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

Science.gov (United States)

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.

Synthetic Aperture Focusing Technique in Ultrasonic Inspection of Coarse Grained Materials

Energy Technology Data Exchange (ETDEWEB)

Stepinski, Tadeusz (Uppsala Univ., Signals and Systems, Box 528, SE-751 20 Uppsala (Sweden))

2007-12-15

Experience from the ultrasonic inspection of nuclear power plants has shown that large focused transducers are relatively effective in suppressing grain (structure) noise. Operation of a large focused transducer can be thought of as an integration (coherent summation) of individual beams reflected from the target and received by individual points at the transducer surface. Synthetic aperture focusing technique (SAFT), in its simplest version mimics an acoustic lens used for focusing beams at a desired point in the region of interest. Thus, SAFT should be able to suppress the grain noise in the similar way as the focused transducer does. This report presents the results of investigation of SAFT algorithms applied for post-processing of ultrasonic data acquired in inspection of coarse grained metals. The performance of SAFT in terms of its spatial (cross-range) resolution and grain noise suppression is studied. The evaluation is made based on the experimental data obtained from the ultrasonic inspection of test specimens with artificial defects (side drilled holes). SAFT algorithms for both contact and immersion mode are introduced and experimentally verified

Entropies from Coarse-graining: Convex Polytopes vs. Ellipsoids

Directory of Open Access Journals (Sweden)

Nikos Kalogeropoulos

2015-09-01

Full Text Available We examine the Boltzmann/Gibbs/Shannon SBGS and the non-additive Havrda-Charvát/Daróczy/Cressie-Read/Tsallis Sq and the Kaniadakis κ-entropy Sκ from the viewpoint of coarse-graining, symplectic capacities and convexity. We argue that the functional form of such entropies can be ascribed to a discordance in phase-space coarse-graining between two generally different approaches: the Euclidean/Riemannian metric one that reflects independence and picks cubes as the fundamental cells in coarse-graining and the symplectic/canonical one that picks spheres/ellipsoids for this role. Our discussion is motivated by and confined to the behaviour of Hamiltonian systems of many degrees of freedom. We see that Dvoretzky’s theorem provides asymptotic estimates for the minimal dimension beyond which these two approaches are close to each other. We state and speculate about the role that dualities may play in this viewpoint.

Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations

Energy Technology Data Exchange (ETDEWEB)

Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai [Los Alamos National Laboratory; Hengartner, Nick [Los Alamos National Laboratory

2008-01-01

We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, 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 coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. 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 are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.

Renormalization and Coarse-graining of Loop Quantum Gravity

OpenAIRE

Charles, Christoph

2017-01-01

The continuum limit of loop quantum gravity is still an open problem. Indeed, no proper dynamics in known to start with and we still lack the mathematical tools to study its would-be continuum limit. In the present PhD dissertation, we will investigate some coarse-graining methods that should become helpful in this enterprise. We concentrate on two aspects of the theory's coarse-graining: finding natural large scale observables on one hand and studying how the dynamics of varying graphs could...

Systematic coarse-graining of the dynamics of entangled polymer melts: the road from chemistry to rheology

International Nuclear Information System (INIS)

Padding, J T; Briels, W J

2011-01-01

For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review current and past computer simulation techniques and critically assess their ability to provide such a link between chemistry and rheology. We distinguish between two classes of coarse-graining levels, which we term coarse-grained molecular dynamics (CGMD) and coarse-grained stochastic dynamics (CGSD). In CGMD the coarse-grained beads are still relatively hard, thus automatically preventing bond crossing. This also implies an upper limit on the number of atoms that can be lumped together (up to five backbone carbon atoms) and therefore on the longest chain lengths that can be studied. To reach a higher degree of coarse-graining, in CGSD many more atoms are lumped together (more than ten backbone carbon atoms), leading to relatively soft beads. In that case friction and stochastic forces dominate the interactions, and action must be undertaken to prevent bond crossing. We also review alternative methods that make use of the tube model of polymer dynamics, by obtaining the entanglement characteristics through a primitive path analysis and by simulation of a primitive chain network. We finally review super-coarse-grained methods in which an entire polymer is represented by a single particle, and comment on ways to include memory effects and transient forces. (topical review)

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

Energy Technology Data Exchange (ETDEWEB)

Grest, Gary S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

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 the 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.

Design of low-power coarse-grained reconfigurable architectures

CERN Document Server

Kim, Yoonjin

2010-01-01

Coarse-grained reconfigurable architecture (CGRA) has emerged as a solution for flexible, application-specific optimization of embedded systems. Helping you understand the issues involved in designing and constructing embedded systems, Design of Low-Power Coarse-Grained Reconfigurable Architectures offers new frameworks for optimizing the architecture of components in embedded systems in order to decrease area and save power. Real application benchmarks and gate-level simulations substantiate these frameworks.The first half of the book explains how to reduce power in the configuration cache. T

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

Science.gov (United States)

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.

Multiresolution Modeling of Semidilute Polymer Solutions: Coarse-Graining Using Wavelet-Accelerated Monte Carlo

Directory of Open Access Journals (Sweden)

Animesh Agarwal

2017-09-01

Full Text Available We present a hierarchical coarse-graining framework for modeling semidilute polymer solutions, based on the wavelet-accelerated Monte Carlo (WAMC method. This framework forms a hierarchy of resolutions to model polymers at length scales that cannot be reached via atomistic or even standard coarse-grained simulations. Previously, it was applied to simulations examining the structure of individual polymer chains in solution using up to four levels of coarse-graining (Ismail et al., J. Chem. Phys., 2005, 122, 234901 and Ismail et al., J. Chem. Phys., 2005, 122, 234902, recovering the correct scaling behavior in the coarse-grained representation. In the present work, we extend this method to the study of polymer solutions, deriving the bonded and non-bonded potentials between coarse-grained superatoms from the single chain statistics. A universal scaling function is obtained, which does not require recalculation of the potentials as the scale of the system is changed. To model semi-dilute polymer solutions, we assume the intermolecular potential between the coarse-grained beads to be equal to the non-bonded potential, which is a reasonable approximation in the case of semidilute systems. Thus, a minimal input of microscopic data is required for simulating the systems at the mesoscopic scale. We show that coarse-grained polymer solutions can reproduce results obtained from the more detailed atomistic system without a significant loss of accuracy.

Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten

Science.gov (United States)

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.

Hybrid continuum-coarse-grained modeling of erythrocytes

Science.gov (United States)

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.

The Martini Coarse-Grained Force Field

NARCIS (Netherlands)

Periole, X.; Marrink, S.J.; Monticelli, Luca; Salonen, Emppu

2013-01-01

The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical

Coarse graining flow of spin foam intertwiners

Science.gov (United States)

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.

Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model

Science.gov (United States)

Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

2017-03-01

A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.

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

Science.gov (United States)

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.

Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model

Science.gov (United States)

Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

2017-01-01

A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg–Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard–Jones fluid in the region close to the liquid–vapor critical point. The procedure is general and can be adapted to other coarse-grained models. PMID:28292890

Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

International Nuclear Information System (INIS)

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

2016-01-01

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 f 0 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 f 0 . 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.

Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

Science.gov (United States)

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.

Calibration and validation of coarse-grained models of atomic systems: application to semiconductor manufacturing

Science.gov (United States)

Farrell, Kathryn; Oden, J. Tinsley

2014-07-01

Coarse-grained models of atomic systems, created by aggregating groups of atoms into molecules to reduce the number of degrees of freedom, have been used for decades in important scientific and technological applications. In recent years, interest in developing a more rigorous theory for coarse graining and in assessing the predictivity of coarse-grained models has arisen. In this work, Bayesian methods for the calibration and validation of coarse-grained models of atomistic systems in thermodynamic equilibrium are developed. For specificity, only configurational models of systems in canonical ensembles are considered. Among major challenges in validating coarse-grained models are (1) the development of validation processes that lead to information essential in establishing confidence in the model's ability predict key quantities of interest and (2), above all, the determination of the coarse-grained model itself; that is, the characterization of the molecular architecture, the choice of interaction potentials and thus parameters, which best fit available data. The all-atom model is treated as the "ground truth," and it provides the basis with respect to which properties of the coarse-grained model are compared. This base all-atom model is characterized by an appropriate statistical mechanics framework in this work by canonical ensembles involving only configurational energies. The all-atom model thus supplies data for Bayesian calibration and validation methods for the molecular model. To address the first challenge, we develop priors based on the maximum entropy principle and likelihood functions based on Gaussian approximations of the uncertainties in the parameter-to-observation error. To address challenge (2), we introduce the notion of model plausibilities as a means for model selection. This methodology provides a powerful approach toward constructing coarse-grained models which are most plausible for given all-atom data. We demonstrate the theory and

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

Science.gov (United States)

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.

MT-ADRES: Multithreading on Coarse-Grained Reconfigurable Architecture

DEFF Research Database (Denmark)

Wu, Kehuai; Kanstein, Andreas; Madsen, Jan

2007-01-01

The coarse-grained reconfigurable architecture ADRES (Architecture for Dynamically Reconfigurable Embedded Systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi......The coarse-grained reconfigurable architecture ADRES (Architecture for Dynamically Reconfigurable Embedded Systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high......-ILP architectures achieve only low parallelism when executing partially sequential code segments, which is also known as Amdahl’s law, this paper proposes to extend ADRES to MT-ADRES (Multi-Threaded ADRES) to also exploit thread-level parallelism. On MT-ADRES architectures, the array can be partitioned in multiple...

Influence of grain structure on the deformation mechanism in martensitic shear reversion-induced Fe-16Cr-10Ni model austenitic alloy with low interstitial content: Coarse-grained versus nano-grained/ultrafine-grained structure

Energy Technology Data Exchange (ETDEWEB)

Challa, V.S.A. [Laboratory for Excellence in Advanced Steel Research, Department of Metallurgical, Materials Engineering, and Biomedical Engineering, University of Texas at El Paso, El Paso, TX 79968 (United States); Misra, R.D.K., E-mail: dmisra2@utep.edu [Laboratory for Excellence in Advanced Steel Research, Department of Metallurgical, Materials Engineering, and Biomedical Engineering, University of Texas at El Paso, El Paso, TX 79968 (United States); Somani, M.C. [Center for Advanced Steels Research, The University of Oulu, P.O. Box 4200, 90014 Oulu (Finland); Wang, Z.D. [State Key Laboratory for Rolling and Automation, Northeastern University, 3-11 Wenhua Road, Shenyang 110819 (China)

2016-04-20

Nanograined/ultrafine-grained (NG/UFG) materials characterized by high strength-high ductility combination are excellent vehicles to obtain an unambiguous understanding of deformation mechanisms vis-à-vis their coarse-grained counterparts. In this context, the innovative concept of phase reversion-induced NG/UFG structure enabled achieving high strength besides comparable ductility, for instance, in metastable austenitic stainless steels. In the phase reversion process, severe deformation of austenite at room temperature (typically ~60–80%) transforms face-centered cubic austenite (γ) to body centered cubic martensite (α′). Upon annealing, martensite reverts to austenite leading to extensive grain refinement. The objective of the present study to fundamentally understand the deformation mechanisms in NG/UFG structure in relation to that of the coarse-grained (CG) structure was accomplished by combining depth-sensing nanoscale experiments on an Fe-16Cr-10Ni model austenitic alloy conducted at different strain rates, followed by the study of structural evolution in the deformed zone using transmission electron microscopy (TEM). In the high strength NG/UFG steel (YS~585 MPa), stacking faults and nanotwins contributed to the enhanced ductility (El~35%), while in the case of low strength (YS~260 MPa) coarse-grained (CG) counterpart, ductility was also high (El~40%), but chiefly due to strain-induced martensite, which points to a clear case of grain size effect (and the corresponding level of strength). The distinct change in the deformation mechanism from stacking faults and twinning-induced plasticity (TWIP) in the NG structure to transformation-induced plasticity (TRIP) in the CG structure is elucidated in terms of austenite stability-strain energy relationship. The insights on the relationship between grain structure (and strength) and deformation mechanisms are envisaged to be important in providing a new direction for the futuristic design of high strength

Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study

International Nuclear Information System (INIS)

Yang, Delian; Wang, Qiang

2015-01-01

We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of N m monomers is uniformly divided into N segments, with the spatial position of each segment corresponding to the center-of-mass of its monomers. We use integral-equation theories suitable for the study of equilibrium properties of polymers, instead of many-chain molecular simulations, to obtain the structural and thermodynamic properties of both original and coarse-grained (CG) systems, and quantitatively examine how the effective pair potentials between CG segments and the thermodynamic properties of CG systems vary with N. Our systematic and simulation-free strategy is much faster than those using many-chain simulations, thus effectively solving the transferability problem in coarse graining, and provides the quantitative basis for choosing the appropriate N-values. It also avoids the problems caused by finite-size effects and statistical uncertainties in many-chain simulations. Taking the simple hard-core Gaussian thread model [K. S. Schweizer and J. G. Curro, Chem. Phys. 149, 105 (1990)] as the original system, we demonstrate our strategy applied to structure-based coarse graining, which is quite general and versatile, and compare in detail the various integral-equation theories and closures for coarse graining. Our numerical results show that the effective CG potentials for various N and closures can be collapsed approximately onto the same curve, and that structure-based coarse graining cannot give thermodynamic consistency between original and CG systems at any N < N m

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

Directory of Open Access Journals (Sweden)

Peter Spijker

2010-06-01

Full Text Available Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.

Coarse-grain modelling of protein-protein interactions

NARCIS (Netherlands)

Baaden, Marc; Marrink, Siewert J.

2013-01-01

Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are

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

OpenAIRE

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

2011-01-01

We investigate how various coarse-graining 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 th...

Parametrizing coarse grained models for molecular systems at equilibrium

KAUST Repository

Kalligiannaki, Evangelia; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plechá č, P.; Harmandaris, V.

2016-01-01

Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing 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 graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

Parametrizing coarse grained models for molecular systems at equilibrium

KAUST Repository

Kalligiannaki, Evangelia

2016-10-18

Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing 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 graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

The Coarse-Grained/Fine-Grained Logic Interface in FPGAs with Embedded Floating-Point Arithmetic Units

Directory of Open Access Journals (Sweden)

Chi Wai Yu

2008-01-01

Full Text Available This paper examines the interface between fine-grained and coarse-grained programmable logic in FPGAs. Specifically, it presents an empirical study that covers the location, pin arrangement, and interconnect between embedded floating point units (FPUs and the fine-grained logic fabric in FPGAs. It also studies this interface in FPGAs which contain both FPUs and embedded memories. The results show that (1 FPUs should have a square aspect ratio; (2 they should be positioned near the center of the FPGA; (3 their I/O pins should be arranged around all four sides of the FPU; (4 embedded memory should be located between the FPUs; and (5 connecting higher I/O density coarse-grained blocks increases the demand for routing resources. The hybrid FPGAs with embedded memory required 12% wider channels than the case where embedded memory is not used.

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

International Nuclear Information System (INIS)

Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plecháč, Petr

2016-01-01

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 entirely 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.

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

Energy Technology Data Exchange (ETDEWEB)

Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Katsoulakis, Markos, E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts at Amherst (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware (United States)

2016-06-01

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 entirely 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.

Comparison of coarse-grained (MARTINI) and atomistic molecular ...

Indian Academy of Sciences (India)

Rajat Desikan

as the root mean square deviation (RMSD) histograms and the inner pore radius profiles from ... ever coarse-grained simulations of membrane-proteins ..... from the MARTINI simulations show greater fluctuations than the all-atom simulations.

Coarse grainings and irreversibility in quantum field theory

International Nuclear Information System (INIS)

Anastopoulos, C.

1997-01-01

In this paper we are interested in studying coarse graining in field theories using the language of quantum open systems. Motivated by the ideas of Hu and Calzetta on correlation histories we employ the Zwanzig projection technique to obtain evolution equations for relevant observables in self-interacting scalar field theories. Our coarse-graining operation consists in concentrating solely on the evolution of the correlation functions of degree less than n, a treatment which corresponds to the familiar truncation of the BBKGY hierarchy at the nth level. We derive the equations governing the evolution of mean-field and two-point functions thus identifying the terms corresponding to dissipation and noise. We discuss possible applications of our formalism, the emergence of classical behavior, and the connection to the decoherent histories framework. copyright 1997 The American Physical Society

Coarse grained model for semiquantitative lipid simulations

NARCIS (Netherlands)

Marrink, SJ; de Vries, AH; Mark, AE

2004-01-01

This paper describes the parametrization of a new coarse grained (CG) model for lipid and surfactant systems. Reduction of the number of degrees of freedom together with the use of short range potentials makes it computationally very efficient. Compared to atomistic models a gain of 3-4 orders of

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

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

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 level 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.

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

International Nuclear Information System (INIS)

Zavadlav, Julija; Praprotnik, Matej; Melo, Manuel N.; Marrink, Siewert J.

2015-01-01

Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties

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

Science.gov (United States)

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 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.

FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

KAUST Repository

Harmandaris, Vagelis

2017-10-03

The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

Multiscale Modeling at Nanointerfaces: Polymer Thin Film Materials Discovery via Thermomechanically Consistent Coarse Graining

Science.gov (United States)

Hsu, David D.

Due to high nanointerfacial area to volume ratio, the properties of "nanoconfined" polymer thin films, blends, and composites become highly altered compared to their bulk homopolymer analogues. Understanding the structure-property mechanisms underlying this effect is an active area of research. However, despite extensive work, a fundamental framework for predicting the local and system-averaged thermomechanical properties as a function of configuration and polymer species has yet to be established. Towards bridging this gap, here, we present a novel, systematic coarse-graining (CG) method which is able to capture quantitatively, the thermomechanical properties of real polymer systems in bulk and in nanoconfined geometries. This method, which we call thermomechanically consistent coarse-graining (TCCG), is a two-bead-per-monomer CG hybrid approach through which bonded interactions are optimized to match the atomistic structure via the Iterative Boltzmann Inversion method (IBI), and nonbonded interactions are tuned to macroscopic targets through parametric studies. We validate the TCCG method by systematically developing coarse-grain models for a group of five specialized methacrylate-based polymers including poly(methyl methacrylate) (PMMA). Good correlation with bulk all-atom (AA) simulations and experiments is found for the temperature-dependent glass transition temperature (Tg) Flory-Fox scaling relationships, self-diffusion coefficients of liquid monomers, and modulus of elasticity. We apply this TCCG method also to bulk polystyrene (PS) using a comparable coarse-grain CG bead mapping strategy. The model demonstrates chain stiffness commensurate with experiments, and we utilize a density-correction term to improve the transferability of the elastic modulus over a 500 K range. Additionally, PS and PMMA models capture the unexplained, characteristically dissimilar scaling of Tg with the thickness of free-standing films as seen in experiments. Using vibrational

MT-ADRES: multi-threading on coarse-grained reconfigurable architecture

DEFF Research Database (Denmark)

Wu, Kehuai; Kanstein, Andreas; Madsen, Jan

2008-01-01

The coarse-grained reconfigurable architecture ADRES (architecture for dynamically reconfigurable embedded systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi......The coarse-grained reconfigurable architecture ADRES (architecture for dynamically reconfigurable embedded systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high......-ILP architectures achieve only low parallelism when executing partially sequential code segments, which is also known as Amdahl's law, this article proposes to extend ADRES to MT-ADRES (multi-threaded ADRES) to also exploit thread-level parallelism. On MT-ADRES architectures, the array can be partitioned...

Superplastic behavior of coarse-grained aluminum alloys

NARCIS (Netherlands)

Chezan, AR; De Hosson, JTM

2005-01-01

In this paper we concentrate on the superplastic behavior and the microstructural evolution of two coarse-grained Al alloys: Al-4.4w/oMg and Al-4.4w/oMg-0.4w/oCu. The values for the strain rate sensitivity index and activation energy suggest that solute drag on dislocation motion is an important

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

Science.gov (United States)

Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

2018-01-01

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Martini Coarse-Grained Force Field : Extension to Carbohydrates

NARCIS (Netherlands)

Lopez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Huenenberger, Philippe H.; Marrink, Siewert J.

2009-01-01

We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The

Coupling a nano-particle with isothermal fluctuating hydrodynamics: Coarse-graining from microscopic to mesoscopic dynamics

Energy Technology Data Exchange (ETDEWEB)

Español, Pep [Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid (Spain); Donev, Aleksandar [Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid (Spain); Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012 (United States)

2015-12-21

We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables, we select the position of the nanoparticle and the total mass and momentum density field of the fluid, which are locally conserved slow variables because they are defined to include the contribution of the nanoparticle. The theory of coarse graining based on the Zwanzing projection operator leads us to a system of stochastic ordinary differential equations that are closed in the relevant variables. We demonstrate that our discrete coarse-grained equations are consistent with a Petrov-Galerkin finite-element discretization of a system of formal stochastic partial differential equations which resemble previously used phenomenological models based on fluctuating hydrodynamics. Key to this connection between our “bottom-up” and previous “top-down” approaches is the use of the same dual orthogonal set of linear basis functions familiar from finite element methods (FEMs), both as a way to coarse-grain the microscopic degrees of freedom and as a way to discretize the equations of fluctuating hydrodynamics. Another key ingredient is the use of a “linear for spiky” weak approximation which replaces microscopic “fields” with a linear FE interpolant inside expectation values. For the irreversible or dissipative dynamics, we approximate the constrained Green-Kubo expressions for the dissipation coefficients with their equilibrium averages. Under suitable approximations, we obtain closed approximations of the coarse-grained dynamics in a manner which gives them a clear physical interpretation and provides explicit microscopic expressions for all of the coefficients appearing in the closure. Our work leads to a model for dilute nanocolloidal suspensions that can be simulated effectively using feasibly short molecular dynamics

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Martini Coarse-Grained Force Field : Extension to RNA

NARCIS (Netherlands)

Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Marrink, Siewert J.; Faustino, Ignacio

2017-01-01

RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain

Deformation bands in ⟨120⟩ grains in coarse-grained aluminium

DEFF Research Database (Denmark)

Bilde-Sørensen, Jørgen

1986-01-01

Coarse-grained aluminium, deformed in tension to a strain of 0.05, was examined in a scanning electron microscope by channelling contrast. Pronounced bands with a width typically of the order of 200 μm were found in some grains with an orientation close to [120]. When observed on surfaces close......)[011](111) and (a/2)[011](111). The Schmid factor for the highest stressed secondary systems has a local minimum of 0.245 at [120]. The application of Frank's equation shows that the only boundaries without long-range stresses that can be formed by combination of the two sets of dislocations, (a/2)- [011...

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

Science.gov (United States)

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.

The Andatza coarse-grained turbidite system (westernmost Pyrenees: Stratigraphy, sedimentology and structural control

Directory of Open Access Journals (Sweden)

A. Bodego

2017-06-01

Full Text Available This is a field-based work that describes the stratigraphy and sedimentology of the Andatza Conglomerate Formation. Based on facies analysis three facies associations of a coarse-grained turbidite system and the related slope have been identified: (1 an inner fan of a turbidite system (or canyon and (2 a low- and (3 a high-gradient muddy slope respectively. The spatial distribution of the facies associations and the palaeocurrent analysis allow to interpret a depositional model for the Andatza Conglomerates consisting of an L-shaped, coarse-grained turbidite system, whose morphology was structurally controlled by synsedimentary basement-involved normal faults. The coarse-grained character of the turbidite system indicates the proximity of the source area, with the presence of a narrow shelf that fed the turbidite canyon from the north.

Exact CTP renormalization group equation for the coarse-grained effective action

International Nuclear Information System (INIS)

Dalvit, D.A.; Mazzitelli, F.D.

1996-01-01

We consider a scalar field theory in Minkowski spacetime and define a coarse-grained closed time path (CTP) effective action by integrating quantum fluctuations of wavelengths shorter than a critical value. We derive an exact CTP renormalization group equation for the dependence of the effective action on the coarse-graining scale. We solve this equation using a derivative expansion approach. Explicit calculation is performed for the λφ 4 theory. We discuss the relevance of the CTP average action in the study of nonequilibrium aspects of phase transitions in quantum field theory. copyright 1996 The American Physical Society

Measuring Crack Length in Coarse Grain Ceramics

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

Vögele, Martin [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany); Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M. (Germany); Holm, Christian; Smiatek, Jens, E-mail: smiatek@icp.uni-stuttgart.de [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany)

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 are 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.

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

International Nuclear Information System (INIS)

Vögele, Martin; Holm, Christian; Smiatek, Jens

2015-01-01

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 are 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

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.

Science.gov (United States)

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.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

Science.gov (United States)

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.

Loop overhead reduction techniques for coarse grained reconfigurable architectures

NARCIS (Netherlands)

Vadivel, K.; Wijtvliet, M.; Jordans, R.; Corporaal, H.

2017-01-01

Due to their flexibility and high performance, Coarse Grained Reconfigurable Array (CGRA) are a topic of increasing research interest. However, CGRAs also have the potential to achieve very high energy efficiency in comparison to other reconfigurable architectures when hardware optimizations are

Hierarchical coarse-graining transform.

Science.gov (United States)

Pancaldi, Vera; King, Peter R; Christensen, Kim

2009-03-01

We present a hierarchical transform that can be applied to Laplace-like differential equations such as Darcy's equation for single-phase flow in a porous medium. A finite-difference discretization scheme is used to set the equation in the form of an eigenvalue problem. Within the formalism suggested, the pressure field is decomposed into an average value and fluctuations of different kinds and at different scales. The application of the transform to the equation allows us to calculate the unknown pressure with a varying level of detail. A procedure is suggested to localize important features in the pressure field based only on the fine-scale permeability, and hence we develop a form of adaptive coarse graining. The formalism and method are described and demonstrated using two synthetic toy problems.

A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

Energy Technology Data Exchange (ETDEWEB)

Markutsya, Sergiy [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Lamm, Monica H., E-mail: mhlamm@iastate.edu [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011 (United States)

2014-11-07

We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

International Nuclear Information System (INIS)

Markutsya, Sergiy; Lamm, Monica H.

2014-01-01

We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems

Free-energy coarse-grained potential for C60

International Nuclear Information System (INIS)

Edmunds, D. M.; Tangney, P.; Vvedensky, D. D.; Foulkes, W. M. C.

2015-01-01

We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C 60 . Potentials generated from this approach exhibit a strong temperature dependence and produce excellent agreement with benchmark fully atomistic molecular dynamics simulations. Parameter sets for analytical fits to this potential are provided at four different temperatures

Shear localization and microstructure in coarse grained beta titanium alloy

Energy Technology Data Exchange (ETDEWEB)

Wang, Bingfeng, E-mail: biw009@ucsd.edu [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China); School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Department of Mechanical and Aerospace Engineering, University of California, San Diego, United States of America (United States); Key Lab of Nonferrous Materials, Ministry of Education, Central South University, Changsha, Hunan (China); Wang, Xiaoyan [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China); School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Li, Zezhou [Department of Mechanical and Aerospace Engineering, University of California, San Diego, United States of America (United States); Ma, Rui [School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Zhao, Shiteng [Department of Mechanical and Aerospace Engineering, University of California, San Diego, United States of America (United States); Xie, Fangyu [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China); School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Zhang, Xiaoyong [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China)

2016-01-15

Adiabatic shear localization plays an important role in the deformation and failure of the coarse grained beta titanium alloy Ti-5 Al-5 Mo-5 V-1 Cr-1 Fe with grain size about 1 mm at high strain rate deformation. Hat shaped specimens with different nominal shear strains are used to induce the formation of shear bands under the controlled shock-loading experiments. The true stress in the specimens can reach about 1040 MPa where the strain is about 1.83. The whole shear localization process lasts about 35 μs. The microstructures within the shear band are investigated by optical microscopy, scanning electron microscopy / electron backscatter diffraction, and transmission electron microscopy. The results show that the width of the shear bands decreases with increasing nominal shear strain, and the grains in the transition region near the shear band are elongated along the shear band, and the core of the shear band consists of the ultrafine deformed grains with width of 0.1 μm and heavy dislocations. With the aims of accommodating the imposed shear strain and maintaining neighboring grain compatibility, the grain subdivision continues to take place within the band. A fiber texture is formed in the core of the shear band. The calculated temperature rise in the shear band can reach about 722 K. Dynamic recovery is responsible for the formation of the microstructure in coarse grained beta titanium alloy.

Time evolution as refining, coarse graining and entangling

International Nuclear Information System (INIS)

Dittrich, Bianca; Steinhaus, Sebastian

2014-01-01

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. (paper)

Time evolution as refining, coarse graining and entangling

Science.gov (United States)

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.

Boltzmann rovibrational collisional coarse-grained model for internal energy excitation and dissociation in hypersonic flows.

Science.gov (United States)

Munafò, A; Panesi, M; Magin, T E

2014-02-01

A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N(2)-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N(2) molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models.

The random phase transducer in ultrasonic NDT of coarse grain stainless steel

International Nuclear Information System (INIS)

Bordier, J.M.; Fink, M.; Le Brun, A.; Cohen-Tenoudji, F.

1993-11-01

Ultrasonic NDT of cast stainless steel is known to be difficult due to a huge loss of focussing of the ultrasonic beam, and to a high level speckle noise generated by the coarse grain structure. In this paper, we describe the principle of the ultrasonic random phase transducer. Experimental results are compared with those obtained with a standard spatial compound technique. We show that the random phase transducer is a good tool to characterize the multiple scattering process generated by these materials. (authors). 7 figs., 11 refs

Coarse-graining complex dynamics

DEFF Research Database (Denmark)

Sibani, Paolo

2013-01-01

Continuous Time Random Walks (CTRW) are widely used to coarse-grain the evolution of systems jumping from a metastable sub-set of their configuration space, or trap, to another via rare intermittent events. The multi-scaled behavior typical of complex dynamics is provided by a fat...... macroscopic variables all produce identical long time relaxation behaviors. Hence, CTRW shed no light on the link between microscopic and macroscopic dynamics. We then highlight how a more recent approach, Record Dynamics (RD) provides a viable alternative, based on a very different set of physical ideas......: while CTRW make use of a renewal process involving identical traps of infinite size, RD embodies a dynamical entrenchment into a hierarchy of traps which are finite in size and possess different degrees of meta-stability. We show in particular how RD produces the stretched exponential, power...

Information Theoretic Tools for Parameter Fitting in Coarse Grained Models

KAUST Repository

Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plechac, Petr

2015-01-01

We study the application of information theoretic tools for model reduction in the case of systems driven by stochastic dynamics out of equilibrium. The model/dimension reduction is considered by proposing parametrized coarse grained dynamics

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

Energy Technology Data Exchange (ETDEWEB)

Limmer, David T., E-mail: dlimmer@princeton.edu [Princeton Center for Theoretical Science, Princeton University, Princeton, New Jersey 08540 (United States); Chandler, David [Department of Chemistry, University of California, Berkeley, California 94609 (United States)

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

Limmer, David T.; Chandler, David

2014-01-01

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

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

Science.gov (United States)

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.

Variational approach to coarse-graining of generalized gradient flows

NARCIS (Netherlands)

Duong, M.H.; Lamacz, A.; Peletier, M.A.; Sharma, U.

2017-01-01

In this paper we present a variational technique that handles coarse-graining and passing to a limit in a unified manner. The technique is based on a duality structure, which is present in many gradient flows and other variational evolutions, and which often arises from a large-deviations principle.

Coarse-grained debris flow dynamics on erodible beds

Science.gov (United States)

Lanzoni, Stefano; Gregoretti, Carlo; Stancanelli, Laura Maria

2017-03-01

A systematic set of flume experiments is used to investigate the features of velocity profiles within the body of coarse-grained debris flows and the dependence of the transport sediment concentration on the relevant parameters (runoff discharge, bed slope, grain size, and form). The flows are generated in a 10 m long laboratory flume, initially filled with a layer consisting of loose debris. After saturation, a prescribed water discharge is suddenly supplied over the granular bed, and the runoff triggers a debris flow wave that reaches nearly steady conditions. Three types of material have been used in the tests: gravel with mean grain size of 3 and 5 mm, and 3 mm glass spheres. Measured parameters included: triggering water discharge, volumetric sediment discharge, sediment concentration, flow depth, and velocity profiles. The dynamic similarity with full-sized debris flows is discussed on the basis of the relevant dimensionless parameters. Concentration data highlight the dependence on the slope angle and the importance of the quasi-static friction angle. The effects of flow rheology on the shape of velocity profiles are analyzed with attention to the role of different stress-generating mechanisms. A remarkable collapse of the dimensionless profiles is obtained by scaling the debris flow velocity with the runoff velocity, and a power law characterization is proposed following a heuristic approach. The shape of the profiles suggests a smooth transition between the different rheological regimes (collisional and frictional) that establish in the upper and lower regions of the flow and is compatible with the presence of multiple length scales dictated by the type of contacts (instantaneous or long lasting) between grains.

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

Science.gov (United States)

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.

Network topology exploration of mesh-based coarse-grain reconfigurable architectures

NARCIS (Netherlands)

Bansal, N.; Gupta, S.; Dutt, N.D.; Nicolau, A.; Gupta, R.

2004-01-01

Several coarse-grain reconfigurable architectures proposed recently consist of a large number of processing elements (PEs) connected in a mesh-like network topology. We study the effects of three aspects of network topology exploration on the performance of applications on these architectures: (a)

Coarse Grained Transport Model for Neutrals in Turbulent SOL Plasmas

Energy Technology Data Exchange (ETDEWEB)

Marandet, Y.; Mekkaoui, A.; Genesio, P.; Rosato, J.; Capes, H.; Godbert-Mouret, L.; Koubiti, M.; Stamm, R., E-mail: yannick.marandet@univ-amu.fr [PIIM, CNRS/Aix-Marseille University, Marseille (France); Reiter, D.; Boerner, P. [IEK4, FZJ, Juelich (Germany)

2012-09-15

Full text: Edge plasmas of magnetic fusion devices exhibit strong intermittent turbulence, which governs perpendicular transport of particles and heat. Turbulent fluxes result from the coarse graining procedure used to derive the transport equation, which entails time averaging of the underlying equations governing the turbulent evolution of the electron and ion fluids. In previous works, we have pointed out that this averaging is not carried out on the Boltzmann equation that describes the transport of neutral particles (atoms, molecules) in current edge code suites (such as SOLPS). Since fluctuations in the far SOL are of order unity, calculating the transport of neutral particles, hence the source terms in plasma fluid equations, in the average plasma background might lead to misleading results. In particular, retaining the effects of fluctuations could affect the estimation of the importance of main chamber recycling, hence first wall sputtering by charge exchange atoms, as well as main chamber impurity contamination and transport. In this contribution, we obtain an exact coarse-grained equation for the average neutral density, assuming that density fluctuations are described by multivariate Gamma statistics. This equation is a scattering free Boltzmann equation, where the ionization rate has been renormalized to account for fluctuations. The coarse grained transport model for neutrals has been implemented in the EIRENE code, and applications in 2D geometry with ITER relevant plasma parameters are presented. Our results open the way for the implementation of the effects of turbulent fluctuations on the transport of neutral particles in coupled plasma/neutral edge codes like B2-EIRENE. (author)

Improved Parameters for the Martini Coarse-Grained Protein Force Field

NARCIS (Netherlands)

de Jong, Djurre H.; Singh, Gurpreet; Bennett, W. F. Drew; Arnarez, Clement; Wassenaar, Tsjerk A.; Schafer, Lars V.; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.

The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too

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

Science.gov (United States)

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.

Microstructure-grain orientation relationship in coarse grain nickel cold-rolled to large strain

International Nuclear Information System (INIS)

Chen, H.S.; Godfrey, A.; Hansen, N.; Xie, J.X.; Liu, Q.

2008-01-01

The relationship between crystallographic orientation and the deformation microstructure formed during cold-rolling to high strains (up to ε vM = 4.5) has been investigated. The starting material was Ni (99.96% purity) with a coarse initial average grain size (approximately 500 μm). Microstructural characterization was carried out using a combination of electron channeling contrast imaging and electron back-scatter diffraction orientation mapping. An orientation dependence of the deformation microstructure was observed even at the highest strain examined. A large increase in the average boundary misorientation is found at strains above ε vM = 1.8 for regions with the {1 1 2} and {1 2 3} orientations. This increase accompanies the structural transition from a medium strain microstructure to a high strain lamellar microstructure. In contrast, the average misorientation in regions of {1 1 0} orientation increases only slowly even up to the highest strain examined

A Snapshot of Present Research at AAU and DTU on Large-Diameter Piles in Coarse-Grained Materials

DEFF Research Database (Denmark)

Leth, C. T.; Sørensen, Søren Peder Hyldal; Klinkvort, Rasmus Tofte

2012-01-01

are developed for piles with diameters up to approximately 2.0 m and are based on a very limited number of tests. Hence, the method has not been validated for piles with diameters of 4 to 6 m. During the last six years extensive studies on non-slender large-diameter piles in coarse-grained material have been...... conducted at Aalborg University (AAU) and at the Technical University of Denmark (DTU). The piles have been investigated by means of physical and numerical modelling. The former consists of both centrifuge tests and tests in a so-called pressure tank (1G tests but with an applied overburden pressure......). The goal of the work has been to investigate the general behaviour of monopiles for nowadays offshore wind turbines and to revise the p-y curves for piles in sand in order to account for diameter on the response of monopiles subjected to both static and cyclic loads. The paper summarizes and compares...

Mineral Elements Content of some Coarse Grains used as staple ...

African Journals Online (AJOL)

Analysis of mineral elements were carried out on some coarse grains used as staple food in Kano metropolis. The levels of Magnesium, Calcium, Manganese, Iron, Copper and Zinc were determined using atomic absorption spectrophotometer (AAS), and that of Sodium and Potassium were obtained using flame photometer ...

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

Science.gov (United States)

Shen, Lin; Yang, Weitao

2016-04-12

We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

The MARTINI force field : Coarse grained model for biomolecular simulations

NARCIS (Netherlands)

Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge; Tieleman, D. Peter; de Vries, Alex H.

2007-01-01

We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To

The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

International Nuclear Information System (INIS)

Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plecháč, Petr

2015-01-01

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 graining 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

The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

Energy Technology Data Exchange (ETDEWEB)

Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware 19716 (United States)

2015-08-28

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 graining 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.

An exactly solvable coarse-grained model for species diversity

Science.gov (United States)

Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

2012-07-01

We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

An exactly solvable coarse-grained model for species diversity

International Nuclear Information System (INIS)

Suweis, Samir; Maritan, Amos; Rinaldo, Andrea

2012-01-01

We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth–death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology. (paper)

Radon diffusion through sandy construction materials: effect of temperature and grain size

International Nuclear Information System (INIS)

Narula, A.K.; Goyal, S.K.; Jain, Ravinder; Kant, Krishan; Yadav, Mani Kant; Chauhan, R.P.; Chakarvarti, S.K.

2013-01-01

Radon appears mainly by diffusion process from the point of origin, say, under ground soil and building materials used in construction of house following alpha decay of radium. The radon diffusion through different building construction materials can be compared by calculating radon diffusion coefficient for them. In the present work, we studied the effect of temperature and grain size on radon diffusion of coarse sand as construction material. The coarse sand was collected from Yamuna river bed, originated from Himalayas. For this study, a steel pipe of diameter 10 cm and length 30 cm., divided into four sectors of equal size, was filled in different sectors with different grain sized (800, 600 and 425 μm) sand as building construction material. A number LR-115 type-II particle track detectors were placed with inter-detector distance of 10 cm in the sectorial compartments. The bottom end of steel pipe assembly was fixed with a radon chamber containing radon source with upper end sealed with a cap. The whole arrangement was then placed into a sand-clay pipe wrapped around by a controlled heating filament, resulting into temperature variations from 25℃ to 60℃. After 100 days interval, the detectors were retrieved processed, and the α - tracks counted for the calculation of radon concentration. It is observed that the radon diffusion coefficient increases with the increase in temperature and decreases with decrease in grain size of the coarse sand. (author)

Multiscale coarse-graining of the protein energy landscape.

Directory of Open Access Journals (Sweden)

Ronald D Hills

2010-06-01

Full Text Available A variety of coarse-grained (CG models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states.

Making coarse grained polymer simulations quantitatively predictive for statics and dynamics

Science.gov (United States)

Kremer, Kurt

2010-03-01

By combining input from short simulation runs of rather small systems with all atomistic details together with properly adapted coarse grained models we are able quantitatively predict static and especially dynamical properties of both pure polymer melts of long fully entangled but also of systems with low molecular weight additives. Comparisons to rather different experiments such as diffusion constant measurements or NMR relaxation experiments show a remarkable quantitative agreement without any adjustable parameter. Reintroduction of chemical details into the coarse grained trajectories allows the study of long time trajectories in all atomistic detail providing the opportunity for rather different means of data analysis. References: V. Harmandaris, K. Kremer, Macromolecules, in press (2009) V. Harmandaris et al, Macromolecules, 40, 7026 (2007) B. Hess, S. Leon, N. van der Vegt, K. Kremer, Soft Matter 2, 409 (2006) D. Fritz et al, Soft Matter 5, 4556 (2009)

Implementing Non Power-of-Two FFTs on Coarse-Grain Reconfigurable Architectures

NARCIS (Netherlands)

Rivaton, Arnaud; Quevremont, Jérôme; Zhang, Q.; Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Nurmi, J.; Takala, J.; Hamalainen, T.D.

2005-01-01

To improve power figures of a dual ARM9 RISC core architecture targeting low-power digital broadcasting applications, the addition of a coarse-grain architecture is considered. This paper introduces two of these structures: PACT's XPP technology and the Montium, developed by the University of

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

Science.gov (United States)

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.

Flow structure of coarse-grained slurry in a horizontal pipe

Czech Academy of Sciences Publication Activity Database

Vlasák, Pavel; Kysela, Bohuš; Chára, Zdeněk

2012-01-01

Roč. 60, č. 2 (2012), s. 115-124 ISSN 0042-790X R&D Projects: GA ČR GAP105/10/1574 Institutional research plan: CEZ:AV0Z20600510 Keywords : coarse-grained slurry * turbulent flow * pressure drop * velocity distribution * flow structure * concentration effect Subject RIV: BK - Fluid Dynamics Impact factor: 0.653, year: 2012

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Short- and medium-term response to storms on three Mediterranean coarse-grained beaches

Science.gov (United States)

Grottoli, Edoardo; Bertoni, Duccio; Ciavola, Paolo

2017-10-01

The storm response of three Italian coarse-grained beaches was investigated to better understand the morphodynamics of coarse-clastic beaches in a microtidal context. Two of the studied sites are located on the eastern side of the country (Portonovo and Sirolo) and the third one (Marina di Pisa) is on the western side. Portonovo and Sirolo are mixed sand and gravel beaches where the storms approach from two main directions, SE and NE. Marina di Pisa is a coarse-grained, gravel-dominated beach, exposed to storms driven by SW winds. Gravel nourishments were undertaken in recent years on the three sites. Beach topography was monitored measuring the same network of cross sections at a monthly (i.e. short-term) to seasonal frequency (i.e. medium-term). Geomorphic changes were examined before and after storm occurrences by means of profile analyses and shoreline position evaluations. The beach orientation and the influence of hard structures are the main factors controlling the transport and accumulation of significant amount of sediments and the consequent high variability of beach morphology over the medium-term. For Marina di Pisa, storms tend to accumulate material towards the upper part of the beach with no shoreline rotation and no chance to recover the initial configuration. Sirolo and Portonovo showed a similar behaviour that is more typical of pocket beaches. Both beaches show shoreline rotation after storms in a clockwise or counter-clockwise direction according to the incoming wave direction. The wider and longer beach at Sirolo allows the accumulation of a thin layer of sediment during storms, rather than at Portonovo where, given its longshore and landward boundaries, the beach material tends to accumulate in greater thickness. After storms, Sirolo and especially Portonovo can quickly recover the initial beach configuration, as soon as another storm of comparable energy approaches from the opposite direction of the previous one. Large morphological

Systematic hierarchical coarse-graining with the inverse Monte Carlo method

Energy Technology Data Exchange (ETDEWEB)

Lyubartsev, Alexander P., E-mail: alexander.lyubartsev@mmk.su.se [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); Naômé, Aymeric, E-mail: aymeric.naome@unamur.be [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); UCPTS Division, University of Namur, 61 Rue de Bruxelles, B 5000 Namur (Belgium); Vercauteren, Daniel P., E-mail: daniel.vercauteren@unamur.be [UCPTS Division, University of Namur, 61 Rue de Bruxelles, B 5000 Namur (Belgium); Laaksonen, Aatto, E-mail: aatto@mmk.su.se [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); Science for Life Laboratory, 17121 Solna (Sweden)

2015-12-28

We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730–3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile.

