Directory of Open Access Journals (Sweden)
Stamatakis Michail
2010-04-01
Full Text Available Abstract Background An adaptive coarse-grained (kinetic Monte Carlo (ACGMC simulation framework is applied to reaction and diffusion dynamics in inhomogeneous domains. The presented model is relevant to the diffusion and dimerization dynamics of epidermal growth factor receptor (EGFR in the presence of plasma membrane heterogeneity and specifically receptor clustering. We perform simulations representing EGFR cluster dissipation in heterogeneous plasma membranes consisting of higher density clusters of receptors surrounded by low population areas using the ACGMC method. We further investigate the effect of key parameters on the cluster lifetime. Results Coarse-graining of dimerization, rather than of diffusion, may lead to computational error. It is shown that the ACGMC method is an effective technique to minimize error in diffusion-reaction processes and is superior to the microscopic kinetic Monte Carlo simulation in terms of computational cost while retaining accuracy. The low computational cost enables sensitivity analysis calculations. Sensitivity analysis indicates that it may be possible to retain clusters of receptors over the time scale of minutes under suitable conditions and the cluster lifetime may depend on both receptor density and cluster size. Conclusions The ACGMC method is an ideal platform to resolve large length and time scales in heterogeneous biological systems well beyond the plasma membrane and the EGFR system studied here. Our results demonstrate that cluster size must be considered in conjunction with receptor density, as they synergistically affect EGFR cluster lifetime. Further, the cluster lifetime being of the order of several seconds suggests that any mechanisms responsible for EGFR aggregation must operate on shorter timescales (at most a fraction of a second, to overcome dissipation and produce stable clusters observed experimentally.
Adaptive Coarse Graining, Environment, Strong Decoherence, and Quasiclassical Realms
Gell-Mann, Murray
2013-01-01
Three ideas are introduced that when brought together characterize the realistic quasiclassical realms of our quantum universe as particular kinds of sets of alternative coarse-grained histories defined by quasiclassical variables: (1) Branch dependent adaptive coarse grainings that can be close to maximally refined and can simplify calculation. (2) Narrative coarse grainings that describe how features of the universe change over time and allow the construction of an environment. (3) A notion of strong decoherence that characterizes realistic mechanisms of decoherence.
Adaptive coarse graining, environment, strong decoherence, and quasiclassical realms
Gell-Mann, Murray; Hartle, James B.
2014-05-01
Three ideas are introduced that when brought together characterize the realistic quasiclassical realms of our quantum universe as particular kinds of sets of alternative coarse-grained histories defined by quasiclassical variables: (i) branch-dependent adaptive coarse grainings that can be close to maximally refined and can simplify calculation, (ii) narrative coarse grainings that describe how features of the universe change over time and allow the construction of an environment, and (iii) a notion of strong decoherence that characterizes realistic mechanisms of decoherence.
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.
Systematic hierarchical coarse-graining with the inverse Monte Carlo method
Lyubartsev, Alexander P.; Naômé, Aymeric; Vercauteren, Daniel P.; Laaksonen, Aatto
2015-12-01
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.
Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
Energy Technology Data Exchange (ETDEWEB)
Zavadlav, Julija; Praprotnik, Matej, E-mail: praprot@cmm.ki.si [Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Melo, Manuel N.; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl [Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen (Netherlands)
2015-06-28
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.
An adaptive coarse graining method for signal transduction in three dimensions
Archuleta, Michelle N.; McDermott, Jason E.; Edwards, Jeremy S.; Resat, Haluk
2013-01-01
The spatio-temporal landscape of the plasma membrane regulates activation and signal transduction of membrane bound receptors by restricting their two-dimensional mobility and by inducing receptor clustering. This regulation also extends to complex formation between receptors and adaptor proteins, which are the intermediate signaling molecules involved in cellular signaling that relay the received cues from cell surface to cytoplasm and eventually to the nucleus. Although their investigation poses challenging technical difficulties, there is a crucial need to understand the impact of the receptor diffusivity, clustering, and spatial heterogeneity, and of receptor-adaptor protein complex formation on the cellular signal transduction patterns. Building upon our earlier studies, we have developed an adaptive coarse-grained Monte Carlo method that can be used to investigate the role of diffusion, clustering and membrane corralling on receptor association and receptor-adaptor protein complex formation dynamics in three dimensions. The new Monte Carlo lattice based approach allowed us to introduce spatial resolution on the 2-D plasma membrane and to model the cytoplasm in three-dimensions. Being a multi-resolution approach, our new method makes it possible to represent various parts of the cellular system at different levels of detail and enabled us to utilize the locally homogeneous assumption when justified (e.g., cytoplasmic region away from the cell membrane) and avoid its use when high spatial resolution is needed (e.g., cell membrane and cytoplasmic region near the membrane) while keeping the required computational complexity manageable. Our results have shown that diffusion has a significant impact on receptor-receptor dimerization and receptor-adaptor protein complex formation kinetics. We have observed an “adaptor protein hopping” mechanism where the receptor binding proteins may hop between receptors to form short-lived transient complexes. This increased
Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses.
Janner, A
2016-05-01
Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article. PMID:27126109
Structure and dynamics of Ebola virus matrix protein VP40 by a coarse-grained Monte Carlo simulation
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.
