, the enthalpic loss (as predicted by the interactions of this coarse-grained model) far outweighs any former stabilization, thus leading to significant barrier to translocation. Finally, we observe reduction in the translocation free-energy barrier for a second Arg9 entering the bilayer in the presence of an initial peptide restrained at the center, again, in qualitative agreement with all-atom force fields. PMID:24506488

Model-Based Assessment of the CO2 Sequestration Potential of Coastal Ocean Alkalinization

NASA Astrophysics Data System (ADS)

Feng, E. Y.; Koeve, W.; Keller, D. P.; Oschlies, A.

2017-12-01

The potential of coastal ocean alkalinization (COA), a carbon dioxide removal (CDR) climate engineering strategy that chemically increases ocean carbon uptake and storage, is investigated with an Earth system model of intermediate complexity. The CDR potential and possible environmental side effects are estimated for various COA deployment scenarios, assuming olivine as the alkalinity source in ice-free coastal waters (about 8.6% of the global ocean's surface area), with dissolution rates being a function of grain size, ambient seawater temperature, and pH. Our results indicate that for a large-enough olivine deployment of small-enough grain sizes (10 µm), atmospheric CO2 could be reduced by more than 800 GtC by the year 2100. However, COA with coarse olivine grains (1000 µm) has little CO2 sequestration potential on this time scale. Ambitious CDR with fine olivine grains would increase coastal aragonite saturation Ω to levels well beyond those that are currently observed. When imposing upper limits for aragonite saturation levels (Ωlim) in the grid boxes subject to COA (Ωlim = 3.4 and 9 chosen as examples), COA still has the potential to reduce atmospheric CO2 by 265 GtC (Ωlim = 3.4) to 790 GtC (Ωlim = 9) and increase ocean carbon storage by 290 Gt (Ωlim = 3.4) to 913 Gt (Ωlim = 9) by year 2100.

A Configurational-Bias-Monte-Carlo Back-Mapping Algorithm for Efficient and Rapid Conversion of Coarse-Grained Water Structures Into Atomistic Models.

PubMed

Loeffler, Troy David; Chan, Henry; Narayanan, Badri; Cherukara, Mathew J; Gray, Stephen K; Sankaranarayanan, Subramanian K R S

2018-06-20

Coarse-grained molecular dynamics (MD) simulations represent a powerful approach to simulate longer time scale and larger length scale phenomena than those accessible to all-atom models. The gain in efficiency, however, comes at the cost of atomistic details. The reverse transformation, also known as back-mapping, of coarse grained beads into their atomistic constituents represents a major challenge. Most existing approaches are limited to specific molecules or specific force-fields and often rely on running a long time atomistic MD of the back-mapped configuration to arrive at an optimal solution. Such approaches are problematic when dealing with systems with high diffusion barriers. Here, we introduce a new extension of the configurational-bias-Monte-Carlo (CBMC) algorithm, which we term the crystalline-configurational-bias-Monte-Carlo (C-CBMC) algortihm, that allows rapid and efficient conversion of a coarse-grained model back into its atomistic representation. Although the method is generic, we use a coarse-grained water model as a representative example and demonstrate the back-mapping or reverse transformation for model systems ranging from the ice-liquid water interface to amorphous and crystalline ice configurations. A series of simulations using the TIP4P/Ice model are performed to compare the new CBMC method to several other standard Monte Carlo and Molecular Dynamics based back-mapping techniques. In all the cases, the C-CBMC algorithm is able to find optimal hydrogen bonded configuration many thousand evaluations/steps sooner than the other methods compared within this paper. For crystalline ice structures such as a hexagonal, cubic, and cubic-hexagonal stacking disorder structures, the C-CBMC was able to find structures that were between 0.05 and 0.1 eV/water molecule lower in energy than the ground state energies predicted by the other methods. Detailed analysis of the atomistic structures show a significantly better global hydrogen positioning when contrasted with the existing simpler back-mapping methods. Our results demonstrate the efficiency and efficacy of our new back-mapping approach, especially for crystalline systems where simple force-field based relaxations have a tendency to get trapped in local minima.

Eye movements during spoken word recognition in Russian children.