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

Science.gov (United States)

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.

Abrasion and algal fouling of coarse material on the Murman littoral

Directory of Open Access Journals (Sweden)

Malavenda S. V.

2017-03-01

Full Text Available On the Murmansk coast of the Barents Sea the boulder littoral zone is widely spread mostly covered by Fucus communities. This is one of the most productive benthic communities of the Barents Sea. The studies of intertidal communities have the long history, but the dynamics of intertidal ecosystems due to surf and storms is not clear. The goal of the work is to identify the leading factors that determine the rate of abrasion of coarse material and fouling algae-macrophytes of the intertidal zone of Murman. The study has been conducted in the Zelenetskaya Bay of the Barents Sea on the basis of the biological station of the MMBI KSC RAS. The rate of abrasion has been carried out during 2004–2013, phyto-overgrowing – 2009–2013. In three pilot landfills 12 samples of coarse material have been exposed during the year (from July to next July. The weight change of the sample as well as species composition and biomass of algae of fouling communities have been investigated. The influence of the surf intensity, temperature of water and air has been analyzed (univariate analysis of variance ANOVA has been applied. It has been shown that on the littoral of the Murmansk coast the abrasion of coarse material is determined primarily by the number of storms, so the storm rate has been proposed. It has been revealed that the density of fouling boulders with macroalgae depends primarily on the intensity of the surf and the average gradient of air temperature. The basis for the emerging communities of annual species are green (Acrosiphonia arcta, Blidingia minima, Spongomorpha aeruginosa and brown algae (Pylaiella littoralis, Dictyosiphon chordaria. These algae groups are found everywhere in Fucus communities of the boulder intertidal zone of the Murman coast and probably they are the intermediate stage of fouling the coarse-grained material

Classical density functional theory & simulations on a coarse-grained model of aromatic ionic liquids.

Science.gov (United States)

Turesson, Martin; Szparaga, Ryan; Ma, Ke; Woodward, Clifford E; Forsman, Jan

2014-05-14

A new classical density functional approach is developed to accurately treat a coarse-grained model of room temperature aromatic ionic liquids. Our major innovation is the introduction of charge-charge correlations, which are treated in a simple phenomenological way. We test this theory on a generic coarse-grained model for aromatic RTILs with oligomeric forms for both cations and anions, approximating 1-alkyl-3-methyl imidazoliums and BF₄⁻, respectively. We find that predictions by the new density functional theory for fluid structures at charged surfaces are very accurate, as compared with molecular dynamics simulations, across a range of surface charge densities and lengths of the alkyl chain. Predictions of interactions between charged surfaces are also presented.

Potential of ultrafine grained materials as high performance penetrator materials

Directory of Open Access Journals (Sweden)

Lee C.S.

2012-08-01

Full Text Available The shear formability and the metal jet formability are important for the kinetic energy penetrator and the chemical energy penetrator, respectively. The shear formability of ultrafine grained (UFG steel was examined, mainly focusing on the effects of the grain shape on the shear characteristics. For this purpose, UFG 4130 steel having the different UFG structures, the lamellar UFG and the equiaxed UFG, was prepared by equal channel angular pressing (ECAP. The lamellar UFG steel exhibited more sharper and localized shear band formation than the equiaxed UFG steel. This is because a lamellar UFG structure was unfavourable against grain rotation which is a main mechanism of the band propagation in UFG materials. Meanwhile, the metal jet formability of UFG OFHC Cu also processed by ECAP was compared to that of coarse grained (CG one by means of dynamic tensile extrusion (DTE tests. CG OFHC Cu exhibited the higher DTE ductility, i.e. better metal jet stability, than UFG OFHC Cu. The initial high strength and the lack of strain hardenability of UFG OFHC Cu were harmful to the metal jet formability.

Lessons Learned from Designing the Montium a Coarse-Grained Reconfigurable Processing Tile

NARCIS (Netherlands)

Smit, Gerardus Johannes Maria; Heysters, P.M.; Rosien, M.A.J.; Molenkamp, Egbert

2004-01-01

In this paper we describe in retrospective the main results of a four year project, called Chameleon. As part of this project we developed a coarse-grained reconfigurable core for DSP algorithms in wirelessdevices denoted MONTIUM. After presenting the main achievements within this project we present

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

Directory of Open Access Journals (Sweden)

Daehyeon Kim

2014-02-01

Full Text Available 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.

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

Science.gov (United States)

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.

Optimization of droplets for UV-NIL using coarse-grain simulation of resist flow

Science.gov (United States)

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.

Effect of cooling rates on the weld heat affected zone coarse grain microstructure

Directory of Open Access Journals (Sweden)

Roman Celin

2018-04-01

Full Text Available The effect of a cooling rate on the S690Q quenched and tempered steel welded joint coarse grain heat affected zone microstructure was investigated using a dilatometer with controlled heating and cooling fixture. Steel samples were heated to a peak temperature of 1350 °C and cooled at the different cooling time Dt8/5. A dilatometric analysis and hardness measurements of the simulated thermal cycle coarse grain samples were done. Transformation start and finish temperature were determined using dilatation vs. temperature data analysis. The microstructure of the sample with a cooling time 5 s consists of martensite, whereas at cooling time 80 s a bainitic microstructure was observed. The investigated steel cooling cycle using simulation approach makes possible to determine the range of an optimum CG HAZ cooling time for the welding.

Testing for entanglement with periodic coarse graining

Science.gov (United States)

Tasca, D. S.; Rudnicki, Łukasz; Aspden, R. S.; Padgett, M. J.; Souto Ribeiro, P. H.; Walborn, S. P.

2018-04-01

Continuous-variable systems find valuable applications in quantum information processing. To deal with an infinite-dimensional Hilbert space, one in general has to handle large numbers of discretized measurements in tasks such as entanglement detection. Here we employ the continuous transverse spatial variables of photon pairs to experimentally demonstrate entanglement criteria based on a periodic structure of coarse-grained measurements. The periodization of the measurements allows an efficient evaluation of entanglement using spatial masks acting as mode analyzers over the entire transverse field distribution of the photons and without the need to reconstruct the probability densities of the conjugate continuous variables. Our experimental results demonstrate the utility of the derived criteria with a success rate in entanglement detection of ˜60 % relative to 7344 studied cases.

Fatigue damage in coarse-grained lean duplex stainless steels

Energy Technology Data Exchange (ETDEWEB)

Strubbia, R., E-mail: strubbia@ifir-conicet.gov.ar; Hereñú, S.; Marinelli, M.C.; Alvarez-Armas, I.

2016-04-06

The present investigation is focused on assessing the effect of a thermal treatment for grain coarsening on the low cycle fatigue damage evolution in two types of Lean Duplex Stainless Steels (LDSSs). The dislocation structure developed during cycling is observed by transmission electron microscopy (TEM). Additionally, a detailed analysis of short crack initiated and grown during low cycle fatigue (LCF) is performed by means of optical and scanning electron (SEM) microscopy in combination with automated electron back-scattered diffraction (EBSD) technique. Though in both coarse-grained LDSSs the short cracks nucleate in the ferrite phase, in each steels its origin is different. The embrittlement caused by the Cr{sub 2}N precipitation and the plastic activity sustained by each phase can explain this difference. The propagation behavior of the short cracks present two alternative growing mechanisms: the crack grows along a favorable slip plane with high Schmid Factor (SF) or the crack alternates between two slip systems. In both cases, the crack follows the path with the smallest tilt angle (β) at a grain boundary.

Cratering efficiency on coarse-grain targets: Implications for the dynamical evolution of asteroid 25143 Itokawa

Science.gov (United States)

Tatsumi, Eri; Sugita, Seiji

2018-01-01

Remote sensing observations made by the spacecraft Hayabusa provided the first direct evidence of a rubble-pile asteroid: 25143 Itokawa. Itokawa was found to have a surface structure very different from other explored asteroids; covered with coarse pebbles and boulders ranging at least from cm to meter size. The cumulative size distribution of small circular depressions on Itokawa, most of which may be of impact origin, has a significantly shallower slope than that on the Moon; small craters are highly depleted on Itokawa compared to the Moon. This deficiency of small circular depressions and other features, such as clustered fragments and pits on boulders, suggest that the boulders on Itokawa might behave like armor, preventing crater formation: the ;armoring effect;. This might contribute to the low number density of small crater candidates. In this study, the cratering efficiency reduction due to coarse-grained targets was investigated based on impact experiments at velocities ranging from ∼ 70 m/s to ∼ 6 km/s using two vertical gas gun ranges. We propose a scaling law extended for cratering on coarse-grained targets (i.e., target grain size ≳ projectile size). We have found that the crater efficiency reduction is caused by energy dissipation at the collision site where momentum is transferred from the impactor to the first-contact target grain, and that the armoring effect can be classified into three regimes: (1) gravity scaled regime, (2) reduced size crater regime, or (3) no apparent crater regime, depending on the ratio of the impactor size to the target grain size and the ratio of the impactor kinetic energy to the disruption energy of a target grain. We found that the shallow slope of the circular depressions on Itokawa cannot be accounted for by this new scaling law, suggesting that obliteration processes, such as regolith convection and migration, play a greater role in the depletion of circular depressions on Itokawa. Based on the new extended

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

NARCIS (Netherlands)

Qi, Yifei; Ingolfsson, Helgi I.; Cheng, Xi; Lee, Jumin; Marrink, Siewert J.; Im, Wonpil

Coarse-grained simulations are widely used to study large biological systems. Nonetheless, building such simulation systems becomes nontrivial, especially when membranes with various lipid types are involved. Taking advantage of the frameworks in all-atom CHARMM-GUI modules, we have developed

On the second law of thermodynamics: The significance of coarse-graining and the role of decoherence

International Nuclear Information System (INIS)

Noorbala, Mahdiyar

2014-01-01

We take up the question why the initial entropy in the universe was small, in the context of evolution of the entropy of a classical system. We note that coarse-graining is an important aspect of entropy evaluation which can reverse the direction of the increase in entropy, i.e., the direction of thermodynamic arrow of time. Then we investigate the role of decoherence in the selection of coarse-graining and explain how to compute entropy for a decohered classical system. Finally, we argue that the requirement of low initial entropy imposes constraints on the decoherence process

Temperature dependent mechanical properties and thermal activation plasticity of nanocrystalline and coarse grained Ni-18.75 at.% Fe alloy

International Nuclear Information System (INIS)

Tabachnikova, E D; Podolskiy, A V; Smirnov, S N; Psaruk, I A; Liao, P K

2014-01-01

Mechanical properties of Ni-18.75 at.% Fe in coarse grained (average grain size 15 gm) and nanocrystalline (average grain size 22 nm) states were studied in uniaxial compression in the temperature range 4.2-350 K. Temperature dependences of the flow stress, strain rate sensitivity and activation volume of plastic deformation were measured. The thermal activation analysis of the experimental data has been fulfilled for the the plastic deformation value of 2 %. It was shown that plastic deformation in temperature range from 35 to 350 K in both studied structural states has the thermally activated type. Comparative analysis of low temperature thermal activation plastic deformation was carried out for the alloy in coarse grained and nanocrystalline states. Empirical estimates of parameters of the dislocation interaction with local barriers and internal stress value estimates were obtained for the both studied structural states. Analysis of the results indicates that different mechanisms control the thermal activation plasticity of the Ni-18.75 at.% Fe alloy in coarse grained and nanocrystalline states. Possible mechanisms, which control plactisity of the studied states, are disscussed

Post-irradiation annealing of coarse-grained model alloys

Energy Technology Data Exchange (ETDEWEB)

Ray, P H.N.; Wilson, C; McElroy, R J [AEA Reactor Services, Harwell (United Kingdom)

1994-12-31

Thermal ageing and irradiation studies have been carried out on three model alloys (JPC, JPB, JPG) that have identical compositions except for different levels of phosphorus and/or copper. They have been irradiated in three conditions, as-received, heat treated to produce a coarse grained microstructure (similar to heat-affected-zone), and in this condition further aged at 450 C to produce a temper embrittled condition. One of the alloy have been subject to a post-irradiation anneal. The effect of these treatments on mechanical property changes has been characterized by Charpy testing and Vickers hardness measurements; the phosphorus segregation has been studied by a combination of STEM and Auger techniques.

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

Science.gov (United States)

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.

Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

Directory of Open Access Journals (Sweden)

Stovgaard Kasper

2010-08-01

Full Text Available Abstract Background Genome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that this gap will disappear in the near future. Small angle X-ray scattering (SAXS is an established low resolution method for routinely determining the structure of proteins in solution. The purpose of this study is to develop a method for the efficient calculation of accurate SAXS curves from coarse-grained protein models. Such a method can for example be used to construct a likelihood function, which is paramount for structure determination based on statistical inference. Results We present a method for the efficient calculation of accurate SAXS curves based on the Debye formula and a set of scattering form factors for dummy atom representations of amino acids. Such a method avoids the computationally costly iteration over all atoms. We estimated the form factors using generated data from a set of high quality protein structures. No ad hoc scaling or correction factors are applied in the calculation of the curves. Two coarse-grained representations of protein structure were investigated; two scattering bodies per amino acid led to significantly better results than a single scattering body. Conclusion We show that the obtained point estimates allow the calculation of accurate SAXS curves from coarse-grained protein models. The resulting curves are on par with the current state-of-the-art program CRYSOL, which requires full atomic detail. Our method was also comparable to CRYSOL in recognizing native structures among native-like decoys. As a proof-of-concept, we combined the coarse-grained Debye calculation with a previously described probabilistic model of protein structure, TorusDBN. This resulted in a significant improvement in the decoy recognition performance. In conclusion, the presented method shows great promise for

An Apparatus for Bed Material Sediment Extraction From Coarse River Beds in Large Alluvial Rivers

Science.gov (United States)

Singer, M. B.; Adam, H.; Cooper, J.; Cepello, S.

2005-12-01

Grain size distributions of bed material sediment in large alluvial rivers are required in applications ranging from habitat mapping, calibration of sediment transport models, high resolution sediment routing, and testing of existing theories of longitudinal and cross steam sediment sorting. However, characterizing bed material sediment from coarse river beds is hampered by difficulties in sediment extraction, a challenge that is generally circumvented via pebble counts on point bars, even though it is unclear whether the bulk grain size distribution of bed sediments is well represented by pebble counts on bars. We have developed and tested a boat-based sampling apparatus and methodology for extracting bulk sediment from a wide range of riverbed materials. It involves the use of a 0.4 x 0.4 x 0.2 meter stainless steel toothed sampler, called the Cooper Scooper, which is deployed from and dragged downstream by the weight of a jet boat. The design is based on that of a river anchor such that a rotating center bar connected to a rope line in the boat aligns the sampler in the downstream direction, the teeth penetrate the bed surface, and the sampler digs into the bed. The sampler is fitted with lead weights to keep it from tipping over. The force of the sampler `biting' into the bed can be felt on the rope line held by a person in the boat at which point they let out slack. The boat then motors to the spot above the embedded sampler, which is hoisted to the water surface via a system of pulleys. The Cooper Scooper is then clipped into a winch and boom assembly by which it is brought aboard. This apparatus improves upon commonly used clamshell dredge samplers, which are unable to penetrate coarse or mixed bed surfaces. The Cooper Scooper, by contrast, extracts statistically representative bed material sediment samples of up to 30 kilograms. Not surprisingly, the sampler does not perform well in very coarse or armored beds (e.g. where surface material size is on the

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

Science.gov (United States)

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.

Coarse-Grained Modeling of Polyelectrolyte Solutions

Science.gov (United States)

Denton, Alan R.; May, Sylvio

2014-03-01

Ionic mixtures, such as electrolyte and polyelectrolyte solutions, have attracted much attention recently for their rich and challenging combination of electrostatic and non-electrostatic interparticle forces and their practical importance, from battery technologies to biological systems. Hydration of ions in aqueous solutions is known to entail ion-specific effects, including variable solubility of organic molecules, as manifested in the classic Hofmeister series for salting-in and salting-out of proteins. The physical mechanism by which the solvent (water) mediates effective interactions between ions, however, is still poorly understood. Starting from a microscopic model of a polyelectrolyte solution, we apply a perturbation theory to derive a coarse-grained model of ions interacting through both long-range electrostatic and short-range solvent-induced pair potentials. Taking these effective interactions as input to molecular dynamics simulations, we calculate structural and thermodynamic properties of aqueous ionic solutions. This work was supported by the National Science Foundation under Grant No. DMR-1106331.

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

International Nuclear Information System (INIS)

Sanyal, Tanmoy; Shell, M. Scott

2016-01-01

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.

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

Energy Technology Data Exchange (ETDEWEB)

Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de [Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin (Germany); Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de; Dzubiella, Joachim, E-mail: joachim.dzubiella@helmholtz-berlin.de [Institut für Physik, Humboldt Universität zu Berlin, Newtonstraße 15, 12489 Berlin (Germany); Institut für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner Platz 1, 14109 Berlin (Germany)

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.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

Science.gov (United States)

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.

Formation of incoherent deformation twin boundaries in a coarse-grained Al-7Mg alloy

Science.gov (United States)

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 -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.

Power-Aware Rationale for Using Coarse-Grained Transponders in IP-Over-WDM Networks

DEFF Research Database (Denmark)

Saldaña Cercos, Silvia; Resendo, Leandro C.; Ribeiro, Moises R. N.

2015-01-01

.e., using 10 Gbps technology)? (2) What is the long-term cost of coarse-grained designs? We define a power-aware mixed integer linear programming (MILP) formulation based on actual modular architectures where modules are upgraded as the network traffic increases. We introduce, for the first time, important...

Coarse-grained model for the interconversion between different crystalline cellulose allomorphs

Energy Technology Data Exchange (ETDEWEB)

Langan, Paul [ORNL

2012-01-01

We present the results of Langevin dynamics simulations on a coarse grained model for crystalline cellulose. In particular, we analyze two different cellulose crystalline forms: cellulose I (the natural form of cellulose) and cellulose IIII (obtained after cellulose I is treated with anhydrous liquid ammonia). Cellulose IIII has been the focus of wide interest in the field of cellulosic biofuels as it can be efficiently hydrolyzed to glucose (its enzymatic degradation rates are up to 5 fold higher than those of cellulose I ). In turn, glucose can eventually be fermented into fuels. The coarse-grained model presented in this study is based on a simplified geometry and on an effective potential mimicking the changes in both intracrystalline hydrogen bonds and stacking interactions during the transition from cellulose I to cellulose IIII. The model accurately reproduces both structural and thermomechanical properties of cellulose I and IIII. The work presented herein describes the structural transition from cellulose I to cellulose IIII as driven by the change in the equilibrium state of two degrees of freedom in the cellulose chains. The structural transition from cellulose I to cellulose IIII is essentially reduced to a search for optimal spatial arrangement of the cellulose chains.

Information Theoretic Tools for Parameter Fitting in Coarse Grained Models

KAUST Repository

Kalligiannaki, Evangelia

2015-01-07

We study the application of information theoretic tools for model reduction in the case of systems driven by stochastic dynamics out of equilibrium. The model/dimension reduction is considered by proposing parametrized coarse grained dynamics and finding the optimal parameter set for which the relative entropy rate with respect to the atomistic dynamics is minimized. The minimization problem leads to a generalization of the force matching methods to non equilibrium systems. A multiplicative noise example reveals the importance of the diffusion coefficient in the optimization problem.

DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

DEFF Research Database (Denmark)

Svaneborg, Carsten; Fellermann, Harold; Rasmussen, Steen

2012-01-01

We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites can...

Rb-Sr geochronology of coarse-grained greywackes and argillites from the Coffs Harbour Block, eastern Australia

International Nuclear Information System (INIS)

Graham, I.J.; Korsch, R.J.

1985-01-01

The Coffs Harbour Block, eastern Australia, includes a sequence of turbidity-current-deposited greywackes and argillites dominated by quartz-poor to quartz-intermediate, volcanic-lithic and feldspathic types. The rocks have a common provenance consisting of dacite with minor andesite and rhyolite, derived from a continental margin volcanic arc. Rb-Sr whole-rock dating of coarse-grained greywackes and argillites suggests that low-grade regional metamorphism (prehnite-pumpellyite to lowest greenschist facies) has completely equilibrated sediments of all grain sizes, giving an age of 318 +- 8 Ma. A subsequent metamorphism which produced thermal biotite on a regional scale over the southern part of the area, re-equilibrated only the fine-grained sediments 238 +- 5 Ma ago; the coarse-grained sediments were unaffected isotopically and still lie on the older isochron. The wide variations in sandstone petrographic modes imply that the older isochron represents neither the age of volcanism in the magmatic arc nor the age of sedimentation at the deposition site, but rather dates the time of earlier metamorphism. (orig.)

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

International Nuclear Information System (INIS)

Poursina, Mohammad; Anderson, Kurt S.

2014-01-01

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

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

Science.gov (United States)

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.

On the representability problem and the physical meaning of coarse-grained models

Energy Technology Data Exchange (ETDEWEB)

Wagner, Jacob W.; Dama, James F.; Durumeric, Aleksander E. P.; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

2016-07-28

In coarse-grained (CG) models where certain fine-grained (FG, i.e., atomistic resolution) observables are not directly represented, one can nonetheless identify indirect the CG observables that capture the FG observable’s dependence on CG coordinates. Often, in these cases it appears that a CG observable can be defined by analogy to an all-atom or FG observable, but the similarity is misleading and significantly undermines the interpretation of both bottom-up and top-down CG models. Such problems emerge especially clearly in the framework of the systematic bottom-up CG modeling, where a direct and transparent correspondence between FG and CG variables establishes precise conditions for consistency between CG observables and underlying FG models. Here we present and investigate these representability challenges and illustrate them via the bottom-up conceptual framework for several simple analytically tractable polymer models. The examples provide special focus on the observables of configurational internal energy, entropy, and pressure, which have been at the root of controversy in the CG literature, as well as discuss observables that would seem to be entirely missing in the CG representation but can nonetheless be correlated with CG behavior. Though we investigate these problems in the framework of systematic coarse-graining, the lessons apply to top-down CG modeling also, with crucial implications for simulation at constant pressure and surface tension and for the interpretations of structural and thermodynamic correlations for comparison to experiment.

Thinning Approximation for Two-Dimensional Scattering Patterns from Coarse-Grained Polymer Melts under Shear Flow

Science.gov (United States)

Hagita, Katsumi; Murashima, Takahiro; Takano, Hiroshi; Kawakatsu, Toshihiro

2017-12-01

We proposed a thinning approximation (TA) for estimation of the two-dimensional (2D) wide-angle scattering patterns from Kremer-Grest polymer melts under shear. In the TA, extra particles are inserted at the middle of bonds for fine-graining of the coarse-grained polymers. For the case without the TA, spots corresponding to the orientation of bonds at a high shear rate are difficult to observe because the bond length of successive particles is comparable to the distance between neighboring particles. With the insertion of the extra particles, a ring pattern originating from the neighboring particles can be moved to a wide-angle region. Thus, we can observe the spots at high shear rates. We also examined the relationship between 2D scattering patterns and the Weissenberg number, which is defined as the product of the shear rate and the longest relaxation time. It is confirmed that the relationship for coarse-grained polymers with the TA is consistent with that of the all-atomistic model of polyethylene.

Coarse-grain parallelism using remote method invocation

Energy Technology Data Exchange (ETDEWEB)

Hebert, A. [Ecole Polytechnique de Montreal, Qc. (Canada)

2003-07-01

The paper describes a user-oriented framework specifically designed to facilitate the development and supervision of coarse-grain parallel applications in reactor physics. The proposed user-oriented framework was designed and implemented in Java, in such a way to obtain a simple and robust application. The proposed approach is based on Java Native Interface(JNI) for integrating the Fortran legacy code and on Remote Method Invocation (RMI) for distributing the calculation load over the farm of processors. Dynamic code downloading over the network is possible. We are presenting the application of this approach to supervision of lattice calculations using the open source Dragon code. The Java layer surrounding Dragon can also be used to construct execution procedures, computational schemes and graphical user interfaces. This approach can be used with any existing legacy Fortran code, as soon as its input/output data structures are Dragon-compatible. (author)

Coarse-graining as a downward causation mechanism

Science.gov (United States)

Flack, Jessica C.

2017-11-01

Downward causation is the controversial idea that `higher' levels of organization can causally influence behaviour at `lower' levels of organization. Here I propose that we can gain traction on downward causation by being operational and examining how adaptive systems identify regularities in evolutionary or learning time and use these regularities to guide behaviour. I suggest that in many adaptive systems components collectively compute their macroscopic worlds through coarse-graining. I further suggest we move from simple feedback to downward causation when components tune behaviour in response to estimates of collectively computed macroscopic properties. I introduce a weak and strong notion of downward causation and discuss the role the strong form plays in the origins of new organizational levels. I illustrate these points with examples from the study of biological and social systems and deep neural networks. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Coarse-grain parallelism using remote method invocation

International Nuclear Information System (INIS)

Hebert, A.

2003-01-01

The paper describes a user-oriented framework specifically designed to facilitate the development and supervision of coarse-grain parallel applications in reactor physics. The proposed user-oriented framework was designed and implemented in Java, in such a way to obtain a simple and robust application. The proposed approach is based on Java Native Interface(JNI) for integrating the Fortran legacy code and on Remote Method Invocation (RMI) for distributing the calculation load over the farm of processors. Dynamic code downloading over the network is possible. We are presenting the application of this approach to supervision of lattice calculations using the open source Dragon code. The Java layer surrounding Dragon can also be used to construct execution procedures, computational schemes and graphical user interfaces. This approach can be used with any existing legacy Fortran code, as soon as its input/output data structures are Dragon-compatible. (author)

Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simblations with Implicit Solvent

NARCIS (Netherlands)

Arnarez, Clement; Uusitalo, Jaakko J.; Masman, Marcelo F.; Ingolfsson, Helgi I.; de Jong, Djurre H.; Melo, Manuel N.; Periole, Xavier; de Vries, Alex H.; Marrink, Siewert J.

Coarse-grained (CG) models allow simulation of larger systems for longer times by decreasing the number of degrees of freedom compared with all-atom models. Here we introduce an implicit-solvent version of the popular CG Martini model, nicknamed Dry Martini. To account for the omitted solvent

Enhanced ductility of surface nano-crystallized materials by modulating grain size gradient

International Nuclear Information System (INIS)

Li, Jianjun; Soh, A K

2012-01-01

Surface nano-crystallized (SNC) materials with a graded grain size distribution on their surfaces have been attracting increasing scientific interest over the past few decades due to their good synergy of high strength and high ductility. However, to date most of the existing studies have focused on the individual contribution of three different aspects, i.e. grain size gradient (GSG), work-hardened region and surface compressive residual stresses, which were induced by surface severe plastic deformation processes, to the improved strength of SNC materials as compared with that of their coarse grained (CG) counterparts. And the ductility of these materials has hardly been studied. In this study, a combination of theoretical analysis and finite element simulations was used to investigate the role of GSG in tuning the ductility of SNC materials. It was found that the ductility of an SNC material can be comparable to that of its CG counterpart, while it simultaneously possessed a much higher strength than its CG core if the optimal GSG thickness and grain size of the topmost phase were adopted. A design map that can be used as a guideline for fabrication of SNC materials was also plotted. Our predictions were also compared with the corresponding experimental results. (paper)

An overview of molecular dynamics simulations of oxidized lipid systems, with a comparison of ELBA and MARTINI force fields for coarse grained lipid simulations

DEFF Research Database (Denmark)

Siani, Pablo; de Souza, R M; Dias, L G

2016-01-01

our new data of all-atom and coarse-grained simulations of hydroperoxidized lipid monolayer and bilayer systems and (iii) provide a comparison of the MARTINI and ELBA coarse grained force fields for lipid bilayer systems. We show that the better electrostatic treatment of interactions in ELBA is able...

Coarse-grained Simulations of Substrate Export through Multidrug Efflux Transporter AcrB

Science.gov (United States)

Jewel, Yead; Dutta, Prashanta; Liu, Jin

2017-11-01

The treatment of bacterial infectious diseases hampered by the overexpression of multidrug resistance (MDR) systems. The MDR system actively pumps the antibiotic drugs as well as other toxic compounds out of the cells. During the pumping, AcrB (one of the key MDR components) undergoes a series of large-scale proton/substrate dependent conformational changes. In this work, we implement a hybrid coarse-grained PACE force field that couples the united-atom protein model with the coarse-grained MARTINI water/lipid, to investigate the conformational changes of AcrB. We first develop the substrate force field which is compatible with PACE, then we implement the force field to explore large scale structural changes of AcrB in microsecond simulations. The effects of the substrate and the protonation states of two key residues: Asp407 and Asp408, are investigated. Our results show that the drug export through AcrB is proton as well as substrate dependent. Our simulations explain molecular mechanisms of substrate transport through AcrB complex, as well as provide valuable insights for designing proper antibiotic drugs. Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM122081.

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

Science.gov (United States)

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.

De Sitter stability and coarse graining

Energy Technology Data Exchange (ETDEWEB)

Markkanen, T. [Imperial College London, Department of Physics, London (United Kingdom); King' s College London, Department of Physics, London (United Kingdom)

2018-02-15

We present a 4-dimensional back reaction analysis of de Sitter space for a conformally coupled scalar field in the presence of vacuum energy initialized in the Bunch-Davies vacuum. In contrast to the usual semi-classical prescription, as the source term in the Friedmann equations we use expectation values where the unobservable information hidden by the cosmological event horizon has been neglected i.e. coarse grained over. It is shown that in this approach the energy-momentum is precisely thermal with constant temperature despite the dilution from the expansion of space due to a flux of energy radiated from the horizon. This leads to a self-consistent solution for the Hubble rate, which is gradually evolving and at late times deviates significantly from de Sitter. Our results hence imply de Sitter space to be unstable in this prescription. The solution also suggests dynamical vacuum energy: the continuous flux of energy is balanced by the generation of negative vacuum energy, which accumulatively decreases the overall contribution. Finally, we show that our results admit a thermodynamic interpretation which provides a simple alternate derivation of the mechanism. For very long times the solutions coincide with flat space. (orig.)

De Sitter stability and coarse graining

International Nuclear Information System (INIS)

Markkanen, T.

2018-01-01

We present a 4-dimensional back reaction analysis of de Sitter space for a conformally coupled scalar field in the presence of vacuum energy initialized in the Bunch-Davies vacuum. In contrast to the usual semi-classical prescription, as the source term in the Friedmann equations we use expectation values where the unobservable information hidden by the cosmological event horizon has been neglected i.e. coarse grained over. It is shown that in this approach the energy-momentum is precisely thermal with constant temperature despite the dilution from the expansion of space due to a flux of energy radiated from the horizon. This leads to a self-consistent solution for the Hubble rate, which is gradually evolving and at late times deviates significantly from de Sitter. Our results hence imply de Sitter space to be unstable in this prescription. The solution also suggests dynamical vacuum energy: the continuous flux of energy is balanced by the generation of negative vacuum energy, which accumulatively decreases the overall contribution. Finally, we show that our results admit a thermodynamic interpretation which provides a simple alternate derivation of the mechanism. For very long times the solutions coincide with flat space. (orig.)

The ELBA force field for coarse-grain modeling of lipid membranes.

Directory of Open Access Journals (Sweden)

Mario Orsi

Full Text Available A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (ε(r = 1. Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC and dioleoylphosphatidylethanolamine (DOPE in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids; this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.

Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

Energy Technology Data Exchange (ETDEWEB)

Cipcigan, Flaviu S., E-mail: flaviu.cipcigan@ed.ac.uk [School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD (United Kingdom); National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Sokhan, Vlad P. [National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Crain, Jason [School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD (United Kingdom); National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Martyna, Glenn J. [IBM T. J. Watson Research Center, Yorktown Heights, NY 10598 (United States)

2016-12-01

One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082–1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230–233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeler through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO-MD. - Highlights: • Electronic coarse graining unites many-body dispersion and polarisation beyond the dipole limit. • It consists of replacing the electrons of a molecule using a quantum harmonic oscillator, called a

Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

International Nuclear Information System (INIS)

Cipcigan, Flaviu S.; Sokhan, Vlad P.; Crain, Jason; Martyna, Glenn J.

2016-01-01

One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082–1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230–233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeler through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO-MD. - Highlights: • Electronic coarse graining unites many-body dispersion and polarisation beyond the dipole limit. • It consists of replacing the electrons of a molecule using a quantum harmonic oscillator, called a

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

Science.gov (United States)

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.

A hybrid particle–field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes

International Nuclear Information System (INIS)

Milano, Giuseppe; De Nicola, Antonio; Kawakatsu, Toshihiro

2013-01-01

This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle–field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale systems and, at the same time, they provide sufficiently detailed chemistry for the mapping scheme adopted. The comparison of the computational costs of our approach with standard molecular dynamics simulations is a function of the system size and the number of processors employed in the parallel calculations. Due to the low amount of data exchange, the larger the number of processors, the better are the performances of the hybrid particle–field models. This feature makes these models very promising ones in the exploration of several problems in biophysics. (paper)

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

Science.gov (United States)

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 �

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

Science.gov (United States)

Knoch, Fabian; Schäfer, Ken; Diezemann, Gregor; Speck, Thomas

2018-01-01

We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

Coarse-Grained Online Monitoring of BTI Aging by Reusing Power-Gating Infrastructure

OpenAIRE

Tenentes, V.; Rossi, D.; Sheng Yang,; Khursheed, S.; Al-Hashimi, B.M.; Gunn, S.R.

2017-01-01

In this paper, we present a novel coarse-grained technique for monitoring online the Bias Temperature Instability (BTI) aging of circuits by exploiting their power gating infrastructure. The proposed technique relies on monitoring the discharge time of the virtual-power-network during stand-by operations, the value of which depends on the threshold voltage of the CMOS devices in the power-gated design (PGD). It does not require any distributed sensors, because the virtual-power network is alr...

Ensemble Empirical Mode Decomposition based methodology for ultrasonic testing of coarse grain austenitic stainless steels.

Science.gov (United States)

Sharma, Govind K; Kumar, Anish; Jayakumar, T; Purnachandra Rao, B; Mariyappa, N

2015-03-01

A signal processing methodology is proposed in this paper for effective reconstruction of ultrasonic signals in coarse grained high scattering austenitic stainless steel. The proposed methodology is comprised of the Ensemble Empirical Mode Decomposition (EEMD) processing of ultrasonic signals and application of signal minimisation algorithm on selected Intrinsic Mode Functions (IMFs) obtained by EEMD. The methodology is applied to ultrasonic signals obtained from austenitic stainless steel specimens of different grain size, with and without defects. The influence of probe frequency and data length of a signal on EEMD decomposition is also investigated. For a particular sampling rate and probe frequency, the same range of IMFs can be used to reconstruct the ultrasonic signal, irrespective of the grain size in the range of 30-210 μm investigated in this study. This methodology is successfully employed for detection of defects in a 50mm thick coarse grain austenitic stainless steel specimens. Signal to noise ratio improvement of better than 15 dB is observed for the ultrasonic signal obtained from a 25 mm deep flat bottom hole in 200 μm grain size specimen. For ultrasonic signals obtained from defects at different depths, a minimum of 7 dB extra enhancement in SNR is achieved as compared to the sum of selected IMF approach. The application of minimisation algorithm with EEMD processed signal in the proposed methodology proves to be effective for adaptive signal reconstruction with improved signal to noise ratio. This methodology was further employed for successful imaging of defects in a B-scan. Copyright © 2014. Published by Elsevier B.V.

Experimental study on waves propagation over a coarse-grained sloping beach

Science.gov (United States)

Hsu, Tai-Wen; Lai, Jian-Wu

2013-04-01

This study investigates velocity fields of wave propagation over a coarse-grained sloping beach using laboratory experiments. The experiment was conducted in a wave flume of 25 m long, 0.5 m wide and 0.6 m high in which a coarse-grained sloping 1:5 beach was placed with two layers ball. The glass ball is D=7.9 cm and the center to center distance of each ball is 8.0 cm. The test section for observing wave and flow fields is located at the middle part of the flume. A piston type wave maker driven by an electromechanical hydraulic serve system is installed at the end of the flume. The intrinsic permeability Kp and turbulent drag coefficient Cf were obtained from steady flow water-head experiments. The flow velocity was measured by the particle image velocimeter (PIV) and digital image process (DIP) techniques. Eleven fields of view (FOVS) were integrated into a complete representation including the outer, surf and swash zone. Details of the definition sketch of the coarse-grained sloping beach model as well as experimental setup are referred to Lai et al. (2008). A high resolution of CCD camera was used to capture the images which was calibrated by the direct linear transform (DCT) algorithm proposed by Abed El-Aziz and Kar-Ara (1971). The water surface between the interface of air and water at each time step are calculated by Otsu' (1978) detect algorithm. The comparison shows that the water surface elevation observed by integrated image agrees well with that of Otsu' detection results. For the flow field measurement, each image pair was cross correlated with 32X32 pixel inter rogation window and a half overlap between adjacent windows. The repeatability and synchronization are the key elements for both wave motion and PIV technique. The wave profiles and flow field were compared during several wave periods to ensure that they can be reproduced by the present system. The water depth is kept as a constant of h=32 cm. The incident wave conditions are set to be wave

Mechanical behavior of ultrafine-grained materials under combined static and dynamic loadings

Directory of Open Access Journals (Sweden)

Guo Y.Z.

2015-01-01

Full Text Available Ultrafine-grained (UFG materials have extensive prospects for engineering application due to their excellent mechanical properties. However, the grain size decrease reduces their strain hardening ability and makes UFG materials more susceptible to deformation instability such as shear localization. In most cases, critical shear strain is taken as the criterion for formation of shear localization under impact loading or adiabatic shear band (ASB. Recently, some researchers found that the formation of ASB was determined only by the dynamic loading process and had nothing to do with its static loading history. They proposed for coarse-grained metals a dynamic stored energy-based criterion for ASB and verified it by some experiments. In this study, we will focus on the shear localization behavior of UFG metals such as UFG titanium and magnesium alloy AZ31. Quasi-static loading and dynamic loading will be applied on the same specimen alternately. The shear localization behavior will be analyzed and the criterion of its formation will be evaluated.

Coarse-grained Simulations of Sugar Transport and Conformational Changes of Lactose Permease

Science.gov (United States)

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

2016-11-01

Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves sugar translocation, H+ transfer, as well as large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the transport of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule across a wild-type LacY during lactose/H+ symport process. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Protonation of Glu325 stabilizes the TDG and inward-facing conformation of LacY. Protonation of Glu269 induces a dramatic protein structural reorganization and causes the expulsion of TDG from LacY to both sides of the membrane. The structural changes occur primarily in the N-terminal domain of LacY. This work is supported by NSF Grants: CBET-1250107 and CBET -1604211.

Weak Galilean invariance as a selection principle for coarse-grained diffusive models.

Science.gov (United States)

Cairoli, Andrea; Klages, Rainer; Baule, Adrian

2018-05-29

How does the mathematical description of a system change in different reference frames? Galilei first addressed this fundamental question by formulating the famous principle of Galilean invariance. It prescribes that the equations of motion of closed systems remain the same in different inertial frames related by Galilean transformations, thus imposing strong constraints on the dynamical rules. However, real world systems are often described by coarse-grained models integrating complex internal and external interactions indistinguishably as friction and stochastic forces. Since Galilean invariance is then violated, there is seemingly no alternative principle to assess a priori the physical consistency of a given stochastic model in different inertial frames. Here, starting from the Kac-Zwanzig Hamiltonian model generating Brownian motion, we show how Galilean invariance is broken during the coarse-graining procedure when deriving stochastic equations. Our analysis leads to a set of rules characterizing systems in different inertial frames that have to be satisfied by general stochastic models, which we call "weak Galilean invariance." Several well-known stochastic processes are invariant in these terms, except the continuous-time random walk for which we derive the correct invariant description. Our results are particularly relevant for the modeling of biological systems, as they provide a theoretical principle to select physically consistent stochastic models before a validation against experimental data.

A coarse-grained model for DNA origami.

Science.gov (United States)

Reshetnikov, Roman V; Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

2018-02-16

Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.

Coarse-grained simulation of polymer-filler blends

Science.gov (United States)

Legters, Gregg; Kuppa, Vikram; Beaucage, Gregory; Univ of Dayton Collaboration; Univ of Cincinnati Collaboration

The practical use of polymers often relies on additives that improve the property of the mixture. Examples of such complex blends include tires, pigments, blowing agents and other reactive additives in thermoplastics, and recycled polymers. Such systems usually exhibit a complex partitioning of the components. Most prior work has either focused on fine-grained details such as molecular modeling of chains at interfaces, or on coarse, heuristic, trial-and-error approaches to compounding (eg: tire industry). Thus, there is a significant gap in our understanding of how complex hierarchical structure (across several decades in length) develops in these multicomponent systems. This research employs dissipative particle thermodynamics in conjunction with a pseudo-thermodynamic parameter derived from scattering experiments to represent polymer-filler interactions. DPD simulations will probe how filler dispersion and hierarchical morphology develops in these complex blends, and are validated against experimental (scattering) data. The outcome of our approach is a practical solution to compounding issues, based on a mutually validating experimental and simulation methodology. Support from the NSF (CMMI-1636036/1635865) is gratefully acknowledged.

Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth

Science.gov (United States)

de la Cruz, Roberto; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás

2017-12-01

The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction-diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction-diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge of

Thermodynamic forces in coarse-grained simulations

Science.gov (United States)

Noid, William

Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

Superplasticity-like deformation of a coarse-grained Al5052 alloy

International Nuclear Information System (INIS)

Chow, K.K.; Chan, K.C.

2000-01-01

In the present paper, hot forming properties of a commercially available coarse-grained Al5052 alloy under uniaxial and biaxial stress states were examined. In hot tensile tests, the alloy exhibits a superplastic-like behaviour with a maximum tensile elongation of 194% at a temperature of 873 K and at an initial strain rate of 2.08 x 10 -1 s -1 . Dislocation slip and grain boundary sliding were considered to be the deformation mechanisms. The alloy was also bulged at a constant polar strain-rate of 2.0 x 10 -1 s -1 and at an optimum temperature of 873 K using elliptical dies with aspect ratios of 1:1, 4:3, 2:1, 8:3 and 4:1. The strain distributions revealed that the strain gradient obtained in the minor axis was much greater than that in major axis. Moreover, it was shown that the deformation behavior of the alloy was basically isotropic and the volume strain of the alloy sheet did not equal to zero which was considered to relate to its cavitation behaviour. (orig.)

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

Science.gov (United States)

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.

Combining an Elastic Network With a Coarse-Grained Molecular Force Field : Structure, Dynamics, and Intermolecular Recognition

NARCIS (Netherlands)

Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.

Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this

Modification of the Surface Topography and Composition of Ultrafine and Coarse Grained Titanium by Chemical Etching.