Sasidevan, V; Sinha, Sitabhra
2016-01-01
The recent trend for acquiring big data assumes that possessing quantitatively more and qualitatively finer data necessarily provides an advantage that may be critical in competitive situations. Using a model complex adaptive system where agents compete for a limited resource using information coarse-grained to different levels, we show that agents having access to more and better data can perform worse than others in certain situations. The relation between information asymmetry and individual payoffs is seen to be complex, depending on the composition of the population of competing agents.
Zeidman, Benjamin D.; Lu, Ning; Wu, David T.
2016-05-01
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.
Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
Zavadlav, Julija; Melo, Manuel N.; Marrink, Siewert J.; Praprotnik, Matej
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
International Nuclear Information System (INIS)
The study of particle coagulation and sintering processes is important in a variety of research studies ranging from cell fusion and dust motion to aerosol formation applications. These processes are traditionally simulated using either Monte-Carlo methods or integro-differential equations for particle number density functions. In this paper, we present a computational technique for cases where we believe that accurate closed evolution equations for a finite number of moments of the density function exist in principle, but are not explicitly available. The so-called equation-free computational framework is then employed to numerically obtain the solution of these unavailable closed moment equations by exploiting (through intelligent design of computational experiments) the corresponding fine-scale (here, Monte-Carlo) simulation. We illustrate the use of this method by accelerating the computation of evolving moments of uni- and bivariate particle coagulation and sintering through short simulation bursts of a constant-number Monte-Carlo scheme.
Liang, Ying; Yang, Gen; Liu, Feng; Wang, Yugang
2016-01-01
Ionizing radiation threatens genome integrity by causing DNA damage. Monte Carlo simulation of the interaction of a radiation track structure with DNA provides a powerful tool for investigating the mechanisms of the biological effects. However, the more or less oversimplification of the indirect effect and the inadequate consideration of high-order chromatin structures in current models usually results in discrepancies between simulations and experiments, which undermine the predictive role of the models. Here we present a biophysical model taking into consideration factors that influence indirect effect to simulate radiation-induced DNA strand breaks in eukaryotic cells with high-order chromatin structures. The calculated yields of single-strand breaks and double-strand breaks (DSBs) for photons are in good agreement with the experimental measurements. The calculated yields of DSB for protons and α particles are consistent with simulations by the PARTRAC code, whereas an overestimation is seen compared with the experimental results. The simulated fragment size distributions for 60Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with 60Co irradiation validates our model in simulating photon irradiation. The general agreement found in α particle irradiation encourages model applicability in the high linear energy transfer range. Moreover, we demonstrate the importance of chromatin high-order structures in shaping the spectrum of initial damage.
Coarse Grained Quantum Dynamics
Agon, Cesar; Kasko, Skyler; Lawrence, Albion
2014-01-01
We consider coarse graining a quantum system divided between short distance and long distance degrees of freedom, which are coupled by the Hamiltonian. Observations using purely long distance observables can be described by the reduced density matrix that arises from tracing out the short-distance observables. The dynamics of this density matrix is that of an open quantum system, and is nonlocal in time, on the order of some short time scale. We describe these dynamics in a model system with a simple hierarchy of energy gaps $\\Delta E_{UV} > \\Delta E_{IR}$, in which the coupling between high-and low-energy degrees of freedom is treated to second order in perturbation theory. We then describe the equations of motion under suitable time averaging, reflecting the limited time resolution of actual experiments, and find an expansion of the master equation in powers of $\\Delta E_{IR}/\\Delta E_{UV}$, in which the failure of the system to be Hamiltonian or even Markovian appears at higher orders in this ratio. We com...
Pandey, R. B.; Farmer, B. L.
2014-11-01
Multi-scale aggregation to network formation of interacting proteins (H3.1) are examined by a knowledge-based coarse-grained Monte Carlo simulation as a function of temperature and the number of protein chains, i.e., the concentration of the protein. Self-assembly of corresponding homo-polymers of constitutive residues (Cys, Thr, and Glu) with extreme residue-residue interactions, i.e., attractive (Cys-Cys), neutral (Thr-Thr), and repulsive (Glu-Glu), are also studied for comparison with the native protein. Visual inspections show contrast and similarity in morphological evolutions of protein assembly, aggregation of small aggregates to a ramified network from low to high temperature with the aggregation of a Cys-polymer, and an entangled network of Glu and Thr polymers. Variations in mobility profiles of residues with the concentration of the protein suggest that the segmental characteristic of proteins is altered considerably by the self-assembly from that in its isolated state. The global motion of proteins and Cys polymer chains is enhanced by their interacting network at the low temperature where isolated chains remain quasi-static. Transition from globular to random coil transition, evidenced by the sharp variation in the radius of gyration, of an isolated protein is smeared due to self-assembly of interacting networks of many proteins. Scaling of the structure factor S(q) with the wave vector q provides estimates of effective dimension D of the mass distribution at multiple length scales in self-assembly. Crossover from solid aggregates (D ˜ 3) at low temperature to a ramified fibrous network (D ˜ 2) at high temperature is observed for the protein H3.1 and Cys polymers in contrast to little changes in mass distribution (D ˜ 1.6) of fibrous Glu- and Thr-chain configurations.