PubMed

Sekerina, Irina A; Brooks, Patricia J

2007-09-01

This study explores incremental processing in spoken word recognition in Russian 5- and 6-year-olds and adults using free-viewing eye-tracking. Participants viewed scenes containing pictures of four familiar objects and clicked on a target embedded in a spoken instruction. In the cohort condition, two object names shared identical three-phoneme onsets. In the noncohort condition, all object names had unique onsets. Coarse-grain analyses of eye movements indicated that adults produced looks to the competitor on significantly more cohort trials than on noncohort trials, whereas children surprisingly failed to demonstrate cohort competition due to widespread exploratory eye movements across conditions. Fine-grain analyses, in contrast, showed a similar time course of eye movements across children and adults, but with cohort competition lingering more than 1s longer in children. The dissociation between coarse-grain and fine-grain eye movements indicates a need to consider multiple behavioral measures in making developmental comparisons in language processing.

Fine-grained rutile in the Gulf of Maine: Diagenetic origin, source rocks, and sedimentary environment of deposition

USGS Publications Warehouse

Valentine, P.C.; Commeau, J.A.

1990-01-01

The Gulf of Maine, an embayment of the New England margin, is floored by shallow, glacially scoured basins that are partly filled with late Pleistocene and Holocene silt and clay containing 0.7 to 1.0 wt percent TiO2 chiefly in the form of silt-size rutile. Much of the rutile in the Gulf of Maine mud probably formed diagenetically in poorly cemented Carboniferous and Triassic coarse-grained sedimentary rocks of Nova Scotia and New Brunswick after the dissolution of titanium-rich detrital minerals (ilmenite, ilmenomagnetite). The diagenesis of rutile in coarse sedimentary rocks (especially arkose and graywacke) followed by erosion, segregation, and deposition (and including recycling of fine-grained rutile from shales) can serve as a model for predicting and prospecting for unconsolidated deposits of fine-grained TiO2. -from Authors

Effects of desolvation barriers and sidechains on local-nonlocal coupling and chevron behaviors in coarse-grained models of protein folding.

PubMed

Chen, Tao; Chan, Hue Sun

2014-04-14

Local-nonlocal coupling is an organizational principle in protein folding. It envisions a cooperative energetic interplay between local conformational preferences and favorable nonlocal contacts. Previous theoretical studies by our group showed that two classes of native-centric coarse-grained models can capture the experimentally observed high degrees of protein folding cooperativity and diversity in folding rates. These models either embody an explicit local-nonlocal coupling mechanism or incorporate desolvation barriers in the models' pairwise interactions. Here a conceptual connection is made between these two paradigmatic coarse-grained interaction schemes by showing that desolvation barriers enhance local-nonlocal coupling. Furthermore, we find that a class of coarse-grained protein models with a single-site representation of sidechains also increases local-nonlocal coupling relative to mainchain models without sidechains. Enhanced local-nonlocal coupling generally leads to higher folding cooperativity and chevron plots with more linear folding arms. For the sidechain models studied, the chevron plot simulated with entirely native-centric intrachain interactions behaves very similarly to the corresponding chevron plots simulated with interactions that are partly modulated by sequence- and denaturant-dependent transfer free energies. In these essentially native-centric models, the mild chevron rollovers in the simulated folding arm are caused by occasionally populated intermediates as well as the movement of the unfolded and putative folding transition states. The strength and limitation of the models are analyzed by comparison with experiment. New formulations of sidechain models that may provide a physical account for nonnative interactions are also explored.

Effective Potentials for Folding Proteins

NASA Astrophysics Data System (ADS)

Chen, Nan-Yow; Su, Zheng-Yao; Mou, Chung-Yu

2006-02-01

A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of the wild-type sequence of protein G and may have provided important hints to the study of protein folding.

The Effect of Grain Size on the Strain Hardening Behavior for Extruded ZK61 Magnesium Alloy

NASA Astrophysics Data System (ADS)

Zhang, Lixin; Zhang, Wencong; Chen, Wenzhen; Duan, Junpeng; Wang, Wenke; Wang, Erde

2017-12-01

The effects of grain size on the tensile and compressive strain hardening behaviors for extruded ZK61 alloys have been investigated by uniaxial tensile and compressive tests along the extrusion directions. Cylindrical tension and compression specimens of extruded ZK61 alloys with various sized grain were fabricated by annealing treatments. Tensile and compressive tests at ambient temperature were conducted at a strain rate of 0.5 × 10-3 s-1. The results indicate that both tensile strain hardening and compressive strain hardening of ZK61 alloys with different grain sizes have an athermal regime of dislocation accumulation in early deformation. The threshold stress value caused dynamic recovery is predominantly related to grain size in tensile strain hardening, but the threshold stress values for different grain sizes are almost identical in compressive strain hardening. There are obvious transition points on the tensile strain hardening curves which indicate the occurrence of dynamic recrystallization (DRX). The tensile strain hardening rate of the coarse-grained alloy obviously decreases faster than that of fine-grained alloys before DRX and the tensile strain hardening curves of different grain sizes basically tend to parallel after DRX. The compressive strain hardening rate of the fine-grained alloy obviously increases faster than that of coarse-grained alloy for twin-induced strain hardening, but compressive strain hardening curves also tend to parallel after twinning is exhausted.