Science.gov (United States)

Nazarov, Denis V; Zemtsova, Elena G; Solokhin, Alexandr Yu; Valiev, Ruslan Z; Smirnov, Vladimir M

2017-01-13

In this study, we present the detailed investigation of the influence of the etching medium (acidic or basic Piranha solutions) and the etching time on the morphology and surface relief of ultrafine grained (UFG) and coarse grained (CG) titanium. The surface relief and morphology have been studied by means of scanning electron microscopy (SEM), atomic force microscopy (AFM), and the spectral ellipsometry. The composition of the samples has been determined by X-ray fluorescence analysis (XRF) and X-ray Photoelectron Spectroscopy (XPS). Significant difference in the etching behavior of UFG and CG titanium has been found. UFG titanium exhibits higher etching activity independently of the etching medium. Formed structures possess higher homogeneity. The variation of the etching medium and time leads to micro-, nano-, or hierarchical micro/nanostructures on the surface. Significant difference has been found between surface composition for UFG titanium etched in basic and acidic Piranha solution. Based on the experimental data, the possible reasons and mechanisms are considered for the formation of nano- and microstructures. The prospects of etched UFG titanium as the material for implants are discussed.

Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

DEFF Research Database (Denmark)

Rossi, G.; Monticelli, L.; Puisto, S. R.

2011-01-01

We hereby introduce a new hybrid thermodynamic-structural approach to the coarse-graining of polymers. The new model is developed within the framework of the MARTINI force-field (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812), which uses mainly thermodynamic properties as targets...... of microseconds. Finally, we tested our model in dilute conditions. The collapse of the polymer chains in a bad solvent and the swelling in a good solvent could be reproduced....

A Coarse-Grained Reconfigurable Architecture with Compilation for High Performance

Directory of Open Access Journals (Sweden)

Lu Wan

2012-01-01

Full Text Available We propose a fast data relay (FDR mechanism to enhance existing CGRA (coarse-grained reconfigurable architecture. FDR can not only provide multicycle data transmission in concurrent with computations but also convert resource-demanding inter-processing-element global data accesses into local data accesses to avoid communication congestion. We also propose the supporting compiler techniques that can efficiently utilize the FDR feature to achieve higher performance for a variety of applications. Our results on FDR-based CGRA are compared with two other works in this field: ADRES and RCP. Experimental results for various multimedia applications show that FDR combined with the new compiler deliver up to 29% and 21% higher performance than ADRES and RCP, respectively.

Microstructural characteristics and toughness of the simulated coarse grained heat affected zone of high strength low carbon bainitic steel

International Nuclear Information System (INIS)

Lan Liangyun; Qiu Chunlin; Zhao Dewen; Gao Xiuhua; Du Linxiu

2011-01-01

Highlights: → Total toughness can be separated into crack initiation energy and crack propagation energy. → Small effective grain size of lath martensite can improve the crack propagation energy. → MA constituent is mainly responsible for the low toughness of coarse bainite specimens. → High angle packet boundary in coarser bainite has few contributions to improving crack propagation energy. - Abstract: The correlation of microstructural characteristics and toughness of the simulated coarse grained heat affected zone (CGHAZ) of low carbon bainitic steel was investigated in this study. The toughness of simulated specimens was examined by using an instrumented Charpy impact tester after the simulation welding test was conducted with different cooling times. Microstructure observation and crystallographic feature analysis were conducted by means of optical microscope and scanning electron microscope equipped with electron back scattered diffraction (EBSD) system, respectively. The main microstructure of simulated specimen changes from lath martensite to coarse bainite with the increase in cooling time. The deterioration of its toughness occurs when the cooling time ranges from 10 to 50 s compared with base metal toughness, and the toughness becomes even worse when the cooling time increases to 90 s or more. The MA (martensite-austenite) constituent is primary responsible for the low toughness of simulated CGHAZ with high values of cooling time because the large MA constituent reduces the crack initiation energy significantly. For crack propagation energy, the small effective grain size of lath martensite plays an important role in improving the crack propagation energy. By contrast, high misorientation packet boundary in coarse bainite seems to have few contributions to the improvement of the toughness because cleavage fracture micromechanism of coarse bainite is mainly controlled by crack initiation.

Microstructural characteristics and toughness of the simulated coarse grained heat affected zone of high strength low carbon bainitic steel

Energy Technology Data Exchange (ETDEWEB)

Lan Liangyun, E-mail: lly.liangyun@gmail.com [State Key Laboratory of Rolling Technology and Automation, Northeastern University, Shenyang 110819 (China); Qiu Chunlin; Zhao Dewen; Gao Xiuhua; Du Linxiu [State Key Laboratory of Rolling Technology and Automation, Northeastern University, Shenyang 110819 (China)

2011-11-25

Highlights: {yields} Total toughness can be separated into crack initiation energy and crack propagation energy. {yields} Small effective grain size of lath martensite can improve the crack propagation energy. {yields} MA constituent is mainly responsible for the low toughness of coarse bainite specimens. {yields} High angle packet boundary in coarser bainite has few contributions to improving crack propagation energy. - Abstract: The correlation of microstructural characteristics and toughness of the simulated coarse grained heat affected zone (CGHAZ) of low carbon bainitic steel was investigated in this study. The toughness of simulated specimens was examined by using an instrumented Charpy impact tester after the simulation welding test was conducted with different cooling times. Microstructure observation and crystallographic feature analysis were conducted by means of optical microscope and scanning electron microscope equipped with electron back scattered diffraction (EBSD) system, respectively. The main microstructure of simulated specimen changes from lath martensite to coarse bainite with the increase in cooling time. The deterioration of its toughness occurs when the cooling time ranges from 10 to 50 s compared with base metal toughness, and the toughness becomes even worse when the cooling time increases to 90 s or more. The MA (martensite-austenite) constituent is primary responsible for the low toughness of simulated CGHAZ with high values of cooling time because the large MA constituent reduces the crack initiation energy significantly. For crack propagation energy, the small effective grain size of lath martensite plays an important role in improving the crack propagation energy. By contrast, high misorientation packet boundary in coarse bainite seems to have few contributions to the improvement of the toughness because cleavage fracture micromechanism of coarse bainite is mainly controlled by crack initiation.

cgHeliParm : analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations

NARCIS (Netherlands)

Faustino, Ignacio; Marrink, S. J.

2017-01-01

Summary: We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of

Coarse-grained simulation of a real-time process control network under peak load

International Nuclear Information System (INIS)

George, A.D.; Clapp, N.E. Jr.

1992-01-01

This paper presents a simulation study on the real-time process control network proposed for the new ANS reactor system at ORNL. A background discussion is provided on networks, modeling, and simulation, followed by an overview of the ANS process control network, its three peak-load models, and the results of a series of coarse-grained simulation studies carried out on these models using implementations of 802.3, 802.4, and 802.5 standard local area networks

Model Reduction and Coarse-Graining Approaches for Multiscale Phenomena

CERN Document Server

Gorban, Alexander N; Theodoropoulos, Constantinos; Kazantzis, Nikolaos K; Öttinger, Hans Christian

2006-01-01

Model reduction and coarse-graining are important in many areas of science and engineering. How does a system with many degrees of freedom become one with fewer? How can a reversible micro-description be adapted to the dissipative macroscopic model? These crucial questions, as well as many other related problems, are discussed in this book. Specific areas of study include dynamical systems, non-equilibrium statistical mechanics, kinetic theory, hydrodynamics and mechanics of continuous media, (bio)chemical kinetics, nonlinear dynamics, nonlinear control, nonlinear estimation, and particulate systems from various branches of engineering. The generic nature and the power of the pertinent conceptual, analytical and computational frameworks helps eliminate some of the traditional language barriers, which often unnecessarily impede scientific progress and the interaction of researchers between disciplines such as physics, chemistry, biology, applied mathematics and engineering. All contributions are authored by ex...

A coarse grained description of time evolution: Irreversible state reduction and time-energy relation

International Nuclear Information System (INIS)

Bonifacio, R.; Milan Univ.

1983-05-01

We show that a proper coarse-grained description of time evolution leads to a finite difference equation with step tau for the density operator. This implies state reduction to the diagonal form in the energy representation and a quasi ergodic behaviour of quantum mechanical ensemble averages. An intrinsic time-energy relation tauΔE>=(h/2π)/2 is proposed, and its equivalence to a time quantization is discussed. (author)

Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential

International Nuclear Information System (INIS)

Neri, Marilisa; Anselmi, Claudio; Carnevale, Vincenzo; Vargiu, Attilio V; Carloni, Paolo

2006-01-01

Outer-membrane proteases T (OmpT) are membrane enzymes used for defense by Gram-negative bacteria. Here we use hybrid molecular mechanics/coarse-grained simulations to investigate the role of large-scale motions of OmpT from Escherichia coli for its function. In this approach, the enzyme active site is treated at the all-atom level, whilst the rest of the protein is described at the coarse-grained level. Our calculations agree well with previously reported all-atom molecular dynamics simulations, suggesting that this approach is well suitable to investigate membrane proteins. In addition, our findings suggest that OmpT large-scale conformational fluctuations might play a role for its biological function, as found for another protease class, the aspartyl proteases

Molecular dynamics simulation of coarse-grained poly(L-lysine) dendrimers.

Science.gov (United States)

Rahimi, Ali; Amjad-Iranagh, Sepideh; Modarress, Hamid

2016-03-01

Poly(L-lysine) (PLL) dendrimer are amino acid based macromolecules and can be used as drug delivery agents. Their branched structure allows them to be functionalized by various groups to encapsulate drug agents into their structure. In this work, at first, an attempt was made on all-atom simulation of PLL dendrimer of different generations. Based on all-atom results, a course-grained model of this dendrimer was designed and its parameters were determined, to be used for simulation of three generations of PLL dendrimer, at two pHs. Similar to the all-atom, the coarse-grained results indicated that by increasing the generation, the dendrimer becomes more spherical. At pH 7, the dendrimer had larger size, whereas at pH 12, due to back folding of branching chains, they had the tendency to penetrate into the inner layers. The calculated radial probability and radial distribution functions confirm that at pH 7, the PLL dendrimer has more cavities and as a result it can encapsulate more water molecules into its inner structure. By calculating the moment of inertia and the aspect ratio, the formation of spherical structure for PLL dendrimer was confirmed.

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

Energy Technology Data Exchange (ETDEWEB)

Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)

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, which 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.

Role of Grain Boundaries under Long-Time Radiation

Science.gov (United States)

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.

Coarse-grained molecular dynamics simulations of the tensile behavior of a thermosetting polymer.

Science.gov (United States)

Yang, Shaorui; Qu, Jianmin

2014-07-01

Using a previously developed coarse-grained model, we conducted large-scale (∼ 85 × 85 × 85 nm(3)) molecular dynamics simulations of uniaxial-strain deformation to study the tensile behavior of an epoxy molding compound, epoxy phenol novolacs (EPN) bisphenol A (BPA). Under the uniaxial-strain deformation, the material is found to exhibit cavity nucleation and growth, followed by stretching of the ligaments separated by the cavities, until the ultimate failure through ligament scissions. The nucleation sites of cavities are rather random and the subsequent cavity growth accounts for much (87%) of the volumetric change during the uniaxial-strain deformation. Ultimate failure of the materials occurs when the cavity volume fraction reaches ∼ 60%. During the entire deformation process, polymer strands in the network are continuously extended to their linear states and broken in the postyielding strain hardening stage. When most of the strands are stretched to their taut configurations, rapid scission of a large number of strands occurs within a small strain increment, which eventually leads to fracture. Finally, through extensive numerical simulations of various loading conditions in addition to uniaxial strain, we find that yielding of the EPN-BPA can be described by the pressure-modified von Mises yield criterion.

Coarse-grained molecular dynamics simulations of the tensile behavior of a thermosetting polymer

Science.gov (United States)

Yang, Shaorui; Qu, Jianmin

2014-07-01

Using a previously developed coarse-grained model, we conducted large-scale (˜85×85×85nm3) molecular dynamics simulations of uniaxial-strain deformation to study the tensile behavior of an epoxy molding compound, epoxy phenol novolacs (EPN) bisphenol A (BPA). Under the uniaxial-strain deformation, the material is found to exhibit cavity nucleation and growth, followed by stretching of the ligaments separated by the cavities, until the ultimate failure through ligament scissions. The nucleation sites of cavities are rather random and the subsequent cavity growth accounts for much (87%) of the volumetric change during the uniaxial-strain deformation. Ultimate failure of the materials occurs when the cavity volume fraction reaches ˜60%. During the entire deformation process, polymer strands in the network are continuously extended to their linear states and broken in the postyielding strain hardening stage. When most of the strands are stretched to their taut configurations, rapid scission of a large number of strands occurs within a small strain increment, which eventually leads to fracture. Finally, through extensive numerical simulations of various loading conditions in addition to uniaxial strain, we find that yielding of the EPN-BPA can be described by the pressure-modified von Mises yield criterion.

Thermal dileptons from coarse-grained transport as fireball probes at SIS energies

International Nuclear Information System (INIS)

Galatyuk, Tetyana; Seck, Florian; Hohler, Paul M.; Rapp, Ralf; Stroth, Joachim

2016-01-01

Utilizing a coarse-graining method to convert hadronic transport simulations of Au+Au collisions at SIS energies into local temperature, baryon and pion densities, we compute the pertinent radiation of thermal dileptons based on an in-medium ρ spectral function that describes available spectra at ultrarelativistic collision energies. In particular, we analyze how far the resulting yields and slopes of the invariant-mass spectra can probe the lifetime and temperatures of the fireball. We find that dilepton radiation sets in after the initial overlap phase of the colliding nuclei of about 7 fm/c, and lasts for about 13 fm/c. This duration closely coincides with the development of the transverse collectivity of the baryons, thus establishing a direct correlation between hadronic collective effects and thermal EM radiation, and supporting a near local equilibration of the system. This fireball ''lifetime'' is substantially smaller than the typical 20-30 fm/c that naive considerations of the density evolution alone would suggest. We furthermore find that the total dilepton yield radiated into the invariant-mass window of M = 0.3-0.7 GeV/c 2 normalized to the number of charged pions, follows a relation to the lifetime found earlier in the (ultra-)relativistic regime of heavy-ion collisions, and thus corroborates the versatility of this tool. The spectral slopes of the invariant-mass spectra above the φ -meson mass provide a thermometer of the hottest phases of the collision, and agree well with the maximal temperatures extracted from the coarse-grained hadron spectra. (orig.)

Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates

NARCIS (Netherlands)

Baron, R; de Vries, AH; Hunenberger, PH; van Gunsteren, WF

2006-01-01

Molecular liquids can be modeled at different levels of spatial resolution. In atomic-level (AL) models, all (heavy) atoms can be explicitly simulated. In coarse-grained (CG) models, particles (beads) that represent groups of covalently bound atoms are used as elementary units. Ideally, a CG model

Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

Science.gov (United States)

Song, Bin; Molinero, Valeria

2013-08-07

Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

Modification of the Surface Topography and Composition of Ultrafine and Coarse Grained Titanium by Chemical Etching

Directory of Open Access Journals (Sweden)

Denis V. Nazarov

2017-01-01

Full Text Available In this study, we present the detailed investigation of the influence of the etching medium (acidic or basic Piranha solutions and the etching time on the morphology and surface relief of ultrafine grained (UFG and coarse grained (CG titanium. The surface relief and morphology have been studied by means of scanning electron microscopy (SEM, atomic force microscopy (AFM, and the spectral ellipsometry. The composition of the samples has been determined by X-ray fluorescence analysis (XRF and X-ray Photoelectron Spectroscopy (XPS. Significant difference in the etching behavior of UFG and CG titanium has been found. UFG titanium exhibits higher etching activity independently of the etching medium. Formed structures possess higher homogeneity. The variation of the etching medium and time leads to micro-, nano-, or hierarchical micro/nanostructures on the surface. Significant difference has been found between surface composition for UFG titanium etched in basic and acidic Piranha solution. Based on the experimental data, the possible reasons and mechanisms are considered for the formation of nano- and microstructures. The prospects of etched UFG titanium as the material for implants are discussed.

Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions.

Science.gov (United States)

Krajniak, Jakub; Zhang, Zidan; Pandiyan, Sudharsan; Nies, Eric; Samaey, Giovanni

2018-06-11

We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non-bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e.g. water molecules or development of polymer morphology during the process of splitting off byproduct molecules. Another concept that could be studied is the degradation of polymeric materials, a very important topic in a recycling of polymer waste. We illustrate the method by simulating the polymerization of polyethylene terephthalate (PET) at the coarse-grained level as an example of a polycondensation reaction with water as a byproduct. The algorithms are implemented in a publicly available software package and are easily accessible using a domain-specific language that describes chemical reactions in an input configuration file. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.

Science.gov (United States)

Fačkovec, B; Vanden-Eijnden, E; Wales, D J

2015-07-28

A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.

Hydrogen accumulation in nanostructured as compared to the coarse-grained tungsten

International Nuclear Information System (INIS)

Gonzalez-Arrabal, R.; Panizo-Laiz, M.; Gordillo, N.; Tejado, E.; Munnik, F.; Rivera, A.; Perlado, J.M.

2014-01-01

Highlights: • Study of the hydrogen behaviour in nanostructured as compare to coarse grained tungsten samples. • Comparison between single (H), sequentially (C plus H) and simultaneously (C and H) implanted samples. • Study of the stability of the nanostructures after implantation at different temperatures. • Implantation energies for H and C above the displacement damage threshold. • Study of the hydrogen behaviour as a function of the implantation temperature. - Abstract: We report on the influence of sample microstructure and of irradiation conditions on the H behaviour in Tungsten (W). For this purpose, commercial coarse grained (CGW) and nanostructured W (NW) samples were implanted with (i) H at room temperature (RT), (ii) sequentially with C and H at RT, and (iii) simultaneously (co-implanted) with C and H at RT. To study the possible effect of implantation temperature on H behaviour, a CGW sample and a NW sample were sequentially implanted with C at RT and with H at 673 K. The H and C implantation fluence was 5 × 10 20 m −2 and the implantation energies were 160 keV for H and 650 keV for C which are above the displacement damage threshold. Scanning electron microscopy images show that nanostructured samples consist of columns with an average diameter of about 100 nm. These nanocolumns are stable under the studied implantations conditions. Moreover, surface modification is absent in all studied samples. X-ray diffraction data illustrate that all samples are mono-phase (α-W phase) and that none of the implantations led to the appearance of secondary phases. Resonant nuclear reaction analysis data show that the H retention in NW samples is larger than in CGW and that synergistic effect has a significant influence on the H retention in CGW samples but not in NW samples

A coarse-grained generalized second law for holographic conformal field theories

Science.gov (United States)

Bunting, William; Fu, Zicao; Marolf, Donald

2016-03-01

We consider the universal sector of a d\\gt 2 dimensional large-N strongly interacting holographic CFT on a black hole spacetime background B. When our CFT d is coupled to dynamical Einstein-Hilbert gravity with Newton constant G d , the combined system can be shown to satisfy a version of the thermodynamic generalized second law (GSL) at leading order in G d . The quantity {S}{CFT}+\\frac{A({H}B,{perturbed})}{4{G}d} is non-decreasing, where A({H}B,{perturbed}) is the (time-dependent) area of the new event horizon in the coupled theory. Our S CFT is the notion of (coarse-grained) CFT entropy outside the black hole given by causal holographic information—a quantity in turn defined in the AdS{}d+1 dual by the renormalized area {A}{ren}({H}{{bulk}}) of a corresponding bulk causal horizon. A corollary is that the fine-grained GSL must hold for finite processes taken as a whole, though local decreases of the fine-grained generalized entropy are not obviously forbidden. Another corollary, given by setting {G}d=0, states that no finite process taken as a whole can increase the renormalized free energy F={E}{out}-{{TS}}{CFT}-{{Ω }}J, with T,{{Ω }} constants set by {H}B. This latter corollary constitutes a 2nd law for appropriate non-compact AdS event horizons.

Impacts into Coarse-Grained Spheres at Moderate Impact Velocities: Implications for Cratering on Asteroids and Planets

Science.gov (United States)

Barnouin, Olivier S.; Daly, R. Terik; Cintala, Mark J.; Crawford, David A.

2018-01-01

The surfaces of many planets and asteroids contain coarsely fragmental material generated by impacts or other geologic processes. The presence of such pre-existing structures may affect subsequent impacts, particularly when the width of the shock is comparable to or smaller than the size of pre-existing structures. Reasonable theoretical predictions and low speed (<300m/s) impact experiments suggest that in such targets the cratering process should be highly dissipative, which would reduce cratering efficiencies and cause a rapid decay in ejection velocity as a function of distance from the impact point. In this study, we assess whether these results apply at higher impact speeds between 0.5 and 2.5 km s-1. This study shows little change in cratering efficiency when 3.18 mm diameter glass beads are launched into targets composed of these same beads. These impacts are very efficient, and ejection velocity decays slowly as function of distance from the impact point. This slow decay in ejection velocity probably indicates a correspondingly slow decay of the shock stresses. However, these experiments reveal that initial interactions between projectile and target strongly influence the cratering process and lead to asymmetries in crater shape and ejection angles, as well as significant variations in ejection velocity at a given launch position. Such effects of asymmetric coupling could be further enhanced by heterogeneity in the initial distribution of grains in the target and by mechanical collisions between grains. These experiments help to explain why so few craters are seen on the rubble-pile asteroid Itokawa: impacts into its coarsely fragmental surface by projectiles comparable to or smaller than the size of these fragments likely yield craters that are not easily recognizable.

Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth

International Nuclear Information System (INIS)

Cruz, Roberto de la; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás

2017-01-01

The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction–diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction–diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge

A note on coarse-grained gravity-flow deposits within proterozoic lacustrine sedimentary rocks, Transvaal sequence, South Africa

Science.gov (United States)

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.

Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.

Directory of Open Access Journals (Sweden)

Frank C Pickard

2014-07-01

Full Text Available A lesson utilizing a coarse-grained (CG Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing web portal (www.charmming.org to the Chemistry at HARvard Macromolecular Mechanics (CHARMM molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the Gō-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG Gō model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field.

Diffusion-accomodated rigid-body translations along grain boundaries in nanostructured materials

International Nuclear Information System (INIS)

Bachurin, D.V.; Nazarov, A.A.; Shenderova, O.A.; Brenner, D.W.

2003-01-01

A model for the structural relaxation of grain boundaries (GBs) in nanostructured materials (NSMs) by diffusion-accommodated rigid body translations along GBs is proposed. The model is based on the results of recent computer simulations that have demonstrated that the GBs in NSMs retain a high-energy structure with random translational states due to severe geometrical constraints applied from neighboring grains (J. Appl. Phys. 78 (1995) 847; Scripta Metall. Mater. 33 (1995) 1245). The shear stresses within a GB caused by non-optimized rigid-body translations (RBTs) can be accommodated by diffusive flow of atoms along a GB. This mechanism is particularly important for low-angle and vicinal GBs, the energy of which noticeably depends on the rigid body translations. At moderate and high temperatures the model yields relaxation times that are very short and therefore GBs in NSMs can attain an equilibrium structure with optimized rigid body translations. In contrast, at room temperature the model predicts that in some metals non-equilibrium structures can be preserved for a long time, which may result in the observation of grain boundary structures different from those in coarse grained polycrystals

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

Science.gov (United States)

Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

2018-04-30

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

Improving the treatment of coarse-grain electrostatics: CVCEL

Energy Technology Data Exchange (ETDEWEB)

Ceres, N.; Lavery, R., E-mail: richard.lavery@ibcp.fr [Bioinformatics: Structures and Interactions, Institut de Biologie et Chimie des Protéines, BMSSI UMR CNRS 5086/Université Lyon I, 7 Passage du Vercors, Lyon 69367 (France)

2015-12-28

We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.

Improving the treatment of coarse-grain electrostatics: CVCEL

International Nuclear Information System (INIS)

Ceres, N.; Lavery, R.

2015-01-01

We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding

Improving the treatment of coarse-grain electrostatics: CVCEL.

Science.gov (United States)

Ceres, N; Lavery, R

2015-12-28

We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.

Cyclic steps and superimposed antidune deposits: important elements of coarse-grained deepwater channel-levée complexes

Science.gov (United States)

Lang, Joerg; Brandes, Christian; Winsemann, Jutta

2017-04-01

The facies distribution and architecture of submarine fans can be strongly impacted by erosion and deposition by supercritical density flows. We present field examples from the Sandino Forearc Basin (southern Central America), where cyclic-step and antidune deposits represent important sedimentary facies of coarse-grained channel-levée complexes. These bedforms occur in all sub-environments of the depositional systems and relate to the different stages of avulsion, bypass, levée construction and channel backfilling. Large-scale scours (18 to 29 m deep, 18 to 25 m wide, 60 to >120 m long) with an amalgamated infill, comprising massive, normally coarse-tail graded or spaced subhorizontally stratified conglomerates and pebbly sandstones, are interpreted as deposits of the hydraulic-jump zone of cyclic steps. These cyclic steps probably formed during avulsion, when high-density flows were routed into the evolving channel. The large-scale scour fills can be distinguished from small-scale channel fills based on the preservation of a steep upper margin and a coarse-grained infill comprising mainly amalgamated hydraulic-jump deposits. Channel fills include repetitive successions deposited by cyclic steps with superimposed antidunes. The hydraulic-jump zone of cyclic-step deposits comprises regularly spaced scours (0.2 to 2.6 m deep, 0.8 to 23 m wide), which are infilled by intraclast-rich conglomerates or pebbly sandstones and display normal coarse-tail grading or backsets. Laterally and vertically these deposits are associated with subhorizontally stratified, low-angle cross-stratified or sinusoidal stratified pebbly sandstones and sandstones (wavelength 0.5 to 18 m), interpreted as representing antidune deposits formed on the stoss-side of the cyclic steps during flow re-acceleration. The field examples indicate that so-called crudely or spaced stratified deposits may commonly represent antidune deposits with varying stratification styles controlled by the aggradation

Lower Badenian coarse-grained Gilbert deltas in the southern margin of the Western Carpathian Foredeep basin

Science.gov (United States)

Nehyba, Slavomír

2018-02-01

Two coarse-grained Gilbert-type deltas in the Lower Badenian deposits along the southern margin of the Western Carpathian Foredeep (peripheral foreland basin) were newly interpreted. Facies characterizing a range of depositional processes are assigned to four facies associations — topset, foreset, bottomset and offshore marine pelagic deposits. The evidence of Gilbert deltas within open marine deposits reflects the formation of a basin with relatively steep margins connected with a relative sea level fall, erosion and incision. Formation, progradation and aggradation of the thick coarse-grained Gilbert delta piles generally indicate a dramatic increase of sediment supply from the hinterland, followed by both relatively continuous sediment delivery and an increase in accommodation space. Deltaic deposition is terminated by relatively rapid and extended drowning and is explained as a transgressive event. The lower Gilbert delta was significantly larger, more areally extended and reveals a more complicated stratigraphic architecture than the upper one. Its basal surface represents a sequence boundary and occurs around the Karpatian/Badenian stratigraphic limit. Two coeval deltaic branches were recognized in the lower delta with partly different stratigraphic arrangements. This different stratigraphic architecture is mostly explained by variations in the sediment delivery and /or predisposed paleotopography and paleobathymetry of the basin floor. The upper delta was recognized only in a restricted area. Its basal surface represents a sequence boundary probably reflecting a higher order cycle of a relative sea level rise and fall within the Lower Badenian. Evidence of two laterally and stratigraphically separated coarse-grained Gilbert deltas indicates two regional/basin wide transgressive/regressive cycles, but not necessarily of the same order. Provenance analysis reveals similar sources of both deltas. Several partial source areas were identified (Mesozoic

Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

Science.gov (United States)

Cipcigan, Flaviu S.; Sokhan, Vlad P.; Crain, Jason; Martyna, Glenn J.

2016-12-01

One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082-1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230-233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeller through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO_MD.

Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts

Science.gov (United States)

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.

Multi-scale coarse-graining of non-conservative interactions in molecular liquids

International Nuclear Information System (INIS)

Izvekov, Sergei; Rice, Betsy M.

2014-01-01

A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger

Multi-scale coarse-graining of non-conservative interactions in molecular liquids

Energy Technology Data Exchange (ETDEWEB)

Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M. [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States)

2014-03-14

A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger

Applying Ultrasonic Phased Array Technology to Examine Austenitic Coarse-Grained Structures for Light Water Reactor Piping

International Nuclear Information System (INIS)

Anderson, Michael T.; Cumblidge, Stephen E.; Doctor, Steven R.

2003-01-01

Pacific Northwest Laboratory is evaluating the capabilities and limitations of phased array (PA) technology to detect service-type flaws in coarse-grained austenitic piping structures. The work is being sponsored by the U.S. Nuclear Regulatory Commission, Office of Research. This paper presents initial work involving the use of PA technology to determine the effectiveness of detecting and accurately characterizing flaws on the far-side of austenitic piping welds

Principal component analysis acceleration of rovibrational coarse-grain models for internal energy excitation and dissociation

Science.gov (United States)

Bellemans, Aurélie; Parente, Alessandro; Magin, Thierry

2018-04-01

The present work introduces a novel approach for obtaining reduced chemistry representations of large kinetic mechanisms in strong non-equilibrium conditions. The need for accurate reduced-order models arises from compression of large ab initio quantum chemistry databases for their use in fluid codes. The method presented in this paper builds on existing physics-based strategies and proposes a new approach based on the combination of a simple coarse grain model with Principal Component Analysis (PCA). The internal energy levels of the chemical species are regrouped in distinct energy groups with a uniform lumping technique. Following the philosophy of machine learning, PCA is applied on the training data provided by the coarse grain model to find an optimally reduced representation of the full kinetic mechanism. Compared to recently published complex lumping strategies, no expert judgment is required before the application of PCA. In this work, we will demonstrate the benefits of the combined approach, stressing its simplicity, reliability, and accuracy. The technique is demonstrated by reducing the complex quantum N2(g+1Σ) -N(S4u ) database for studying molecular dissociation and excitation in strong non-equilibrium. Starting from detailed kinetics, an accurate reduced model is developed and used to study non-equilibrium properties of the N2(g+1Σ) -N(S4u ) system in shock relaxation simulations.

Multiaxial creep of fine grained 0.5Cr-0.5Mo-0.25V and coarse grained 1Cr-0.5Mo steels

International Nuclear Information System (INIS)

Browne, R.J.; Flewitt, P.E.J.; Lonsdale, D.

1991-01-01

To explore the multiaxial creep response of materials used for electrical power generating plant, two steels, a fine grained 0.5Cr-0.5Mo-0.25V steel in a normalised and tempered condition with high creep ductility and a coarse grained 1Cr-0.5Mo steel in a quenched and tempered condition with low uniaxial creep ductility, have been selected. A range of multiaxial stress testing techniques which span the stress states that would allow identification of any technique dependent variables has been used. The deformation and failure of the normalised and tempered 0.5Cr-0.5Mo-0.25V steel for a range of multiaxial test techniques and, therefore, stress states may be described by an equivalent stress criterion. The results from the multiaxial tests carried out on the fully bainitic 1Cr-0.5Mo steel show that the multiaxial stress rupture criterion (MSRC) varies with stress state; at high triaxiality (notch), it is controlled by the maximum principal stress, whereas at low triaxiality (shear) it is dependent on both maximum principal stress and equivalent stress. Furthermore, a simple description of stress state based on maximum principal and equivalent stress does not define this uniquely, since the MSRC derived from uniaxial and torsion testing does not describe the failure of notch, tube, or double shear tests. (author)

Statistical properties of the coarse-grained velocity gradient tensor in turbulence: Monte-Carlo simulations of the tetrad model

International Nuclear Information System (INIS)

Pumir, Alain; Naso, Aurore

2010-01-01

A proper description of the velocity gradient tensor is crucial for understanding the dynamics of turbulent flows, in particular the energy transfer from large to small scales. Insight into the statistical properties of the velocity gradient tensor and into its coarse-grained generalization can be obtained with the help of a stochastic 'tetrad model' that describes the coarse-grained velocity gradient tensor based on the evolution of four points. Although the solution of the stochastic model can be formally expressed in terms of path integrals, its numerical determination in terms of the Monte-Carlo method is very challenging, as very few configurations contribute effectively to the statistical weight. Here, we discuss a strategy that allows us to solve the tetrad model numerically. The algorithm is based on the importance sampling method, which consists here of identifying and sampling preferentially the configurations that are likely to correspond to a large statistical weight, and selectively rejecting configurations with a small statistical weight. The algorithm leads to an efficient numerical determination of the solutions of the model and allows us to determine their qualitative behavior as a function of scale. We find that the moments of order n≤4 of the solutions of the model scale with the coarse-graining scale and that the scaling exponents are very close to the predictions of the Kolmogorov theory. The model qualitatively reproduces quite well the statistics concerning the local structure of the flow. However, we find that the model generally tends to predict an excess of strain compared to vorticity. Thus, our results show that while some physical aspects are not fully captured by the model, our approach leads to a very good description of several important qualitative properties of real turbulent flows.

String-like collective motion in the α- and β-relaxation of a coarse-grained polymer melt

Science.gov (United States)

Pazmiño Betancourt, Beatriz A.; Starr, Francis W.; Douglas, Jack F.

2018-03-01

Relaxation in glass-forming liquids occurs as a multi-stage hierarchical process involving cooperative molecular motion. First, there is a "fast" relaxation process dominated by the inertial motion of the molecules whose amplitude grows upon heating, followed by a longer time α-relaxation process involving both large-scale diffusive molecular motion and momentum diffusion. Our molecular dynamics simulations of a coarse-grained glass-forming polymer melt indicate that the fast, collective motion becomes progressively suppressed upon cooling, necessitating large-scale collective motion by molecular diffusion for the material to relax approaching the glass-transition. In each relaxation regime, the decay of the collective intermediate scattering function occurs through collective particle exchange motions having a similar geometrical form, and quantitative relationships are derived relating the fast "stringlet" collective motion to the larger scale string-like collective motion at longer times, which governs the temperature-dependent activation energies associated with both thermally activated molecular diffusion and momentum diffusion.

From point process observations to collective neural dynamics: Nonlinear Hawkes process GLMs, low-dimensional dynamics and coarse graining.

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

Abbott, Lauren J.; Stevens, Mark J., E-mail: msteve@sandia.gov [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States)

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.

Coarse-grained molecular simulations of allosteric cooperativity

Energy Technology Data Exchange (ETDEWEB)

Nandigrami, Prithviraj; Portman, John J. [Department of Physics, Kent State University, Kent, Ohio 44242 (United States)

2016-03-14

Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein’s functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca{sup 2+} ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein’s conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca{sup 2+} with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop’s structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

DEFF Research Database (Denmark)

Kato, Yuki; Gorodkin, Jan; Havgaard, Jakob Hull

2017-01-01

. Methods: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes...... without alignment. Results: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity. Conclusions: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs....

Coarse-Grained Model for Water Involving a Virtual Site.

Science.gov (United States)

Deng, Mingsen; Shen, Hujun

2016-02-04

In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones.

A coarse-grained model for synergistic action of multiple enzymes on cellulose

Directory of Open Access Journals (Sweden)

Asztalos Andrea

2012-08-01

Full Text Available Abstract Background Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. Results We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. Conclusions Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures

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

International Nuclear Information System (INIS)

Abbott, Lauren J.; Stevens, Mark J.

2015-01-01

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 atomistic simulations

GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.

Science.gov (United States)

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

2017-08-15

Predicting the 3D structure of RNA molecules is a key feature towards predicting their functions. Methods which work at atomic or nucleotide level are not suitable for large molecules. In these cases, coarse-grained prediction methods aim to predict a shape which could be refined later by using more precise methods on smaller parts of the molecule. We developed a complete method for sampling 3D RNA structure at a coarse-grained model, taking a secondary structure as input. One of the novelties of our method is that a second step extracts two best possible structures close to the native, from a set of possible structures. Although our method benefits from the first version of GARN, some of the main features on GARN2 are very different. GARN2 is much faster than the previous version and than the well-known methods of the state-of-art. Our experiments show that GARN2 can also provide better structures than the other state-of-the-art methods. GARN2 is written in Java. It is freely distributed and available at http://garn.lri.fr/. melanie.boudard@lri.fr or johanne.cohen@lri.fr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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

Energy Technology Data Exchange (ETDEWEB)

Solano Canchaya, José G.; Dequidt, Alain, E-mail: alain.dequidt@univ-bpclermont.fr; Goujon, Florent; Malfreyt, Patrice [Institut de Chimie de Clermont-Ferrand, Université Blaise Pascal, Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand (France); CNRS, UMR 6296, ICCF, F-63178 Aubiere (France)

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 and 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.

Relationship Between Bake Hardening, Snoek-Köster and Dislocation-Enhanced Snoek Peaks in Coarse Grained Low Carbon Steel

Directory of Open Access Journals (Sweden)

Li Weijuan

2016-09-01

Full Text Available In the present work, specimens prepared from coarse grained low carbon steel with different prestrains were baked and then, their bake hardening (BH property and internal friction were determined. TEM was used to characterize the dislocation structure in BH treated samples. The measurements of internal friction in prestrained samples and baked samples were carried out using a multifunctional internal friction apparatus. The results indicate that, in coarse grained low carbon steel, the bake hardening properties (BH values were negative, which were increased by increasing the prestrain from 2 to 5%, and then were decreased by increasing the prestrain from 5 to 10%. In the specimen with prestrain 5%, the BH value reached the maximum value and the height of Snoek-Köster peak was observed to be the maximum alike. With increasing the prestrain, both of the BH value and Snoek-Köster peak heights are similarly varied. It is concluded that Snoek-Köster and dislocation-enhanced Snoek peaks, caused by the interactions between interstitial solute carbon atoms and dislocations, can be used in further development of the bake hardening steels.

Anomalous g-Factors for Charged Leptons in a Fractional Coarse-Grained Approach

International Nuclear Information System (INIS)

Helayël-Neto, J. A.; Weberszpil, J.

2014-01-01

We here propose to extend the concept of helicity to include it in a fractional scenario and we write down the left- and the right-handed Weyl equations from first principles in this extended framework. Next, by coupling the different fractional Weyl sectors by means of a mass parameter, we arrive at the fractional version of Dirac's equation which, whenever coupled to an external electromagnetic field and reduced to the nonrelativistic regime, yields a fractional Pauli-type equation. From the latter, we are able to present an explicit expression for the gyromagnetic ratio of charged fermions in terms of the fractionality parameter. We then focus our efforts to relate the coarse-grained property of space-time to fractionality and to the (g-2) anomalies of the different leptonic species

Non-Steady Oscillatory Flow in Coarse Granular Materials

DEFF Research Database (Denmark)

Andersen, O. H.; Gent, M. R. A. van; Meer, J. W. van der

1992-01-01

Stationary and oscillatory flow through coarse granular materials have been investigated experimentally at Delft Hydraulics in their oscillating water tunnel with the objective of determining the coefficients of the extended Forchheimer equation. Cylinders, spheres and different types of rock have....... Further, for the non-stationary term, the virtual mass coefficient will be derived....

A Bayesian framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems

Energy Technology Data Exchange (ETDEWEB)

Farrell, Kathryn, E-mail: kfarrell@ices.utexas.edu; Oden, J. Tinsley, E-mail: oden@ices.utexas.edu; Faghihi, Danial, E-mail: danial@ices.utexas.edu

2015-08-15

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.

A Bayesian framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems

Science.gov (United States)

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.

Coarse grain model for coupled thermo-mechano-chemical processes and its application to pressure-induced endothermic chemical reactions

International Nuclear Information System (INIS)

Antillon, Edwin; Banlusan, Kiettipong; Strachan, Alejandro

2014-01-01

We extend a thermally accurate model for coarse grain dynamics (Strachan and Holian 2005 Phys. Rev. Lett. 94 014301) to enable the description of stress-induced chemical reactions in the degrees of freedom internal to the mesoparticles. Similar to the breathing sphere model, we introduce an additional variable that describes the internal state of the particles and whose dynamics is governed both by an internal potential energy function and by interparticle forces. The equations of motion of these new variables are derived from a Hamiltonian and the model exhibits two desired features: total energy conservation and Galilean invariance. We use a simple model material with pairwise interactions between particles and study pressure-induced chemical reactions induced by hydrostatic and uniaxial compression. These examples demonstrate the ability of the model to capture non-trivial processes including the interplay between mechanical, thermal and chemical processes of interest in many applications. (paper)

Intrinsic Mechanisms of Ductile-brittle Transition for F460 Steel Welding Coarse Grained Heat Affected Zones with Different Heat Inputs

Directory of Open Access Journals (Sweden)

LI Jing

2016-08-01

Full Text Available Coarse grain heat affected zone (HAZ of F460 steel was simulated by a Gleeble 3800 thermo-mechanical simulator. The microstructure, critical event of the HAZ formed at various heat inputs (E were characterized and determined by optical microscopy (OM and scanning electronic microscopy (SEM, and cleavage fracture stress σf was also calculated by ABAQUS software. Based on above systematic analysis, the intrinsic mechanism of ductile-brittle transition for F460 steel heat affected zones with different heat inputs were revealed. The results indicate that:with the improvement of heat input, the microstructures in sequence are a minority of lath martensite and massive fine lath bainite, more lath bainite with less granular bainite, more granular bainite with less lath bainite, bulky of granular bainite; and the maximum size of the original austenite grain and bainite packet becomes bigger with the improvement of heat input. The size of bainite packet is critical event of the cleavage fracture for coarse grain heat affected zone specimens with various heat inputs by comparing the relationships among residual crack length, original austenite grain size and bainite packet size. With the decreasing of the bainitic packet, the ductile to brittle transition temperature decreases. In addition, cleavage fracture stress σf is also calculated by ABAQUS software, σf gradually decreases with the increase of the heat input, which can explain the intrinsic mechanism of ductile to brittle transition temperature Tk with the change of the heat input.

On the importance of grain size in luminescence dating using quartz

DEFF Research Database (Denmark)

Timar-Gabor, A.; Buylaert, Jan-Pieter; Guralnik, B.

2017-01-01

Chinese loess, thus pointing to a potential worldwide phenomenon. While age underestimation is often attributed to signal saturation problems, this is not the case for fine grain material, which saturates at higher doses than coarse grains, yet begins to underestimate true ages earlier. Here we examine...

Application of physical and numerical simulations for interpretation of peripheral coarse grain structure during hot extrusion of AA7020 aluminum alloy

NARCIS (Netherlands)

Eivani, A.R.; Zhou, J.

2017-01-01

In this research, hot compression test is used to simulate the metallurgical phenomena occurring in the peripheral part of AA7020 aluminum alloy extrudates during hot extrusion and leading to the formation of the peripheral coarse grain (PCG) structure. The temperature profiles at a tracking

Investment strategy due to the minimization of portfolio noise level by observations of coarse-grained entropy

OpenAIRE

Krzysztof Urbanowicz; Janusz A. Holyst

2004-01-01

Using a recently developed method of noise level estimation that makes use of properties of the coarse grained-entropy we have analyzed the noise level for the Dow Jones index and a few stocks from the New York Stock Exchange. We have found that the noise level ranges from 40 to 80 percent of the signal variance. The condition of a minimal noise level has been applied to construct optimal portfolios from selected shares. We show that implementation of a corresponding threshold investment stra...