Directory of Open Access Journals (Sweden)
R. B. Pandey
2015-09-01
Full Text Available The self-organizing dynamics of lysozymes (an amyloid protein with 148 residues with different numbers of protein chains, Nc = 1,5,10, and 15 (concentration 0.004 – 0.063 is studied by a coarse-grained Monte Carlo simulation with knowledge-based residue-residue interactions. The dynamics of an isolated lysozyme (Nc = 1 is ultra-slow (quasi-static at low temperatures and becomes diffusive asymptotically on raising the temperature. In contrast, the presence of interacting proteins leads to concentration induced protein diffusion at low temperatures and concentration-tempering sub-diffusion at high temperatures. Variation of the radius of gyration of the protein with temperature shows a systematic transition from a globular structure (at low T to a random coil (high T conformation when the proteins are isolated. The crossover from globular to random coil becomes sharper upon increasing the protein concentration (i.e. with Nc = 5,10, with larger Rg at higher temperatures and concentration; Rg becomes smaller on adding more protein chains (e.g. Nc = 15 a non-monotonic response to protein concentration. Analysis of the structure factor (S(q provides an estimate of the effective dimension (D ≥ 3, globular conformation at low temperature, and D ∼ 1.7, random coil, at high temperatures of the isolated protein. With many interacting proteins, the morphology of the self-assembly varies with scale, i.e. at the low temperature (T = 0.015, D ∼ 2.9 on the scale comparable to the radius of gyration of the protein, and D ∼ 2.3 at the large scale over the entire sample. The global network of fibrils appears at high temperature (T = 0.021 with D ∼ 1.7 (i.e. a random coil morphology at large scale involving tenuous distribution of micro-globules (at small scales.
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-tailed distribu......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......-law and logarithmic relaxation behaviors ubiquitous in complex dynamics, together with the sub-diffusive time dependence of the Mean Square Displacement characteristic of single particles moving in a complex environment....
Coarse graining flow of spin foam intertwiners
Dittrich, Bianca; Seth, Cameron J; Steinhaus, Sebastian
2016-01-01
Simplicity constraints play a crucial role in the construction of spin foam models, yet their effective behaviour on larger scales is scarcely explored. In this article we introduce intertwiner and spin net models for the quantum group $\\text{SU}(2)_k \\times \\text{SU}(2)_k$, which implement the simplicity constraints analogous to 4D 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. 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 2D topological phase, BC spin net models flow away from the initial simplicity constraints and converge to several different ...
Quasiclassical Coarse Graining and Thermodynamic Entropy
Gell-Mann, Murray; Gell-Mann, Murray; Hartle, James
2006-01-01
Our everyday descriptions of the universe are highly coarse-grained, following only a tiny fraction of the variables necessary for a perfectly fine-grained description. Coarse graining in classical physics is made natural by our limited powers of observation and computation. But in the modern quantum mechanics of closed systems, some measure of coarse graining is inescapable because there are no non-trivial, probabilistic, fine-grained descriptions. This essay explores the consequences of that fact: Quantum theory allows for various coarse-grained descriptions some of which are mutually incompatible. For most purposes, however, we are interested in the small subset of ``quasiclassical descriptions'' defined by ranges of values of averages over small volumes of densities of conserved quantities such as energy and momentum and approximately conserved quantities such as baryon number. The near-conservation of these quasiclassical quantities results in approximate decoherence, predictability, and local equilibriu...
Coarse graining lessons from simple examples
Akritas, P; Yarevsky, E
2001-01-01
We assess Coarse Graining by studying different partitions of the phase space of the Baker transformation and the periodic torus automorphisms. It turns out that the shape of autocorrelation functions for the Baker transformation is more or less reproduced. However, for certain partitions the decay rates turn out to be irrelevant, even decay may stop in a finite time. For the periodic torus automorphisms, Coarse Graining introduces artificial dumping.
Coarse-grained Modeling of DNA Curvature
Freeman, Gordon S; Lequieu, Joshua P; Whitmer, Jonathan K; de Pablo, Juan J
2014-01-01
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient exploration of binding configurations. It is known that the local structure of DNA can significantly affect its protein-binding properties (i.e. intrinsic curvature in DNA-histone complexes). In a step towards comprehensive DNA-protein modeling, we expand the 3SPN.2 coarse-grained model to include intrinsic shape, and validate the refined model against experimental data including melting temperature, local flexibility, persistence length, and minor groove width profile.
Multiresolution Modeling of Polymer Solutions: Wavelet-Based Coarse-Graining and Reverse-Mapping
Ismail, Ahmed; Adorf, Carl Simon; Agarwal, Animesh; Iacovella, Christopher R.
2014-03-01
Unlike multiscale methods, which encompass multiple simulation techniques, multiresolution models uses one modeling technique at different length and time scales. We present a combined coarse-graining and reverse-mapping framework for modeling of semidilute polymer solutions, based on the wavelet-accelerated Monte Carlo (WAMC) method, which forms a hierarchy of resolutions to model polymers at length scales that cannot be reached via atomistic or even ``standard'' coarse-grained simulations. A universal scaling function is obtained so that potentials do not need to be recomputed as the scale of the system is changed. We show that coarse-grained polymer solutions can reproduce results obtained from the simulations of the more detailed atomistic system to a reasonable degree of accuracy. Reverse mapping proceeds similarly: using probability distributions obtained from coarse-graining the bond lengths, angles, torsions, and the non-bonded potentials, we can reconstruct a more detailed polymer consistent with both geometric constraints and energetic considerations. Using a ``convergence factor'' within a Monte Carlo-based energy optimization scheme, we can successfully reconstruct entire atomistic configurations from coarse-grained descriptions.