Radiation breakage of DNA: a model based on random-walk chromatin structure

NASA Technical Reports Server (NTRS)

Ponomarev, A. L.; Sachs, R. K.

2001-01-01

Monte Carlo computer software, called DNAbreak, has recently been developed to analyze observed non-random clustering of DNA double strand breaks in chromatin after exposure to densely ionizing radiation. The software models coarse-grained configurations of chromatin and radiation tracks, small-scale details being suppressed in order to obtain statistical results for larger scales, up to the size of a whole chromosome. We here give an analytic counterpart of the numerical model, useful for benchmarks, for elucidating the numerical results, for analyzing the assumptions of a more general but less mechanistic "randomly-located-clusters" formalism, and, potentially, for speeding up the calculations. The equations characterize multi-track DNA fragment-size distributions in terms of one-track action; an important step in extrapolating high-dose laboratory results to the much lower doses of main interest in environmental or occupational risk estimation. The approach can utilize the experimental information on DNA fragment-size distributions to draw inferences about large-scale chromatin geometry during cell-cycle interphase.

Using phase information to enhance speckle noise reduction in the ultrasonic NDE of coarse grain materials

NASA Astrophysics Data System (ADS)

Lardner, Timothy; Li, Minghui; Gachagan, Anthony

2014-02-01

Materials with a coarse grain structure are becoming increasingly prevalent in industry due to their resilience to stress and corrosion. These materials are difficult to inspect with ultrasound because reflections from the grains lead to high noise levels which hinder the echoes of interest. Spatially Averaged Sub-Aperture Correlation Imaging (SASACI) is an advanced array beamforming technique that uses the cross-correlation between images from array sub-apertures to generate an image weighting matrix, in order to reduce noise levels. This paper presents a method inspired by SASACI to further improve imaging using phase information to refine focusing and reduce noise. A-scans from adjacent array elements are cross-correlated using both signal amplitude and phase to refine delay laws and minimize phase aberration. The phase-based and amplitude-based corrected images are used as inputs to a two-dimensional cross-correlation algorithm that will output a weighting matrix that can be applied to any conventional image. This approach was validated experimentally using a 5MHz array a coarse grained Inconel 625 step wedge, and compared to the Total Focusing Method (TFM). Initial results have seen SNR improvements of over 20dB compared to TFM, and a resolution that is much higher.

Construction of continuous cooling transformation (CCT) diagram using Gleeble for coarse grained heat affected zone of SA106 grade B steel

NASA Astrophysics Data System (ADS)

Vimalan, G.; Muthupandi, V.; Ravichandran, G.

2018-05-01

A continuous cooling transformation diagram is constructed for simulated coarse grain heat affected zone (CGHAZ) of SA106 grade B carbon steel. Samples are heated to a peak temperature of 1200°C in the Gleeble thermo mechanical simulator and then cooled at different cooling rates varying from 0.1°C/s to 100°C/s. Microstructure of the specimens simulated at different cooling rates were characterised by optical microscopy and hardness was assessed by Vicker's hardness test and micro-hardness test. Transformation temperatures and the corresponding phase fields were identified from dilatometric curves and the same could be confirmed by correlating with the microstructures at room temperature. These data were used to construct the CCT diagram. Phase fields were found to have ferrite, pearlite, bainite and martensite or their combinations. With the help of this CCT diagram it is possible to predict the microstructure and hardness of coarse grain HAZ experiencing different cooling rates. The constructed CCT diagram becomes an important tool in evaluating the weldability of SA106 grade B carbon steel.

Coarse-Graining of Polymer Dynamics via Energy Renormalization

NASA Astrophysics Data System (ADS)

Xia, Wenjie; Song, Jake; Phelan, Frederick; Douglas, Jack; Keten, Sinan

The computational prediction of the properties of polymeric materials to serve the needs of materials design and prediction of their performance is a grand challenge due to the prohibitive computational times of all-atomistic (AA) simulations. Coarse-grained (CG) modeling is an essential strategy for making progress on this problem. While there has been intense activity in this area, effective methods of coarse-graining have been slow to develop. Our approach to this fundamental problem starts from the observation that integrating out degrees of freedom of the AA model leads to a strong modification of the configurational entropy and cohesive interaction. Based on this observation, we propose a temperature-dependent systematic renormalization of the cohesive interaction in the CG modeling to recover the thermodynamic modifications in the system and the dynamics of the AA model. Here, we show that this energy renormalization approach to CG can faithfully estimate the diffusive, segmental and glassy dynamics of the AA model over a large temperature range spanning from the Arrhenius melt to the non-equilibrium glassy states. Our proposed CG strategy offers a promising strategy for developing thermodynamically consistent CG models with temperature transferability.