Dynamics of Coarse-grained Model of Filled Rubber Composite under Deformation

Science.gov (United States)

Hagita, Katsumi; Ueno, Shinichi; Bito, Yasumasa; Takano, Hiroshi; Doi, Masao; Morita, Hiroshi

2010-03-01

We presented a result of coarse-grained Molecular Dynamics simulation of filled polymer melts with Sulfur-crosslink under deformation based on the Kremer-Grest Model. Because all polymer chains are connected to one network gel, the size of simulation box under periodic boundary conditions (PBC) is set to about 33nm. We put 4 fillers, 80 polymer chains of 1024 particles, and many crosslink into the PBC box. One filler consists of 1280 particles of the C1280 fullerene structure. A repulsive force from the center of the filler is applied to the particles of C1280 in order to make a sphere whose diameter is about 15nm. Some patterns of distribution of the fillers are examined. The stress-strain curves estimated by applying a deformation to the system in simulations qualitatively agree with those in experiments. It is successful to show hysteresis on the S-S curve between elongation / release of the filled rubber.

Probing finite coarse-grained virtual Feynman histories with sequential weak values

Science.gov (United States)

Georgiev, Danko; Cohen, Eliahu

2018-05-01

Feynman's sum-over-histories formulation of quantum mechanics has been considered a useful calculational tool in which virtual Feynman histories entering into a coherent quantum superposition cannot be individually measured. Here we show that sequential weak values, inferred by consecutive weak measurements of projectors, allow direct experimental probing of individual virtual Feynman histories, thereby revealing the exact nature of quantum interference of coherently superposed histories. Because the total sum of sequential weak values of multitime projection operators for a complete set of orthogonal quantum histories is unity, complete sets of weak values could be interpreted in agreement with the standard quantum mechanical picture. We also elucidate the relationship between sequential weak values of quantum histories with different coarse graining in time and establish the incompatibility of weak values for nonorthogonal quantum histories in history Hilbert space. Bridging theory and experiment, the presented results may enhance our understanding of both weak values and quantum histories.

Producing laminated NiAl with bimodal distribution of grain size by solid–liquid reaction treatment

DEFF Research Database (Denmark)

Fan, G.H.; Wang, Q.W.; Du, Y.

2014-01-01

The prospect of combining laminated structure design and grain size tailoring to toughen brittle materials is examined. Laminated NiAl consisting of coarse-grained layers and fine-grained layers was fabricated by solid–liquid reaction treatment of stacking Ni and Al foils. The fracture toughness...

Coarse-grained parallel genetic algorithm applied to a nuclear reactor core design optimization problem

International Nuclear Information System (INIS)

Pereira, Claudio M.N.A.; Lapa, Celso M.F.

2003-01-01

This work extends the research related to generic algorithms (GA) in core design optimization problems, which basic investigations were presented in previous work. Here we explore the use of the Island Genetic Algorithm (IGA), a coarse-grained parallel GA model, comparing its performance to that obtained by the application of a traditional non-parallel GA. The optimization problem consists on adjusting several reactor cell parameters, such as dimensions, enrichment and materials, in order to minimize the average peak-factor in a 3-enrichment zone reactor, considering restrictions on the average thermal flux, criticality and sub-moderation. Our IGA implementation runs as a distributed application on a conventional local area network (LAN), avoiding the use of expensive parallel computers or architectures. After exhaustive experiments, taking more than 1500 h in 550 MHz personal computers, we have observed that the IGA provided gains not only in terms of computational time, but also in the optimization outcome. Besides, we have also realized that, for such kind of problem, which fitness evaluation is itself time consuming, the time overhead in the IGA, due to the communication in LANs, is practically imperceptible, leading to the conclusion that the use of expensive parallel computers or architecture can be avoided

Source and depositional processes of coarse-grained limestone event beds in Frasnian slope deposits (Kostomłoty-Mogiłki quarry, Holy Cross Mountains, Poland)

Science.gov (United States)

Vierek, Aleksandra

2010-10-01

The Kostomłoty-Mogiłki succession is situated in the Kostomłoty transitional zone between the shallow-water Kielce stromatoporoid-coral platform and the deeper Łysogóry basin. In the Kostomłoty-Mogiłki quarry, the upper part of the Szydłówek Beds and Kostomłoty Beds are exposed. The Middle-Upper Frasnian Kostomłoty Beds are composed of shales, micritic and nodular limestones with abundant intercalations of detrital limestones. The dark shales and the micritic and nodular limestones record background sedimentation. The interbedded laminated and detrital limestones reflect high-energy deposition (= event beds). These event beds comprise laminated calcisiltites, fine-grained calcarenites, coarse-grained grain-supported calcirudites fabrics, and matrix-supported calcirudites. The material of these event beds was supplied by both erosion of the carbonate-platform margin and cannibalistic erosion of penecontemporaneous detrital limestones building the slope of this platform. Storms and the tectonic activity were likely the main causes of erosion. Combined and gravity flows were the transporting mechanisms involved in the reworking and redeposition.

Dynamic magnetization models for soft ferromagnetic materials with coarse and fine domain structures

Energy Technology Data Exchange (ETDEWEB)

Zirka, S.E., E-mail: zirka@email.dp.ua [Department of Physics and Technology, Dnepropetrovsk National University, Gagarin 72, 49050 Dnepropetrovsk (Ukraine); Moroz, Y.I. [Department of Physics and Technology, Dnepropetrovsk National University, Gagarin 72, 49050 Dnepropetrovsk (Ukraine); Steentjes, S.; Hameyer, K. [Institute of Electrical Machines, RWTH Aachen University, Schinkelstr. 4, 52056 Aachen (Germany); Chwastek, K. [Faculty of Electrical Engineering, Czestochowa University of Technology, al. AK 17, 42-201 Czestochowa (Poland); Zurek, S. [Megger Instruments Ltd., Archcliffe Road, Dover, Kent, CT17 9EN (United Kingdom); Harrison, R.G. [Department of Electronics, Carleton University, Ottawa, Canada K1S 5B6 (Canada)

2015-11-15

We consider dynamic models, both numerical and analytical, that reproduce the magnetization field H(B) and the energy loss in ferromagnetic sheet materials with different domain structures. Conventional non-oriented (NO) and grain-oriented (GO) electrical steels are chosen as typical representatives of fine-domain and coarse-domain materials. The commonly-accepted loss separation procedures in these materials are critically analyzed. The use of a well-known simplified (“classical”) expression for the eddy-current loss is identified as the primary source of mistaken evaluations of excess loss in NO steel, in which the loss components can only be evaluated using the Maxwell (penetration) equation. The situation is quite different in GO steel, in which the loss separation is uncertain, but the total dynamic loss is several times higher than that explained by any version (numerical or analytical) of the classical approach. To illustrate the uncertainty of the loss separation in GO steel, we show that the magnetization field, and thus the total loss, in this material can be represented with equal accuracy using either the existing three-component approach or our proposed two-component technique, which makes no distinction between classical eddy-current and excess fields and losses. - Highlights: • Critical analysis of a ferromagnetic-material loss-separation principle. • This is to warn materials-science engineers about the inaccuracies resulting from this principle. • A transient model having a single dynamic component is proposed.

Investment strategy due to the minimization of portfolio noise level by observations of coarse-grained entropy

Science.gov (United States)

Urbanowicz, Krzysztof; Hołyst, Janusz A.

2004-12-01

Using a recently developed method of noise level estimation that makes use of properties of the coarse-grained entropy, we have analyzed the noise level for the Dow Jones index and a few stocks from the New York Stock Exchange. We have found that the noise level ranges from 40% to 80% of the signal variance. The condition of a minimal noise level has been applied to construct optimal portfolios from selected shares. We show that the implementation of a corresponding threshold investment strategy leads to positive returns for historical data.

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

Directory of Open Access Journals (Sweden)

Vakser Ilya A

2011-07-01

Full Text Available Abstract Background Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom pairs in the non-interaction state. Results The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the DOCKGROUND resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results. Conclusions A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of

Representing environment-induced helix-coil transitions in a coarse grained peptide model

Science.gov (United States)

Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine

2016-10-01

Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that

Time evolution of the coarse-graining-smoothed Wigner operator in an amplitude dissipative channel: from a pure state to a mixed state

International Nuclear Information System (INIS)

He, Rui; Fan, Hong-yi

2014-01-01

Based on the solution to the master equation of the density operator describing the amplitude dissipative channel, we derive the time evolution law of the coarse-graining-smoothed Wigner operator in this channel, which demonstrates how an initial pure state evolves into a mixed state, exhibiting decoherence

Twist-writhe partitioning in a coarse-grained DNA minicircle model

Science.gov (United States)

Sayar, Mehmet; Avşaroǧlu, Barış; Kabakçıoǧlu, Alkan

2010-04-01

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular-dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality, and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion; therefore, our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.

Systematic methods for defining coarse-grained maps in large biomolecules.

Science.gov (United States)

Zhang, Zhiyong

2015-01-01

Large biomolecules are involved in many important biological processes. It would be difficult to use large-scale atomistic molecular dynamics (MD) simulations to study the functional motions of these systems because of the computational expense. Therefore various coarse-grained (CG) approaches have attracted rapidly growing interest, which enable simulations of large biomolecules over longer effective timescales than all-atom MD simulations. The first issue in CG modeling is to construct CG maps from atomic structures. In this chapter, we review the recent development of a novel and systematic method for constructing CG representations of arbitrarily complex biomolecules, in order to preserve large-scale and functionally relevant essential dynamics (ED) at the CG level. In this ED-CG scheme, the essential dynamics can be characterized by principal component analysis (PCA) on a structural ensemble, or elastic network model (ENM) of a single atomic structure. Validation and applications of the method cover various biological systems, such as multi-domain proteins, protein complexes, and even biomolecular machines. The results demonstrate that the ED-CG method may serve as a very useful tool for identifying functional dynamics of large biomolecules at the CG level.

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

Science.gov (United States)

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

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

Science.gov (United States)

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

Construction of continuous cooling transformation (CCT) diagram using Gleeble for coarse grained heat affected zone of SA106 grade B steel

Science.gov (United States)

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.

Grain interaction effects in polycrystalline Cu

DEFF Research Database (Denmark)

Thorning, C.; Somers, Marcel A.J.; Wert, John A.

2005-01-01

Crystal orientation maps for a grain in a deformed Cu polycrystal have been analysed with the goal of understanding the effect of grain interactions on orientation subdivision. The polycrystal was incrementally strained in tension to 5, 8, 15 and 25% extension; a crystal orientation map...... was measured after each strain increment. The measurements are represented as rotations from the initial crystal orientation. A coarse domain structure forms in the initial 5% strain increment and persists at higher strains. Crystal rotations for all coarse domains in the grain are consistent with the full...... range of Tailor solutions for axisymmetric strain; grain interactions are not required to account for the coarse domain structure. Special orientation domains extend 20-100 µm into the grain at various locations around its periphery. The special orientation domain morphologies include layers along...

Exploration of conformational changes in lactose permease upon sugar binding and proton transfer through coarse-grained simulations.

Science.gov (United States)

Jewel, Yead; Dutta, Prashanta; Liu, Jin

2017-10-01

Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H + symport process. Lactose/H + symport is a highly complex process that involves sugar translocation, H + transfer, and large-scale protein conformational changes. The complete picture of lactose/H + symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-d-galactopyranosyl-1-thio- β-d-galactopyranoside (TDG) molecule to a wild-type LacY. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from ∼5.5 µs simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with double electron-electron resonance and thiol cross-linking experiments. Our analysis suggests that the conformational changes of LacY are a cumulative consequence of interdomain H-bonds breaking at the periplasmic side, interdomain salt-bridge formation at the cytoplasmic side, and the TDG orientational changes during the transition. © 2017 Wiley Periodicals, Inc.

Coarse-grained representation of the quasi adiabatic propagator path integral for the treatment of non-Markovian long-time bath memory

Science.gov (United States)

Richter, Martin; Fingerhut, Benjamin P.

2017-06-01

The description of non-Markovian effects imposed by low frequency bath modes poses a persistent challenge for path integral based approaches like the iterative quasi-adiabatic propagator path integral (iQUAPI) method. We present a novel approximate method, termed mask assisted coarse graining of influence coefficients (MACGIC)-iQUAPI, that offers appealing computational savings due to substantial reduction of considered path segments for propagation. The method relies on an efficient path segment merging procedure via an intermediate coarse grained representation of Feynman-Vernon influence coefficients that exploits physical properties of system decoherence. The MACGIC-iQUAPI method allows us to access the regime of biological significant long-time bath memory on the order of hundred propagation time steps while retaining convergence to iQUAPI results. Numerical performance is demonstrated for a set of benchmark problems that cover bath assisted long range electron transfer, the transition from coherent to incoherent dynamics in a prototypical molecular dimer and excitation energy transfer in a 24-state model of the Fenna-Matthews-Olson trimer complex where in all cases excellent agreement with numerically exact reference data is obtained.

Coarse and nano emulsions for effective delivery of the natural pest control agent pulegone for stored grain protection.

Science.gov (United States)

Golden, Gilad; Quinn, Elazar; Shaaya, Eli; Kostyukovsky, Moshe; Poverenov, Elena

2018-04-01

One of the most significant contributors to the global food crisis is grain loss during storage, mainly caused by pest insects. Currently, there are two main methods used for insect pest control: fumigation and grain protection using contact insecticides. As some chemical insecticides can harm humans and the environment, there is a global tendency to reduce their use by finding alternative eco-friendly approaches. In this study, the natural pest-managing agent pulegone was encapsulated into coarse and nano emulsions. The emulsions were characterized using spectroscopic and microscopic methods and their stability and pulegone release ability were examined. The insecticidal activity of the prepared formulations against two stored product insects, rice weevil (Sitophilus oryzae L.) and red flour beetle (Tribolium castaneum Herbst), was demonstrated. The nano emulsion-based formulation offered significant advantages and provided powerful bioactivity, with high (> 90%) mortality rates for as long as 5 weeks for both insects, whereas coarse emulsions showed high efficacy for only 1 week. The developed pulegone-based nano emulsions could serve as a model for an effective alternative method for pest control. Although pulegone is from a natural source, toxicological studies should be performed before the widespread application of pulegone or pulegone-containing essential oils to dry food products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

A new algorithm for construction of coarse-grained sites of large biomolecules.

Science.gov (United States)

Li, Min; Zhang, John Z H; Xia, Fei

2016-04-05

The development of coarse-grained (CG) models for large biomolecules remains a challenge in multiscale simulations, including a rigorous definition of CG representations for them. In this work, we proposed a new stepwise optimization imposed with the boundary-constraint (SOBC) algorithm to construct the CG sites of large biomolecules, based on the s cheme of essential dynamics CG. By means of SOBC, we can rigorously derive the CG representations of biomolecules with less computational cost. The SOBC is particularly efficient for the CG definition of large systems with thousands of residues. The resulted CG sites can be parameterized as a CG model using the normal mode analysis based fluctuation matching method. Through normal mode analysis, the obtained modes of CG model can accurately reflect the functionally related slow motions of biomolecules. The SOBC algorithm can be used for the construction of CG sites of large biomolecules such as F-actin and for the study of mechanical properties of biomaterials. © 2015 Wiley Periodicals, Inc.

Elastic deformation and failure in protein filament bundles: Atomistic simulations and coarse-grained modeling.

Science.gov (United States)

Hammond, Nathan A; Kamm, Roger D

2008-07-01

The synthetic peptide RAD16-II has shown promise in tissue engineering and drug delivery. It has been studied as a vehicle for cell delivery and controlled release of IGF-1 to repair infarcted cardiac tissue, and as a scaffold to promote capillary formation for an in vitro model of angiogenesis. The structure of RAD16-II is hierarchical, with monomers forming long beta-sheets that pair together to form filaments; filaments form bundles approximately 30-60 nm in diameter; branching networks of filament bundles form macroscopic gels. We investigate the mechanics of shearing between the two beta-sheets constituting one filament, and between cohered filaments of RAD16-II. This shear loading is found in filament bundle bending or in tensile loading of fibers composed of partial-length filaments. Molecular dynamics simulations show that time to failure is a stochastic function of applied shear stress, and that for a given loading time behavior is elastic for sufficiently small shear loads. We propose a coarse-grained model based on Langevin dynamics that matches molecular dynamics results and facilities extending simulations in space and time. The model treats a filament as an elastic string of particles, each having potential energy that is a periodic function of its position relative to the neighboring filament. With insight from these simulations, we discuss strategies for strengthening RAD16-II and similar materials.

Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations

DEFF Research Database (Denmark)

Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit

2012-01-01

Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic...... resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates...

Representing the Marginal Stability of Peptides in Coarse Grained Models

Science.gov (United States)

Sayar, Mehmet; Dalgicdir, Cahit; Ramezanghorbani, Farhad

Tertiary structure of proteins is only marginally stable; such that the folded structure is separated from local minima by as little as 10 kcal/mol. In particular for intrinsically disordered peptides, this marginal stability is key to understanding their complex behavior. Bottom-up coarse grained (CG) models for proteins/peptides which rely on structural and/or thermodynamic reference data from experiments or all atom simulations inherently focus on the equilibrium structure and fail to capture the conformational dynamics of the molecule. In this study, we present a CG model for a synthetic peptide, LK, which successfully captures the conformational flexibility of the molecule in different environments. LK peptide is composed of leucine and lysine residues and displays a stark conformational transition from a degenerate conformation in dilute solution to a fully stable alpha-helix at macroscopic and molecular interfaces. In this study we demonstrate that by carefully combining atomistic references from both the unfolded and folded states, one can create a CG model that can represent not only the folded state, but also the conformational transitions that the peptide exhibits in response to changes in the environment. M. Sayar thanks TÜBİTAK (Grant No. 212T184) and TÜBA Distinguished Young Scientist Award (2012 awardee) for financial support.

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

Science.gov (United States)

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).

A hierarchical coarse-grained (all-atom to all residue) approach to peptides (P1, P2) binding with a graphene sheet

Science.gov (United States)

Pandey, Ras; Kuang, Zhifeng; Farmer, Barry; Kim, Sang; Naik, Rajesh

2012-02-01

Recently, Kim et al. [1] have found that peptides P1: HSSYWYAFNNKT and P2: EPLQLKM bind selectively to graphene surfaces and edges respectively which are critical in modulating both the mechanical as well as electronic transport properties of graphene. Such distinctions in binding sites (edge versus surface) observed in electron micrographs were verified by computer simulation by an all-atomic model that captures the pi-pi bonding. We propose a hierarchical approach that involves input from the all-atom Molecular Dynamics (MD) study (with atomistic detail) into a coarse-grained Monte Carlo simulation to extend this study further to a larger scale. The binding energy of a free amino acid with the graphene sheet from all-atom simulation is used in the interaction parameter for the coarse-grained approach. Peptide chain executes its stochastic motion with the Metropolis algorithm. We investigate a number of local and global physical quantities and find that peptide P1 is likely to bind more strongly to graphene sheet than P2 and that it is anchored by three residues ^4Y^5W^6Y. [1] S.N. Kim et al J. Am. Chem. Soc. 133, 14480 (2011).

Competing Grain Boundary and Interior Deformation Mechanisms with Varying Sizes

Energy Technology Data Exchange (ETDEWEB)

Zhang, Wei [University of Tennessee (UT); Gao, Yanfei [ORNL; Nieh, T. G. [University of Tennessee, Knoxville (UTK)

2018-01-01

In typical coarse-grained alloys, the dominant plastic deformations are dislocation gliding or climbing, and material strengths can be tuned by dislocation interactions with grain boundaries, precipitates, solid solutions, and other defects. With the reduction of grain size, the increase of material strengths follows the classic Hall-Petch relationship up to nano-grained materials. Even at room temperatures, nano-grained materials exhibit strength softening, or called the inverse Hall-Petch effect, as grain boundary processes take over as the dominant deformation mechanisms. On the other hand, at elevated temperatures, grain boundary processes compete with grain interior deformation mechanisms over a wide range of the applied stress and grain sizes. This book chapter reviews and compares the rate equation model and the microstructure-based finite element simulations. The latter explicitly accounts for the grain boundary sliding, grain boundary diffusion and migration, as well as the grain interior dislocation creep. Therefore the explicit finite element method has clear advantages in problems where microstructural heterogeneities play a critical role, such as in the gradient microstructure in shot peening or weldment. Furthermore, combined with the Hall-Petch effect and its breakdown, the above competing processes help construct deformation mechanism maps by extending from the classic Frost-Ashby type to the ones with the dependence of grain size.

Unconfined twist : a simple method to prepare ultrafine grained metallic materials.

Energy Technology Data Exchange (ETDEWEB)

Zhao, Y. (Yonghao); Liao, Xiaozhou; Zhu, Y. T. (Yuntian Theodore)

2004-01-01

A new simple method - unconfined twist was employed to prepare ultrafine grained (UFG) Fe,wire. A coarse grained (CG) Fe wire with a diameter of 0.85 mm was fixed at one end, and twisted at the other end. After maximum twist before fracture, in the cross-sectional plane, concentrically deformed layers with a width of several micrometers formed surrounding the center axis of the wire. The near-surface deformed layers consist of lamella grains with a width in submicrometer range. In the longitudinal plane, deformed bands (with a width of several micrometers) formed uniformly, which were composed of lamella crystallites (with a width in submicrometer range). The tensile yield strength and ultimate strength of the twisted Fe wire are increased by about 150% and 100% compared with the values of its CG counterpart.

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

Science.gov (United States)

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.

Algorithm for simulation of quantum many-body dynamics using dynamical coarse-graining

International Nuclear Information System (INIS)

Khasin, M.; Kosloff, R.

2010-01-01

An algorithm for simulation of quantum many-body dynamics having su(2) spectrum-generating algebra is developed. The algorithm is based on the idea of dynamical coarse-graining. The original unitary dynamics of the target observables--the elements of the spectrum-generating algebra--is simulated by a surrogate open-system dynamics, which can be interpreted as weak measurement of the target observables, performed on the evolving system. The open-system state can be represented by a mixture of pure states, localized in the phase space. The localization reduces the scaling of the computational resources with the Hilbert-space dimension n by factor n 3/2 (ln n) -1 compared to conventional sparse-matrix methods. The guidelines for the choice of parameters for the simulation are presented and the scaling of the computational resources with the Hilbert-space dimension of the system is estimated. The algorithm is applied to the simulation of the dynamics of systems of 2x10 4 and 2x10 6 cold atoms in a double-well trap, described by the two-site Bose-Hubbard model.

The attachment of α -synuclein to a fiber: A coarse-grain approach

Science.gov (United States)

Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.

2017-03-01

We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson's disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet. Flexible linkers between the particles enable sampling of the tertiary structure. This novel model is applied here to study the growth of an amyloid fibril, by calculating the free energy profile of a protein attaching to the end of a fibril. The simulation results suggest that the attaching protein readily becomes trapped in a mis-folded state, thereby inhibiting further growth of the fibril until the protein has readjusted to conform to the fibril structure, in line with experimental findings and previous simulations on small fragments of other proteins.

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.

Science.gov (United States)

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.

Randomly grain growth in metallic materials

Energy Technology Data Exchange (ETDEWEB)

Ramirez, A. [Instituto Politecnico Nacional, (SEPI-ESIME), Unidad Profesional Ticoman, Av. Ticoman 600, Del. G.A.M., C.P. 07340 Distrito Federal, Mexico (Mexico); Instituto Politecnico Nacional, (SEPI-ESIQIE), Unidad Profesional Zacatenco, Edif. 6 y Edif. Z planta baja C.P.07300, Distrito Federal, Mexico (Mexico)], E-mail: adaramil@yahoo.com.mx; Chavez, F. [Instituto Politecnico Nacional, (SEPI-ESIQIE), Unidad Profesional Zacatenco, Edif. 6 y Edif. Z planta baja C.P.07300, Distrito Federal, Mexico (Mexico); Demedices, L. [Instituto Politecnico Nacional, (SEPI-ESIME), Unidad Profesional Ticoman, Av. Ticoman 600, Del. G.A.M., C.P. 07340 Distrito Federal, Mexico (Mexico); Instituto Politecnico Nacional, (SEPI-ESIQIE), Unidad Profesional Zacatenco, Edif. 6 y Edif. Z planta baja C.P.07300, Distrito Federal, Mexico (Mexico); Cruz, A.; Macias, M. [Instituto Politecnico Nacional, (SEPI-ESIQIE), Unidad Profesional Zacatenco, Edif. 6 y Edif. Z planta baja C.P.07300, Distrito Federal, Mexico (Mexico)

2009-10-30

Computational modeling of grain structures is a very important topic in materials science. In this work, the development of the computational algorithms for a mathematical model to predict grain nucleation and grain growth is presented. The model place a number of nucleated points randomly in a liquid pool according with the solid and liquid fractions (X{sub sol} and X{sub liq}) of metal solute and the local temperature distribution (SS{sub I,J}). Then these points grows isotropically until obtain a grain structure with straight interfaces. Different grain morphologies such as columnar and equiaxed can be obtained as a function of the temperature distributions and growth directions.

Randomly grain growth in metallic materials

International Nuclear Information System (INIS)

Ramirez, A.; Chavez, F.; Demedices, L.; Cruz, A.; Macias, M.

2009-01-01

Computational modeling of grain structures is a very important topic in materials science. In this work, the development of the computational algorithms for a mathematical model to predict grain nucleation and grain growth is presented. The model place a number of nucleated points randomly in a liquid pool according with the solid and liquid fractions (X sol and X liq ) of metal solute and the local temperature distribution (SS I,J ). Then these points grows isotropically until obtain a grain structure with straight interfaces. Different grain morphologies such as columnar and equiaxed can be obtained as a function of the temperature distributions and growth directions.

A Coarse-Grained Molecular Dynamics Study of DLPC, DMPC, DPPC, and DSPC Mixtures in Aqueous Solution

Directory of Open Access Journals (Sweden)

Roghayeh Abedi Karjiban

2013-01-01

Full Text Available The structural and dynamics properties of the bilayer comprising 128 molecules of dipalmitoylphosphatidylcholine (DPPC, dilauroylphosphatidylcholine (DLPC, dimyristoylphosphatidylcholine (DMPC, and distearoylphosphatidylcholine (DSPC in water were investigated using a coarse-grained molecular dynamics (CG-MD simulation technique. The model mixture system was simulated at 298 K under semi-isotropic pressure conditions. The aggregation was initiated from the random configurations followed by the formation of a bilayer over a period of 500 ns. The calculated values of the area per lipid, thickness, and lateral diffusion for the mixed model were different from when a single lipid was used. Our results confirmed that the chain length of the lipid molecules strongly affects the phospholipid bilayer’s physical properties.

Transferable coarse-grained model for perfluorosulfonic acid polymer membranes

Science.gov (United States)

Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru

2017-09-01

Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

Energy Technology Data Exchange (ETDEWEB)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de [Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt (Germany)

2014-12-14

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 from 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.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

International Nuclear Information System (INIS)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der

2014-01-01

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 from 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

Deformation and fracture of Coarse-grained Model of Filled Rubber Composites

Science.gov (United States)

Hagita, Katsumi; Morita, Hiroshi; Doi, Masao; Takano, Hiroshi

2011-03-01

We presented a result of coarse-grained Molecular Dynamics simulation of filled polymer melts with Sulfur-crosslink under deformation based on the Kremer-Grest Model. Under uni-axial deformation (extension) by setting Poisson's ratio to less than 0.5, facture of this polymer nanocomoposites occurs due to volume increase for increasing the strain. In order to study facture behavior, we use the original Lennard Jones potential formula (with attractive part) as interaction between polymers. The size of simulation box under periodic boundary conditions (PBC) is set to about 133nm. We put 2048 fillers, 5120 polymer chains of 1024 particles, and many crosslink into the PBC box. Due to the crosslink, all polymer chains are connected to one network gel. One filler consists of 320 particles of the C320 fullerene structure. A repulsive force from the center of the filler is applied to the particles of C320 in order to make a sphere whose diameter is about 7nm. We can observe the fracture occurs due to void created near surface of fillers for the case that interaction between polymer and filler is relatively non- attractive. Various cases of Poisson's ratio and interaction between polymer and filler are examined.

An accurate coarse-grained model for chitosan polysaccharides in aqueous solution.

Directory of Open Access Journals (Sweden)

Levan Tsereteli

Full Text Available Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides. The model is validated against experimental data for Chitosan molecules in solution with various degree of deacetylation, and is shown to closely reproduce the available experimental data. For long polymers, subtle differences of the free energy maps of the glycosidic links are found to significantly affect the measurable polymer properties. Therefore, for titratable monomers the free energy maps of the corresponding links are updated according to the current charge of the monomers. We then characterize the microscopic and mesoscopic structural properties of large chitosan polysaccharides in solution for a wide range of solvent pH and ionic strength, and investigate the effect of polymer length and degree and pattern of deacetylation on the polymer properties.

An accurate coarse-grained model for chitosan polysaccharides in aqueous solution.

Science.gov (United States)

Tsereteli, Levan; Grafmüller, Andrea

2017-01-01

Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides. The model is validated against experimental data for Chitosan molecules in solution with various degree of deacetylation, and is shown to closely reproduce the available experimental data. For long polymers, subtle differences of the free energy maps of the glycosidic links are found to significantly affect the measurable polymer properties. Therefore, for titratable monomers the free energy maps of the corresponding links are updated according to the current charge of the monomers. We then characterize the microscopic and mesoscopic structural properties of large chitosan polysaccharides in solution for a wide range of solvent pH and ionic strength, and investigate the effect of polymer length and degree and pattern of deacetylation on the polymer properties.

Effect of inter-critically reheating temperature on microstructure and properties of simulated inter-critically reheated coarse grained heat affected zone in X70 steel

International Nuclear Information System (INIS)

Zhu, Zhixiong; Kuzmikova, Lenka; Li, Huijun; Barbaro, Frank

2014-01-01

This study investigated the influence of the inter-critical reheating temperature on the microstructure and mechanical properties of a coarse grained heat affected zone (CGHAZ) in an API 5L grade X70 pipeline steel seam weld. A Gleeble 3500 thermo-mechanical simulator was employed to duplicate particular weld thermal cycles in order to accurately assess specific regions of the weld HAZ. Detailed microstructural analysis, including investigation of the martensite–austenite (M–A) constituent, was performed using optical microscope (OM), scanning electron microscope (SEM) and selective etching techniques. It is shown that the fracture toughness of the CGHAZ is significantly reduced following exposure to a subsequent inter-critical thermal cycle. Fracture toughness gradually improves as the inter-critical temperature is increased, but does not return to the value of the original CGHAZ due to the presence of isolated large M–A particles and coarse microstructure. Significance of M–A particles to the HAZ fracture toughness is first related to the location of particles along prior austenite grain boundaries, followed by the size of individual M–A particles

Grain boundary and triple junction diffusion in nanocrystalline copper

Energy Technology Data Exchange (ETDEWEB)

Wegner, M., E-mail: m.wegner@uni-muenster.de; Leuthold, J.; Peterlechner, M.; Divinski, S. V., E-mail: divin@uni-muenster.de [Institut für Materialphysik, Universität Münster, Wilhelm-Klemm-Straße 10, D-48149, Münster (Germany); Song, X., E-mail: xysong@bjut.edu.cn [College of Materials Science and Engineering, Beijing University of Technology, 100124 Beijing (China); Wilde, G. [Institut für Materialphysik, Universität Münster, Wilhelm-Klemm-Straße 10, D-48149, Münster (Germany); Institute of Nanochemistry and Nanobiology, School of Environmental and Chemical Engineering, Shanghai University, 200444 Shanghai (China)

2014-09-07

Grain boundary and triple junction diffusion in nanocrystalline Cu samples with grain sizes, 〈d〉, of ∼35 and ∼44 nm produced by spark plasma sintering were investigated by the radiotracer method using the {sup 63}Ni isotope. The measured diffusivities, D{sub eff}, are comparable with those determined previously for Ni grain boundary diffusion in well-annealed, high purity, coarse grained, polycrystalline copper, substantiating the absence of a grain size effect on the kinetic properties of grain boundaries in a nanocrystalline material at grain sizes d ≥ 35 nm. Simultaneously, the analysis predicts that if triple junction diffusion of Ni in Cu is enhanced with respect to the corresponding grain boundary diffusion rate, it is still less than 500⋅D{sub gb} within the temperature interval from 420 K to 470 K.

Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations

DEFF Research Database (Denmark)

Koivuniemi, A.; Vuorela, T.; Kovanen, P. T.

2012-01-01

molecular dynamics simulations to unravel the mechanisms associated with the CETP-mediated lipid exchange. To this end we used both atomistic and coarse-grained models whose results were consistent with each other. We found CETP to bind to the surface of high density lipoprotein (HDL) -like lipid droplets......Cholesteryl ester transfer protein (CETP) transports cholesteryl esters, triglycerides, and phospholipids between different lipoprotein fractions in blood plasma. The inhibition of CETP has been shown to be a sound strategy to prevent and treat the development of coronary heart disease. We employed...... evidence that helix X acts as a lid which conducts lipid exchange by alternating the open and closed states. The findings have potential for the design of novel molecular agents to inhibit the activity of CETP....

Multiscale crystal defect dynamics: A coarse-grained lattice defect model based on crystal microstructure

Science.gov (United States)

Lyu, Dandan; Li, Shaofan

2017-10-01

Crystal defects have microstructure, and this microstructure should be related to the microstructure of the original crystal. Hence each type of crystals may have similar defects due to the same failure mechanism originated from the same microstructure, if they are under the same loading conditions. In this work, we propose a multiscale crystal defect dynamics (MCDD) model that models defects by considering its intrinsic microstructure derived from the microstructure or material genome of the original perfect crystal. The main novelties of present work are: (1) the discrete exterior calculus and algebraic topology theory are used to construct a scale-up (coarse-grained) dual lattice model for crystal defects, which may represent all possible defect modes inside a crystal; (2) a higher order Cauchy-Born rule (up to the fourth order) is adopted to construct atomistic-informed constitutive relations for various defect process zones, and (3) an hierarchical strain gradient theory based finite element formulation is developed to support an hierarchical multiscale cohesive (process) zone model for various defects in a unified formulation. The efficiency of MCDD computational algorithm allows us to simulate dynamic defect evolution at large scale while taking into account atomistic interaction. The MCDD model has been validated by comparing of the results of MCDD simulations with that of molecular dynamics (MD) in the cases of nanoindentation and uniaxial tension. Numerical simulations have shown that MCDD model can predict dislocation nucleation induced instability and inelastic deformation, and thus it may provide an alternative solution to study crystal plasticity.

Effect of coarse {gamma} grain size on the dynamic and static recrystallisation during hot working in microalloyed Nb and Nb-Ti steels

Energy Technology Data Exchange (ETDEWEB)

Fernandez, A.I.; Abad, R.; Lopez, B.; Rodriguez-Ibabe, J.M. [Centro de Estudios e Investigaciones Tecnicas de Guipuzcoa (CEIT), San Sebastian (Spain)

1998-10-01

The effect of coarse austenite grain size on the dynamic and static recrystallisation kinetics of two microalloyed Nb and Nb-Ti steels has been investigated in the present work. To characterize the dynamic recrystallisation behaviour of the austenite, continuous-torsion tests were carried out after the reheating of the specimen at different temperatures in the range 1000-1420 C. It has been observed that the occurrence of dynamic recrystallisation is dependent on the initial grain size and the deformation conditions (temperature and strain-rate). Decreasing values of the Zener-Hollomon parameter (Z) and grain size promotes dynamic recrystallisation. However for the coarser grain sizes no peaks appear on the flow curves above a determined value of Z. This value seems to decrease with increasing the grain size. An equation to predict the {epsilon}{sub p} peak strain for a wide range of grain sizes has been obtained for both steels. The effect of strain on the static recrystallisation of the austenite, having a large grain size, has been also studied. Interrupted-torsion tests were performed to determined the fractional softening. A quadratic dependence of t{sub 0.5} on strain has been observed, denoting a less dependence of recrystallisation on strain than proposed previously by other authors in the range of lower grain sizes. (orig.) 22 refs.

A Tri-modal 2024 Al -B4C composites with super-high strength and ductility: Effect of coarse-grained aluminum fraction on mechanical behavior

Directory of Open Access Journals (Sweden)

Alireza Abdollahi

2014-12-01

Full Text Available In this study, ultrafine grained 2024 Al alloy based B4C particles reinforced composite was produced by mechanical milling and hot extrusion. Mechanical milling was used to synthesize the nanostructured Al2024 in attrition mill under argon atmosphere up to 50h. A similar process was used to produce Al2024-5%wt. B4C composite powder. To produce trimodal composites, milled powders were combined with coarse grained aluminum in 30 and 50 wt% and then were exposed to hot extrusion at 570°C. The microstructure of hot extruded samples were studied by optical microscope, Transmission electron microscope (TEM and scanning electron microscope (SEM equipped with EDS spectroscopy. The mechanical properties of samples were compared by using tensile, compression and hardness tests. The results showed that the strength, after 50 h milling and addition of 5wt% B4C, increased from 340 to 582 MPa and the hardness increased from 87 HBN to 173 HBN, but the elongation decreased from 14 to 0.5%. By adding the coarse-grained aluminum powder, the strength and hardness decreased slightly, but the increases in return. Ductility increase is the result of increase in dislocation movements and strength increase is the result of restriction in plastic deformation by nanostructured regions. Furthermore, the strength and hardness of trimodal composites were higher, but their ductility was lower.

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

Science.gov (United States)

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

Grain-boundary engineering applied to grain growth in a high temperature material

International Nuclear Information System (INIS)

Huda, Z.

1993-01-01

Crystallography of grain boundaries are determined for a high temperature material, before and after grain growth processes, so as to study the induction of special properties useful for application in components of a gas-turbine engine. The philosophy of grain-boundary engineering is applied to grain growth in APK-6, a powder formed nickel-base superalloy so as to establish the possible structure/property relationships. The alloy in the as received condition is shown to possess a strong texture and contained coincident site lattices (CSL) boundaries with most boundaries having sigma values in the range of 3 > sigma > 25. A normal grain-growth heat treatment result in a good population of low angle grain boundaries, and drastically reduces the proportion of CSL boundaries. A strong [011] annealing texture is observed after an intermediate grain growth; most grain boundaries, here, tend to be high angle indicating a possibility of possessing special properties. (author)

Preparation of bimodal grain size 7075 aviation aluminum alloys and their corrosion properties

Directory of Open Access Journals (Sweden)

Wenming TIAN

2017-10-01

Full Text Available The bimodal grain size metals show improved strength and ductility compared to traditional metals; however, their corrosion properties are unknown. In order to evaluate the corrosion properties of these metals, the bimodal grain size 7075 aviation aluminum alloys containing different ratios of coarse (100 μm in diameter and fine (10 μm in diameter grains were prepared by spark plasma sintering (SPS. The effects of grain size as well as the mixture degree of coarse and fine grains on general corrosion were estimated by immersion tests, electrochemical measurements and complementary techniques such as scanning electron microscope (SEM and transmission electron microscope-energy disperse spectroscopy (TEM-EDS. The results show that, compared to fine grains, the coarse grains have a faster dissolution rate in acidic NaCl solution due to the bigger size, higher alloying elements content and larger area fraction of second phases in them. In coarse grains, the hydrogen ions have a faster reduction rate on cathodic second phases, therefore promoting the corrosion propagation. The mixture of coarse and fine grains also increases the electrochemical heterogeneity of alloys in micro-scale, and thus the increased mixture degree of these grains in metal matrix accelerates the corrosion rate of alloys in acidic NaCl solution.

Estimation of a noise level using coarse-grained entropy of experimental time series of internal pressure in a combustion engine

International Nuclear Information System (INIS)

Litak, Grzegorz; Taccani, Rodolfo; Radu, Robert; Urbanowicz, Krzysztof; HoIyst, Janusz A.; Wendeker, MirosIaw; Giadrossi, Alessandro

2005-01-01

We report our results on non-periodic experimental time series of pressure in a single cylinder spark ignition engine. The experiments were performed for different levels of loading. We estimate the noise level in internal pressure calculating the coarse-grained entropy from variations of maximal pressures in successive cycles. The results show that the dynamics of the combustion is a non-linear multidimensional process mediated by noise. Our results show that so defined level of noise in internal pressure is not monotonous function of loading

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

Science.gov (United States)

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.

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

Energy Technology Data Exchange (ETDEWEB)

Li, Chunhua [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States); Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Su, Jiguo, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [College of Science, Yanshan University, Qinhuangdao 066004 (China); Zhang, Yang, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States)

2016-07-07

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

Coarse-grained molecular simulation of epidermal growth factor receptor protein tyrosine kinase multi-site self-phosphorylation.

Directory of Open Access Journals (Sweden)

John G Koland

2014-01-01

Full Text Available Upon the ligand-dependent dimerization of the epidermal growth factor receptor (EGFR, the intrinsic protein tyrosine kinase (PTK activity of one receptor monomer is activated, and the dimeric receptor undergoes self-phosphorylation at any of eight candidate phosphorylation sites (P-sites in either of the two C-terminal (CT domains. While the structures of the extracellular ligand binding and intracellular PTK domains are known, that of the ∼225-amino acid CT domain is not, presumably because it is disordered. Receptor phosphorylation on CT domain P-sites is critical in signaling because of the binding of specific signaling effector molecules to individual phosphorylated P-sites. To investigate how the combination of conventional substrate recognition and the unique topological factors involved in the CT domain self-phosphorylation reaction lead to selectivity in P-site phosphorylation, we performed coarse-grained molecular simulations of the P-site/catalytic site binding reactions that precede EGFR self-phosphorylation events. Our results indicate that self-phosphorylation of the dimeric EGFR, although generally believed to occur in trans, may well occur with a similar efficiency in cis, with the P-sites of both receptor monomers being phosphorylated to a similar extent. An exception was the case of the most kinase-proximal P-site-992, the catalytic site binding of which occurred exclusively in cis via an intramolecular reaction. We discovered that the in cis interaction of P-site-992 with the catalytic site was facilitated by a cleft between the N-terminal and C-terminal lobes of the PTK domain that allows the short CT domain sequence tethering P-site-992 to the PTK core to reach the catalytic site. Our work provides several new mechanistic insights into the EGFR self-phosphorylation reaction, and demonstrates the potential of coarse-grained molecular simulation approaches for investigating the complexities of self-phosphorylation in

Transport properties of olivine grain boundaries from electrical conductivity experiments

Science.gov (United States)

Pommier, Anne; Kohlstedt, David L.; Hansen, Lars N.; Mackwell, Stephen; Tasaka, Miki; Heidelbach, Florian; Leinenweber, Kurt

2018-05-01

Grain boundary processes contribute significantly to electronic and ionic transports in materials within Earth's interior. We report a novel experimental study of grain boundary conductivity in highly strained olivine aggregates that demonstrates the importance of misorientation angle between adjacent grains on aggregate transport properties. We performed electrical conductivity measurements of melt-free polycrystalline olivine (Fo90) samples that had been previously deformed at 1200 °C and 0.3 GPa to shear strains up to γ = 7.3. The electrical conductivity and anisotropy were measured at 2.8 GPa over the temperature range 700-1400 °C. We observed that (1) the electrical conductivity of samples with a small grain size (3-6 µm) and strong crystallographic preferred orientation produced by dynamic recrystallization during large-strain shear deformation is a factor of 10 or more larger than that measured on coarse-grained samples, (2) the sample deformed to the highest strain is the most conductive even though it does not have the smallest grain size, and (3) conductivity is up to a factor of 4 larger in the direction of shear than normal to the shear plane. Based on these results combined with electrical conductivity data for coarse-grained, polycrystalline olivine and for single crystals, we propose that the electrical conductivity of our fine-grained samples is dominated by grain boundary paths. In addition, the electrical anisotropy results from preferential alignment of higher-conductivity grain boundaries associated with the development of a strong crystallographic preferred orientation of the grains.