The gravitational description of coarse grained microstates
Energy Technology Data Exchange (ETDEWEB)
Alday, Luis F. [Institute for Theoretical Physics and Spinoza Institute, Utrecht University, 3508 TD Utrecht (Netherlands); Boer, Jan de [Instituut voor Theoretische Fysica, Valckenierstraat 65, 1018XE Amsterdam (Netherlands); Messamah, Ilies [Instituut voor Theoretische Fysica, Valckenierstraat 65, 1018XE Amsterdam (Netherlands)
2006-12-15
In this paper we construct a detailed map from pure and mixed half-BPS states of the D1-D5 system to half-BPS solutions of type IIB supergravity. Using this map, we can see how gravity arises through coarse graining microstates, and we can explicitly confirm the microscopic description of conical defect metrics, the M = 0 BTZ black hole and of small black rings. We find that the entropy associated to the natural geometric stretched horizon typically exceeds that of the mixed state from which the geometry was obtained.
An algebraic approach to coarse graining
Markopoulou, F
2000-01-01
We propose that Kreimer's method of Feynman diagram renormalization via a Hopf algebra of rooted trees can be fruitfully employed in the analysis of block spin renormalization or coarse graining of inhomogeneous statistical systems. Examples of such systems include spin foam formulations of non-perturbative quantum gravity as well as lattice gauge and spin systems on irregular lattices and/or with spatially varying couplings. We study three examples which are Z_2 lattice gauge theory on irregular 2-dimensional lattices, Ising/Potts models with varying bond strengths and (1+1)-dimensional spin foam models.
Coarse-Grain Modeling of Energetic Materials
Brennan, John
2015-06-01
Mechanical and thermal loading of energetic materials can incite responses over a wide range of spatial and temporal scales due to inherent nano- and microscale features. Many energy transfer processes within these materials are atomistically governed, yet the material response is manifested at the micro- and mesoscale. The existing state-of-the-art computational methods include continuum level approaches that rely on idealized field-based formulations that are empirically based. Our goal is to bridge the spatial and temporal modeling regimes while ensuring multiscale consistency. However, significant technical challenges exist, including that the multiscale methods linking the atomistic and microscales for molecular crystals are immature or nonexistent. To begin addressing these challenges, we have implemented a bottom-up approach for deriving microscale coarse-grain models directly from quantum mechanics-derived atomistic models. In this talk, a suite of computational tools is described for particle-based microscale simulations of the nonequilibrium response of energetic solids. Our approach builds upon recent advances both in generating coarse-grain models under high strains and in developing a variant of dissipative particle dynamics that includes chemical reactions.
Equilibrium behavior of coarse-grained chaos
Egolf, David A.; Ballard, Christopher C.; Esty, C. Clark
2015-03-01
A wide variety of systems exhibiting spatiotemporal chaos have been shown to be extensive, in that their fractal dimensions grow linearly with volume. Ruelle argued that this extensivity is evidence that these systems can be viewed as a gas of weakly-interacting regions. We have tested this idea by performing large-scale computational studies of spatiotemporal chaos in the 1D complex Ginzburg-Landau equation, and we have found that aspects of the coarse-grained system are well-described not only as a gas, but as an equilibrium gas -- in particular, a Tonks gas (and variants) in the grand canonical ensemble. Furthermore, for small system sizes, the average number of particles in the corresponding Tonks gas exhibits oscillatory, decaying deviations from extensivity in agreement with deviations in the fractal dimension found by Fishman and Egolf. This result not only supports Ruelle's picture but also suggests that the coarse-grained behavior of this far-from-equilibrium system might be understood using equilibrium statistical mechanics.
Coarse graining in spin foam models
Energy Technology Data Exchange (ETDEWEB)
Markopoulou, Fotini
2003-03-07
We formulate the problem of finding the low-energy limit of spin foam models as a coarse-graining problem in the sense of statistical physics. This suggests that renormalization group methods may be used to find that limit. However, since spin foams are models of spacetime at the Planck scale, novel issues arise: these microscopic models are sums over irregular, background-independent lattices. We show that all of these issues can be addressed by the recent application of the Kreimer Hopf algebra for quantum field theory renormalization to non-perturbative statistical physics. The main difference from the standard renormalization group is that the Hopf algebra executes block transformations in parts of the lattice only but in a controlled manner so that the end result is a fully block-transformed lattice.
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.
Model Reduction and Coarse-Graining Approaches for Multiscale Phenomena
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 spectral signature generator
Lam, K. P.; Austin, J. C.; Day, C. R.
2007-01-01
This paper investigates the method for object fingerprinting in the context of element specific x-ray imaging. In particular, the use of spectral descriptors that are illumination invariant and viewpoint independent for pattern identification was examined in some detail. To improve generating the relevant "signature", the spectral descriptor constructed is enhanced with a differentiator which has built-in noise filtration capability and good localisation properties, thus facilitating the extraction of element specific features at a coarse-grained level. In addition to the demonstrable efficacy in identifying significant image intensity transitions that are associated with the underlying physical process of interest, the method has the distinct advantage of being conceptually simple and computationally efficient. These latter properties allow the descriptor to be further utilised by an intelligent system capable of performing a fine-grained analysis of the extracted pattern signatures. The performance of the spectral descriptor has been studied in terms of the quality of the signature vectors that it generated, quantitatively based on the established framework of Spectral Information Measure (SIM). Early results suggested that such a multiscale approach of image sequence analysis offers a considerable potential for real-time applications.