A coarse-grained biophysical model of sequence evolution and the population size dependence of the speciation rate

PubMed Central

Khatri, Bhavin S.; Goldstein, Richard A.

2015-01-01

Speciation is fundamental to understanding the huge diversity of life on Earth. Although still controversial, empirical evidence suggests that the rate of speciation is larger for smaller populations. Here, we explore a biophysical model of speciation by developing a simple coarse-grained theory of transcription factor-DNA binding and how their co-evolution in two geographically isolated lineages leads to incompatibilities. To develop a tractable analytical theory, we derive a Smoluchowski equation for the dynamics of binding energy evolution that accounts for the fact that natural selection acts on phenotypes, but variation arises from mutations in sequences; the Smoluchowski equation includes selection due to both gradients in fitness and gradients in sequence entropy, which is the logarithm of the number of sequences that correspond to a particular binding energy. This simple consideration predicts that smaller populations develop incompatibilities more quickly in the weak mutation regime; this trend arises as sequence entropy poises smaller populations closer to incompatible regions of phenotype space. These results suggest a generic coarse-grained approach to evolutionary stochastic dynamics, allowing realistic modelling at the phenotypic level. PMID:25936759

Coarse-grained simulations of protein-protein association: an energy landscape perspective.

PubMed

Ravikumar, Krishnakumar M; Huang, Wei; Yang, Sichun

2012-08-22

Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

From point process observations to collective neural dynamics: Nonlinear Hawkes process GLMs, low-dimensional dynamics and coarse graining

PubMed Central

Truccolo, Wilson

2017-01-01

This review presents a perspective on capturing collective dynamics in recorded neuronal ensembles based on multivariate point process models, inference of low-dimensional dynamics and coarse graining of spatiotemporal measurements. A general probabilistic framework for continuous time point processes reviewed, with an emphasis on multivariate nonlinear Hawkes processes with exogenous inputs. A point process generalized linear model (PP-GLM) framework for the estimation of discrete time multivariate nonlinear Hawkes processes is described. The approach is illustrated with the modeling of collective dynamics in neocortical neuronal ensembles recorded in human and non-human primates, and prediction of single-neuron spiking. A complementary approach to capture collective dynamics based on low-dimensional dynamics (“order parameters”) inferred via latent state-space models with point process observations is presented. The approach is illustrated by inferring and decoding low-dimensional dynamics in primate motor cortex during naturalistic reach and grasp movements. Finally, we briefly review hypothesis tests based on conditional inference and spatiotemporal coarse graining for assessing collective dynamics in recorded neuronal ensembles. PMID:28336305

From point process observations to collective neural dynamics: Nonlinear Hawkes process GLMs, low-dimensional dynamics and coarse graining.

PubMed

Truccolo, Wilson

2016-11-01

This review presents a perspective on capturing collective dynamics in recorded neuronal ensembles based on multivariate point process models, inference of low-dimensional dynamics and coarse graining of spatiotemporal measurements. A general probabilistic framework for continuous time point processes reviewed, with an emphasis on multivariate nonlinear Hawkes processes with exogenous inputs. A point process generalized linear model (PP-GLM) framework for the estimation of discrete time multivariate nonlinear Hawkes processes is described. The approach is illustrated with the modeling of collective dynamics in neocortical neuronal ensembles recorded in human and non-human primates, and prediction of single-neuron spiking. A complementary approach to capture collective dynamics based on low-dimensional dynamics ("order parameters") inferred via latent state-space models with point process observations is presented. The approach is illustrated by inferring and decoding low-dimensional dynamics in primate motor cortex during naturalistic reach and grasp movements. Finally, we briefly review hypothesis tests based on conditional inference and spatiotemporal coarse graining for assessing collective dynamics in recorded neuronal ensembles. Published by Elsevier Ltd.

Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective

PubMed Central

Ravikumar, Krishnakumar M.; Huang, Wei; Yang, Sichun

2012-01-01

Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes. PMID:22947945