Reaction and relaxation in a coarse-grained fluvial system following catchment-wide disturbance

Science.gov (United States)

Tunnicliffe, Jon; Brierley, Gary; Fuller, Ian C.; Leenman, Anya; Marden, Mike; Peacock, Dave

2018-04-01

The Waiapu River catchment (drainage area of 1734-km2) is one of the most prolific conveyors of sediment in the world, annually delivering roughly 35 Mt of fine material to the ocean from eroding gullies, hillslopes, and reworked sediment on valley floors. Tectonic and geologic influences, in combination with a dynamic climate influenced by tropical cyclones and clearance of vegetation from steep hillslopes, predisposes this region to high rates of erosion. The bedload sediment regime of the river is strongly influenced by several exceptionally large gullies and gully complexes that produce a coarse-grained, poorly sorted sediment mixture. Rapid abrasion and breakdown leads to high rates of suspended sediment yield. A wave of bedload material, manifesting as elevated bed levels and significant widening of active alluvial fills, has been triggered by large inputs of hillslope material from a few key tributary catchments following Cyclone Bola in 1988. We review the evidence for the relaxation process of the sedimentary system in the subsequent 29 years, appraising some of the legacy effects that may endure, as associated with reworking of the considerable alluvial stores within the Waiapu system. We use Structure-from-Motion (SfM) techniques and archival aerial photos to quantify changes in sediment storage at the base of two major gully systems in recent decades. A record of over 850 cross section surveys at 62 sites on 10 rivers throughout the catchment (1958-2017) indicates recent transition from a trend of continuous accumulation to downcutting and remobilisation of valley-bottom deposits. The channel cross sections provide a minimum estimate of sediment flux from source areas to the lower reaches of the river, giving a rudimentary but spatially extensive picture of the wave of material cascading through the drainage network. The largest impacts occur in the upper steepland rivers, closest to the landslide-derived sediment supply. Transport rates here, as

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

Science.gov (United States)

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.

Extension of 239+240Pu sediment geochronology to coarse-grained marine sediments

Science.gov (United States)

Kuehl, Steven A.; Ketterer, Michael E.; Miselis, Jennifer L.

2012-01-01

Sediment geochronology of coastal sedimentary environments dominated by sand has been extremely limited because concentrations of natural and bomb-fallout radionuclides are often below the limit of measurement using standard techniques. ICP-MS analyses of 239+240Pu from two sites representative of traditionally challenging (i.e., low concentration) environments provide a "proof of concept" and demonstrate a new application for bomb-fallout radiotracers in the study of sandy shelf-seabed dynamics. A kasten core from the New Zealand shelf in the Southern Hemisphere (low fallout), and a vibracore from the sandy nearshore of North Carolina (low particle surface area) both reveal measurable 239+240Pu activities at depth. In the case of the New Zealand site, independently verified steady-state sedimentation results in a 239+240Pu profile that mimics the expected atmospheric fallout. The depth profile of 239+240Pu in the North Carolina core is more uniform, indicating significant sediment resuspension, which would be expected in this energetic nearshore environment. This study, for the first time, demonstrates the utility of 239+240Pu in the study of sandy environments, significantly extending the application of bomb-fallout isotopes to coarse-grained sediments, which compose the majority of nearshore regions.

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

International Nuclear Information System (INIS)

Sinitskiy, Anton V.; Voth, Gregory A.

2015-01-01

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

Coarse-grained modelling of triglyceride crystallisation: a molecular insight into tripalmitin tristearin binary mixtures by molecular dynamics simulations

Science.gov (United States)

Pizzirusso, Antonio; Brasiello, Antonio; De Nicola, Antonio; Marangoni, Alejandro G.; Milano, Giuseppe

2015-12-01

The first simulation study of the crystallisation of a binary mixture of triglycerides using molecular dynamics simulations is reported. Coarse-grained models of tristearin (SSS) and tripalmitin (PPP) molecules have been considered. The models have been preliminarily tested in the crystallisation of pure SSS and PPP systems. Two different quenching procedures have been tested and their performances have been analysed. The structures obtained from the crystallisation procedures show a high orientation order and a high content of molecules in the tuning fork conformation, comparable with the crystalline α phase. The behaviour of melting temperatures for the α phase of the mixture SSS/PPP obtained from the simulations is in qualitative agreement with the behaviour that was experimentally determined.

Coarse-grained modelling of triglyceride crystallisation: a molecular insight into tripalmitin tristearin binary mixtures by molecular dynamics simulations

International Nuclear Information System (INIS)

Pizzirusso, Antonio; De Nicola, Antonio; Milano, Giuseppe; Brasiello, Antonio; Marangoni, Alejandro G

2015-01-01

The first simulation study of the crystallisation of a binary mixture of triglycerides using molecular dynamics simulations is reported. Coarse-grained models of tristearin (SSS) and tripalmitin (PPP) molecules have been considered. The models have been preliminarily tested in the crystallisation of pure SSS and PPP systems. Two different quenching procedures have been tested and their performances have been analysed. The structures obtained from the crystallisation procedures show a high orientation order and a high content of molecules in the tuning fork conformation, comparable with the crystalline α phase. The behaviour of melting temperatures for the α phase of the mixture SSS/PPP obtained from the simulations is in qualitative agreement with the behaviour that was experimentally determined. (paper)

Deformation Behavior of a Coarse-Grained Mg-8Al-1.5Ca-0.2Sr Magnesium Alloy at Elevated Temperatures

Science.gov (United States)

Lou, Yan; Liu, Xiao

2018-02-01

The compression tests were carried out on a coarse-grained Mg-8Al-1.5Ca-0.2Sr magnesium alloy samples at temperatures from 300 to 450 °C and strain rates from 0.001 to 10 s-1. The flow stress curves were analyzed using the double-differentiation method, and double minima were detected on the flow curves. The first set of minima is shown to identify the critical strain for twinning, while the second set indicates the critical strain for the initiation of dynamic recrystallization (DRX). Twin variant selection was numerically identified by comprehensive analysis of the Schmid factors for different deformation modes and the accommodation strains imposed on neighboring grains. It was found that twinning is initiated before DRX. Dynamic recrystallization volume increases with strain rate at a given deformation temperature. At high strain rate, various twin variants are activated to accommodate deformation, leading to the formation of twin intersections and high DRX volume. Fully dynamic recrystallized structure can be obtained at both high and low strain rates due to the high mobility of the grain and twin boundaries at the temperature of 400 °C.

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

Science.gov (United States)

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.

Demixing by a Nematic Mean Field: Coarse-Grained Simulations of Liquid Crystalline Polymers

Energy Technology Data Exchange (ETDEWEB)

Ramírez-Hernández, Abelardo; Hur, Su-Mi; Armas-Pérez, Julio; Cruz, Monica; de Pablo, Juan

2017-03-01

Liquid crystalline polymers exhibit a particular richness of behaviors that stems from their rigidity and their macromolecular nature. On the one hand, the orientational interaction between liquid-crystalline motifs promotes their alignment, thereby leading to the emergence of nematic phases. On the other hand, the large number of configurations associated with polymer chains favors formation of isotropic phases, with chain stiffness becoming the factor that tips the balance. In this work, a soft coarse-grained model is introduced to explore the interplay of chain stiffness, molecular weight and orientational coupling, and their role on the isotropic-nematic transition in homopolymer melts. We also study the structure of polymer mixtures composed of stiff and flexible polymeric molecules. We consider the effects of blend composition, persistence length, molecular weight and orientational coupling strength on the melt structure at the nano-and mesoscopic levels. Conditions are found where the systems separate into two phases, one isotropic and the other nematic. We confirm the existence of non-equilibrium states that exhibit sought-after percolating nematic domains, which are of interest for applications in organic photovoltaic and electronic devices.

A coarse-grained model for the simulations of biomolecular interactions in cellular environments

International Nuclear Information System (INIS)

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2014-01-01

The interactions of bio-molecules constitute the key steps of cellular functions. However, in vivo binding properties differ significantly from their in vitro measurements due to the heterogeneity of cellular environments. Here we introduce a coarse-grained model based on rigid-body representation to study how factors such as cellular crowding and membrane confinement affect molecular binding. The macroscopic parameters such as the equilibrium constant and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these model parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific cellular environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular diffusion and diffusion-limited reactions. Furthermore, the binding constants of membrane proteins are currently difficult to measure. We provide quantitative estimations about how the binding of membrane proteins deviates from soluble proteins under different degrees of membrane confinements. The simulation results provide biological insights to the functions of membrane receptors on cell surfaces. Overall, our studies establish a connection between the details of molecular interactions and the heterogeneity of cellular environments

Electrons scattered inside small dust grains of various materials

International Nuclear Information System (INIS)

Richterova, Ivana; Beranek, Martin; Pavlu, Jiri; Nemecek, Zdenek; Safrankova, Jana

2010-01-01

The dust grain charge in an electron beam is given by a difference in numbers of electrons that fall onto the grain and those leaving it. Electrons with energies exceeding 1 keV can penetrate through submicron-sized dust grains. If the grain is small enough, a yield of these electrons reaches unity but they leave a part of their energy inside the grain and this energy excites secondary electrons. The paper presents a hybrid Monte Carlo code that simulates paths of the primary electrons inside a spherical grain and provides the yield of scattered electrons and their energy spectrum as a function of the grain size and material. This code is based on the Richterovaet al. [Phys. Rev. B 74, 235430 (2006)] model but it includes several corrections important for light materials like carbon or ice. The model was verified using experimental results obtained on large planar samples. For spherical samples, we have found that the yield of scattered electrons reaches unity for 50 nm Au grains illuminated by 5 keV electrons, whereas the same effect can be observed on ≅1000 nm carbon grains.

Modelling airborne dispersion of coarse particulate material

International Nuclear Information System (INIS)

Apsley, D.D.

1989-03-01

Methods of modelling the airborne dispersion and deposition of coarse particulates are presented, with the emphasis on the heavy particles identified as possible constituents of releases from damaged AGR fuel. The first part of this report establishes the physical characteristics of the irradiated particulate in airborne emissions from AGR stations. The second part is less specific and describes procedures for extending current dispersion/deposition models to incorporate a coarse particulate component: the adjustment to plume spread parameters, dispersion from elevated sources and dispersion in conjunction with building effects and plume rise. (author)

The effect of coarse second-phase particles on the rate of grain refinement during severe deformation processing

DEFF Research Database (Denmark)

Apps, P.J.; Bowen, Jacob R.; Prangnell, P.B.

2003-01-01

The effect of second-phase particles on the rate of grain refinement during severe deformation processing has been investigated, by comparing the microstructure evolution in an AA8079 aluminium alloy, containing 2.5 vol.% of ~2 μm particles, with that in a high purity, single-phase, Al-0.13% Mg a...... by an effective strain of only five in the particle-containing alloy, compared to ten in the single-phase material. The mechanisms that contribute to this acceleration of the grain refinement process are discussed.......The effect of second-phase particles on the rate of grain refinement during severe deformation processing has been investigated, by comparing the microstructure evolution in an AA8079 aluminium alloy, containing 2.5 vol.% of ~2 μm particles, with that in a high purity, single-phase, Al-0.13% Mg...... alloy, deformed identically by ECAE to an effective strain of ten. The materials were analysed by high-resolution EBSD orientation mapping, which revealed that grain refinement occurred at a dramatically higher rate in the particle-containing alloy. A submicron grain structure could be achieved...

Time evolution of coarse-grained entropy in classical and quantum motions of strongly chaotic systems

Science.gov (United States)

Gu, Yan; Wang, Jiao

1997-02-01

We study relaxation of an ensemble of cat maps with initially localized phase-space distributions. Calculations of the coarse-grained entropy Sɛ ( t) for both classical and quantum motions are presented. It is shown that, within the relaxation period, both classical and quantum entropies increase with a nearly constant rate which can be identified as the largest Lyapunov exponent of the classical cat. After an empirical relaxation time, the time behavior for two entropies becomes different. While the classical entropy increases to the equilibrium entropy Seqm and stays there, its quantum analogue fluctuates incessantly around a mean overlineSɛ which is less than Seqm. We regard the entropy difference ΔS = S eqm - overlineSɛ as a measure of nonergodicity of the quantum motion of strongly chaotic systems and investigate its dependence on the Planck constant h. For fixed initial phase-space distributions, numerical results suggest that there is a scaling law ΔSαhβ with β ≈ 0.72 in the semiclassical regime.

Mechanism of ultra low friction of multilayer graphene studied by coarse-grained molecular simulation.

Science.gov (United States)

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.

Grain boundaries of nanocrystalline materials - their widths, compositions, and internal structures

International Nuclear Information System (INIS)

Fultz, B.; Frase, H.N.

2000-01-01

Nanocrystalline materials contain many atoms at and near grain boundaries. Sufficient numbers of Moessbauer probe atoms can be situated in grain boundary environments to make a clear contribution to the measured Moessbauer spectrum. Three types of measurements on nanocrystalline materials are reported here, all using Moessbauer spectrometry in conjunction with X-ray diffractometry, transmission electron microscopy, or small angle neutron scattering. By measuring the fraction of atoms contributing to the grain boundary component in a Moessbauer spectrum, and by knowing the grain size of the material, it is possible to deduce the average width of grain boundaries in metallic alloys. It is found that these widths are approximately 0.5 nm for fcc alloys and slightly larger than 1.0 nm for bcc alloys.Chemical segregation to grain boundaries can be measured by Moessbauer spectrometry, especially in conjunction with small angle neutron scattering. Such measurements on Fe-Cu and Fe 3 Si-Nb were used to study how nanocrystalline materials could be stabilized against grain growth by the segregation of Cu and Nb to grain boundaries. The segregation of Cu to grain boundaries did not stabilize the Fe-Cu alloys against grain growth, since the grain boundaries were found to widen and accept more Cu atoms during annealing. The Nb additions to Fe 3 Si did suppress grain growth, perhaps because of the low mobility of Nb atoms, but also perhaps because Nb atoms altered the chemical ordering in the alloy.The internal structure of grain boundaries in nanocrystalline materials prepared by high-energy ball milling is found to be unstable against internal relaxations at low temperatures. The Moessbauer spectra of the nanocrystalline samples showed changes in the hyperfine fields attributable to movements of grain boundary atoms. In conjunction with SANS measurements, the changes in grain boundary structure induced by cryogenic exposure and annealing at low temperature were found to be

Magnetic properties of different grain-sized particles of sediments from the Okinawa Trough and their relationships to sedimentary environment

Institute of Scientific and Technical Information of China (English)

LI Ping; LI Peiying; ZHANG Xiaolong; CAO Chengxiao; XU Xingyong; DU Jun; LIU Lejun

2005-01-01

Multiple magnetic parameters were measured for nine different grain-sized fractions separated from the sediment samples that are representatives of four different sedimentary environments of the Okinawa Trough. Based on the measured results, the contributions of different grain-sized particles to total magnetic susceptibility of bulk sediments, the magnetic mineral assemblage and magnetic domain state as well as their relationships to sedimentary environment were discussed. Our research shows that the magnetic mineral is dominated by magnetite with a small amount of hematite and is primarily in pseudo-single-domain state. That indicates that the different sedimentary environments in the Okinawa Trough have certain correlation in material provenance. The magnetic minerals enrich in different grain-sized particles in response to different sedimentary environments. The contribution of the grain sizes from coarse to fine to coarse and fine to the magnetic susceptibility from the west to the east is in accordance with terrigenous material transportation from continental shelf of the East China Sea to the Okinawa Trough. It also shows difference in magnetic properties as a result of some environmental factors.

Effect of ageing on tensile behavior of ultrafine grained Al 6061 alloy

Energy Technology Data Exchange (ETDEWEB)

Rao, P. Nageswara [Department of Metallurgical and Materials Engineering & Centre of Nanotechnology, IIT Roorkee, Roorkee 247667 (India); Singh, Dharmendra [Department of Mechanical Engineering, Government Engineering College, Bikaner 304001 (India); Brokmeier, Heinz-Günter [Helmholtz Zentrum Geesthacht, Max Planck Straße 1, Geb 33, D-21502 Geesthacht (Germany); Jayaganthan, R., E-mail: rjayafmt@iitr.ernet.in [Department of Metallurgical and Materials Engineering & Centre of Nanotechnology, IIT Roorkee, Roorkee 247667 (India)

2015-08-12

In the present investigation, the ageing behavior of ultrafine grained (UFG) Al 6061 alloy, processed through multi-directional forging (MDF) at cryogenic temperature was investigated. The evolution of microstructure was investigated through transmission electron microscopy and electron back scattered diffraction technique. The results indicate that homogeneous microstructure with an ultrafine grain morphology (average size 250 nm) was achieved through cryogenic forging of the alloy subjected to prior solutionising treatment. Tensile testing at room temperature revealed that MDFed material after ageing led to significant improvement in work hardening and its tensile ductility. Strengthening of the matrix through various mechanisms has been quantified with the existing models to estimate the yield strength of the as forged and peak aged material. The precipitation hardening response in UFG material is found to be 35% lower than that of the coarse grained material as observed in the present work.

Structure of grain boundaries in hexagonal materials

International Nuclear Information System (INIS)

Sarrazit, F.

1998-05-01

The work presented in this thesis describes experimental and theoretical aspects associated with the structure of grain boundaries in hexagonal materials. It has been found useful to classify grain boundaries as low-angle, special or general on the basis of their structure. High-angle grain boundaries were investigated in tungsten carbide (WC) using conventional electron microscopy techniques, and three examples characteristic of the interfaces observed in this material were studied extensively. Three-dimensionally periodic patterns are proposed as plausible reference configurations, and the Burgers vectors of observed interfacial dislocations were predicted using a theory developed recently. The comparison of experimental observations with theoretical predictions proved to be difficult as contrast simulation techniques require further development for analysis to be completed confidently. Another part of this work involves the characterisation of high-angle grain boundaries in zinc oxide (ZnO) using circuit mapping. Two boundaries displayed structural features characteristic of the 'special' category, however, one boundary presented features which did not conform to this model. It is proposed that the latter observation shows a structural transition from the special to a more general type. Material fluxes involved in defect interactions were considered using the topological framework described in this work. A genera) expression was derived for the total flux arising which allows the behaviour of line-defects to be studied in complex interfacial processes. (author)

Coarse-grained modeling of hybrid block copolymer system

Science.gov (United States)

Su, Yongrui

This thesis is comprised of three major projects of my research. In the first project, I proposed a nanoparticle model and combined it with the Theoretically Informed Coarse Grained (TICG) model for pure polymer systems and the grand canonical slip springs model developed in our group to build a new model for entangled nanocomposites. With Molecule Dynamics(MD) simulation, I studied the mechanic properties of the nanocomposites, for example the influence of nanoparticles size and volume fraction on entanglements, the diffusion of polymers and nanoparticles, and the influence of nanoparticles size and volume fraction on viscosity et al.. We found that the addition of small-size nanoparticles reduces the viscosity of the nanocomposites, which is in contrary to what Einstein predicted a century ago. However, when particle increases its size to micrometers the Einstein predictions is recovered. From our simulation, we believe that small-size nanoparticles can more effectively decrease the entanglements of nanocomposites than larger particles. The free volume effect introduced by small-size nanoparticles also helps decrease the viscosity of the whole system. In the second project, I combined the Ohta-Kawasaki (OK) model [3] and the Covariance Matrix Adaptation Evolutionary Strategy(CMA-ES) to optimize the block copolymer blends self-assembly in the hole-shrink process. The aim is to predict the optimal composition and the optimal surface energy to direct the block copolymer blends self-assembly process in the confined hole. After optimization in the OK model, we calibrated the optimal results by the more reliable TICG model and got the same morphology. By comparing different optimization process, we found that the homopolymers which are comprised of the same monomers as either block of the block copolymer can form a perfect perforated hole and might have better performance than the pure block copolymer. While homopolymers which are comprised of a third-party monomers

Grain boundary corrosion of copper canister weld material

International Nuclear Information System (INIS)

Gubner, Rolf; Andersson, Urban; Linder, Mats; Nazarov, Andrej; Taxen, Claes

2006-01-01

The proposed design for a final repository for spent fuel and other long-lived residues in Sweden is based on the multi-barrier principle. The waste will be encapsulated in sealed cylindrical canisters, which will then be placed in granite bedrock and surrounded by compacted bentonite clay. The canister design is based on a thick cast inner container fitted inside a corrosion-resistant copper canister. During fabrication of the outer copper canisters there will be some unavoidable grain growth in the welded areas. As grains grow, they will tend to concentrate impurities within the copper at the new grain boundaries. The work described in this report was undertaken to determine whether there is any possibility of enhanced corrosion at grain boundaries within the copper canister, based on the recommendations of the report SKB-TR--01-09 (INIS ref. 32025363). Grain boundary corrosion of copper is not expected to be a problem for the copper canisters in a repository. However, as one step in the experimental verification it is necessary to study grain boundary corrosion of copper in an environment where it may occur. A literature study aimed to find one or several solutions that are aggressive with respect to grain boundary corrosion of copper. Copper specimens cut from welds of real copper canisters where exposed to aerated ammonium hydroxide solution for a period of 14 days at 80 degrees C and 10 bar pressure. The samples were investigated prior to exposure using the scanning Kelvin probe technique to characterize anodic and cathodic areas on the samples. The degree of corrosion was determined by optical microscopy. No grain boundary corrosion could be observed in the autoclave experiments, however, a higher rate of corrosion was observed for the weld material compared to the base material. The work suggests that grain boundary corrosion of copper weld material is most unlikely to adversely affect SKB's copper canisters under the conditions in the repository

Grain boundary corrosion of copper canister weld material

Energy Technology Data Exchange (ETDEWEB)

Gubner, Rolf; Andersson, Urban; Linder, Mats; Nazarov, Andrej; Taxen, Claes [Corrosion and Metals Research Inst. (KIMAB), Stockholm (Sweden)

2006-01-15

The proposed design for a final repository for spent fuel and other long-lived residues in Sweden is based on the multi-barrier principle. The waste will be encapsulated in sealed cylindrical canisters, which will then be placed in granite bedrock and surrounded by compacted bentonite clay. The canister design is based on a thick cast inner container fitted inside a corrosion-resistant copper canister. During fabrication of the outer copper canisters there will be some unavoidable grain growth in the welded areas. As grains grow, they will tend to concentrate impurities within the copper at the new grain boundaries. The work described in this report was undertaken to determine whether there is any possibility of enhanced corrosion at grain boundaries within the copper canister, based on the recommendations of the report SKB-TR--01-09 (INIS ref. 32025363). Grain boundary corrosion of copper is not expected to be a problem for the copper canisters in a repository. However, as one step in the experimental verification it is necessary to study grain boundary corrosion of copper in an environment where it may occur. A literature study aimed to find one or several solutions that are aggressive with respect to grain boundary corrosion of copper. Copper specimens cut from welds of real copper canisters where exposed to aerated ammonium hydroxide solution for a period of 14 days at 80 degrees C and 10 bar pressure. The samples were investigated prior to exposure using the scanning Kelvin probe technique to characterize anodic and cathodic areas on the samples. The degree of corrosion was determined by optical microscopy. No grain boundary corrosion could be observed in the autoclave experiments, however, a higher rate of corrosion was observed for the weld material compared to the base material. The work suggests that grain boundary corrosion of copper weld material is most unlikely to adversely affect SKB's copper canisters under the conditions in the repository.

Study for effective use of fishery byproducts as alternative earth materials focusing on their water retention

International Nuclear Information System (INIS)

Kobayashi, Kaoru; Nakafusa, Satoru; Nishimura, Tomoyoshi; Morii, Toshihiro

2011-01-01

Capillary barriers have been known and widely used in geoenvironmental engineering applications as soil cover for typical rainfall infiltration control systems. The capillary barrier is consisting of a fine-grained soil layer placed over a coarse-grained soil layer. The applications of capillary barriers are significantly useful to preventing infiltration into waste materials. Natural gravel or coarse-grained soil material had a exhaustion problems in practices. On the contrary, shells a kind of fishery byproduct, are classified as industrial waste in laws concerning waste disposal. The majority of shells are piled and left near the fishing port without controlling system. Therefore, it is proposed that the crushed shells are available to layer material instead of natural coarse-grained soil. This solution is considered to great contribute developing of recycle for fisher byproduct shells and is related to environment conservation. Water retention for crushed shells, however, never been fully investigate. This study focuses on the ability of crushed shells to capillary barrier applications. The soil-water characteristic curve for crushed shells with three different grain size distributions was determined using the modified SWCC testing apparatus. Also, it is observed using a conventional model equipment that the getting of fine sand into crushed shell layer is prevented. (author)

Erosion and deposition by supercritical density flows during channel avulsion and backfilling: Field examples from coarse-grained deepwater channel-levée complexes (Sandino Forearc Basin, southern Central America)

Science.gov (United States)

Lang, Jörg; Brandes, Christian; Winsemann, Jutta

2017-03-01

Erosion and deposition by supercritical density flows can strongly impact the facies distribution and architecture of submarine fans. Field examples from coarse-grained channel-levée complexes from the Sandino Forearc Basin (southern Central America) show that cyclic-step and antidune deposits represent common sedimentary facies of these depositional systems and relate to the different stages of avulsion, bypass, levée construction and channel backfilling. During channel avulsion, large-scale scour-fill complexes (18 to 29 m deep, 18 to 25 m wide, 60 to > 120 m long) were incised by supercritical density flows. The multi-storey infill of the large-scale scour-fill complexes comprises amalgamated massive, normally coarse-tail graded or widely spaced subhorizontally stratified conglomerates and pebbly sandstones, interpreted as deposits of the hydraulic-jump zone of cyclic steps. The large-scale scour-fill complexes can be distinguished from small-scale channel fills based on the preservation of a steep upper margin and a coarse-grained infill comprising mainly amalgamated hydraulic-jump zone deposits. Channel fills include repeated successions deposited by cyclic steps with superimposed antidunes. The deposits of the hydraulic-jump zone of cyclic steps comprise regularly spaced scours (0.2 to 2.6 m deep, 0.8 to 23 m long) infilled by intraclast-rich conglomerates or pebbly sandstones, displaying normal coarse-tail grading or backsets. These deposits are laterally and vertically associated with subhorizontally stratified, low-angle cross-stratified or sinusoidally stratified sandstones and pebbly sandstones, which were deposited by antidunes on the stoss side of the cyclic steps during flow re-acceleration. The field examples indicate that so-called spaced stratified deposits may commonly represent antidune deposits with varying stratification styles controlled by the aggradation rate, grain-size distribution and amalgamation. The deposits of small-scale cyclic

Interpretation of sedimentological processes of coarse-grained deposits applying a novel combined cluster and discriminant analysis

Directory of Open Access Journals (Sweden)

Farics Éva

2017-10-01

Full Text Available The main aim of this paper is to determine the depositional environments of an Upper-Eocene coarse-grained clastic succession in the Buda Hills, Hungary. First of all, we measured some commonly used parameters of samples (size, amount, roundness and sphericity in a much more objective overall and faster way than with traditional measurement approaches, using the newly developed Rock Analyst application. For the multivariate data obtained, we applied Combined Cluster and Discriminant Analysis (CCDA in order to determine homogeneous groups of the sampling locations based on the quantitative composition of the conglomerate as well as the shape parameters (roundness and sphericity. The result is the spatial pattern of these groups, which assists with the interpretation of the depositional processes. According to our concept, those sampling sites which belong to the same homogeneous groups were likely formed under similar geological circumstances and by similar geological processes.

Dynamics of the Glycophorin A Dimer in Membranes of Native-Like Composition Uncovered by Coarse-Grained Molecular Dynamics Simulations.

Science.gov (United States)

Flinner, Nadine; Schleiff, Enrico

2015-01-01

Membranes are central for cells as borders to the environment or intracellular organelle definition. They are composed of and harbor different molecules like various lipid species and sterols, and they are generally crowded with proteins. The membrane system is very dynamic and components show lateral, rotational and translational diffusion. The consequence of the latter is that phase separation can occur in membranes in vivo and in vitro. It was documented that molecular dynamics simulations of an idealized plasma membrane model result in formation of membrane areas where either saturated lipids and cholesterol (liquid-ordered character, Lo) or unsaturated lipids (liquid-disordered character, Ld) were enriched. Furthermore, current discussions favor the idea that proteins are sorted into the liquid-disordered phase of model membranes, but experimental support for the behavior of isolated proteins in native membranes is sparse. To gain insight into the protein behavior we built a model of the red blood cell membrane with integrated glycophorin A dimer. The sorting and the dynamics of the dimer were subsequently explored by coarse-grained molecular dynamics simulations. In addition, we inspected the impact of lipid head groups and the presence of cholesterol within the membrane on the dynamics of the dimer within the membrane. We observed that cholesterol is important for the formation of membrane areas with Lo and Ld character. Moreover, it is an important factor for the reproduction of the dynamic behavior of the protein found in its native environment. The protein dimer was exclusively sorted into the domain of Ld character in the model red blood cell plasma membrane. Therefore, we present structural information on the glycophorin A dimer distribution in the plasma membrane in the absence of other factors like e.g. lipid anchors in a coarse grain resolution.

Dynamics of the Glycophorin A Dimer in Membranes of Native-Like Composition Uncovered by Coarse-Grained Molecular Dynamics Simulations.

Directory of Open Access Journals (Sweden)

Nadine Flinner

Full Text Available Membranes are central for cells as borders to the environment or intracellular organelle definition. They are composed of and harbor different molecules like various lipid species and sterols, and they are generally crowded with proteins. The membrane system is very dynamic and components show lateral, rotational and translational diffusion. The consequence of the latter is that phase separation can occur in membranes in vivo and in vitro. It was documented that molecular dynamics simulations of an idealized plasma membrane model result in formation of membrane areas where either saturated lipids and cholesterol (liquid-ordered character, Lo or unsaturated lipids (liquid-disordered character, Ld were enriched. Furthermore, current discussions favor the idea that proteins are sorted into the liquid-disordered phase of model membranes, but experimental support for the behavior of isolated proteins in native membranes is sparse. To gain insight into the protein behavior we built a model of the red blood cell membrane with integrated glycophorin A dimer. The sorting and the dynamics of the dimer were subsequently explored by coarse-grained molecular dynamics simulations. In addition, we inspected the impact of lipid head groups and the presence of cholesterol within the membrane on the dynamics of the dimer within the membrane. We observed that cholesterol is important for the formation of membrane areas with Lo and Ld character. Moreover, it is an important factor for the reproduction of the dynamic behavior of the protein found in its native environment. The protein dimer was exclusively sorted into the domain of Ld character in the model red blood cell plasma membrane. Therefore, we present structural information on the glycophorin A dimer distribution in the plasma membrane in the absence of other factors like e.g. lipid anchors in a coarse grain resolution.

A multi-state coarse grained modeling approach for an intrinsically disordered peptide

Science.gov (United States)

Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

2017-09-01

Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα 14 is disordered in dilute solutions; however, it strictly adopts the α -helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α -helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

Grain boundary engineering for structure materials of nuclear reactors

Science.gov (United States)

Tan, L.; Allen, T. R.; Busby, J. T.

2013-10-01

Grain boundary engineering (GBE), primarily implemented by thermomechanical processing, is an effective and economical method of enhancing the properties of polycrystalline materials. Among the factors affecting grain boundary character distribution, literature data showed definitive effect of grain size and texture. GBE is more effective for austenitic stainless steels and Ni-base alloys compared to other structural materials of nuclear reactors, such as refractory metals, ferritic and ferritic-martensitic steels, and Zr alloys. GBE has shown beneficial effects on improving the strength, creep strength, and resistance to stress corrosion cracking and oxidation of austenitic stainless steels and Ni-base alloys.

Grain boundary engineering for structure materials of nuclear reactors

Energy Technology Data Exchange (ETDEWEB)

Tan, L., E-mail: tanl@ornl.gov [Materials Science and Technology Division, Oak Ridge National Laboratory (United States); Allen, T.R. [Department of Engineering Physics, University of Wisconsin–Madison (United States); Busby, J.T. [Materials Science and Technology Division, Oak Ridge National Laboratory (United States)

2013-10-15

Grain boundary engineering (GBE), primarily implemented by thermomechanical processing, is an effective and economical method of enhancing the properties of polycrystalline materials. Among the factors affecting grain boundary character distribution, literature data showed definitive effect of grain size and texture. GBE is more effective for austenitic stainless steels and Ni-base alloys compared to other structural materials of nuclear reactors, such as refractory metals, ferritic and ferritic–martensitic steels, and Zr alloys. GBE has shown beneficial effects on improving the strength, creep strength, and resistance to stress corrosion cracking and oxidation of austenitic stainless steels and Ni-base alloys.

Effects of Nb on microstructure and continuous cooling transformation of coarse grain heat-affected zone in 610 MPa class high-strength low-alloy structural steels

International Nuclear Information System (INIS)

Zhang, Y.Q.; Zhang, H.Q.; Liu, W.M.; Hou, H.

2009-01-01

Continuous cooling transformation diagrams of the coarse grain heat-affected zone and microstructure after continuous cooling were investigated for 610 MPa class high-strength low-alloy (HSLA) structural steels with and without niobium. For the steel without Nb, grain boundary ferrite, degenerate pearlite and acicular ferrite are produced at slower cooling rates. Bainite phase is formed at faster cooling rates. However, for the steel with Nb, granular bainite is dominant at a large range of cooling rates. At cooling rates 32 K/s, Nb addition has no obvious influence on transformation start temperature, but it influences microstructure transformation significantly. Martensite is observed in steel with Nb at faster cooling rates, but not produced in steel without Nb

Numerical simulation of the mechanical behavior of ultrafine- and coarse-grained Zr-Nb alloys over a wide range of strain rates

Science.gov (United States)

Serbenta, V. A.; Skripnyak, N. V.; Skripnyak, V. A.; Skripnyak, E. G.

2017-12-01

This paper presents the results on the development of theoretical methods of evaluation and prediction of mechanical properties of Zr-Nb alloys over a range of strain rates from 10-3 to 103 s-1. The mechanical behavior of coarse- and ultrafine-grained Zr-1Nb (E110) was investigated numerically. The ranges of strain rates and temperatures in which the mechanical behavior of Zr-1Nb alloy can be described using modified models of Johnson-Cook and Zerilli-Armstrong were defined. The results can be used in engineering analysis of designed technical systems for nuclear reactors.

Grain scale stresses and strains determination by X-ray diffraction; Contribution a l'analyse par diffractometrie X des deformations et des contraintes a l'echelle des grains

Energy Technology Data Exchange (ETDEWEB)

Huang, W

2007-03-15

A new methodology for strain and stress analysis by X ray diffraction (XRD) in single crystal was developed. It can be applied to determine the second order stress (in grain scale) in single and multi-crystal material with non-cubic lattice. This method is based on the method Ortner I. It has introduced the metric tensor G which is deduced from the lattice space measured by XRD. In the developed method, when the crystal reference is non-orthonormal, an orthonormal reference associated with the crystal basis is defined, so all calculation could be done with usual calculation laws. The use of the least square method allows the acquisition of many more measurements than the six absolute necessary. Then a better metric tensor G is calculated and the statistical error is obtained. This developed method was applied in a bi crystal copper. The experimental results have shown that this method is also effective. The second order residuals stresses for coarse Zn grains in a galvanized coating were determined after annealing. The four coarse grains with different orientations were also characterized and demonstrated the elastic and plastic deformation mechanism in a grain or between the grains during in situ tensile loading. So this method is well able to determine the strains and stresses in grain scale in a mono crystal or multi crystal with any crystalline structure. (author)

Relating water and air flow characteristics in coarse granular materials

DEFF Research Database (Denmark)

Andreasen, Rune Røjgaard; Canga, Eriona; Poulsen, Tjalfe Gorm

2013-01-01

Water pressure drop as a function of velocity controls w 1 ater cleaning biofilter operation 2 cost. At present this relationship in biofilter materials must be determined experimentally as no 3 universal link between pressure drop, velocity and filter material properties have been established. 4...... Pressure drop - velocity in porous media is much simpler and faster to measure for air than for water. 5 For soils and similar materials, observations show a strong connection between pressure drop – 6 velocity relations for air and water, indicating that water pressure drop – velocity may be estimated 7...... from air flow data. The objective of this study was, therefore, to investigate if this approach is valid 8 also for coarse granular biofilter media which usually consists of much larger particles than soils. In 9 this paper the connection between the pressure drop – velocity relationships for air...

Quantitative grain-scale ferroic domain volume fractions and domain switching strains from three-dimensional X-ray diffraction data

DEFF Research Database (Denmark)

Oddershede, Jette; Majkut, Marta; Caosyd, Qinghua

2015-01-01

A method for the extension of the three-dimensional X-ray diffraction technique to allow the extraction of domain volume fractions in polycrystalline ferroic materials is presented. This method gives access to quantitative domain volume fractions of hundreds of independent embedded grains within...... are applied to tetragonal coarse-grained Ba0.88Ca0.12Zr0.06Ti0.94O3 and rhombohedral fine-grained (0.82)Bi0.5Na0.5TiO3–(0.18)Bi0.5K0.5TiO3 electroceramic materials. The fitted volume fraction information is used to calculate grain-scale non-180° ferroelectric domain switching strains. The absolute errors...

Pore-size distribution and compressibility of coarse sandy subsoil with added biochar

DEFF Research Database (Denmark)

Petersen, C. T.; Hansen, E.; Larsen, H. H.

2016-01-01

Sustainable agricultural production on coarse sandy soil is constrained by the restricted growth of roots, and poor water and nutrient retention. Amending the soil with biochar can reduce these problems, but the processes involved are not known in detail. We investigated in the laboratory...... the effects of two fine-grained gasification biochars made of straw (LTST) and other materials (LTSN) and of one fast pyrolysis straw biochar (FPST) on pore-size distribution and soil compressibility when added to coarse sandy subsoil. Water retention and therefore pore-size distribution were affected...... systematically. All biochars converted drainable pore space with pore diameters in the range 60–300 µm into water-retaining pores of size 0.2–60 µm, which was taken as an estimate of available water capacity (AWC). Effects were linear over the whole range of biochar (0–4% by mass). The effect of LTST and LTSN...

Computational Calculation Of The Ionization Energies Of The Human Prion Protein By The Coarse-grain Method

Science.gov (United States)

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.

Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field

Energy Technology Data Exchange (ETDEWEB)

Wang Zunjing; Deserno, Markus, E-mail: zwang@cmu.ed, E-mail: deserno@andrew.cmu.ed [Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213 (United States)

2010-09-15

We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.

Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field

International Nuclear Information System (INIS)

Wang Zunjing; Deserno, Markus

2010-01-01

We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

Energy Technology Data Exchange (ETDEWEB)

Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K., E-mail: jonathan.doye@chem.ox.ac.uk [Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ (United Kingdom); Randisi, Ferdinando [Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU (United Kingdom); Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Šulc, Petr [Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065 (United States); Ouldridge, Thomas E. [Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ (United Kingdom); Tsukanov, Roman; Nir, Eyal [Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva (Israel); Louis, Ard A. [Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

2015-06-21

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

International Nuclear Information System (INIS)

Snodin, Benedict E. K.; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; Šulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

2015-01-01

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na + ] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

Science.gov (United States)

Fonseca, Pedro; Romano, Flavio; Schreck, John S.; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.

2018-04-01

Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.

Coarse grained MD simulations of a fracture of filler-filled polymer nanocomposites under uniaxial elongation

Science.gov (United States)

Hagita, Katsumi; Morita, Hiroshi; Takano, Hiroshi

We performed coarse grained molecular dynamics (MD) simulations based on Kremer-Grest model in order to investigate a fracture of polymer nanocomposites filled with spherical nanoparticles (NPs) under uniaxial elongation with a Poisson ratio of 0.4. In our model, the NP consists of 320 surface beads and one center bead. In order to make the NP spherical, a harmonic potential is applied to the surface particles from the center of the NP. Here, the initial volume fraction of the NPs is about 20%. The dependences of the fracture on the interactions between the NPs and polymers were examined. In order to observe the creation of nanovoids, the interaction among the polymers was set to be attractive. When the NP-polymer interaction is attractive, nanovoids appear in the bulk of polymers. On the other hand, for repulsive NP-polymer interaction, nanovoids are created at the surface between the polymers and NPs. At the same time, segregation of NPs is observed. We found that these behaviors depend on crosslink densities.

Molecular modeling of polycarbonate materials: Glass transition and mechanical properties

Science.gov (United States)

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.

Grain-growth law during Stage 1 sintering of materials

International Nuclear Information System (INIS)

He Zeming; Ma, J.

2002-01-01

This work investigates the grain-growth behaviour of powder compact during Stage 1 sintering (<90{%} theoretical density). It is widely accepted that grain size is an important state variable in the constitutive modelling in material sintering. However, it is noted that all the existing grain-growth laws proposed in the literature do not incorporate the effect of externally applied stress independently. In this work, a grain-growth law with externally applied stress as a variable was proposed. Alumina powders were forge-sintered at different applied stresses to examine the proposed grain-growth relationship. The proposed grain-growth law was then applied to model the grain-growth process on the sinter forging of tool steel. It is shown that the present proposed grain-growth law provides a good description on the experimental results. (author)

A new insight into ductile fracture of ultrafine-grained Al-Mg alloys.

Science.gov (United States)

Yu, Hailiang; Tieu, A Kiet; Lu, Cheng; Liu, Xiong; Liu, Mao; Godbole, Ajit; Kong, Charlie; Qin, Qinghua

2015-04-08

It is well known that when coarse-grained metals undergo severe plastic deformation to be transformed into nano-grained metals, their ductility is reduced. However, there are no ductile fracture criteria developed based on grain refinement. In this paper, we propose a new relationship between ductile fracture and grain refinement during deformation, considering factors besides void nucleation and growth. Ultrafine-grained Al-Mg alloy sheets were fabricated using different rolling techniques at room and cryogenic temperatures. It is proposed for the first time that features of the microstructure near the fracture surface can be used to explain the ductile fracture post necking directly. We found that as grains are refined to a nano size which approaches the theoretical minimum achievable value, the material becomes brittle at the shear band zone. This may explain the tendency for ductile fracture in metals under plastic deformation.

Luna 24 regolith breccias: A possible source of the fine size material of the Luna 24 regolith

Science.gov (United States)

Rode, O. D.; Lindstrom, M. M.

1994-01-01

The regolith breccias from the Luna 24 core were analyzed. The Luna 24 regolith is a mixture of fine and coarse grain materials. The comparable analysis of the grain size distributions, the modal and chemical compositions of the breccias, and the regolith from the same levels show that the friable slightly litificated breccia with a friable fine grain matrix may be a source of fine grain material of the Luna 24 present day regolith.

Rheological analysis of fine-grained natural debris-flow material

Science.gov (United States)

Major, Jon J.; Pierson, Thomas C.; ,

1990-01-01

Experiments were conducted on large samples of fine-grained material (???2mm) from a natural debris flow using a wide-gap concentric-cylinder viscometer. The rheological behavior of this material is compatible with a Bingham model at shear rates in excess of 5 sec. At lesser shear rates, rheological behavior of the material deviates from the Bingham model, and when sand concentration of the slurry exceeds 20 percent by volume, particle interaction between sand grains dominates the mechanical behavior. Yield strength and plastic viscosity are extremely sensitive to sediment concentration.

Investigation of the thermophysical properties of oxide ceramic materials at liquid-helium temperatures

International Nuclear Information System (INIS)

Taranov, A. V.; Khazanov, E. N.