Buchert coarse-graining and the classical energy conditions
Visser, Matt
2015-01-01
So-called "Buchert averaging" is actually a coarse-graining procedure, where fine detail is "smeared out" due to limited spatio-temporal resolution. For technical reasons, (to be explained herein), "averaging" is not really an appropriate term, and I shall consistently describe the process as a "coarse-graining". Because Einstein gravity is nonlinear the coarse-grained Einstein tensor is typically not equal to the Einstein tensor of the coarse-grained spacetime geometry. The discrepancy can be viewed as an "effective" stress-energy, and this "effective" stress-energy often violates the classical energy conditions. To keep otherwise messy technical issues firmly under control, I shall work with conformal-FLRW (CFLRW) cosmologies. These CFLRW-based models are particularly tractable, and are also particularly attractive observationally: the CMB is not distorted. In this CFLRW context one can prove some rigorous theorems regarding the interplay between Buchert coarse-graining, tracelessness of the effective stres...
Perez Sirkin, Yamila A; Factorovich, Matías H; Molinero, Valeria; Scherlis, Damian A
2016-06-14
The vapor pressure of water is a key property in a large class of applications from the design of membranes for fuel cells and separations to the prediction of the mixing state of atmospheric aerosols. Molecular simulations have been used to compute vapor pressures, and a few studies on liquid mixtures and solutions have been reported on the basis of the Gibbs Ensemble Monte Carlo method in combination with atomistic force fields. These simulations are costly, making them impractical for the prediction of the vapor pressure of complex materials. The goal of the present work is twofold: (1) to demonstrate the use of the grand canonical screening approach ( Factorovich , M. H. J. Chem. Phys. 2014 , 140 , 064111 ) to compute the vapor pressure of solutions and to extend the methodology for the treatment of systems without a liquid-vapor interface and (2) to investigate the ability of computationally efficient high-resolution coarse-grained models based on the mW monatomic water potential and ions described exclusively with short-range interactions to reproduce the relative vapor pressure of aqueous solutions. We find that coarse-grained models of LiCl and NaCl solutions faithfully reproduce the experimental relative pressures up to high salt concentrations, despite the inability of these models to predict cohesive energies of the solutions or the salts. A thermodynamic analysis reveals that the coarse-grained models achieve the experimental activity coefficients of water in solution through a compensation of severely underestimated hydration and vaporization free energies of the salts. Our results suggest that coarse-grained models developed to replicate the hydration structure and the effective ion-ion attraction in solution may lead to this compensation. Moreover, they suggest an avenue for the design of coarse-grained models that accurately reproduce the activity coefficients of solutions. PMID:27196963
Non-commutativity from coarse grained classical probabilities
Wetterich, C
2010-01-01
Non-commutative quantum physics at the atom scale can arise from coarse graining of a classical statistical ensemble at the Planck scale. Position and momentum of an isolated particle are classical observables which remain computable in terms of the coarse grained information. However, the commuting classical product of position and momentum observables is no longer defined in the coarse grained system, which is therefore described by incomplete statistics. The microphysical classical statistical ensemble at the Planck scale admits an alternative non-commuting product structure for position and momentum observables which is compatible with the coarse graining. Measurement correlations for isolated atoms are based on this non-commutative product structure. We present an explicit example for these ideas. It also realizes the discreteness of the spin observable within a microphysical classical statistical ensemble.
Coarse-Grained Simulations of Membranes under Tension
Neder, Jörg; Nielaba, Peter; Schmid, Friederike
2010-01-01
We investigate the properties of membranes under tension by Monte-Carlo simulations of a generic coarse-grained model for lipid bilayers. We give a comprising overview of the behavior of several membrane characteristics, such as the area per lipid, the monolayer overlap, the nematic order, and pressure profiles. Both the low-temperature regime, where the membranes are in a gel phase, and the high-temperature regime, where they are in the fluid phase, are considered. In the gel state, the membrane is hardly influenced by tension. In the fluid state, high tensions lead to structural changes in the membrane, which result in different compressibility regimes. The ripple state, which is found at tension zero in the transition regime between the fluid and the gel phase, disappears under tension and gives way to an interdigitated phase. We also study the membrane fluctuations in the fluid phase. In the low tension regime the data can be fitted nicely to a suitably extended elastic theory. At higher tensions the elas...
Conveying of Coarse-Grained Particles in Pipes
Vlasák, P.; Chára, Z.; Konfršt, J. (Jiří); Sobota , J.; Kysela, B. (Bohuš)
2013-01-01
The effect of slurry velocity and concentration on the coarse-grained particle–water mixtures flow behavior and pressure drops was studied in horizontal and inclined pipes of inner diameter 100 mm. The study revealed that the coarse-grained particle-water mixtures were significantly stratified, the particles moved principally in a layer close to the pipe invert, for higher flow velocities particle saltation becomes dominant mode of conveying. Frictional pressure drops in vertical pipe ...
Energy-conserving coarse-graining of complex molecules.