2008-01-01

The main regularities in the transport of thermal phonons in oxide ceramic materials are investigated at liquid-helium temperatures. The dependences of the thermophysical characteristics of ceramic materials on their structural parameters (such as the grain size R, the grain boundary thickness d, and the structure of grain boundaries) are analyzed. It is demonstrated that, in dense coarse-grained ceramic materials with qR>>1 (where q is the phonon wave vector), the grain boundaries and the grain size are the main factors responsible for the thermophysical characteristics of the material at liquid-helium temperatures. A comparative analysis of the thermophysical characteristics of optically transparent ceramic materials based on the Y 3 Al 5 O 12 (YAG) and Y 2 O 3 cubic oxides synthesized under different technological conditions is performed using the proposed criterion

Structure and dynamics of Ebola virus matrix protein VP40 by a coarse-grained Monte Carlo simulation

Science.gov (United States)

Pandey, Ras; Farmer, Barry

Ebola virus matrix protein VP40 (consisting of 326 residues) plays a critical role in viral assembly and its functions such as regulation of viral transcription, packaging, and budding of mature virions into the plasma membrane of infected cells. How does the protein VP40 go through structural evolution during the viral life cycle remains an open question? Using a coarse-grained Monte Carlo simulation we investigate the structural evolution of VP40 as a function of temperature with the input of a knowledge-based residue-residue interaction. A number local and global physical quantities (e.g. mobility profile, contact map, radius of gyration, structure factor) are analyzed with our large-scale simulations. Our preliminary data show that the structure of the protein evolves through different state with well-defined morphologies which can be identified and quantified via a detailed analysis of structure factor.

SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

Science.gov (United States)

Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio

2015-02-10

Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.

SmartCell: An Energy Efficient Coarse-Grained Reconfigurable Architecture for Stream-Based Applications

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Liang Cao

2009-01-01

Full Text Available This paper presents SmartCell, a novel coarse-grained reconfigurable architecture, which tiles a large number of processor elements with reconfigurable interconnection fabrics on a single chip. SmartCell is able to provide high performance and energy efficient processing for stream-based applications. It can be configured to operate in various modes, such as SIMD, MIMD, and systolic array. This paper describes the SmartCell architecture design, including processing element, reconfigurable interconnection fabrics, instruction and control process, and configuration scheme. The SmartCell prototype with 64 PEs is implemented using 0.13  m CMOS standard cell technology. The core area is about 8.5  , and the power consumption is about 1.6 mW/MHz. The performance is evaluated through a set of benchmark applications, and then compared with FPGA, ASIC, and two well-known reconfigurable architectures including RaPiD and Montium. The results show that the SmartCell can bridge the performance and flexibility gap between ASIC and FPGA. It is also about 8% and 69% more energy efficient than Montium and RaPiD systems for evaluated benchmarks. Meanwhile, SmartCell can achieve 4 and 2 times more throughput gains when comparing with Montium and RaPiD, respectively. It is concluded that SmartCell system is a promising reconfigurable and energy efficient architecture for stream processing.

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

Science.gov (United States)

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.

Interpretation of sedimentological processes of coarse-grained deposits applying a novel combined cluster and discriminant analysis

Science.gov (United States)

Farics, Éva; Farics, Dávid; Kovács, József; Haas, János

2017-10-01

The main aim of this paper is to determine the depositional environments of an Upper-Eocene coarse-grained clastic succession in the Buda Hills, Hungary. First of all, we measured some commonly used parameters of samples (size, amount, roundness and sphericity) in a much more objective overall and faster way than with traditional measurement approaches, using the newly developed Rock Analyst application. For the multivariate data obtained, we applied Combined Cluster and Discriminant Analysis (CCDA) in order to determine homogeneous groups of the sampling locations based on the quantitative composition of the conglomerate as well as the shape parameters (roundness and sphericity). The result is the spatial pattern of these groups, which assists with the interpretation of the depositional processes. According to our concept, those sampling sites which belong to the same homogeneous groups were likely formed under similar geological circumstances and by similar geological processes. In the Buda Hills, we were able to distinguish various sedimentological environments within the area based on the results: fan, intermittent stream or marine.

Hysteresis of liquid adsorption in porous media by coarse-grained Monte Carlo with direct experimental validation

Energy Technology Data Exchange (ETDEWEB)

Zeidman, Benjamin D. [Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401 (United States); Lu, Ning [Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401 (United States); Wu, David T., E-mail: dwu@mines.edu [Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401 (United States); Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401 (United States)

2016-05-07

The effects of path-dependent wetting and drying manifest themselves in many types of physical systems, including nanomaterials, biological systems, and porous media such as soil. It is desirable to better understand how these hysteretic macroscopic properties result from a complex interplay between gasses, liquids, and solids at the pore scale. Coarse-Grained Monte Carlo (CGMC) is an appealing approach to model these phenomena in complex pore spaces, including ones determined experimentally. We present two-dimensional CGMC simulations of wetting and drying in two systems with pore spaces determined by sections from micro X-ray computed tomography: a system of randomly distributed spheres and a system of Ottawa sand. Results for the phase distribution, water uptake, and matric suction when corrected for extending to three dimensions show excellent agreement with experimental measurements on the same systems. This supports the hypothesis that CGMC can generate metastable configurations representative of experimental hysteresis and can also be used to predict hysteretic constitutive properties of particular experimental systems, given pore space images.

Evolution of twinning in extruded AZ31 alloy with bimodal grain structure

Energy Technology Data Exchange (ETDEWEB)

Garcés, G., E-mail: ggarces@cenim.csic.es [Department of Physical Metallurgy, National Centre for Metallurgical Research CENIM-CSIC, Av. De Gregorio del Amo 8, 28040 Madrid (Spain); Oñorbe, E. [CIEMAT, Division of Structural Materials, Avenida Complutense, 40, 28040 Madrid (Spain); Gan, W. [German Engineering Materials Science Centre at MLZ, Helmholtz-Zentrum Geesthacht, Lichtebergstr. 1, D-85747 Garching (Germany); Máthis, K. [Department of Physics of Materials, Faculty of Mathematics and Physics, Charles University, KeKarlovu 5, 121 16 Praha 2 (Czech Republic); Tolnai, D. [Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Max-Planck-Str. 1, 21502 Geesthacht (Germany); Horváth, K. [Department of Physics of Materials, Faculty of Mathematics and Physics, Charles University, KeKarlovu 5, 121 16 Praha 2 (Czech Republic); Pérez, P.; Adeva, P. [Department of Physical Metallurgy, National Centre for Metallurgical Research CENIM-CSIC, Av. De Gregorio del Amo 8, 28040 Madrid (Spain)

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 recrystallized 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.

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

Science.gov (United States)

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.

Preferential Flow Paths and Recirculation-Disrupting Jets in the Leeside of Self-Forming Coarse-Grained Laboratory Bedforms

Science.gov (United States)

Lichtner, D.; Christensen, K. T.; Best, J.; Blois, G.

2014-12-01

Exchange of fluid in the near-subsurface of a streambed is influenced by turbulence in the free flow, as well as by bed topography and permeability. Macro-roughness elements such as bedforms are known to produce pressure gradients that drive fluid into the streambed on their stoss sides and out of the bed on their lee sides. To study the modification of the near-bed flow field by self-forming permeable bedforms, laboratory experiments were conducted in a 5 mm wide flume filled with 1.3 mm glass beads. The narrow width of the flume permitted detailed examination of the fluid exiting the bed immediately downstream of a bedform. Dense 2-D velocity field measurements were gathered using particle image velocimetry (PIV). In up to 8% of instantaneous PIV realizations, the flow at the near-bed presented a component perpendicular to the streambed, indicating flow across the interface. At the downstream side of the bedform, such flow disrupted the mean recirculation pattern that is typically observed in finer sediment beds. It is hypothesized that the coarse grain size and the resulting high bed permeability promote such near-surface jet events. A qualitative analysis of raw image frames indicated that an in-place jostling of sediment is associated with these jets thus suggesting that subsurface flow may be characterized by impulsive events. These observations are relevant to hyporheic exchange rates in coarse sediments and can have strong morphodynamic implications as they can explain the lack of ripples and characteristics of dunes in high permeability gravels. Overall, further study of the flow structure over highly permeable streambeds is needed to understand subsurface exchange and bedform initiation.

Optimal number of coarse-grained sites in different components of large biomolecular complexes.

Science.gov (United States)

Sinitskiy, Anton V; Saunders, Marissa G; Voth, Gregory A

2012-07-26

The computational study of large biomolecular complexes (molecular machines, cytoskeletal filaments, etc.) is a formidable challenge facing computational biophysics and biology. To achieve biologically relevant length and time scales, coarse-grained (CG) models of such complexes usually must be built and employed. One of the important early stages in this approach is to determine an optimal number of CG sites in different constituents of a complex. This work presents a systematic approach to this problem. First, a universal scaling law is derived and numerically corroborated for the intensity of the intrasite (intradomain) thermal fluctuations as a function of the number of CG sites. Second, this result is used for derivation of the criterion for the optimal number of CG sites in different parts of a large multibiomolecule complex. In the zeroth-order approximation, this approach validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems (e.g., individual biomolecules). The first-order corrections to this rule are derived and numerically checked by the case studies of the Escherichia coli ribosome and Arp2/3 actin filament junction. In different ribosomal proteins, the optimal number of amino acids per CG site is shown to differ by a factor of 3.5, and an even wider spread may exist in other large biomolecular complexes. Therefore, the method proposed in this paper is valuable for the optimal construction of CG models of such complexes.

Investigation of pier scour in coarse-bed streams in Montana, 2001 through 2007

Science.gov (United States)

Holnbeck, Stephen R.

2011-01-01

A primary goal of ongoing field research of bridge scour is improvement of scour-prediction equations so that pier-scour depth is predicted accurately-an important element of hydraulic analysis and design of highway bridges that cross streams, rivers, and other waterways. Scour depth for piers in streambeds with a mixture of sand, gravel, cobbles, and boulders (coarse-bed streams, which are common in Montana) generally is less than the scour depth in finer-grained (sandy) streambeds under similar conditions. That difference is attributed to an armor layer of coarser material. Pier-scour data from the U.S. Geological Survey were used in this study to develop a bed-material correction factor, which was incorporated into the Federal Highway Administration's recommended equation for computing pier scour. This report describes results of a study of pier scour in coarse-bed streams at 59 bridge sites during 2001-2007 in the mountain and foothill regions of western Montana. Respective drainage areas ranged from about 3 square miles (mi2) to almost 20,000 mi2. Data collected and analyzed for this study included 103 pier-scour measurements; the report further describes data collection, shows expansion of the national coarse pier-scour database, discusses use of the new data in evaluation of relative accuracy of various predictive equations, and demonstrates how differences in size and gradation between surface bed material and shallow-subsurface bed material might relate to pier scour. Nearly all measurements were made under clear-water conditions with no incoming sediment supply to the bridge opening. Half of the measurements showed approach velocities that equaled or surpassed the critical velocity for incipient motion of bed material, possibly indicating that measurements were made very near the threshold between clear-water and live-bed scour, where maximum scour was shown in laboratory studies. Data collected in this study were compared to selected pier-scour data from

Equation for the superfluid gap obtained by coarse graining the Bogoliubov-de Gennes equations throughout the BCS-BEC crossover

Science.gov (United States)

Simonucci, S.; Strinati, G. C.

2014-02-01

We derive a nonlinear differential equation for the gap parameter of a superfluid Fermi system by performing a suitable coarse graining of the Bogoliubov-de Gennes (BdG) equations throughout the BCS-BEC crossover, with the aim of replacing the time-consuming solution of the original BdG equations by the simpler solution of this novel equation. We perform a favorable numerical test on the validity of this new equation over most of the temperature-coupling phase diagram, by an explicit comparison with the full solution of the original BdG equations for an isolated vortex. We also show that the new equation reduces both to the Ginzburg-Landau equation for Cooper pairs in weak coupling close to the critical temperature and to the Gross-Pitaevskii equation for composite bosons in strong coupling at low temperature.

The effect of grain size on dynamic tensile extrusion behaviour

Directory of Open Access Journals (Sweden)

Park Leeju

2015-01-01

Full Text Available Dynamic tensile extrusion (DTE tests were conducted on coarse grained and ultrafine grained (UFG OFHC Cu, Interstitial free (IF Steel, and pure Ta. Equal channel angular pressing (ECAP of 16passes with Bc for Cu, IF Steel and 4 passes for Ta was employed to fabricated UFG materials. DTE tests were carried out by launching the sphere samples (Dia. 7.62 mm to the conical extrusion die at a speed of ∼500 m/sec. The fragmentation behavior of the soft-recovered fragments were examined and compared with each other. The DTE fragmentation behavior of CG and UFG was numerically simulated by the LS-DYNA FEM code.

Systematic NMR Analysis of Stable Isotope Labeled Metabolite Mixtures in Plant and Animal Systems: Coarse Grained Views of Metabolic Pathways

Science.gov (United States)

Chikayama, Eisuke; Suto, Michitaka; Nishihara, Takashi; Shinozaki, Kazuo; Hirayama, Takashi; Kikuchi, Jun

2008-01-01

Background Metabolic phenotyping has become an important ‘bird's-eye-view’ technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of ‘top-down’ chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. Methodology/Principal Findings The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 1H and 13C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each 13C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient 13C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. Conclusions/Significance Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of 13C atoms of

Tools for Material Design and Selection

Science.gov (United States)

Wehage, Kristopher

The present thesis focuses on applications of numerical methods to create tools for material characterization, design and selection. The tools generated in this work incorporate a variety of programming concepts, from digital image analysis, geometry, optimization, and parallel programming to data-mining, databases and web design. The first portion of the thesis focuses on methods for characterizing clustering in bimodal 5083 Aluminum alloys created by cryomilling and powder metallurgy. The bimodal samples analyzed in the present work contain a mixture of a coarse grain phase, with a grain size on the order of several microns, and an ultra-fine grain phase, with a grain size on the order of 200 nm. The mixing of the two phases is not homogeneous and clustering is observed. To investigate clustering in these bimodal materials, various microstructures were created experimentally by conventional cryomilling, Hot Isostatic Pressing (HIP), Extrusion, Dual-Mode Dynamic Forging (DMDF) and a new 'Gradient' cryomilling process. Two techniques for quantitative clustering analysis are presented, formulated and implemented. The first technique, the Area Disorder function, provides a metric of the quality of coarse grain dispersion in an ultra-fine grain matrix and the second technique, the Two-Point Correlation function, provides a metric of long and short range spatial arrangements of the two phases, as well as an indication of the mean feature size in any direction. The two techniques are implemented on digital images created by Scanning Electron Microscopy (SEM) and Electron Backscatter Detection (EBSD) of the microstructures. To investigate structure--property relationships through modeling and simulation, strategies for generating synthetic microstructures are discussed and a computer program that generates randomized microstructures with desired configurations of clustering described by the Area Disorder Function is formulated and presented. In the computer program, two

Grain-size segregation and levee formation in geophysical mass flows

Science.gov (United States)

Johnson, C.G.; Kokelaar, B.P.; Iverson, Richard M.; Logan, M.; LaHusen, R.G.; Gray, J.M.N.T.

2012-01-01

Data from large-scale debris-flow experiments are combined with modeling of particle-size segregation to explain the formation of lateral levees enriched in coarse grains. The experimental flows consisted of 10 m3 of water-saturated sand and gravel, which traveled ∼80 m down a steeply inclined flume before forming an elongated leveed deposit 10 m long on a nearly horizontal runout surface. We measured the surface velocity field and observed the sequence of deposition by seeding tracers onto the flow surface and tracking them in video footage. Levees formed by progressive downslope accretion approximately 3.5 m behind the flow front, which advanced steadily at ∼2 m s−1during most of the runout. Segregation was measured by placing ∼600 coarse tracer pebbles on the bed, which, when entrained into the flow, segregated upwards at ∼6–7.5 cm s−1. When excavated from the deposit these were distributed in a horseshoe-shaped pattern that became increasingly elevated closer to the deposit termination. Although there was clear evidence for inverse grading during the flow, transect sampling revealed that the resulting leveed deposit was strongly graded laterally, with only weak vertical grading. We construct an empirical, three-dimensional velocity field resembling the experimental observations, and use this with a particle-size segregation model to predict the segregation and transport of material through the flow. We infer that coarse material segregates to the flow surface and is transported to the flow front by shear. Within the flow head, coarse material is overridden, then recirculates in spiral trajectories due to size-segregation, before being advected to the flow edges and deposited to form coarse-particle-enriched levees.

HIGH-FIDELITY SIMULATION-DRIVEN MODEL DEVELOPMENT FOR COARSE-GRAINED COMPUTATIONAL FLUID DYNAMICS

Energy Technology Data Exchange (ETDEWEB)

Hanna, Botros N.; Dinh, Nam T.; Bolotnov, Igor A.

2016-06-01

Nuclear reactor safety analysis requires identifying various credible accident scenarios and determining their consequences. For a full-scale nuclear power plant system behavior, it is impossible to obtain sufficient experimental data for a broad range of risk-significant accident scenarios. In single-phase flow convective problems, Direct Numerical Simulation (DNS) and Large Eddy Simulation (LES) can provide us with high fidelity results when physical data are unavailable. However, these methods are computationally expensive and cannot be afforded for simulation of long transient scenarios in nuclear accidents despite extraordinary advances in high performance scientific computing over the past decades. The major issue is the inability to make the transient computation parallel, thus making number of time steps required in high-fidelity methods unaffordable for long transients. In this work, we propose to apply a high fidelity simulation-driven approach to model sub-grid scale (SGS) effect in Coarse Grained Computational Fluid Dynamics CG-CFD. This approach aims to develop a statistical surrogate model instead of the deterministic SGS model. We chose to start with a turbulent natural convection case with volumetric heating in a horizontal fluid layer with a rigid, insulated lower boundary and isothermal (cold) upper boundary. This scenario of unstable stratification is relevant to turbulent natural convection in a molten corium pool during a severe nuclear reactor accident, as well as in containment mixing and passive cooling. The presented approach demonstrates how to create a correction for the CG-CFD solution by modifying the energy balance equation. A global correction for the temperature equation proves to achieve a significant improvement to the prediction of steady state temperature distribution through the fluid layer.

Coarse-grained molecular dynamics modeling of the kinetics of lamellar block copolymer defect annealing

Science.gov (United States)

Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

2016-01-01

State-of-the-art block copolymer (BCP)-directed self-assembly (DSA) methods still yield defect densities orders of magnitude higher than is necessary in semiconductor fabrication despite free-energy calculations that suggest equilibrium defect densities are much lower than is necessary for economic fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that bulk simulations yield an exponential drop in defect heal rate above χN˜30. Thin films show no change in rate associated with the energy barrier below χN˜50, significantly higher than the χN values found previously for self-consistent field theory studies that neglect fluctuations. Above χN˜50, the simulations show an increase in energy barrier scaling with 1/2 to 1/3 of the bulk systems. This is because thin films always begin healing at the free interface or the BCP-underlayer interface, where the increased A-B contact area associated with the transition state is minimized, while the infinitely thick films cannot begin healing at an interface.

Coarse-Grain QoS-Aware Dynamic Instance Provisioning for Interactive Workload in the Cloud

Directory of Open Access Journals (Sweden)

Jianxiong Wan

2014-01-01

Full Text Available Cloud computing paradigm renders the Internet service providers (ISPs with a new approach to deliver their service with less cost. ISPs can rent virtual machines from the Infrastructure-as-a-Service (IaaS provided by the cloud rather than purchasing them. In addition, commercial cloud providers (CPs offer diverse VM instance rental services in various time granularities, which provide another opportunity for ISPs to reduce cost. We investigate a Coarse-grain QoS-aware Dynamic Instance Provisioning (CDIP problem for interactive workload in the cloud from the perspective of ISPs. We formulate the CDIP problem as an optimization problem where the objective is to minimize the VM instance rental cost and the constraint is the percentile delay bound. Since the Internet traffic shows a strong self-similar property, it is hard to get an analytical form of the percentile delay constraint. To address this issue, we purpose a lookup table structure together with a learning algorithm to estimate the performance of the instance provisioning policy. This approach is further extended with two function approximations to enhance the scalability of the learning algorithm. We also present an efficient dynamic instance provisioning algorithm, which takes full advantage of the rental service diversity, to determine the instance rental policy. Extensive simulations are conducted to validate the effectiveness of the proposed algorithms.

Connecting macroscopic observables and microscopic assembly events in amyloid formation using coarse grained simulations.

Directory of Open Access Journals (Sweden)

Noah S Bieler

Full Text Available The pre-fibrillar stages of amyloid formation have been implicated in cellular toxicity, but have proved to be challenging to study directly in experiments and simulations. Rational strategies to suppress the formation of toxic amyloid oligomers require a better understanding of the mechanisms by which they are generated. We report Dynamical Monte Carlo simulations that allow us to study the early stages of amyloid formation. We use a generic, coarse-grained model of an amyloidogenic peptide that has two internal states: the first one representing the soluble random coil structure and the second one the [Formula: see text]-sheet conformation. We find that this system exhibits a propensity towards fibrillar self-assembly following the formation of a critical nucleus. Our calculations establish connections between the early nucleation events and the kinetic information available in the later stages of the aggregation process that are commonly probed in experiments. We analyze the kinetic behaviour in our simulations within the framework of the theory of classical nucleated polymerisation, and are able to connect the structural events at the early stages in amyloid growth with the resulting macroscopic observables such as the effective nucleus size. Furthermore, the free-energy landscapes that emerge from these simulations allow us to identify pertinent properties of the monomeric state that could be targeted to suppress oligomer formation.

Starch degradability of dry and ensiled high-moisture grains of corn hybrids with different textures at different grinding degrees

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Wagner dos Reis

2011-02-01

Full Text Available This research evaluated corn grains with flint and dent texture (ensiled high-moisture or dried, submitted to grinding degrees, using the in situ ruminal degradation technique. Three rumen canulated adult sheeps were used in a complete randomized design, using a factorial outline 2 x 2 x 3, with two corn hybrids (flint and dent texture, two conservation methods (ensiled high-moisture and dry and three grinding degress (whole, coarsely and finely ground, corresponding to the sieve of 12; 10 and 8 mm. Starch soluble fraction (A of the dent hybrid ensiled corn grains was greater comparing to the dry materials and in both conservation forms this fraction was reduced in the flint texture hybrid, while the insoluble fraction potentially degradable (B the opposite occurred. The degradation potential was higher in grains ensiled in two textures. The ensiled allowed more starch effective degradation in relation to dry grain in two textures and the grains dent texture hybrid also increased such degradation in both conservation methods. The dent texture and the ensiled high-moisture grains proved the best option considering the starch degradability. Regardless of the conservation forms, the grains of corn hybrid flint texture should be finely ground, for providing higher ruminal degradation, while for the dent texture hybrid, the coarsely and whole grinding are the most suitable for ensiled and dry grain, respectively.

Mechanics of biopolymer materials: Single chains to bulk properties

NARCIS (Netherlands)

Amuasi, H.E.; Storm, C.

2010-01-01

We outline the first stages in the multiscale modeling of biopolymer materials, starting with the statistical mechanics of single stiff chains. In the first coarse graining step, we demonstrate how to integrate out the single polymer degrees of freedom in supramolecular assemblies of such

Computational Investigation of Effects of Grain Size on Ballistic Performance of Copper

Science.gov (United States)

He, Ge; Dou, Yangqing; Guo, Xiang; Liu, Yucheng

2018-01-01

Numerical simulations were conducted to compare ballistic performance and penetration mechanism of copper (Cu) with four representative grain sizes. Ballistic limit velocities for coarse-grained (CG) copper (grain size ≈ 90 µm), regular copper (grain size ≈ 30 µm), fine-grained (FG) copper (grain size ≈ 890 nm), and ultrafine-grained (UG) copper (grain size ≈ 200 nm) were determined for the first time through the simulations. It was found that the copper with reduced grain size would offer higher strength and better ductility, and therefore renders improved ballistic performance than the CG and regular copper. High speed impact and penetration behavior of the FG and UG copper was also compared with the CG coppers strengthened by nanotwinned (NT) regions. The comparison results showed the impact and penetration resistance of UG copper is comparable to the CG copper strengthened by NT regions with the minimum twin spacing. Therefore, besides the NT-strengthened copper, the single phase copper with nanoscale grain size could also be a strong candidate material for better ballistic protection. A computational modeling and simulation framework was proposed for this study, in which Johnson-Cook (JC) constitutive model is used to predict the plastic deformation of Cu; the JC damage model is to capture the penetration and fragmentation behavior of Cu; Bao-Wierzbicki (B-W) failure criterion defines the material's failure mechanisms; and temperature increase during this adiabatic penetration process is given by the Taylor-Quinney method.

Electrical properties of grain boundaries in polycrystalline materials under intrinsic or low doping

International Nuclear Information System (INIS)

Chowdhury, M H; Kabir, M Z

2011-01-01

An analytical model is developed to study the electrical properties (electric field and potential distributions, potential energy barrier height and polarization phenomenon) of polycrystalline materials at intrinsic or low doping for detector and solar cell applications by considering an arbitrary amount of grain boundary charge and a finite width of grain boundary region. The general grain boundary model is also applicable to highly doped polycrystalline materials. The electric field and potential distributions are obtained by solving Poisson's equation in both depleted grains and grain boundary regions. The electric field and potential distributions across the detector are analysed under various doping, trapping and applied biases. The electric field collapses, i.e. a nearly zero-average electric field region exists in some part of the biased detector at high trapped charge densities at the grain boundaries. The model explains the conditions of existence of a zero-average field region, i.e. the polarization mechanisms in polycrystalline materials. The potential energy barrier at the grain boundary exists if the electric field changes its sign at the opposite side of the grain boundary. The energy barrier does not exist in all grain boundaries in the low-doped polycrystalline detector and it never exists in intrinsic polycrystalline detectors under applied bias condition provided that there is no charge trapping in the grain.

Dynamics of deposited fly-ash and fine grained magnetite in sandy material of different porosity (column experiments)

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Kapicka, Ales; Kodesova, Radka; Petrovsky, Eduard; Grison, Hana

2010-05-01

Several studies confirm that soil magnetometry can serve as proxy of industrial immisions as well as heavy-metal contamination. The important assumption for magnetic mapping of contaminated soils is that atmospherically deposited particulate matter, including the ferrimagnetic phase, accumulates in the top soil horizons and remains there over long period. Only if this is true, large areas can be reliably mapped using soil magnetometry, and, moreover, this method can be used also for long-term monitoring. However, in soil types such as sandy soils with different porosity or soils with substantial variability of water regime, translocation of the deposited anthropogenic particles may result in biased (underestimated) values of the measured topsoil magnetic susceptibility. From the physical point of view, this process may be considered as colloid transport through porous medium. In our column experiments in laboratory we used three technical sands with different particle sizes (0,63 - 1.25mm, 0,315-0,80mm, 0,10-0,63mm). Sands in cylinders were contaminated on the surface by fly-ashes from coal-burning power plant (mean grain size 10μm) and fine grained Fe3O4 (grain size < 20 μm). Soil moisture sensors were used to monitor water regime within the sand columns after controlled rain simulation and temperature distribution in sand column was measured as well. Vertical migration of ferrimagnetic particles-tracers presented in the fly-ash was measured by SM 400 Kappameter. By means of magnetic susceptibility distribution we studied two parameters: gradual shift of peak concentration of contaminants (relative to surface layer) and maximum penetration depth. Results indicated that after rain simulation (pulls infiltration of defined water volume) the positions of peak values moved downwards compared to the initial state and gradual decrease of susceptibility peak values were detected in all studied sand formations. Fly-ash migrated more or less freely in coarse sand

Conformational temperature-dependent behavior of a histone H2AX: a coarse-grained Monte Carlo approach via knowledge-based interaction potentials.

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Miriam Fritsche

Full Text Available Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential.We find a variety of equilibrium structures including global globular configurations at low normalized temperature (T* = 0.014, combination of segmental globules and elongated chains (T* = 0.016,0.017, predominantly elongated chains (T* = 0.019,0.020, as well as universal SAW conformations at high normalized temperature (T* ≥ 0.023. The radius of gyration of the protein exhibits a non-monotonic temperature dependence with a maximum at a characteristic temperature (T(c* = 0.019 where a crossover occurs from a positive (stretching at T* ≤ T(c* to negative (contraction at T* ≥ T(c* thermal response on increasing T*.

Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

Science.gov (United States)

Kapoor, Abhijeet; Travesset, Alex

2014-03-01

We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.

Investigation on the crystallography of the transformation products of reverted austenite in intercritically reheated coarse grained heat affected zone

International Nuclear Information System (INIS)

You, Yang; Shang, Chengjia; Chen, Liang; Subramanian, Sundaresa

2013-01-01

Highlights: ► Area of reverted austenite is traced out by crystallographic information. ► Bainite and martensite regions were confirmed within it. ► The martensite region is considered as the blocky MA particles. ► Martensite region has high deformation to initiate fracture. ► More uniform transformation of the reverted austenite is good for toughness. -- Abstract: In present study the intercritically reheated coarse grained heat affected zone (ICCGHAZ) showing the worst impact toughness in the heat affected zone of multi-pass welding was simulated by Gleeble-1500, and its microstructure was investigated in detail by means of scanning electron microscope (SEM) and electron backscattering diffraction (EBSD). With the crystallographic information from EBSD scanning the area of a single reverted austenite grain which formed during the thermal cycles of second pass simulation was traced out. Within it two regions with different characteristic both in morphology and crystallography were found out, showing an un-uniform transformation of the reverted austenite. The region I is a bainitic region containing larger bainitic ferrite grains, while the region II is made up of several clusters containing tiny grains. Based on the crystallographic information each cluster was determined as martensite island thereby should be considered as blocky Martensite/Austenite constituent (M/A), which is hard phase and harmful for toughness. Analysis on the level of deformation shows that the region II is much higher deformed than the region I, indicating there is high stress concentration within the region II. The possible influence of the region I and the region II on fracture is discussed under the early proposed M/A’s fracture-initiating mechanisms. It suggests that the main cause of the toughness reduction is the un-uniform transformation of the reverted austenite, and the toughness performance of the ICCGHAZ could be improved if the transformation of the reverted

Insight of Transmembrane Processes of Self-Assembling Nanotubes Based on a Cyclic Peptide Using Coarse Grained Molecular Dynamics Simulation.

Science.gov (United States)

Fu, Yankai; Yan, Tingxuan; Xu, Xia

2017-09-28

Transmembrane self-assembling cyclic peptide (SCP) nanotubes are promising candidates for delivering specific molecules through cell membranes. The detailed mechanisms behind the transmembrane processes, as well as stabilization factors of transmembrane structures, are difficult to elucidate through experiments. In this study, the effects of peptide sequence and oligomeric state on the transmembrane capabilities of SCP nanotubes and the perturbation of embedded SCP nanotubes acting on the membrane were investigated based on coarse grained molecular dynamics simulation. The simulation results reveal that hydrophilic SCP oligomers result in the elevation of the energy barrier while the oligomerization of hydrophobic SCPs causes the reduction of the energy barrier, further leading to membrane insertion. Once SCP nanotubes are embedded, membrane properties such as density, thickness, ordering state and lateral mobility are adjusted along the radial direction. This study provides insight into the transmembrane strategy of SCP nanotubes and sheds light on designing novel transport systems.

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

Science.gov (United States)

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.

Fine-grained, local maps and coarse, global representations support human spatial working memory.

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Mohammad Zia Ul Haq Katshu

Full Text Available While sensory processes are tuned to particular features, such as an object's specific location, color or orientation, visual working memory (vWM is assumed to store information using representations, which generalize over a feature dimension. Additionally, current vWM models presume that different features or objects are stored independently. On the other hand, configurational effects, when observed, are supposed to mainly reflect encoding strategies. We show that the location of the target, relative to the display center and boundaries, and overall memory load influenced recall precision, indicating that, like sensory processes, capacity limited vWM resources are spatially tuned. When recalling one of three memory items the target distance from the display center was overestimated, similar to the error when only one item was memorized, but its distance from the memory items' average position was underestimated, showing that not only individual memory items' position, but also the global configuration of the memory array may be stored. Finally, presenting the non-target items at recall, consequently providing landmarks and configurational information, improved precision and accuracy of target recall. Similarly, when the non-target items were translated at recall, relative to their position in the initial display, a parallel displacement of the recalled target was observed. These findings suggest that fine-grained spatial information in vWM is represented in local maps whose resolution varies with distance from landmarks, such as the display center, while coarse representations are used to store the memory array configuration. Both these representations are updated at the time of recall.

Fine-Grained, Local Maps and Coarse, Global Representations Support Human Spatial Working Memory

Science.gov (United States)

Katshu, Mohammad Zia Ul Haq; d'Avossa, Giovanni

2014-01-01

While sensory processes are tuned to particular features, such as an object's specific location, color or orientation, visual working memory (vWM) is assumed to store information using representations, which generalize over a feature dimension. Additionally, current vWM models presume that different features or objects are stored independently. On the other hand, configurational effects, when observed, are supposed to mainly reflect encoding strategies. We show that the location of the target, relative to the display center and boundaries, and overall memory load influenced recall precision, indicating that, like sensory processes, capacity limited vWM resources are spatially tuned. When recalling one of three memory items the target distance from the display center was overestimated, similar to the error when only one item was memorized, but its distance from the memory items' average position was underestimated, showing that not only individual memory items' position, but also the global configuration of the memory array may be stored. Finally, presenting the non-target items at recall, consequently providing landmarks and configurational information, improved precision and accuracy of target recall. Similarly, when the non-target items were translated at recall, relative to their position in the initial display, a parallel displacement of the recalled target was observed. These findings suggest that fine-grained spatial information in vWM is represented in local maps whose resolution varies with distance from landmarks, such as the display center, while coarse representations are used to store the memory array configuration. Both these representations are updated at the time of recall. PMID:25259601

Enhanced mechanical behaviors of gradient nano-grained austenite stainless steel by means of ultrasonic impact treatment

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Xinjun Yang

Full Text Available The gradient nano-grained (GNG structure was formed on the top layer of AISI 304 in the presence of coarse grains (CG by means of ultrasonic impact treatment (UIT. The impact velocity was 5 m/s and the coverage changed from 3000% to 9000% in order to obtain the microstructure GNG/CG materials. The tensile test and small punch test (SPT were further carried out in order to investigate the mechanical behaviors of the GNG/CG 304 at the different stress states. The results indicated that the yield strength of GNG/CG 304 obtained by tensile test and SPT increased at the small expense of ductility. The stress triaxiality T played an important role in the deformation behavior of GNG/CG 304. An increased T-value in the region of biaxial stretching of small punch specimen (T = 2/3 led to an improved ductility compared with that noted in the case of uniaxial tensile specimen. The strain rate sensitivity m of GNG/CG 304 was 0.0468 that was estimated to be 25-fold greater than the coarse material. The yield strength of GNG/CG 304 at 400 °C was 1.6-fold greater than the coarse material at ambient temperature due to the thermal stability of the GNG layer. Thus, the GNG structure could improve the comprehensive mechanical performances of AISI 304 with a balance of strength and ductility. Keywords: GNG structure, Mechanical behaviors, Small punch test, Ultrasonic impact treatment, Austenite stainless steel

Protein folding simulations: from coarse-grained model to all-atom model.

Science.gov (United States)

Zhang, Jian; Li, Wenfei; Wang, Jun; Qin, Meng; Wu, Lei; Yan, Zhiqiang; Xu, Weixin; Zuo, Guanghong; Wang, Wei

2009-06-01

Protein folding is an important and challenging problem in molecular biology. During the last two decades, molecular dynamics (MD) simulation has proved to be a paramount tool and was widely used to study protein structures, folding kinetics and thermodynamics, and structure-stability-function relationship. It was also used to help engineering and designing new proteins, and to answer even more general questions such as the minimal number of amino acid or the evolution principle of protein families. Nowadays, the MD simulation is still undergoing rapid developments. The first trend is to toward developing new coarse-grained models and studying larger and more complex molecular systems such as protein-protein complex and their assembling process, amyloid related aggregations, and structure and motion of chaperons, motors, channels and virus capsides; the second trend is toward building high resolution models and explore more detailed and accurate pictures of protein folding and the associated processes, such as the coordination bond or disulfide bond involved folding, the polarization, charge transfer and protonate/deprotonate process involved in metal coupled folding, and the ion permeation and its coupling with the kinetics of channels. On these new territories, MD simulations have given many promising results and will continue to offer exciting views. Here, we review several new subjects investigated by using MD simulations as well as the corresponding developments of appropriate protein models. These include but are not limited to the attempt to go beyond the topology based Gō-like model and characterize the energetic factors in protein structures and dynamics, the study of the thermodynamics and kinetics of disulfide bond involved protein folding, the modeling of the interactions between chaperonin and the encapsulated protein and the protein folding under this circumstance, the effort to clarify the important yet still elusive folding mechanism of protein BBL

Coarse graining of entanglement classes in 2 ×m ×n systems

Science.gov (United States)

Hebenstreit, M.; Gachechiladze, M.; Gühne, O.; Kraus, B.

2018-03-01

We consider three-partite pure states in the Hilbert space C2⊗Cm⊗Cn and investigate to which states a given state can be locally transformed with a nonvanishing probability. Whenever the initial and final states are elements of the same Hilbert space, the problem can be solved via the characterization of the entanglement classes which are determined via stochastic local operations and classical communication (SLOCC). In the particular case considered here, the matrix pencil theory can be utilized to address this point. In general, there are infinitely many SLOCC classes. However, when considering transformations from higher to lower dimensional Hilbert spaces, an additional hierarchy among the classes can be found. This hierarchy of SLOCC classes coarse grains SLOCC classes which can be reached from a common resource state of higher dimension. We first show that a generic set of states in C2⊗Cm⊗Cn for n =m is the union of infinitely many SLOCC classes, which can be parameterized by m -3 parameters. However, for n ≠m there exists a single SLOCC class which is generic. Using this result, we then show that there is a full-measure set of states in C2⊗Cm⊗Cn such that any state within this set can be transformed locally to a full measure set of states in any lower dimensional Hilbert space. We also investigate resource states, which can be transformed to any state (not excluding any zero-measure set) in the smaller dimensional Hilbert space. We explicitly derive a state in C2⊗Cm⊗C2 m -2 which is the optimal common resource of all states in C2⊗Cm⊗Cm . We also show that for any n m .

Separation of the Stern and diffuse layer in coarse-grained models: the cases of phosphatidyl serine, phosphatidic acid, and PIP2 monolayers.

Science.gov (United States)

Vangaveti, S; Travesset, A

2014-12-28

We present here a method to separate the Stern and diffuse layer in general systems into two regions that can be analyzed separately. The Stern layer can be described in terms of Bjerrum pairing and the diffuse layer in terms of Poisson-Boltzmann theory (monovalent) or strong coupling theory plus a slowly decaying tail (divalent). We consider three anionic phospholipids: phosphatidyl serine, phosphatidic acid, and phosphatidylinositol(4,5)bisphosphate (PIP2), which we describe within a minimal coarse-grained model as a function of ionic concentration. The case of mixed lipid systems is also considered, which shows a high level of binding cooperativity as a function of PIP2 localization. Implications for existing experimental systems of lipid heterogeneities are also discussed.

Experimental investigation of coarse particle conveying in pipes

Directory of Open Access Journals (Sweden)

Vlasak Pavel

2015-01-01

Full Text Available The advanced knowledge of particle-water mixture flow behaviour is important for safe, reliable, and economical design and operation of the freight pipelines. The effect of the mixture velocity and concentration on the coarse particle – water mixtures flow behaviour was experimentally investigated on an experimental pipe loop of inner diameter D = 100 mm with horizontal, vertical, and inclined pipe sections. Narrow particle size distribution basalt pebbles were used as model of coarse-grained solid particles. The radiometric method was used to measure particle concentration distribution in pipe cross-section. Mixture flow behaviour and particles motion along the pipe invert were studied in a pipe viewing section. The study revealed that the coarse particlewater mixtures in the horizontal and inclined pipe sections were significantly stratified. The particles moved principally in a layer close to the pipe invert. However, for higher and moderate flow velocities the particles moved also in the central part of the pipe cross-section, and particle saltation was found to be dominant mode of particle conveying.

Blocking of grain reorientation in self-doped alumina materials

International Nuclear Information System (INIS)

Suarez, M.; Fernandez, A.; Menendez, J.L.; Ramirez-Rico, J.; Torrecillas, R.

2011-01-01

Alumina nanoparticles 10-20 nm in diameter were nucleated on alumina particles, 150 nm average diameter, by a colloidal route followed by calcination. It is shown that after sintering, the final grain size is up to 20% smaller due to the addition of the alumina nanoparticles. Electron backscattered diffraction analysis shows that whereas a correlation in the relative crystalline orientations between neighbouring grains exists in the pure materials, the addition of alumina nanoparticles results in a random crystalline orientation.

Ultrasonic Characterization of Cast Austenitic Stainless Steel Microstructure: Discrimination between Equiaxed- and Columnar-Grain Material – An Interim Study

Energy Technology Data Exchange (ETDEWEB)

Ramuhalli, Pradeep; Good, Morris S.; Diaz, Aaron A.; Anderson, Michael T.; Watson, Bruce E.; Peters, Timothy J.; Dixit, Mukul; Bond, Leonard J.

2009-10-27

Ultrasonic nondestructive evaluation (NDE) and inspection of cast austenitic stainless steel (CASS) components used in the nuclear power industry is neither as effective nor reliable as is needed due to detrimental effects upon the interrogating ultrasonic beam and interference from ultrasonic backscatter. The root cause is the coarse-grain microstructure inherent to this class of materials. Some ultrasonic techniques perform better for particular microstructural classifications and this has led to the hypothesis that an ultrasonic inspection can be optimized for a particular microstructural class, if a technique exists to reliably classify the microstructure for feedback to the inspection. This document summarizes scoping experiments of in-situ ultrasonic methods for classification and/or characterization of the material microstructures in CASS components from the outside surface of a pipe. The focus of this study was to evaluate ultrasonic methods and provide an interim report that documents results and technical progress. An initial set of experiments were performed to test the hypothesis that in-service characterization of cast austenitic stainless steel (CASS) is feasible, and that, if reliably performed, such data would provide real-time feedback to optimize in-service inspections in the field. With this objective in mind, measurements for the experiment were restricted to techniques that should be robust if carried forward to eventual field implementation. Two parameters were investigated for their ability to discriminate between different microstructures in CASS components. The first parameter was a time-of-flight ratio of a normal incidence shear wave to that of a normal incidence longitudinal wave (TOFRSL). The ratio removed dependency on component thickness which may not be accurately reported in the field. The second parameter was longitudinal wave attenuation. The selected CASS specimens provided five equiaxed-grain material samples and five columnar-grain

The effects of the finest grains on the mechanical behaviours of nanocrystalline materials

International Nuclear Information System (INIS)

Hu Lingling; Huo Ruxiao; Zhou Jianqiu; Wang Ying; Zhang Shu

2012-01-01

This article proposes a new constitutive model to account for effects of the finest grains, with sizes ranging from 2 to 4 nm, on the mechanical behaviours of nanocrystalline (NC) materials. In this model, the normal nanograins (ranging from 20 to 100 nm) were treated as though they were composed of a grain interior (GI) and a grain boundary (GB) affected zone (GBAZ). The finest grains were considered to be part of the GBAZ, denoted as super triple junctions (STJs). For the initial plastic deformation stage of the NC materials, a phenomenological constitutive equation was suggested to predict the deformation behaviours of the GBAZ. The formation of GB dislocation (GBD) pileups provides dramatic strain hardening in deformed NC materials and thereby enhances their ductility. Then, the constitutive equations to describe the plastic deformation of the GI and the GBAZ lattice region were established. In this stage, the GBAZ are already saturated with GBD pileups, and GI deformation is the dominant mechanism. Finally, the mechanical model for the NC materials with the finest grains was built using the self-consistent method, and an overall moderate “work hardening,” sustained over a long range of plastic strain, was predicted. The effects of TJs/STJs on the deformation mechanism were quantitatively analysed. The analysis demonstrated that the existence of the finest grains will simultaneously lead to good strength and good ductility.

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

Science.gov (United States)

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.

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

Energy Technology Data Exchange (ETDEWEB)

Knott, Michael [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Best, Robert B., E-mail: robertbe@helix.nih.gov [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States)

2014-05-07

Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an “induced fit” or “conformational selection” mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

International Nuclear Information System (INIS)

Knott, Michael; Best, Robert B.

2014-01-01

Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an “induced fit” or “conformational selection” mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD

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

Science.gov (United States)

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

Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

Energy Technology Data Exchange (ETDEWEB)

MacDermaid, Christopher M., E-mail: chris.macdermaid@temple.edu; Klein, Michael L.; Fiorin, Giacomo, E-mail: giacomo.fiorin@temple.edu [Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801 (United States); Kashyap, Hemant K. [Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); DeVane, Russell H. [Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069 (United States); Shinoda, Wataru [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Klauda, Jeffery B. [Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)

2015-12-28

The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.

Grain-size effects on PIXE and INAA analysis of IAEA-336 lichen reference material

Science.gov (United States)

Marques, A. P.; Freitas, M. C.; Wolterbeek, H. Th.; Verburg, T. G.; De Goeij, J. J. M.

2007-02-01

IAEA-336 lichen certified reference material was used to compare outcomes from INAA and PIXE elemental analyses, in relationship with grain size. The IAEA material (grain size lichen reference material's particle size distribution follows a bimodal distribution, which is turning more and more monomodal after further fine sieving. Replicates of each fraction were analysed by INAA and PIXE. Results for Cl, K, Mn, Fe and Zn by both techniques were compared by application of z-values tested against the criterion ∣ z∣ limited amount of lichen material as "seen" in the PIXE analysis and the grain size distribution in the lichen material were no causes of measurable differences between the results of both techniques. However, fractionation into smaller grain sizes showed to be associated with lower element content, for Na, Cl, K, Mn and Sr even up to a factor of 2. The observed increases of the proportion of algae in the smaller grain-size fractions and the possible accumulation capacity for certain elements in the fungal part of the lichen may explain the observed phenomenon. The sieving process and consequently the discarding of part of the material have lead to a change of the properties of the original sample, namely algae/fungus percentage and elemental contents.

How coarse is too coarse for salmon spawning substrates?

Science.gov (United States)

Wooster, J. K.; Riebe, C. S.; Ligon, F. K.; Overstreet, B. T.

2009-12-01

Populations of Pacific salmon species have declined sharply in many rivers of the western US. Reversing these declines is a top priority and expense of many river restoration projects. To help restore salmon populations, managers often inject gravel into rivers, to supplement spawning habitat that has been depleted by gravel mining and the effects of dams—which block sediment and thus impair habitat downstream by coarsening the bed where salmon historically spawned. However, there is little quantitative understanding nor a methodology for determining when a river bed has become too coarse for salmon spawning. Hence there is little scientific basis for selecting sites that would optimize the restoration benefits of gravel injection (e.g., sites where flow velocities are suitable but bed materials are too coarse for spawning). To develop a quantitative understanding of what makes river beds too coarse for salmon spawning, we studied redds and spawning use in a series of California and Washington rivers where salmon spawning ability appears to be affected by coarse bed material. Our working hypothesis is that for a given flow condition, there is a maximum “threshold” particle size that a salmon of a given size is able to excavate and/or move as she builds her redd. A second, related hypothesis is that spawning use should decrease and eventually become impossible with increasing percent coverage by immovable particles. To test these hypotheses, we quantified the sizes and spatial distributions of immovably coarse particles in a series of salmon redds in each river during the peak of spawning. We also quantified spawning use and how it relates to percent coverage by immovable particles. Results from our studies of fall-run chinook salmon (Oncorhynchus tshawytsha) in the Feather River suggest that immovable particle size varies as a function of flow velocity over the redd, implying that faster water helps fish move bigger particles. Our Feather River study also

Bimodal grain-size distribution of Chinese loess, and its palaeoclimatic implications

NARCIS (Netherlands)

Sun, D.G.; Bloemendal, J.; Rea, D.K.; An, Z.S.; Vandenberghe, J.; Lu, H.; Su, R.; Liu, T.S.

2004-01-01

Grain-size analysis indicates that Chinese loess generally shows a bimodal distribution with a coarse and a fine component. The coarse component, comprising the main part of the loess, has pronounced kurtosis and is well sorted, which is interpreted to be the product of dust storms generated by

Mechanical behavior and strengthening mechanisms in ultrafine grain precipitation-strengthened aluminum alloy

International Nuclear Information System (INIS)

Ma, Kaka; Wen, Haiming; Hu, Tao; Topping, Troy D.; Isheim, Dieter; Seidman, David N.; Lavernia, Enrique J.; Schoenung, Julie M.

2014-01-01

To provide insight into the relationships between precipitation phenomena, grain size and mechanical behavior in a complex precipitation-strengthened alloy system, Al 7075 alloy, a commonly used aluminum alloy, was selected as a model system in the present study. Ultrafine-grained (UFG) bulk materials were fabricated through cryomilling, degassing, hot isostatic pressing and extrusion, followed by a subsequent heat treatment. The mechanical behavior and microstructure of the materials were analyzed and compared directly to the coarse-grained (CG) counterpart. Three-dimensional atom-probe tomography was utilized to investigate the intermetallic precipitates and oxide dispersoids formed in the as-extruded UFG material. UFG 7075 exhibits higher strength than the CG 7075 alloy for each equivalent condition. After a T6 temper, the yield strength (YS) and ultimate tensile strength (UTS) of UFG 7075 achieved 734 and 774 MPa, respectively, which are ∼120 MPa higher than those of the CG equivalent. The strength of as-extruded UFG 7075 (YS: 583 MPa, UTS: 631 MPa) is even higher than that of commercial 7075-T6. More importantly, the strengthening mechanisms in each material were established quantitatively for the first time for this complex precipitation-strengthened system, accounting for grain-boundary, dislocation, solid-solution, precipitation and oxide dispersoid strengthening contributions. Grain-boundary strengthening was the predominant mechanism in as-extruded UFG 7075, contributing a strength increment estimated to be 242 MPa, whereas Orowan precipitation strengthening was predominant in the as-extruded CG 7075 (∼102 MPa) and in the T6-tempered materials, and was estimated to contribute 472 and 414 MPa for CG-T6 and UFG-T6, respectively

Sedimentary differentiation of aeolian grains at the White Sands National Monument, New Mexico, USA

Science.gov (United States)

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 (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

Grain growth control and transparency in spark plasma sintered self-doped alumina materials

International Nuclear Information System (INIS)

Suarez, M.; Fernandez, A.; Menendez, J.L.; Torrecillas, R.

2009-01-01

Doping alumina particles with aluminum alkoxides allows dense spark plasma sintered (SPSed) materials to be obtained that have a refined grain size compared to pure materials, which is critical for their transparency. An optical model considering pore and grain size distributions has been developed to obtain information about porosity in dense materials. This work suggests that the atomic diffusion mechanisms do not depend on the sintering technique. A reduction in the activation energy by a factor of 2 has been found in SPSed materials.

A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry.

Directory of Open Access Journals (Sweden)

Satyan Sharma

Full Text Available The resemblance of lipid membrane models to physiological membranes determines how well molecular dynamics (MD simulations imitate the dynamic behavior of cell membranes and membrane proteins. Physiological lipid membranes are composed of multiple types of phospholipids, and the leaflet compositions are generally asymmetric. Here we describe an approach for self-assembly of a Coarse-Grained (CG membrane model with physiological composition and leaflet asymmetry using the MARTINI force field. An initial set-up of two boxes with different types of lipids according to the leaflet asymmetry of mammalian cell membranes stacked with 0.5 nm overlap, reliably resulted in the self-assembly of bilayer membranes with leaflet asymmetry resembling that of physiological mammalian cell membranes. Self-assembly in the presence of a fragment of the plasma membrane protein syntaxin 1A led to spontaneous specific positioning of phosphatidylionositol(4,5bisphosphate at a positively charged stretch of syntaxin consistent with experimental data. An analogous approach choosing an initial set-up with two concentric shells filled with different lipid types results in successful assembly of a spherical vesicle with asymmetric leaflet composition. Self-assembly of the vesicle in the presence of the synaptic vesicle protein synaptobrevin 2 revealed the correct position of the synaptobrevin transmembrane domain. This is the first CG MD method to form a membrane with physiological lipid composition as well as leaflet asymmetry by self-assembly and will enable unbiased studies of the incorporation and dynamics of membrane proteins in more realistic CG membrane models.

Multiple age components in individual molybdenite grains

Science.gov (United States)

Aleinikoff, John N.; Creaser, Robert A.; Lowers, Heather; Magee, Charles W.; Grauch, Richard I.

2012-01-01

Re–Os geochronology of fractions composed of unsized, coarse, and fine molybdenite from a pod of unusual monazite–xenotime gneiss within a granulite facies paragneiss, Hudson Highlands, NY, yielded dates of 950.5 ± 2.5, 953.8 ± 2.6, and 941.2 ± 2.6 Ma, respectively. These dates are not recorded by co-existing zircon, monazite, or xenotime. SEM–BSE imagery of thin sections and separated grains reveals that most molybdenite grains are composed of core and rim plates that are approximately perpendicular. Rim material invaded cores, forming irregular contacts, probably reflecting dissolution/reprecipitation. EPMA and LA-ICP-MS analyses show that cores and rims have different trace element concentrations (for example, cores are relatively enriched in W). On the basis of inclusions of zircon with metamorphic overgrowths, we conclude that molybdenite cores and rims formed after high-grade regional metamorphism. The discovery of cores and rims in individual molybdenite grains is analogous to multi-component U-Pb geochronometers such as zircon, monazite, and titanite; thus, molybdenite should be carefully examined before dating to ensure that the requirement of age homogeneity is fulfilled.

Microphase separation and the formation of ion conductivity channels in poly(ionic liquid)s: A coarse-grained molecular dynamics study

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Coarse-grained molecular dynamics modeling of the kinetics of lamellar BCP defect annealing

Science.gov (United States)

Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

2015-03-01

Directed self-assembly of block copolymers (BCPs) is a process that has received great interest in the field of nanomanufacturing in the past decade, and great strides towards forming high quality aligned patterns have been made. But state of the art methods still yield defectivities orders of magnitude higher than is necessary in semi-conductor fabrication even though free energy calculations suggest that equilibrium defectivities are much lower than is necessary for economic semi-conductor fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that infinitely thick films yield an exponential drop in defect heal rate above χN ~ 30. Below χN ~ 30, the rate of transport was similar to the rate at which the transition state was reached so that the overall rate changed only slightly. The energy barrier in periodic simulations increased with 0.31 χN on average. Thin film simulations show no change in rate associated with the energy barrier below χN ~ 50, and then show an increase in energy barrier scaling with 0.16χN. Thin film simulations always begin to heal at either the free interface or the BCP-underlayer interface where the increased A-B contact area associated with the transition state will be minimized, while the infinitely thick films must start healing in the bulk where the A-B contact area is increased. It is also found that cooperative chain movement is required for the defect to start healing.

Influence of High Temperature Treatment on Mechanical Behavior of a Coarse-grained Marble

Science.gov (United States)

Rong, G.; Peng, J.; Jiang, M.

2017-12-01

High temperature has a significant influence on the physical and mechanical behavior of rocks. With increasing geotechnical engineering structures concerning with high temperature problems such as boreholes for oil or gas production, underground caverns for storage of radioactive waste, and deep wells for injection of carbon dioxides, etc., it is important to study the influence of temperature on the physical and mechanical properties of rocks. This paper experimentally investigates the triaxial compressive properties of a coarse-grained marble after exposure to different high temperatures. The rock specimens were first heated to a predetermined temperature (200, 400, and 600 oC) and then cooled down to room temperature. Triaxial compression tests on these heat-treated specimens subjected to different confining pressures (i.e., 0, 5, 10, 15, 20, 25, 30, 35, and 40 MPa) were then conducted. Triaxial compression tests on rock specimens with no heat treatment were also conducted for comparison. The results show that the high temperature treatment has a significant influence on the microstructure, porosity, P-wave velocity, stress-strain relation, strength and deformation parameters, and failure mode of the tested rock. As the treatment temperature gradually increases, the porosity slightly increases and the P-wave velocity dramatically decreases. Microscopic observation on thin sections reveals that many micro-cracks will be generated inside the rock specimen after high temperature treatment. The rock strength and Young's modulus show a decreasing trend with increase of the treatment temperature. The ductility of the rock is generally enhanced as the treatment temperature increases. In general, the high temperature treatment weakens the performance of the tested rock. Finally, a degradation parameter is defined and a strength degradation model is proposed to characterize the strength behavior of heat-treated rocks. The results in this study provide useful data for

Recycled Coarse Aggregate Produced by Pulsed Discharge in Water

Science.gov (United States)

Namihira, Takao; Shigeishi, Mitsuhiro; Nakashima, Kazuyuki; Murakami, Akira; Kuroki, Kaori; Kiyan, Tsuyoshi; Tomoda, Yuichi; Sakugawa, Takashi; Katsuki, Sunao; Akiyama, Hidenori; Ohtsu, Masayasu

In Japan, the recycling ratio of concrete scraps has been kept over 98 % after the Law for the Recycling of Construction Materials was enforced in 2000. In the present, most of concrete scraps were recycled as the Lower Subbase Course Material. On the other hand, it is predicted to be difficult to keep this higher recycling ratio in the near future because concrete scraps increase rapidly and would reach to over 3 times of present situation in 2010. In addition, the demand of concrete scraps as the Lower Subbase Course Material has been decreased. Therefore, new way to reuse concrete scraps must be developed. Concrete scraps normally consist of 70 % of coarse aggregate, 19 % of water and 11 % of cement. To obtain the higher recycling ratio, the higher recycling ratio of coarse aggregate is desired. In this paper, a new method for recycling coarse aggregate from concrete scraps has been developed and demonstrated. The system includes a Marx generator and a point to hemisphere mesh electrode immersed in water. In the demonstration, the test piece of concrete scrap was located between the electrodes and was treated by the pulsed discharge. After discharge treatment of test piece, the recycling coarse aggregates were evaluated under JIS and TS and had enough quality for utilization as the coarse aggregate.

Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array

International Nuclear Information System (INIS)

Van Essen, B.; Panda, R.; Wood, A.; Ebeling, C.; Hauck, S.

2010-01-01

Functional units provide the backbone of any spatial accelerator by providing the computing resources. The desire for having rich and expensive functional units is in tension with producing a regular and energy-efficient computing fabric. This paper explores the design trade-off between complex, universal functional units and simpler, limited functional units. We show that a modest amount of specialization reduces the area-delay-energy product of an optimized architecture to 0.86x a baseline architecture. Furthermore, we provide a design guideline that allows an architect to customize the contents of the computing fabric just by examining the profile of benchmarks within the application domains. Functional units are the core of compute-intensive spatial accelerators. They perform the computation of interest with support from local storage and communication structures. Ideally, the functional units will provide rich functionality, supporting operations ranging from simple addition, to fused multiply-adds, to advanced transcendental functions and domain specific operations like add-compare-select. However, the total opportunity cost to support the more complex operations is a function of the cost of the hardware, the rate of occurrence of the operation in the application domain, and the inefficiency of emulating the operation with simpler operators. Examples of operations that are typically emulated in spatial accelerators are division and trigonometric functions, which can be solved using table-lookup based algorithms and the CORDIC algorithm. One reason to avoid having direct hardware support for complex operations in a tiled architecture like a Coarse-Grained Reconfigurable Array (CGRA) is that the expensive hardware will typically need to be replicated in some or all of the architecture's tiles. Tiled architecture are designed such that their tiles are either homogeneous or heterogeneous. Homogeneous architectures are simpler to design but heterogeneous

Coarse sediment oil persistence laboratory studies and model

International Nuclear Information System (INIS)

Humphrey, B.; Harper, J.R.

1993-01-01

To gain understanding of the factors which affect the fate of stranded oil on coarse sediment beaches, a series of oil penetration and tidal flushing experiments was conducted in columns containing sediments of two grain sizes: granules and pebbles. The experiments included changing oil properties by weathering and by emulsification. Factors examined included permeability, effective porosity, and residual capacity of the sediment for oil. The laboratory data provided input to an oil persistence model for coarse sediment beaches, and the model was modified on the basis of the new data. The permeability measurements suggest that the permeability of pebble/granule mixtures is close to that of the smaller component. For low viscosity oils, the permeability in coarse sediments is rapid enough to match the fall and rise of tidal water. Effective porosity of the pebbles was ca 90% of the measured porosity, but for both the granules and a 50-50 pebble/granule mixture, the effective porosity was ca 75% of measured porosity. Results of tidal flushing simulation imply that flushing may be rapid but not efficient. The emulsion completely entered the sediment in the case of pebbles only. 2 refs., 6 figs., 3 tabs

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

Science.gov (United States)

Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet

2013-12-01

One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

Science.gov (United States)

Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

2017-05-01

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

International Nuclear Information System (INIS)

Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet; Peter, Christine

2013-01-01

One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

Energy Technology Data Exchange (ETDEWEB)

Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet, E-mail: msayar@ku.edu.tr [College of Engineering, Koç University, 34450 Istanbul (Turkey); Peter, Christine [Max Planck Institute for Polymer Research, 55128 Mainz (Germany); Department of Chemistry, University of Konstanz, 78547 Konstanz (Germany)

2013-12-21

One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

Development of Multiscale Materials Modeling Techniques and Coarse- Graining Strategies for Predicting Materials Degradation in Extreme Irradiation Environments

Energy Technology Data Exchange (ETDEWEB)

Wirth, Brian [Univ. of Tennessee, Knoxville, TN (United States)

2016-01-12

Exposure of metallic structural materials to irradiation environments results in significant microstructural evolution, property changes and performance degradation, which limits the extended operation of current generation light water reactors and restricts the design of advanced fission and fusion reactors [1-8]. This effect of irradiation on materials microstructure and properties is a classic example of an inherently multiscale phenomenon, as schematically illustrated in Figure 1a. Pertinent processes range from the atomic nucleus to structural component length scales, spanning more than 15 orders of magnitude. Time scales bridge more than 22 orders of magnitude, with the shortest being less than a femtosecond [1,8]. Further, the mix of radiation-induced features formed and the corresponding property degradation depend on a wide range of material and irradiation variables. This emphasizes the importance of closely integrating models with high-resolution experimental characterization of the evolving radiation- damaged microstructure, including measurements performed in-situ during irradiation. In this article, we review some recent successes through the use of closely coordinated modeling and experimental studies of the defect cluster evolution in irradiated body-centered cubic materials, followed by a discussion of outstanding challenges still to be addressed, which are necessary for the development of comprehensive models of radiation effects in structural materials.

Role of Neutral Lipids in Tear Fluid Lipid Layer: Coarse-Grained Simulation Study

DEFF Research Database (Denmark)

Telenius, J.; Koivuniemi, A.; Kulovesi, P.

2012-01-01

Tear fluid lipid layer (TFLL) residing at the air-water interface of tears has been recognized to play an important role in the development of dry eye syndrome. Yet, the composition, structure, and mechanical properties of TFLL are only partly known. Here, we report results of coarse...

Dependency of annealing behaviour on grain size in Al–TiC ...

Indian Academy of Sciences (India)

This work investigates the effect of grain size on annealing behaviour in both coarse-grained and ultrafinegrained Al–TiC composite processed by accumulative roll bonding (ARB). Microstructural analysis indicates that annealingbehaviour of the specimens are essentially determined by the level of strain accumulation or ...

Automatic kinetic Monte-Carlo modeling for impurity atom diffusion in grain boundary structure of tungsten material

Directory of Open Access Journals (Sweden)

Atsushi M. Ito

2017-08-01

Full Text Available The diffusion process of hydrogen and helium in plasma-facing material depends on the grain boundary structures. Whether a grain boundary accelerates or limits the diffusion speed of these impurity atoms is not well understood. In the present work, we proposed the automatic modeling of a kinetic Monte-Carlo (KMC simulation to treat an asymmetric grain boundary structure that corresponds to target samples used in fusion material experiments for retention and permeation. In this method, local minimum energy sites and migration paths for impurity atoms in the grain boundary structure are automatically found using localized molecular dynamics. The grain boundary structure was generated with the Voronoi diagram. Consequently, we demonstrate that the KMC simulation for the diffusion process of impurity atoms in the generated grain boundary structure of tungsten material can be performed.

The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

International Nuclear Information System (INIS)

Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian; Sugii, Taisuke

2015-01-01

We investigate the volumetric glass transition temperature T g in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T g increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T g in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T g is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment

Emerging quasi-0D states at vanishing total entropy of the 1D hard sphere system: A coarse-grained similarity to the car parking problem

Science.gov (United States)

Frusawa, Hiroshi

2014-05-01

A coarse-grained system of one-dimensional (1D) hard spheres (HSs) is created using the Delaunay tessellation, which enables one to define the quasi-0D state. It is found from comparing the quasi-0D and 1D free energy densities that a frozen state due to the emergence of quasi-0D HSs is thermodynamically more favorable than fluidity with a large-scale heterogeneity above crossover volume fraction of ϕc=e/(1+e)=0.731⋯ , at which the total entropy of the 1D state vanishes. The Delaunay-based lattice mapping further provides a similarity between the dense HS system above ϕc and the jamming limit in the car parking problem.

Emerging quasi-0D states at vanishing total entropy of the 1D hard sphere system: A coarse-grained similarity to the car parking problem

International Nuclear Information System (INIS)

Frusawa, Hiroshi

2014-01-01

A coarse-grained system of one-dimensional (1D) hard spheres (HSs) is created using the Delaunay tessellation, which enables one to define the quasi-0D state. It is found from comparing the quasi-0D and 1D free energy densities that a frozen state due to the emergence of quasi-0D HSs is thermodynamically more favorable than fluidity with a large-scale heterogeneity above crossover volume fraction of ϕ c =e/(1+e)=0.731⋯ , at which the total entropy of the 1D state vanishes. The Delaunay-based lattice mapping further provides a similarity between the dense HS system above ϕ c and the jamming limit in the car parking problem.

Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

Science.gov (United States)

Ghobadi, Ahmadreza F; Jayaraman, Arthi

2016-02-28

In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

Numerical modelling of intergranular fracture in polycrystalline materials and grain size effects

Directory of Open Access Journals (Sweden)

P. Wriggers

2011-07-01

Full Text Available In this paper, the phenomenon of intergranular fracture in polycrystalline materials is investigated using a nonlinear fracture mechanics approach. The nonlocal cohesive zone model (CZM for finite thickness interfaces recently proposed by the present authors is used to describe the phenomenon of grain boundary separation. From the modelling point of view, considering the dependency of the grain boundary thickness on the grain size observed in polycrystals, a distribution of interface thicknesses is obtained. Since the shape and the parameters of the nonlocal CZM depend on the interface thickness, a distribution of interface fracture energies is obtained as a consequence of the randomness of the material microstructure. Using these data, fracture mechanics simulations are performed and the homogenized stress-strain curves of 2D representative volume elements (RVEs are computed. Failure is the result of a diffuse microcrack pattern leading to a main macroscopic crack after coalescence, in good agreement with the experimental observation. Finally, testing microstructures characterized by different average grain sizes, the computed peak stresses are found to be dependent on the grain size, in agreement with the trend expected according to the Hall-Petch law.

SANITY OF CORN GRAINS AS A FUNCTION OF GENETIC MATERIAL

Directory of Open Access Journals (Sweden)

L. F. Oliveira

2018-02-01

Full Text Available Diseases that occur in corn crops can cause great losses to farmers and consumers of its product and derivatives. So, was evaluated the sanity of maize grains in different genetic materials. The grains used were obtained from the crop of 2014/2015 on a farm in the city of Sorriso, State of Mato Grosso. For this, grain samples were collected from hybrids P3630H, 30F53YH, P2830H, and P3844H. The standard test ("Blotter Test" allowed noticing the incidence of Aspergillus sp., Fusarium sp. and Penicillium sp. Data were submitted to analysis of variance and Scott-Knott test at 5% probability. In treatments with the resistant genetic material the genus with the highest incidence was Penicillium sp. (82%, followed by Fusarium sp. (68.75% and Aspergillus sp. (15.25%. The hybrid with the lower incidence of Fusarium sp. was P2830H (59%. The hybrid with greater resistance to Aspergillus sp. and Penicillium sp. was P3844H (5 and 55%, respectively. The most susceptible hybrid to pathogens Aspergillus sp., Fusarium sp. and Penicillium sp. was 30F53YH (37, 79 and 94%, respectively. For the better sanitary quality of grains, based on the observed data, it is recommended to use the hybrid P2830H

Spatially resolved acoustic spectroscopy for rapid imaging of material microstructure and grain orientation

International Nuclear Information System (INIS)

Smith, Richard J; Li, Wenqi; Coulson, Jethro; Clark, Matt; Somekh, Michael G; Sharples, Steve D

2014-01-01

Measuring the grain structure of aerospace materials is very important to understand their mechanical properties and in-service performance. Spatially resolved acoustic spectroscopy is an acoustic technique utilizing surface acoustic waves to map the grain structure of a material. When combined with measurements in multiple acoustic propagation directions, the grain orientation can be obtained by fitting the velocity surface to a model. The new instrument presented here can take thousands of acoustic velocity measurements per second. The spatial and velocity resolution can be adjusted by simple modification to the system; this is discussed in detail by comparison of theoretical expectations with experimental data. (paper)

Phase behaviour of macromolecular liquid crystalline materials. Computational studies at the molecular level

International Nuclear Information System (INIS)

Stimson, Lorna M.

2003-01-01

Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a single dendrimer molecule in the gas phase at the atomistic level, semi-atomistic molecular dynamics of a single molecule in liquid crystalline solvents and a coarse-grained molecular dynamics study of the dendrimer in the bulk. The coarse-grained model has been developed and parameterized using the results of the atomistic and semi-atomistic work. The single molecule studies showed that the liquid crystalline dendrimer was able to change its structure by conformational changes in the flexible chains that link the mesogenic groups to the core. Structural change was seen under the application of a mean field ordering potential in the gas phase, and in the presence of liquid crystalline solvents. No liquid crystalline phases were observed for the bulk phase studies of the coarse-grained model. However, when the length of the mesogenic units was increased there was some evidence for microphase separation in these systems. (author)

Sticking properties of ice grains

Science.gov (United States)

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.

Burst Testing and Analysis of Superalloy Disks With a Dual Grain Microstructure

Science.gov (United States)

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.

Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Yu, Hang; Ma, Wen [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Han, Wei [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)

2015-12-28

Parkinson’s disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and {sup 3}J(H{sub N}H{sub C{sub α}})-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

Effective potentials from complex simulations: a potential-matching algorithm and remarks on coarse-grained potentials

International Nuclear Information System (INIS)

Toth, Gergely

2007-01-01

The projection of complex interactions onto simple distance-dependent or angle-dependent classical mechanical functions is a long-standing theoretical challenge in the field of computational sciences concerning biomolecules, colloids, aggregates and simple systems as well. The construction of an effective potential may be based on theoretical assumptions, on the application of fitting procedures on experimental data and on the simplification of complex molecular simulations. Recently, a force-matching method was elaborated to project the data of Car-Parrinello ab initio molecular dynamics simulations onto two-particle classical interactions (Izvekov et al 2004 J. Chem. Phys. 120 10896). We have developed a potential-matching algorithm as a practical analogue of this force-matching method. The algorithm requires a large number of configurations (particle positions) and a single value of the potential energy for each configuration. We show the details of the algorithm and the test calculations on simple systems. The test calculation on water showed an example in which a similar structure was obtained for qualitatively different pair interactions. The application of the algorithm on reverse Monte Carlo configurations was tried as well. We detected inconsistencies in a part of our calculations. We found that the coarse graining of potentials cannot be performed perfectly both for the structural and the thermodynamic data. For example, if one applies an inverse method with an input of the pair-correlation function, it provides energetics data for the configurations uniquely. These energetics data can be different from the desired ones obtained by all atom simulations, as occurred in the testing of our potential-matching method

Experimental investigation of coarse particles-water mixture flow in horizontal and inclined pipes

Czech Academy of Sciences Publication Activity Database

Vlasák, Pavel; Chára, Zdeněk; Krupička, Jan; Konfršt, Jiří

2014-01-01

Roč. 62, č. 3 (2014), s. 241-247 ISSN 0042-790X R&D Projects: GA ČR GAP105/10/1574 Institutional support: RVO:67985874 Keywords : hydraulic pipelining * coarse-grained slurry * pressure drops * pipe inclination * concentration distribution Subject RIV: BK - Fluid Dynamics Impact factor: 1.486, year: 2014

High-Resolution Single-Grain Diffraction of Polycrystalline Materials

DEFF Research Database (Denmark)

Lienert, Ulrich; Ribárik, Gábor; Ungar, Tamas

2017-01-01

. The microstructure usually influences the materials properties critically. It has been demonstrated that, by using high-energy synchrotron radiation, diffraction peaks off individual grains can be recorded in-situ during processing. Important information such as the orientation, average strain, and size...... of individual grains can be obtained, even if the peak shapes are commonly not analyzed. However, it is also well-known that the shape of diffraction peaks, if observed with sufficient resolution, contains significant information about the microstructure. While the intensity distribution in reciprocal space...... of a perfect lattice consists of delta functions located at the reciprocal lattice points, defects induce characteristic peak broadening. In order to exploit the wealth of microstructural information contained in broadened diffraction peaks, the intensity distribution has to be characterized in all three...

Grain-size effects on PIXE and INAA analysis of IAEA-336 lichen reference material

International Nuclear Information System (INIS)

Marques, A.P.; Freitas, M.C.; Wolterbeek, H.Th.; Verburg, T.G.; Goeij, J.J.M. de

2007-01-01

IAEA-336 lichen certified reference material was used to compare outcomes from INAA and PIXE elemental analyses, in relationship with grain size. The IAEA material (grain size <125 μm) was ground and sieved through nylon nets with 64 μm, 41 μm and 20 μm pores. Particle sizes were determined by Laser Light Scattering technique: the data indicate that, after sieving, the IAEA-336 lichen reference material's particle size distribution follows a bimodal distribution, which is turning more and more monomodal after further fine sieving. Replicates of each fraction were analysed by INAA and PIXE. Results for Cl, K, Mn, Fe and Zn by both techniques were compared by application of z-values tested against the criterion vertical bar z vertical bar < 3 for approval of results at the 99.7% confidence level. Under the conditions of this study, the limited amount of lichen material as 'seen' in the PIXE analysis and the grain size distribution in the lichen material were no causes of measurable differences between the results of both techniques. However, fractionation into smaller grain sizes showed to be associated with lower element content, for Na, Cl, K, Mn and Sr even up to a factor of 2. The observed increases of the proportion of algae in the smaller grain-size fractions and the possible accumulation capacity for certain elements in the fungal part of the lichen may explain the observed phenomenon. The sieving process and consequently the discarding of part of the material have lead to a change of the properties of the original sample, namely algae/fungus percentage and elemental contents

H2O grain size and the amount of dust in Mars' residual North polar cap

Science.gov (United States)

Kieffer, H.H.

1990-01-01

In Mars' north polar cap the probable composition of material residual from the annual condensation cycle is a mixture of fine dust and H2O grains of comparable size and abundance. However, metamorphism of such material will gradually lower its albedo by increasing the size of the H2O grains only. If the cap is undergoing net annual sublimation (as inferred from water vapor observations), late summer observations should be of old ice with H2O grain sizes of 100 ??m or more. Ice of this granularity containing 30% fine dust has a reflectivity similar to that of dust alone; the observed albedo and computed ice grain size imply dust concentrations of 1 part per 1000 or less. The brightness of the icy areas conflicts with what would be expected for a residual cap deposited by an annual cycle similar to that observed by Viking and aged for thousands of years. The residual cap surface cannot be "old dirty' ice. It could be old, coarse, and clean; or it could be young, fine, and dirty. This brings into question both the source of the late summer water vapor and the formation rate of laminated terrain. -Author

Optically stimulated luminescence techniques in retrospective dosimetry using single grains of quartz extracted from unheated materials

Energy Technology Data Exchange (ETDEWEB)

Joerkov Thomsen, Kristina

2004-02-01

This work investigates the possibility of applying optically stimulated luminescence (OSL) in retrospective dose determinations using unheated materials. It focuses on identifying materials suitable for use in assessment of doses absorbed as a consequence of radiation accidents (i.e. accident dosimetry). Special attention has been paid to quartz extracted from unheated building materials such as concrete and mortar. The single-aliquot regeneration-dose (SAR) protocol has been used to determine absorbed doses in small aliquots as well as single grains of quartz. It is shown that OSL measurements of single grains of quartz extracted from poorly-bleached building materials can provide useful information on radiation accident doses, even when the luminescence sensitivity is low. Sources of variance in well-bleached single grain dose distributions have been investigated in detail and it is concluded that the observed variability in the data is consistent with the sum (in quadrature) of a component, which depends on the number of photons detected from each grain, and a fixed component independent of light level. Dose depth profiles through laboratory irradiated concrete bricks have successfully been measured and minimum detection limits of less than 100 mGy are derived. Measurements of thermal transfer in single grains of poorly-bleached quartz show that thermal transfer is variable on a grain-to-grain basis and that it can be a source of variance in single-grain dose distributions. Furthermore, the potential of using common household and workplace chemicals, such as table salt, washing powder and water softener, in retrospective dosimetry has been investigated. It is concluded that such materials should be considered as retrospective dosimeters in the event of a radiation accident. (au)

Spinodal decomposition in fine grained materials

Indian Academy of Sciences (India)

Unknown

ηηi has a value of unity inside the ith grain, decreases smoothly through the grain boundary region to zero out- side the grain. For a symmetric alloy of composition, c = 0⋅⋅5, our results show that microstructural evolution depends largely on the difference in the grain boundary energies, γγgb, of A-rich (αα) and B-rich (ββ) ...

The influence of grain size on the strain-induced martensite formation in tensile straining of an austenitic 15Cr–9Mn–Ni–Cu stainless steel

International Nuclear Information System (INIS)

Kisko, A.; Misra, R.D.K.; Talonen, J.; Karjalainen, L.P.

2013-01-01

In order to improve understanding on the behavior of ultrafine-grained austenitic stainless steels during deformation, the influence of the austenite grain size and microstructure on the strain-induced martensite transformation was investigated in an austenitic 15Cr–9Mn–Ni–Cu (Type 204Cu) stainless steel. By different reversion treatments of the 60% cold-rolled sheet, varying grain sizes from ultrafine (0.5 μm), micron-scale (1.5 μm), fine (4 μm) to coarse (18 μm) were obtained. Some microstructures also contained a mixture of ultrafine or micron-scale and coarse initially cold-worked austenite grains. Samples were tested in tensile loading and deformation structures were analyzed after 2%, 10% and 20% engineering strains by means of martensite content measurements, scanning electron microscope together with a electron backscatter diffraction device and transmission electron microscope. The results showed that the martensite nucleation sites and the rate of transformation vary. In ultrafine grains strain-induced α′-martensite nucleates at grain boundaries and twins, whereas in coarser grains as well as in coarse-grained retained austenite, α′-martensite formation occurs at shear bands, sometimes via ε-martensite. The transformation rate of strain-induced α′-martensite decreases with decreasing grain size to 1.5 μm. However, the rate is fastest in the microstructure containing a mixture of ultrafine and retained cold-worked austenite grains. There the ultrafine grains transform quite readily to martensite similarly as the coarse retained austenite grains, where the previous cold-worked microstructure is still partly remaining

The influence of processing on microstructure and properties of iron aluminides

Energy Technology Data Exchange (ETDEWEB)

Wright, R.N.; Wright, J.K. [Idaho National Engineering Lab., Idaho Falls, ID (United States)

1996-08-01

An Fe-28%Al alloy containing 5% Cr has been synthesized by reaction of elemental powders, followed by consolidation using hot extrusion. The resulting material is fully dense, homogeneous, and has a grain size of less than 5{mu}m. Reaction synthesis results in an Al{sub 2}O{sub 3} dispersion that is uniformly dispersed during hot extrusion. Under some circumstances the hot extruded material undergoes secondary recrystallization, resulting in grain sizes greater than 25 millimeters. The fine grained material exhibits improved yield strength compared to the coarse grained material up to test temperatures of 800{degrees}C. Creep testing has shown that the coarse grained material has significantly improved time to rupture compared to fine grained material. The oxide dispersion strengthened material has significantly improved creep resistance compared to conventional powder metallurgy material. With proper heat treatment, the coarse grained material exhibits time to rupture of 425 hours at 650{degrees}C and a stress of 75 MPa, compared to 40 hours for conventional material of similar composition.

Significance of grain boundaries and stacking faults on hydrogen storage properties of Mg2Ni intermetallics processed by high-pressure torsion

International Nuclear Information System (INIS)

Hongo, Toshifumi; Edalati, Kaveh; Arita, Makoto; Matsuda, Junko; Akiba, Etsuo; Horita, Zenji

2015-01-01

Mg 2 Ni intermetallics are processed using three different routes to produce three different microstructural features: annealing at high temperature for coarse grain formation, severe plastic deformation through high-pressure torsion (HPT) for nanograin formation, and HPT processing followed by annealing for the introduction of stacking faults. It is found that both grain boundaries and stacking faults are significantly effective to activate the Mg 2 Ni intermetallics for hydrogen storage at 423 K (150 °C). The hydrogenation kinetics is also considerably enhanced by the introduction of large fractions of grain boundaries and stacking faults while the hydrogenation thermodynamics remains unchanged. This study shows that, similar to grain boundaries and cracks, stacking faults can act as quick pathways for the transportation of hydrogen in the hydrogen storage materials

De determination for young samples using the standardised OSL response of coarse-grain quartz

International Nuclear Information System (INIS)

Burbidge, C.I.; Duller, G.A.T.; Roberts, H.M.

2006-01-01

It has recently been shown that it is possible to construct standardised curves of the sensitivity corrected growth in optically stimulated luminescence (OSL) with exposure to ionising radiation, and that they may be used in the dating of quartz and polymineral samples. Standardised growth curves are particularly advantageous where measurement time is limited, as once they have been defined, only the natural signal and the response to a subsequent test dose are required in order to determine the equivalent dose of a sub-sample. The present study is concerned with the application of the standardised growth curve approach to OSL dating of Holocene age samples. Systematic changes in the shape of the standardised growth curve of coarse-grain quartz are identified as the size of the test dose is varied, because of non-proportionality between the test dose and the luminescence test response. The effect is characterised by fitting the change in gradient of the standardised growth curve as test dose is varied. An equation is defined to describe standardised growth as a function of regenerative dose and test dose. Regenerative dose responses of other samples in this study are treated as unknowns and recovered through different growth curves to compare precision and accuracy of various methods of D e determination. The standardised growth curve is found to yield similar precision to conventional fits of single aliquot regenerative data, but slightly poorer accuracy. The standardised growth curve approach was refined by incorporating the measurement of one regenerative response for each aliquot as well as its natural signal. Measurements of this additional data point for aliquots of 22 samples were used to adjust the standardised growth equation, improving its accuracy. The incorporation of this additional data point also indicated a systematic uncertainty of 2.4% in the estimates of D e

Into the deep: A coarse-grained carbonate turbidite thalweg generated by gigantic submarine chutes

Science.gov (United States)

Mulder, Thierry; Gillet, Hervé; Reijmer, John; Droxler, André; cavailhes, Thibault; Hanquiez, Vincent; Fauquembergue, Kelly; Bujan, Stéphane; Blanck, David; bashah, Sara; Guiastrennec, Léa; Fabregas, Natacha; Recouvreur, Audrey; Seibert, Chloé

2017-04-01

New high-resolution multibeam mapping, in the Southeastern Bahamas, images in exquisite details the southern part of Exuma Sound, and its unchartered transition area to the deep abyssal plain of the Western North Atlantic bounded by the Bahama Escarpment (BE) between San Salvador Island and Samana Cay, referred here to the San Salvador abyssal plain. The transition area is locally referred to as Crooked Island Passage, loosely delineated by Crooked, Long, and Conception Islands, Rum and Samana Cays. Surprisingly in such a pure carbonate landscape, the newly established map reveals the detailed and complex morphology of a giant valley formed by numerous gravity flows originated in Exuma Sound itself, in addition to many secondary slope gullies and smaller tributaries draining the surrounding upper slopes. The valley referred here as the Exuma canyon system starts with a perched valley with low sinuosity, characterized by several flow restrictions and knickpoints initiated by the presence of drowned isolated platforms and merging tributaries. The valley abruptly transforms itself into a deep incised canyon, rivaling the depth of the Colorado Grand Canyon, through two major knickpoints with outsized chutes exceeding several hundred of meters in height, a total of 1600-1800 m. The sudden transformation of the wide valley into a deep narrow canyon, occurring when the flows incised deep into an underlying lower Cretaceous drowned carbonate platform, generates a huge hydraulic jump and creates an enormous plunge pool and related deposits with mechanisms comparable to the ones operating along giant subaerial waterfalls. The high kinetic flow energy, constrained by this narrow and deeply incised canyon, formed, when it is released at its mouth in the abyssal plain, a wide deep-sea channel with well-developed levees and fan, made of coarse-grained carbonate defined layers separated by fine carbonate sediments mixed with fine siliciclastics transported along the BE by the

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

Science.gov (United States)

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.

Influence of grain size and exchange interaction on the LLB modeling procedure

Science.gov (United States)

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

2016-12-01

Reliably predicting bit-error rates in realistic heat-assisted magnetic recording simulations is a challenging task. Integrating the Landau-Lifshitz-Bloch (LLB) equation, within a coarse graining approach, can reduce the computational effort to determine the magnetization dynamics in the vicinity of the Curie temperature, compared to solving the atomistic Landau-Lifshitz-Gilbert equation. If the aim is that the dynamics of both approaches coincide, temperature dependent material functions, such as the zero-field equilibrium magnetization as well as the parallel and normal susceptibilities, must be modeled carefully in order to use them as input in the LLB equation. We present an extensive study on how these functions depend on grain size and exchange interactions. We show that, if the size or the exchange constant of a reference grain is modified, the material functions can be scaled, according to the changed Curie temperature, yielding negligible errors. This is shown to be valid for volume changes of up to ±40% and variations of the exchange constant of up to ±10%. Besides the temperature dependent material curves, computed switching probabilities also agree well with probabilities separately determined for each system. Our study suggests that there is no need to recalculate the required LLB input functions for each particle. Within the presented limits, it is sufficient to scale them to the Curie temperature of the altered system.

Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.

Science.gov (United States)

Flechsig, Holger

2016-02-01

ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter

The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

Energy Technology Data Exchange (ETDEWEB)

Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt (Germany); Sugii, Taisuke, E-mail: taisuke.sugii.zs@hitachi.com [Center for Technology Innovation – Mechanical Engineering, Research & Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034 (Japan)

2015-12-28

We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.

Reconstruction of Single-Grain Orientation Distribution Functions for Crystalline Materials

DEFF Research Database (Denmark)

Hansen, Per Christian; Sørensen, Henning Osholm; Sükösd, Zsuzsanna

2009-01-01

for individual grains of the material in consideration. We study two iterative large-scale reconstruction algorithms, the algebraic reconstruction technique (ART) and conjugate gradients for least squares (CGLS), and demonstrate that right preconditioning is necessary in both algorithms to provide satisfactory...

Sticking properties of ice grains

Directory of Open Access Journals (Sweden)

Jongmanns M.

2017-01-01

Full Text Available 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.

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study.