Español, Pep; Serrano, Mar; Pagonabarraga, Ignacio; Zúñiga, Ignacio
2016-05-25
Coarse-graining (CG) of complex molecules is a method to reach time scales that would be impossible to access through brute force molecular simulations. In this paper, we formulate a coarse-grained model for complex molecules using first principles caculations that ensures energy conservation. Each molecule is described in a coarse way by a thermal blob characterized by the position and momentum of the center of mass of the molecule, together with its internal energy as an additional degree of freedom. This level of description gives rise to an entropy-based framework instead of the usual one based on the configurational free energy (i.e. potential of mean force). The resulting dynamic equations, which account for an appropriate description of heat transfer at the coarse-grained level, have the structure of the dissipative particle dynamics with energy conservation (DPDE) model but with a clear microscopic underpinning. Under suitable approximations, we provide explicit microscopic expressions for each component (entropy, mean force, friction and conductivity coefficients) appearing in the coarse-grained model. These quantities can be computed directly using MD simulations. The proposed non-isothermal coarse-grained model is thermodynamically consistent and opens up a first principles CG strategy for the study of energy transport issues that are not accessible using current isothermal models. PMID:27127809
Coarse-graining the Lin-Maldacena geometries
International Nuclear Information System (INIS)
The Lin-Maldacena geometries are nonsingular gravity duals to degenerate vacuum states of a family of field theories with SU(2|4) supersymmetry. In this note, we show that at large N, where the number of vacuum states is large, there is a natural 'macroscopic' description of typical states, giving rise to a set of coarse-grained geometries. For a given coarse-grained state, we can associate an entropy related to the number of underlying microstates. We find a simple formula for this entropy in terms of the data that specify the geometry. We see that this entropy function is zero for the original microstate geometries and maximized for a certain 'typical state' geometry, which we argue is the gravity dual to the zero-temperature limit of the thermal state of the corresponding field theory. Finally, we note that the coarse-grained geometries are singular if and only if the entropy function is non-zero
Coarse-graining two-dimensional turbulence via dynamical optimization
Turkington, Bruce; Thalabard, Simon
2015-01-01
A model reduction technique based on an optimization principle is employed to coarse-grain inviscid, incompressible fluid dynamics in two dimensions. In this reduction the spectrally-truncated vorticity equation defines the microdynamics, while the macroscopic state space consists of quasi-equilibrium trial probability densities on the microscopic phase space, which are parameterized by the means and variances of the low modes of the vorticity. A macroscopic path therefore represents a coarse-grained approximation to the evolution of a nonequilibrium ensemble of microscopic solutions. Closure in terms of the vector of resolved variables, namely, the means and variances of the low modes, is achieved by minimizing over all feasible paths the time integral of their mean-squared residual with respect to the Liouville equation. The equations governing the optimal path are deduced from Hamilton-Jacobi theory. The coarse-grained dynamics derived by this optimization technique contains a scale-dependent eddy viscosit...
Systematic coarse-graining in nucleation theory
International Nuclear Information System (INIS)
In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 − 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al., J. Chem. Phys. 139, 074309 (2013)] conducted in the experimental accessible supersaturation regime for Lennard-Jones argon. We argue that this is due to the truncated state space the literature mostly relies on, where the number of atoms in a nucleus is considered the only relevant order parameter. We here formulate the nonequilibrium statistical mechanics of nucleation in an extended state space, where the internal energy and momentum of the nuclei are additionally incorporated. We show that the extended model explains the lack in agreement between the molecular dynamics simulations by Diemand et al. and the truncated state space. We demonstrate additional benefits of using the extended state space; in particular, the definition of a nucleus temperature arises very naturally and can be shown without further approximation to obey the fluctuation law of McGraw and LaViolette. In addition, we illustrate that our theory conveniently allows to extend existing theories to richer sets of order parameters
REVLD: A coarse-grained model for polymers
A.G. Bailey; C.P. Lowe; A.P. Sutton
2009-01-01
A new model for polymers is presented. REVLD (Rigid, Excluded Volume, Langevin Dynamics) is similar to the coarse-grained, bead spring model for linear chains except that the inter-bead distance is rigidly constrained instead of using an inter-bead potential to encapsulate the connectivity. Static a
Coarse graining and scaling in dissipative particle dynamics
DEFF Research Database (Denmark)
Füchslin, Rudolf M; Fellermann, Harold; Eriksson, Anders;
2009-01-01
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent the applicability of the method to the whole mesoscopic ...
Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations
Bulacu, Monica; Goga, Nicolae; Zhao, Wei; Rossi, Giulia; Monticelli, Luca; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.
2013-01-01
Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules.
Martini Coarse-Grained Force Field : Extension to Carbohydrates
Lopez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Huenenberger, Philippe H.; Marrink, Siewert J.; Hünenberger, Philippe H.
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 car
Free-energy coarse-grained potential for C60
International Nuclear Information System (INIS)
We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C60. 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
Dileptons in a coarse-grained transport approach
van Hees, H; Weil, J; Bleicher, M
2015-01-01
We calculate dilepton spectra in heavy-ion collisions using a coarse-graining approach to the simulation of the created medium with the UrQMD transport model. This enables the use of dilepton-production rates evaluated in equilibrium quantum-field theory at finite temperatures and chemical potentials.
Coarse-graining and scaling in dissipative particle dynamics
DEFF Research Database (Denmark)
Fuechslin, Rudolf; Fellermann, Harold; Eriksson, Anders;
2009-01-01
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent the applicability of the method to the whole mesoscopic...
Notes on coarse grainings and functions of observables
Dvurecenskij, A; Pulmannova, S; Ylinen, K
2004-01-01
Using the Naimark dilation theory we investigate the question under what conditions an observable which is a coarse graining of another observable is a function of it. To this end, conditions for the separability and for the Boolean structure of an observable are given.
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.
Coarse Grainings and Irreversibility in Quantum Field Theory
Anastopoulos, C
1997-01-01
In this paper we are interested in the studying coarse-graining in field theories using the language of quantum open systems. Motivated by the ideas of Calzetta and Hu 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 from statistical mechanics truncation of the BBKGY hierarchy at the n-th 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 behaviour and the connection to the decoherent histories framework.
A nucleotide-level coarse-grained model of RNA
Šulc, Petr; Ouldridge, Thomas E; Doye, Jonathan P K; Louis, Ard A
2014-01-01
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.
Determination of the scale of coarse graining in earthquake network
Abe, Sumiyoshi
2009-01-01
In a recent paper [S. Abe and N. Suzuki, Europhys. Lett., 65 (2004) 581], the concept of earthquake network has been introduced in order to describe complexity of seismicity. There, the cell size, which is the scale of coarse graining needed for constructing an earthquake network, has remained as a free parameter. Here, a method is presented for determining it based on the scaling behavior of the network. Quite remarkably, both the exponent of the power-law connectivity distribution and the clustering coefficient are found to approach the respective universal values and remain invariant as the cell size becomes larger than a certain value, $l_*$, which depends on the number of events contained in the analysis, in general. This $l_*$ fixes the scale of coarse graining. Universality of the result is demonstrated for all of the networks constructed from the data independently taken from California, Japan and Iran.
Vesicles and vesicle fusion: coarse-grained simulations
DEFF Research Database (Denmark)
Shillcock, Julian C.
2010-01-01
Biological cells are highly dynamic, and continually move material around their own volume and between their interior and exterior. Much of this transport encapsulates the material inside phospholipid vesicles that shuttle to and fro, fusing with, and budding from, other membranes. A feature...... of vesicles that is crucial for this transport is their ability to fuse to target membranes and release their contents to the distal side. In industry, some personal care products contain vesicles to help transport reagents across the skin, and research on drug formulation shows that packaging active...... compounds inside vesicles delays their clearance from the blood stream. In this chapter, we survey the biological role and physico-chemical properties of phospholipids, and describe progress in coarse-grained simulations of vesicles and vesicle fusion. Because coarse-grained simulations retain only those...
Experimental investigation of coarse-grained particles in pipes
Vlasák, P.; Chára, Z.; Konfršt, J. (Jiří); Kysela, B. (Bohuš)
2013-01-01
The effect of solid concentration and mixture velocity on the flow behaviour and pressure drops of coarse-grained particle-water mixtures in the turbulent flow was experimentally investigated. Concentration distribution in the pipe cross-section was also studied. Graded basalt pebbles as a model of solid particles were studied on an experimental pipe loop with horizontal, vertical, and inclined sections of smooth stainless steel pipes of inner diameter D = 100 mm. The study revealed that the ...
Systematic and Simulation-Free Coarse Graining of Polymeric Systems: A Structure-based Study
Yang, Delian; Wang, Qiang
2015-03-01
We propose a systematic and simulation-free strategy for coarse graining of multicomponent polymeric systems, where we use the Polymer Reference Interaction Site Model theory, instead of many-chain molecular simulations, to calculate the structure and thermodynamic properties of both the original and coarse-grained (CG) models, and quantitatively examine how the effective CG pair potentials and properties of CG systems vary with the coarse-graining level. Our strategy is general and versatile, is much faster than those using many-chain simulations, and practically solves the transferability problem of coarse graining. As an example, here we apply it to structure-based coarse graining of homopolymer melts, which matches the structure correlations of CG segments between the original and CG systems. Our numerical results clearly show that structure-based coarse graining cannot give thermodynamic consistency between the original and CG systems at any coarse-graining level due to the information loss of coarse graining.
Coarse-graining two-dimensional turbulence via dynamical optimization
Turkington, Bruce; Chen, Qian-Yong; Thalabard, Simon
2016-10-01
A model reduction technique based on an optimization principle is employed to coarse-grain inviscid, incompressible fluid dynamics in two dimensions. In this reduction the spectrally-truncated vorticity equation defines the microdynamics, while the macroscopic state space consists of quasi-equilibrium trial probability densities on the microscopic phase space, which are parameterized by the means and variances of the low modes of the vorticity. A macroscopic path therefore represents a coarse-grained approximation to the evolution of a nonequilibrium ensemble of microscopic solutions. Closure in terms of the vector of resolved variables, namely, the means and variances of the low modes, is achieved by minimizing over all feasible paths the time integral of their mean-squared residual with respect to the Liouville equation. The equations governing the optimal path are deduced from Hamilton-Jacobi theory. The coarse-grained dynamics derived by this optimization technique contains a scale-dependent eddy viscosity, modified nonlinear interactions between the low mode means, and a nonlinear coupling between the mean and variance of each low mode. The predictive skill of this optimal closure is validated quantitatively by comparing it against direct numerical simulations. These tests show that good agreement is achieved without adjusting any closure parameters.
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.
High capacitance of coarse-grained carbide derived carbon electrodes
Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury
2016-02-01
We report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. Using a titanium carbide (TiC) precursor, we synthesized 70-250 μm sized particles with high surface area and a narrow pore size distribution. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. The material showcased capacitance above 100 F g-1 at sweep rates as high as 250 mV s-1 in organic electrolyte. 250-1000 micron thick dense CDC films with up to 80 mg cm-2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.