Science.gov (United States)

Condon, Joshua E; Jayaraman, Arthi

2017-10-04

Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (T m ) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (T a ) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA T m in these systems, as the number of ONA-star polymer arms increase, the assembly temperature T a increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.

Grain Size of Recall Practice for Lengthy Text Material: Fragile and Mysterious Effects on Memory

Science.gov (United States)

Wissman, Kathryn T.; Rawson, Katherine A.

2015-01-01

The current research evaluated the extent to which the grain size of recall practice for lengthy text material affects recall during practice and subsequent memory. The "grain size hypothesis" states that a smaller vs. larger grain size will increase retrieval success during practice that in turn will enhance subsequent memory for…

Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

Science.gov (United States)

Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

2015-04-14

We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

Coarse-grained description of cosmic structure from Szekeres models

International Nuclear Information System (INIS)

Sussman, Roberto A.; Gaspar, I. Delgado; Hidalgo, Juan Carlos

2016-01-01

We show that the full dynamical freedom of the well known Szekeres models allows for the description of elaborated 3-dimensional networks of cold dark matter structures (over-densities and/or density voids) undergoing ''pancake'' collapse. By reducing Einstein's field equations to a set of evolution equations, which themselves reduce in the linear limit to evolution equations for linear perturbations, we determine the dynamics of such structures, with the spatial comoving location of each structure uniquely specified by standard early Universe initial conditions. By means of a representative example we examine in detail the density contrast, the Hubble flow and peculiar velocities of structures that evolved, from linear initial data at the last scattering surface, to fully non-linear 10–20 Mpc scale configurations today. To motivate further research, we provide a qualitative discussion on the connection of Szekeres models with linear perturbations and the pancake collapse of the Zeldovich approximation. This type of structure modelling provides a coarse grained—but fully relativistic non-linear and non-perturbative —description of evolving large scale cosmic structures before their virialisation, and as such it has an enormous potential for applications in cosmological research

Thermal and microstructural properties of fine-grained material at the Viking Lander 1 site

Science.gov (United States)

Paton, M. D.; Harri, A.-M.; Savijärvi, H.; Mäkinen, T.; Hagermann, A.; Kemppinen, O.; Johnston, A.

2016-06-01

As Viking Lander 1 touched down on Mars one of its footpads fully penetrated a patch of loose fine-grained drift material. The surrounding landing site, as observed by VL-1, was found to exhibit a complex terrain consisting of a crusted surface with an assortment of rocks, large dune-like drifts and smaller patches of drift material. We use a temperature sensor attached to the buried footpad and covered in fine-grained material to determine the thermal properties of drift material at the VL-1 site. The thermal properties are used to investigate the microstructure of the drift material and understand its relevance to surface-atmosphere interactions. We obtained a thermal inertia value of 103 ± 22 tiu. This value is in the upper range of previous thermal inertia estimates of martian dust as measured from orbit and is significantly lower than the regional thermal inertia of the VL-1 site, of around 283 tiu, obtained from orbit. We estimate a thermal inertia of around 263 ± 29 tiu for the duricrust at the VL-1 site. It was noted the patch of fine-grained regolith around the footpad was about 20-30 K warmer compared to similar material beyond the thermal influence of the lander. An effective diameter of 8 ± 5 μm was calculated for the particles in the drift material. This is larger than atmospheric dust and large compared to previous estimates of the drift material particle diameter. We interpret our results as the presence of a range of particle sizes, <8 μm, in the drift material with the thermal properties being controlled by a small amount of large particles (∼8 μm) and its cohesion being controlled by a large amount of smaller particles. The bulk of the particles in the drift material are therefore likely comparable in size to that of atmospheric dust. The possibility of larger particles being locked into a fine-grained material has implications for understanding the mobilisation of wind blown materials on Mars.

Effect of solvent on the structure of a protein (H3.1) with a coarse-grained model with knowledge-based interactions

Science.gov (United States)

Pandey, Ras; Farmer, Barry

2013-03-01

Quality of solvent plays a critical role in modulating the structure of a protein along with the temperature. Using a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV) we examine the structure and dynamics of a histone (H3.1). The empty lattice sites constitute the effective solvent medium in which the protein is embedded. Residue-solvent characteristic interaction is based on the hydropathy index while the residue-residue interaction is used from the knowledge-based contact matrices derived from ensembles of protein structures in the protein data bank. Large scale simulations are performed to analyze the structure of protein for a range of residue-solvent interaction strength, a measure of the solvent quality with each potential. Unlike the monotonic thermal response, the radius of gyration of the protein exhibits non-monotonic dependence of the solvent strength. Quantitative comparison of the structure and dynamics emerging from three knowledge-based potentials will be presented in this talk. This work is supported by Air Force Research Laboratory.

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

Science.gov (United States)

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...

The material from Lampung as coarse aggregate to substitute andesite for concrete-making

Science.gov (United States)

Amin, M.; Supriyatna, Y. I.; Sumardi, S.

2018-01-01

Andesite stone is usually used for split stone material in the concrete making. However, its availability is decreasing. Lampung province has natural resources that can be used for coarse aggregate materials to substitute andesite stone. These natural materials include limestone, feldspar stone, basalt, granite, and slags from iron processing waste. Therefore, a research on optimizing natural materials in Lampung to substitute andesite stone for concrete making is required. This research used laboratory experiment method. The research activities included making cubical object samples of 150 x 150 x 150 mm with material composition referring to a standard of K.200 and w/c 0.61. Concrete making by using varying types of aggregates (basalt, limestone, slag) and aggregate sizes (A = 5-15 mm, B = 15-25 mm, and 25-50 mm) was followed by compressive strength test. The results showed that the obtained optimal compressive strengths for basalt were 24.47 MPa for 50-150 mm aggregate sizes, 21.2 MPa for 15-25 mm aggregate sizes, and 20.7 MPa for 25-50 mm aggregate sizes. These results of basalt compressive strength values were higher than the same result for andesite (19.69 MPa for 50-150 mm aggregate sizes), slag (22.72 MPa for 50-150 mm aggregate sizes), and limestone (19.69 Mpa for 50-150 mm aggregate sizes). These results indicated that basalt, limestone, and slag aggregates were good enough to substitute andesite as materials for concrete making. Therefore, natural resources in Lampung can be optimized as construction materials in concrete making.

Modification of the grain structure of austenitic welds for improved ultrasonic inspectability

International Nuclear Information System (INIS)

Wagner, Sabine; Dugan, Sandra; Stubenrauch, Steffen; Jacobs, Oliver

2013-01-01

Welding is an essential part of the fabrication of austenitic stainless steel components used in industrial plants, such as those designed for nuclear power generation, chemical processing, conventional power generation and, increasingly, for production of renewable energy. The welded austenitic material presents major challenges for ultrasonic inspection due to the grain structure of the weld metal. The typically coarse grain structure, in combination with the elastic anisotropy of the material, leads to increased scattering and affects sound wave propagation in the weld. These effects result in a reduced signal-to-noise ratio, and complicate the interpretation of signals and the localisation of defects by ultrasonic inspection. This paper presents the results of a research project dealing with efforts to influence grain growth in the weld during the welding process, in particular during the solidification process, in order to produce smaller grains. The objective was to achieve improved sound propagation through the weld, so that inspectability can be improved. The welding process was modified by the application of alternating magnetic fields at different frequencies, as well as different temperature cycles and pulsed arc technology. Metallographic sections of the test welds show that modification of the grain structure can be achieved by the use of these techniques. For further optimisation, test blocks for ultrasonic testing were manufactured with testflaws to study sound propagation through the modified weld and to assess the detectability of test flaws. The results of this investigation are of importance in assessing the integrity of highly stressed components in industrial installations, particularly for those components with stringent requirements on safety and quality.

Abnormal growth of faceted (WC) grains in a (Co) liquid matrix

International Nuclear Information System (INIS)

Park, Y.J.; Yoon, D.Y.

1996-01-01

If the grains dispersed in a liquid matrix are spherical, their surface atomic structure is expected to be rough (diffuse), and their coarsening has been observed to be controlled by diffusion in the matrix. They do not, furthermore, undergo abnormal growth. On the other hand, in some compound material systems, the grains in liquid matrices are faceted and often show abnormal coarsening behavior. Their faceted surface planes are expected to be singular (atomically flat) and therefore grow by a defect-assisted process and two-dimensional (2-D) nucleation. Contrary to the usual coarsening theories, their growth velocity is not linearly dependent on the driving force arising from the grain size difference. If the growth of the faceted grains occurs by 2-D nucleation, the rate is expected to increase abruptly at a critical supersaturation, as has been observed in crystal growth in melts and solutions. It is proposed that this growth mechanism leads to the abnormal grain coarsening. The 2-D nucleation theory predicts that there is a threshold initial grain size for the abnormal grain growth (AGG), and the propensity for AGG will increase with the heat-treatment temperature. The AGG behavior will also vary with the defects in the grains. These predictions are qualitatively confirmed in the sintered WC-Co alloy prepared from fine (0.85-microm) and coarse (5.48-microm) WC powders and their mixtures. The observed dependence of the AGG behavior on the sintering temperature and the milling of the WC powder is also qualitatively consistent with the predicted behavior

Martensitic Transformation in Ultrafine-Grained Stainless Steel AISI 304L Under Monotonic and Cyclic Loading

Directory of Open Access Journals (Sweden)

Heinz Werner Höppel

2012-02-01

Full Text Available The monotonic and cyclic deformation behavior of ultrafine-grained metastable austenitic steel AISI 304L, produced by severe plastic deformation, was investigated. Under monotonic loading, the martensitic phase transformation in the ultrafine-grained state is strongly favored. Under cyclic loading, the martensitic transformation behavior is similar to the coarse-grained condition, but the cyclic stress response is three times larger for the ultrafine-grained condition.

Mechanical properties of granular materials: A variational approach to grain-scale simulations

Energy Technology Data Exchange (ETDEWEB)

Holtzman, R.; Silin, D.B.; Patzek, T.W.

2009-01-15

The mechanical properties of cohesionless granular materials are evaluated from grain-scale simulations. A three-dimensional pack of spherical grains is loaded by incremental displacements of its boundaries. The deformation is described as a sequence of equilibrium configurations. Each configuration is characterized by a minimum of the total potential energy. This minimum is computed using a modification of the conjugate gradient algorithm. Our simulations capture the nonlinear, path-dependent behavior of granular materials observed in experiments. Micromechanical analysis provides valuable insight into phenomena such as hysteresis, strain hardening and stress-induced anisotropy. Estimates of the effective bulk modulus, obtained with no adjustment of material parameters, are in agreement with published experimental data. The model is applied to evaluate the effects of hydrate dissociation in marine sediments. Weakening of the sediment is quantified as a reduction in the effective elastic moduli.

Thermal stability of the grain structure in the W-2V and W-2V-0.5Y2O3 alloys produced by hot isostatic pressing

International Nuclear Information System (INIS)

Martínez, J.; Savoini, B.; Monge, M.A.; Muñoz, A.; Armstrong, D.E.J.; Pareja, R.

2013-01-01

Highlights: • W-2V and ODS W-2V-0.5Y 2 O 3 alloys have been produced following a powder metallurgy route. • Grain microstructure and microhardness have been studied after isothermal treatments in vacuum. • Both alloys exhibit a duplex grain size population: a submicron-sized grain and a coarse grained one. • The Y 2 O 3 addition inhibits growth of the coarse grains for T 2 O 3 nanoparticles enhance the microhardness of W-2V-0.5Y 2 O 3 . -- Abstract: W-2V and ODS W-2V-0.5Y 2 O 3 alloys have been produced following a powder metallurgy route consisting of mechanical alloying and a subsequent high isostatic pressing HIP at 1573 K. The grain microstructure and microhardness recovery of the alloys have been studied in samples subjected to isothermal treatments in vacuum in temperature range 1073–1973 K. Both alloys exhibit a duplex grain size distribution consisting of a submicron-sized grain and a coarse-grained population. It has been found that the Y 2 O 3 addition inhibits growth of the coarse grains at T 2 O 3 , respectively, was observed at T ≥ 1573 K. It resulted that the rate constant for grain growth is 30 times higher in W-2V-0.5Y 2 O 3 than in W-2V. The considerable enhancement of the microhardness in the W-2V-0.5Y 2 O 3 appears to be associated to dispersion strengthening

Influence of nano-inclusions' grain boundaries on crack propagation modes in materials

International Nuclear Information System (INIS)

Karakasidis, T.E.; Charitidis, C.A.

2011-01-01

The effect of nano-inclusions on materials' strength and toughness has attracted great interest in recent years. It has been shown that tuning the morphological and microstructural features of materials can tailor their fracture modes. The existence of a characteristic size of inclusions that favours the fracture mode (i.e. transgranular or intergranular) has been experimentally observed but also predicted by a 2D model based on energetic arguments which relates the crack propagation mode to the ratio of the interface area between the crystalline inclusion and the matrix with the area of the crystallite inclusion in a previous work. In the present work, a 3D model is proposed in order to extend the 2D model and take into account the influence of the size of grain boundary zone on the toughening/hardening behavior of the material as it was observed experimentally in the literature. The model relates crack propagation mode to the ratio of the volume of the grain boundary zone between the crystalline inclusion and the matrix with the volume of the nano-inclusion. For a ratio below a critical value, transgranular propagation is favoured while for larger values, intergranular propagation is favoured. We also demonstrate that the extent of the grain boundary region also can significantly affect this critical value. The results of the model are in agreement with the literature experimental observations related to the toughening/hardening behavior as a function of the size of crystalline inclusions as well as the width of the grain boundary regions.

Scope of millet grains as an extender in meat products.

Science.gov (United States)

Talukder, Suman; Sharma, B D

2015-01-01

India stood first for millet production in the world and plays a significant role in meat production and consumption too. To meet the demand of health conscious consumers for healthy and nutritious meat food item, the incorporation of millet grains and its byproducts to the meat products by the processors can serve the purpose. The multidimensional positive nutritional and functional characteristics millet grain not only improve the acceptability of the meat products but also increase its own demand as a main coarse food grain in competition to the wheat and rice over the world.

Coarse-grain parallel solution of few-group neutron diffusion equations

International Nuclear Information System (INIS)

Sarsour, H.N.; Turinsky, P.J.

1991-01-01

The authors present a parallel numerical algorithm for the solution of the finite difference representation of the few-group neutron diffusion equations. The targeted architectures are multiprocessor computers with shared memory like the Cray Y-MP and the IBM 3090/VF, where coarse granularity is important for minimizing overhead. Most of the work done in the past, which attempts to exploit concurrence, has concentrated on the inner iterations of the standard outer-inner iterative strategy. This produces very fine granularity. To coarsen granularity, the authors introduce parallelism at the nested outer-inner level. The problem's spatial domain was partitioned into contiguous subregions and assigned a processor to solve for each subregion independent of all other subregions, hence, processors; i.e., each subregion is treated as a reactor core with imposed boundary conditions. Since those boundary conditions on interior surfaces, referred to as internal boundary conditions (IBCs), are not known, a third iterative level, the recomposition iterations, is introduced to communicate results between subregions

Monte Carlo tests of small-world architecture for coarse-grained networks of the United States railroad and highway transportation systems

Science.gov (United States)

Aldrich, Preston R.; El-Zabet, Jermeen; Hassan, Seerat; Briguglio, Joseph; Aliaj, Enela; Radcliffe, Maria; Mirza, Taha; Comar, Timothy; Nadolski, Jeremy; Huebner, Cynthia D.

2015-11-01

Several studies have shown that human transportation networks exhibit small-world structure, meaning they have high local clustering and are easily traversed. However, some have concluded this without statistical evaluations, and others have compared observed structure to globally random rather than planar models. Here, we use Monte Carlo randomizations to test US transportation infrastructure data for small-worldness. Coarse-grained network models were generated from GIS data wherein nodes represent the 3105 contiguous US counties and weighted edges represent the number of highway or railroad links between counties; thus, we focus on linkage topologies and not geodesic distances. We compared railroad and highway transportation networks with a simple planar network based on county edge-sharing, and with networks that were globally randomized and those that were randomized while preserving their planarity. We conclude that terrestrial transportation networks have small-world architecture, as it is classically defined relative to global randomizations. However, this topological structure is sufficiently explained by the planarity of the graphs, and in fact the topological patterns established by the transportation links actually serve to reduce the amount of small-world structure.

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

Science.gov (United States)

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.

The Role of Carbon in Grain Refinement of Cast CrFeCoNi High-Entropy Alloys

Science.gov (United States)

Liu, X. W.; Liu, L.; Liu, G.; Wu, X. X.; Lu, D. H.; Yao, J. Q.; Jiang, W. M.; Fan, Z. T.; Zhang, W. B.

2018-06-01

As a promising engineering material, high-entropy alloys (HEAs) CrFeCoNi system has attracted extensive attention worldwide. Their cast alloys are of great importance because of their great formability of complex components, which can be further improved through the transition of the columnar to equiaxed grains and grain refinement. In the current work, the influence of C contents on the grain structures and mechanical properties of the as-cast high-entropy alloy CrFeCoNi was chosen as the target and systematically studied via a hybrid approach of the experiments and thermodynamic calculations. The alloys with various C additions were prepared by arc melting and drop cast. The as-cast macrostructure and microstructure were characterized using optical microscopy, scanning electron microscopy, and transmission electron microscopy. The cast HEAs transform from coarse columnar grains into equiaxed grains with the C level increased to ≥ 2 at. pct and the size of equiaxed grains is further decreased with the increasing C addition. It is revealed that the interdendritic segregation of Cr and C results in grain boundary precipitation of M23C6 carbides. The grain refinement is attributed to the additional constitutional supercoiling from the C addition. The yield stress and tensile strength at room temperature are improved due to the transition of columnar to equiaxed grains and grain refinement.

Environmental monitoring of Columbia River sediments: Grain-size distribution and contaminant association

Energy Technology Data Exchange (ETDEWEB)

Blanton, M.L.; Gardiner, W.W.; Dirkes, R.L.

1995-04-01

Based on the results of this study and literature review, the following conclusions can be made: Sediment grain size and TOC (total organic carbon) influence contaminant fate and transport (in general, sediments with higher TOC content and finer grain-size distribution can have higher contaminant burdens than sediments from a given river section that have less TOC and greater amounts of coarse-grained sediments). Physiochemical sediment characteristics are highly variable among monitoring sites along the Columbia River. Sediment grain characterization and TOC analysis should be included in interpretations of sediment-monitoring data.

Environmental monitoring of Columbia River sediments: Grain-size distribution and contaminant association

International Nuclear Information System (INIS)

Blanton, M.L.; Gardiner, W.W.; Dirkes, R.L.

1995-04-01

Based on the results of this study and literature review, the following conclusions can be made: Sediment grain size and TOC (total organic carbon) influence contaminant fate and transport (in general, sediments with higher TOC content and finer grain-size distribution can have higher contaminant burdens than sediments from a given river section that have less TOC and greater amounts of coarse-grained sediments). Physiochemical sediment characteristics are highly variable among monitoring sites along the Columbia River. Sediment grain characterization and TOC analysis should be included in interpretations of sediment-monitoring data

Annealing behavior of a cast Mg-Gd-Y-Zr alloy with necklace fine grains developed under hot deformation

Energy Technology Data Exchange (ETDEWEB)

Yang, Yi [Educational Key Laboratory of Nonferrous Metal Materials Science and Engineering, School of Materials Science and Engineering, Central South University, Changsha 410083 (China); Yang, Xuyue, E-mail: yangxuyue@mail.csu.edu.cn [Educational Key Laboratory of Nonferrous Metal Materials Science and Engineering, School of Materials Science and Engineering, Central South University, Changsha 410083 (China); Nonferrous Metal Oriented Advanced Structural Materials and Manufacturing Cooperative Innovation Center, Central South University, Changsha 410083 (China); Xiao, Zhenyu; Zhang, Duxiu [Educational Key Laboratory of Nonferrous Metal Materials Science and Engineering, School of Materials Science and Engineering, Central South University, Changsha 410083 (China); Wang, Jun [Institute for Frontier Materials, Deakin University, Geelong, VIC 3216 (Australia); Sakai, Taku [UEC Tokyo (The University of Electro-Communications), Chofu, Tokyo 182-8585 (Japan)

2017-03-14

The microstructure and texture development of a cast Mg-Gd-Y-Zr alloy during hot deformation and subsequent annealing were investigated by optical microscopy (OM) and electron backscattered diffraction (EBSD) technology. Initial microstructures with partially and fully developed new fine grains (NFGs), separately attended by continuous or interrupted hot forging, were various mixed grain structures composed of NFGs in necklace and retained coarse grains. It is shown that, during annealing, the development of grain size can be divided into three stages: i.e. an incubation of grain growth, a rapid coarsening and a normal grain growth. After a long time annealing of over 10{sup 4} ks at 693 K, the average grain size for samples continuous compressed to ε=1.2 and those interrupted compressed to ε=1.6 were close. Moreover, orientations of such strain-induced fine grains were relatively randomly distributed, leading to a weakened basal texture, while the basal plane of retained coarse grains were perpendicular to the forging direction. Such texture even became weaker during subsequent annealing. The results show that the development of necklace NFGs during hot deformation can be effective for homogeneous grain refinement under subsequent annealing.

Grain Boundary Segregation in Metals

CERN Document Server

Lejcek, Pavel

2010-01-01

Grain boundaries are important structural components of polycrystalline materials used in the vast majority of technical applications. Because grain boundaries form a continuous network throughout such materials, their properties may limit their practical use. One of the serious phenomena which evoke these limitations is the grain boundary segregation of impurities. It results in the loss of grain boundary cohesion and consequently, in brittle fracture of the materials. The current book deals with fundamentals of grain boundary segregation in metallic materials and its relationship to the grain boundary structure, classification and other materials properties.

Micro/nano composited tungsten material and its high thermal loading behavior

Energy Technology Data Exchange (ETDEWEB)

Fan, Jinglian, E-mail: fjl@csu.edu.cn; Han, Yong; Li, Pengfei; Sun, Zhiyu; Zhou, Qiang

2014-12-15

Tungsten (W) is considered as promising candidate material for plasma facing components (PFCs) in future fusion reactors attributing to its many excellent properties. Current commercial pure tungsten material in accordance with the ITER specification can well fulfil the performance requirements, however, it has defects such as coarse grains, high ductile–brittle transition temperature (DBTT) and relatively low recrystallization temperature compared with its using temperature, which cannot meet the harsh wall loading requirement of future fusion reactor. Grain refinement has been reported to be effective in improving the thermophysical and mechanical properties of W. In this work, rare earth oxide (Y{sub 2}O{sub 3}/La{sub 2}O{sub 3}) and carbides (TiC/ZrC) were used as dispersion phases to refine W grains, and micro/nano composite technology with a process of “sol gel – heterogeneous precipitation – spray drying – hydrogen reduction – ordinary consolidation sintering” was invented to introduce these second-phase particles uniformly dispersed into W grains and grain-boundaries. Via this technology, fine-grain W materials with near-full density and relatively high mechanical properties compared with traditional pure W material were manufactured. Preliminary transient high-heat flux tests were performed to evaluate the thermal response under plasma disruption conditions, and the results show that the W materials prepared by micro/nano composite technology can endure high-heat flux of 200 MW/m{sup 2} (5 ms)

The influences of impurity content, tensile strength, and grain size on in-service temper embrittlement of CrMoV steels

International Nuclear Information System (INIS)

Cheruvu, N.S.; Seth, B.B.

1989-01-01

The influences of impurity levels, grain size, and tensile strength on in-service temper embrittlement of CrMoV steels have been investigated. The samples for this study were taken from steam turbine CrMoV rotors which had operated for 15 to 26 years. The effects of grain size and tensile strength on embrittlement susceptibility were separated by evaluating the embrittlement behavior of two rotor forgings made from the same ingot after an extended step-cooling treatment. Among the residual elements in the steels, only P produces a significant embrittlement. The variation of P and tensile strength has no effect on in-service temper embrittlement susceptibility, as measured by the shift in fracture appearance transition temperature (FATT). However, the prior austenite grain size plays a major role in service embrittlement. The fine grain steels with a grain size of ASTM No. 9 or higher are virtually immune to in-service embrittlement. In steels having duplex grain sizes, embrittlement susceptibility is controlled by the size of coarser grains. For a given steel chemistry, the coarse grain steel is more susceptible to in-service embrittlement, and a decrease in ASTM grain size number from 4 to 0/1 increases the shift in FATT by 61 degrees C (10/10 degrees F). It is demonstrated that long-term service embrittlement can be simulated, except in very coarse grain steels, by using the extended step-cooling treatment. The results of step-cooling studies show that the coarse grain rotor steels take longer time during service to reach a fully embrittled state than the fine grain rotor steels

Grain boundary corrosion of copper canister material

International Nuclear Information System (INIS)

Fennell, P.A.H.; Graham, A.J.; Smart, N.R.; Sofield, C.J.

2001-03-01

The proposed design for a final repository for spent fuel and other long-lived residues in Sweden is based on the multi-barrier principle. The waste will be encapsulated in sealed cylindrical canisters, which will then be placed in granite bedrock and surrounded by compacted bentonite clay. The canister design is based on a thick cast inner container fitted inside a corrosion-resistant copper canister. During fabrication of the outer copper canisters there will be some unavoidable grain growth in the welded areas. As grains grow they will tend to concentrate impurities within the copper at the new grain boundaries. The work described in this report was undertaken to determine whether there is any possibility of enhanced corrosion at grain boundaries within the copper canister. The potential for grain boundary corrosion was investigated by exposing copper specimens, which had undergone different heat treatments and hence had different grain sizes, to aerated artificial bentonite-equilibrated groundwater with two concentrations of chloride, for increasing periods of time. The degree of grain boundary corrosion was determined by atomic force microscopy (AFM) and optical microscopy. AFM showed no increase in grain boundary 'ditching' for low chloride groundwater. In high chloride groundwater the surface was covered uniformly with a fine-grained oxide. No increases in oxide thickness were observed. No significant grain boundary attack was observed using optical microscopy either. The work suggests that in aerated artificial groundwaters containing chloride ions, grain boundary corrosion of copper is unlikely to adversely affect SKB's copper canisters

Micromechanical Modeling of Grain Boundaries Damage in a Copper Alloy Under Creep

International Nuclear Information System (INIS)

Voese, Markus

2015-01-01

In order to include the processes on the scale of the grain structure into the description of the creep behaviour of polycrystalline materials, the damage development of a single grain boundary has been initially investigated in the present work. For this purpose, a special simulationmethod has been used, whose resolution procedure based on holomorphic functions. The mechanisms taken into account for the simulations include nucleation, growth by grain boundary diffusion, coalescence and shrinkage until complete sintering of grain boundary cavities. These studies have then been used to develop a simplified cavitation model, which describes the grain boundary damage by two state variables and the time-dependent development by a mechanism-oriented rate formulation. To include the influence of grain boundaries within continuum mechanical considerations of polycrystals, an interface model has been developed, that incorporates both damage according to the simplified cavitation model and grain boundary sliding in dependence of a phenomenological grain boundary viscosity. Furthermore a micromechanical model of a polycrystal has been developed that allows to include a material's grain structure into the simulation of the creep behaviour by means of finite element simulations. Thereby, the deformations of individual grains are expressed by a viscoplastic single crystal model and the grain boundaries are described by the proposed interface model. The grain structure is represented by a finite element model, in which the grain boundaries are modelled by cohesive elements. From the evaluation of experimental creep data, the micromechanical model of a polycrystal has been calibrated for a copper-antimony alloy at a temperature of 823 K. Thereby, the adjustment of the single crystal model has been carried out on the basis of creep rates of pure copper single crystal specimens. The experimental determination of grain boundary sliding and grain boundary porosity for coarse-grained

A Multi-Wavelength Grain-by-Grain Survey of Lunar Soils in Search of Rare Materials

Science.gov (United States)

Crites, S.; Lucey, P. G.; Viti, T.

2014-12-01

The Moon is unique among terrestrial planets for its lack of an atmosphere and global tectonic or volcanic processes. These factors and its position in the inner solar system mean that it is a potential repository of meteoritic material from all of the terrestrial planets. The National Research Council's 2007 report on the Scientific Context for the Exploration of the Moon highlighted this unique possibility and defined the search for rare materials including those from the early Earth as a key goal for future lunar exploration. Armstrong et al. (2002) estimated that Earth material could be present at the 7 ppm level in surface lunar regolith and emphasized that since a single gram of lunar fines contains over 10 million particles, the search for terran material in lunar soils should begin with the current stock of lunar samples. Joy et al. (2012) demonstrated that mineral and lithologic relics of impactors can survive and be recognized in lunar samples, and recent work by Burchell et al. (2014) suggests that fossil fragments from Earth could survive the extreme shocks associated with transport to the Moon. Following the concept laid out by Armstrong et al. (2002), we are conducting a survey of lunar soil samples using microscopic hyperspectral imaging spectroscopy across visible, near-infrared, and thermal infrared wavelengths to conduct a search for rare particles, including those that could be sourced from the early Earth. Our system currently consists of three microscopic imaging spectrometers with ~30 micron spatial resolution, permitting resolved imaging of individual grains. Fields of view of at least 1 cm and scan rates near 1 mm/sec permit rapid processing of relatively large quantities of sample. Existing spectrometers cover the 0.5 to 2.5 micron region, permitting detection and characterization of the common iron-bearing lunar minerals olivine and pyroxene, and the 8-14 micron region, which permits detection of other, rarer minerals of interest such as

Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids.

Science.gov (United States)

Poma, Adolfo B; Chwastyk, Mateusz; Cieplak, Marek

2017-10-25

We study the mechanical response of cellulose and β-amyloid microfibrils to three types of deformation: tensile, indentational, and shear. The cellulose microfibrils correspond to the allomorphs Iα or Iβ whereas the β-amyloid microfibrils correspond to the polymorphs of either two- or three-fold symmetry. This response can be characterized by three elastic moduli, namely, Y L , Y T , and S. We use a structure-based coarse-grained model to analyze the deformations in a unified manner. We find that each of the moduli is almost the same for the two allomorphs of cellulose but Y L is about 20 times larger than Y T (140 GPa vs. 7 GPa), indicating the existence of significant anisotropy. For cellulose we note that the anisotropy results from the involvement of covalent bonds in stretching. For β-amyloid, the sense of anisotropy is opposite to that of cellulose. In the three-fold symmetry case, Y L is about half of Y T (3 vs. 7) whereas for two-fold symmetry the anisotropy is much larger (1.6 vs. 21 GPa). The S modulus is derived to be 1.2 GPa for three-fold symmetry and one half of it for the other symmetry and 3.0 GPa for cellulose. The values of the moduli reflect deformations in the hydrogen-bond network. Unlike in our theoretical approach, no experiment can measure all three elastic moduli with the same apparatus. However, our theoretical results are consistent with various measured values: typical Y L for cellulose Iβ ranges from 133 to 155 GPa, Y T from 2 to 25 GPa, and S from 1.8 to 3.8 GPa. For β-amyloid, the experimental values of S and Y T are about 0.3 GPa and 3.3 GPa respectively, while the value of Y L has not been reported.

A comparative study of the luminescence characteristics of polymineral fine grains and coarse-grained K-, and Na-rich feldspars

DEFF Research Database (Denmark)

Tsukamoto, Sumiko; Jain, Mayank; Murray, Andrew S.

2012-01-01

for K-feldspar samples, when a preheat temperature of 250 °C for 60 s is used. After preheating to a higher temperature (320 °C for 60 s) all samples show a TL reduction around 410 °C in the blue detection window. Pulse annealing experiments for IRSL and pIRIR signals for preheats between 320 °C and 500...... °C indicate that the signal stabilities are similar among the different feldspar types, when a higher preheat temperature (>320 °C) is used. Thermal activation energies for IRSL and pIRIR signals are largest in K-feldspar and smallest in polymineral fine grains, in both blue and UV detection windows...... for both fast time-resolved (TR) and continuous wave (CW) signals. These results suggest that IRSL and pIRIR signals in polymineral fine grains originate mainly from Na-feldspar grains; these signals are less thermally stable than those from K-feldspar, but a more stable signal (presumably from K...

Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: Does a stronger acid make a stiffer hydrogen bond?

Science.gov (United States)

Houjou, Hirohiko

2011-10-01

Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m-1 for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.

Bake hardening of ultra-fine grained low carbon steel produced by constrained groove pressing

International Nuclear Information System (INIS)

Alihosseini, H.; Dehghani, K.

2012-01-01

Highlights: ► BH of UFG low carbon steel sheets was studied. ► Three passes of CGP are used for producing of UFG sheets. ► Maximum BH was achieved to the UFG specimen pre-strained 8% by baking at 250 °C. - Abstract: In the present work, the bake hardening of ultra-fine grained low carbon steel was compared with that of its coarse-grain counterpart. The ultra-fine grained sheets were produced by applying three passes of constrained groove pressing resulting the grains of 260–270 nm. The microstructure of ultra-fine grain specimens were characterized using electron back-scatter diffraction technique. Then, the bake hardenability of ultra-fine grain and coarse-grain samples were compared by pre-straining to 4, 6 and 8% followed by baking at 150 °C and 250 °C for 20 min. The results show that in case of baking at 250 °C, there was an increase about 108%, 93%, and 72% in the bake hardening for 4%, 6% and 8% pre-strain, respectively. As for baking at 150 °C, these values were 170%, 168%, and 100%, respectively for 4%, 6% and 8% pre-strain. The maximum in bake hardenability (103 MPa) and final yield stress (563 MPa) were pertaining to the ultra-fine grain specimen pre-strained 8% followed by baking at 250 °C.

Continuous Production of Isomalto-oligosaccharides by Thermo-inactivated Cells of Aspergillus niger J2 with Coarse Perlite as an Immobilizing Material.

Science.gov (United States)

Huang, Zhihua; Li, Zhihong; Su, Yongjian; Zhu, Yongfeng; Zeng, Wei; Chen, Guiguang; Liang, Zhiqun

2018-02-13

The coarse perlite 40-80 mesh was selected as an immobilizing material and put into a packed bed reactor (PBR) to continuously convert maltose to isomalto-oligosaccharides (IMOs). The PBR was prepared by mixing the thermo-inactivated cells (TIC) from Aspergillus niger J2 strain with the coarse perlite, then the mixture was put into an overpressure-resistant column. Compared with diatomite 40-80 mesh and thin perlite 80-120 mesh in PBR, coarse perlite was chosen as the best filtration aid, when the ratio of coarse perlite versus TIC was 1:1. The thermal and pH stability of the free and immobilized TIC and the optimum conditions for the transglycosylation reactions were determined. The results show that approximately 75 and 82% and 87 and 91% of α-glucosidase activity were reserved for free and immobilized TIC at temperatures from 30 to 60 °C and pH from 3.00 to 7.00 for 12 h, respectively. With 30% malt syrup under the conditions of 50 °C and pH 4.00, a mini-scale packed bed reactor (Mi-PBR) and medium-scale packed bed reactor (Me-PBR) could continuously produce IMO over 25 and 34 days with the yield of effective IMO (eIMO) ≥ 35% and total IMO (tIMO) ≥ 50%, respectively. The strategy of mixing the coarse perlite with TIC in PBR is a novel approach to continuously produce IMO and has great application potential in industry.

Austenite grain growth and microstructure control in simulated heat affected zones of microalloyed HSLA steel

Energy Technology Data Exchange (ETDEWEB)

Zhang, Lei [Department of Machine Tools and Factory Management, Technical University of Berlin, Pascalstraße 8 – 9, 10587, Berlin (Germany); Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205, Berlin (Germany); Kannengiesser, Thomas [Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205, Berlin (Germany); Institute of Materials and Joining Technology, Otto von Guericke University Magdeburg, Universitetsplatz 2, 39106, Magdeburg (Germany)

2014-09-08

The roles of microalloying niobium, titanium and vanadium for controlling austenite grain growth, microstructure evolution and hardness were investigated at different simulated heat affected zones (HAZ) for high strength low alloy (HSLA) S690QL steel. High resolution FEG-SEM has been used to characterize fine bainitic ferrite, martensite and nanosized second phases at simulated coarse and fine grain HAZs. It was found that for Ti bearing steel (Ti/N ratio is 2) austenite grain had the slowest growth rate due to the presence of most stable TiN. The fine cuboidal particles promoted intragranular acicular ferrite (IGF) formation. Nb bearing steel exhibited relatively weaker grain growth retardation compared with titanium bearing steels and a mixed microstructure of bainite and martensite was present for all simulated HAZs. IGF existed at coarse grain HAZ of Ti+V bearing steel but it was totally replaced by bainite at fine grain HAZs. Hardness result was closely related to the morphology of bainitic ferrite, intragranular ferrite and second phases within ferrite. The microstructure and hardness results of different simulated HAZs were in good agreement with welded experimental results.

the use of statistical grain-size method in analysing borehole

African Journals Online (AJOL)

of medium-coarse grained sandstones, sub-angular to sub-rounded ... rainy season. Figure 1: Nsukka section of the Nsukka-Okigwe Cuesta. 6 0. 8 0. 100. 120. 140 ...... and also to improve the quality of drinking water, several boreholes were ...

A method to calculate flux distribution in reactor systems containing materials with grain structure

International Nuclear Information System (INIS)

Stepanek, J.

1980-01-01

A method is proposed to compute the neutron flux spatial distribution in slab, spherical or cylindrical systems containing zones with close grain structure of material. Several different types of equally distributed particles embedded in the matrix material are allowed in one or more zones. The multi-energy group structure of the flux is considered. The collision probability method is used to compute the fluxes in the grains and in an ''effective'' part of the matrix material. Then the overall structure of the flux distribution in the zones with homogenized materials is determined using the DPN ''surface flux'' method. Both computations are connected using the balance equation during the outer iterations. The proposed method is written in the code SURCU-DH. Two testcases are computed and discussed. One testcase is the computation of the eigenvalue in simplified slab geometry of an LWR container of one zone with boral grains equally distributed in an aluminium matrix. The second is the computation of the eigenvalue in spherical geometry of the HTR pebble-bed cell with spherical particles embedded in a graphite matrix. The results are compared to those obtained by repeated use of the WIMS Code. (author)

New Experiences in Dike Construction with Soil-Ash Composites and Fine-Grained Dredged Materials

Directory of Open Access Journals (Sweden)

Duszyński Remigiusz

2017-12-01

Full Text Available The supporting structure inside a coastal dike is often made of dredged non-uniform sand with good compaction properties. Due to the shortage of natural construction material for both coastal and river dikes and the surplus of different processed materials, new experiments were made with sand-ash mixtures and fine-grained dredged materials to replace both dike core and dike cover materials resulting in economical, environmentally friendly and sustainable dikes. Ash from EC Gdańsk and dredged sand from the Vistula river were mixed to form an engineering material used for dike construction. The optimum sand-ash composites were applied at a field test site to build a large-scale research dike. Fine-grained dredged materials from Germany were chosen to be applied in a second full-scale research dike in Rostock. All materials were investigated according to the standards for soil mechanical analysis. This includes basic soil properties, mechanical characteristics, such as grain-size distribution, compaction parameters, compressibility, shear strength, and water permeability. In the field, the infiltration of water into the dike body as well as the erosion resistance of the cover material against overflowing water was determined. Results of both laboratory and field testing are discussed in this paper. In conclusion, the mixing of bottom ash with mineral soil, such as relatively uniform dredged sand, fairly improves the geotechnical parameters of the composite, compared to the constituents. Depending on the composite, the materials may be suitable to build a dike core or an erosion-resistant dike cover.

New Experiences in Dike Construction with Soil-Ash Composites and Fine-Grained Dredged Materials

Science.gov (United States)

Duszyński, Remigiusz; Duszyńska, Angelika; Cantré, Stefan

2017-12-01

The supporting structure inside a coastal dike is often made of dredged non-uniform sand with good compaction properties. Due to the shortage of natural construction material for both coastal and river dikes and the surplus of different processed materials, new experiments were made with sand-ash mixtures and fine-grained dredged materials to replace both dike core and dike cover materials resulting in economical, environmentally friendly and sustainable dikes. Ash from EC Gdańsk and dredged sand from the Vistula river were mixed to form an engineering material used for dike construction. The optimum sand-ash composites were applied at a field test site to build a large-scale research dike. Fine-grained dredged materials from Germany were chosen to be applied in a second full-scale research dike in Rostock. All materials were investigated according to the standards for soil mechanical analysis. This includes basic soil properties, mechanical characteristics, such as grain-size distribution, compaction parameters, compressibility, shear strength, and water permeability. In the field, the infiltration of water into the dike body as well as the erosion resistance of the cover material against overflowing water was determined. Results of both laboratory and field testing are discussed in this paper. In conclusion, the mixing of bottom ash with mineral soil, such as relatively uniform dredged sand, fairly improves the geotechnical parameters of the composite, compared to the constituents. Depending on the composite, the materials may be suitable to build a dike core or an erosion-resistant dike cover.

Searching for an Improved Spectral Match to TES and IRIS Sinus Meridiani Spectra: Coatings and Cemented Materials

Science.gov (United States)

Kirkland, L. E.; Herr, K. C.; Adams, P. M.

2001-05-01

A region on Mars within Sinus Meridiani has been interpreted as a surface partially covered by coarse-grained (gray) hematite, using spectra measured by the 1996 Global Surveyor Thermal Emission Spectrometer (TES) [Lane et al., 1999; Christensen et al., 2000]. The band strengths recorded by TES of this region are consistent with either coarse-grained hematite, or cemented poorly crystalline or cemented fine-grained hematite. The band strengths are inconsistent with unconsolidated, poorly crystalline or fine-grained hematite, including nanophase hematite dust [Christensen et al., 2000]. Currently the gray hematite interpretation is based on bands centered near 22 and 33 microns. TES also records a band centered near 18 microns that was used in early hematite interpretations [Lane et al., 1999]. However, it was noted [Kirkland et al., 1999a] that the 18 micron band is too narrow in both TES and the 1971 Mariner Mars IRIS spectra to be a good match to typical spectra of well-crystalline hematite [e.g. Salisbury et al., 1991]. The 18 micron band is near the very strong 15 micron atmospheric CO2 band, but if anything the nearby CO2 band should cause the 18 micron band to appear wider, not narrower. In addition, the higher spectral resolution of IRIS allows improved separation of the bands [Kirkland et al., 1999b]. More recent publications no longer show the TES 18 micron band [e.g. Lane et al., 2000; Christensen et al., 2000], which temporarily resolved the issue. However, we feel it is important to understand why TES and IRIS spectra exhibit an 18 micron band that is too narrow to match typical spectra of coarse-grained hematite. Smooth-surfaced cemented (e.g. ferricrete) or coated materials (e.g. desert varnish) have spectral contrast that is consistent with the observed IRIS and TES band contrast. On Mars, one possible source for cemented material or coatings would be the nanophase hematite dust. Cemented materials may occur in bulk (e.g. duricrust or ferricrete), or

Quantitative mineralogy and preliminary pore-water chemistry of candidate buffer and backfill materials for a nuclear fuel waste disposal vault

International Nuclear Information System (INIS)

Quigley, R.M.

1984-07-01

The quantitative mineralogy of seven candidate buffer and backfill materials for a nuclear fuel waste disposal vault is presented. Two of the materials were coarse grained: one a blended very pure silica sand, and the other a crushed plagioclase-rich granite or granodiorite. Five materials were fine-grained soils containing abundant clay minerals. Of these, three were fairly pure, Cretaceous, ash-derived bentonites that contained up to 3 percent of soluble sulphates; one was a freshwater glacial clay containing 59 percent interlayered smectite-illite; and one was a crushed Paleozoic shale containing abundant illite and chlorite. The adsorbed cation regimes and the pore-water chemistry of the clays are discussed