Moving Beyond Watson-Crick Models of Coarse Grained DNA
Dorfman, Kevin; Linak, Margaret; Tourdot, Richard
2012-02-01
DNA structure possesses several levels of complexity, ranging from the sequence of bases (primary structure) to base pairing (secondary structure) to its three-dimensional shape (tertiary structure) and can produce a wide variety of conformations in addition to canonical double stranded DNA. By including non-Watson-Crick interactions in a coarse-grained model, we developed a system that not only can capture the traditional B-form double helix, but also can adopt a wide variety of other DNA conformations. In our experimentally parameterized, coarse-grained DNA model we are able to reproduce the microscopic features of double-stranded DNA without the need for explicit constraints and capture experimental melting curves for a number of short DNA hairpins. We demonstrate the utility of the model by simulating more complex tertiary structures such as the folding of the thrombin aptamer, which includes G-quartets, and strand invasion during triplex formation. Our results highlight the importance of non-canonical interactions in DNA coarse- grained models.
Adaptive Multilevel Monte Carlo Simulation
Hoel, H
2011-08-23
This work generalizes a multilevel forward Euler Monte Carlo method introduced in Michael B. Giles. (Michael Giles. Oper. Res. 56(3):607–617, 2008.) for the approximation of expected values depending on the solution to an Itô stochastic differential equation. The work (Michael Giles. Oper. Res. 56(3):607– 617, 2008.) proposed and analyzed a forward Euler multilevelMonte Carlo method based on a hierarchy of uniform time discretizations and control variates to reduce the computational effort required by a standard, single level, Forward Euler Monte Carlo method. This work introduces an adaptive hierarchy of non uniform time discretizations, generated by an adaptive algorithmintroduced in (AnnaDzougoutov et al. Raùl Tempone. Adaptive Monte Carlo algorithms for stopped diffusion. In Multiscale methods in science and engineering, volume 44 of Lect. Notes Comput. Sci. Eng., pages 59–88. Springer, Berlin, 2005; Kyoung-Sook Moon et al. Stoch. Anal. Appl. 23(3):511–558, 2005; Kyoung-Sook Moon et al. An adaptive algorithm for ordinary, stochastic and partial differential equations. In Recent advances in adaptive computation, volume 383 of Contemp. Math., pages 325–343. Amer. Math. Soc., Providence, RI, 2005.). This form of the adaptive algorithm generates stochastic, path dependent, time steps and is based on a posteriori error expansions first developed in (Anders Szepessy et al. Comm. Pure Appl. Math. 54(10):1169– 1214, 2001). Our numerical results for a stopped diffusion problem, exhibit savings in the computational cost to achieve an accuracy of ϑ(TOL),from(TOL−3), from using a single level version of the adaptive algorithm to ϑ(((TOL−1)log(TOL))2).
Nguyen, Hung; Van, Thanh Dac; Le, Ly
2015-10-01
The novel hyperactive antifreeze protein (AFP) of Antarctic sea ice bacterium Colwellia sp. provides a target for studying the protection of psychrophilic microgoranisms against freezing environment. Interestingly, the Colwellia sp. hyperactive antifreeze protein (ColAFP) was crystallized without the structural dynamic characteristics. Here, the result indicated, through coarse grained simulation of ColAFP under various subfreezing temperature, that ColAFP remains active at temperature of equal and greater than 275 K (∼2 °C). Extensive simulation analyses also revealed the adaptive mechanism of ColAFP in subfreezing environment. Our result provides a structural dynamic understanding of the ColAFP.
A system for coarse-grained location-based synchronisation
Coelho, André; Silva, Mário; José, Rui
2010-01-01
This paper describes a system for supporting coarse-grained location-based synchronisation. This type of synchronisation may occur when people need only some awareness about the location of others within the specific context of an on-going activity. We have identified a number of reference scenarios for this type of synchronisation and we have implemented and deployed a prototype to evaluate the type of support provided. The results of the evaluation suggest a good acceptance of the overall concept, indicating that this might be a valuable approach for many of the indicated scenarios, possibly replacing or complementing existing synchronisation practices.
Coarse-grained parallelism for full-core transport calculations
International Nuclear Information System (INIS)
In this paper we analyze the synergy between the Domain Decomposition Method and the Coarse-Mesh Finite Difference technique. In contrast to massively parallel computations, we construct a coarse-grained parallelism for daily run calculations on standard SIMD workstations based on shared memory architecture. We evaluate the effectiveness of the algorithm for several high-fidelity calculations spanning different types of color-sets up to the full-core. We show that CPU times for a best-estimate 2D calculation of the EPR can be reduced from several days to few hours using a standard workstation. (author)
Symmetry-based coarse-graining of evolved dynamical networks
Karalus, Steffen
2015-01-01
Networks with prescribed subdiffusive dynamical behavior can be generated by evolutionary optimization applied to the spectrum of the graph Laplacian. When the evolution algorithm is constrained to preserve degree-regularity, the evolved networks display an abundance of certain motifs arranged into loops and long linear segments. We use algebraic graph theory to construct the quotient networks induced by the symmetries underlying the motifs. The resulting coarse-grained networks display improved pectral properties and provide an intuitive view of how the anomalous diffusive properties are realized in the evolved structures.
MICROTHREAD BASED (MTB) COARSE GRAINED FAULT TOLERANCE SUPERSCALAR PROCESSOR ARCHITECTURE
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
Fault tolerance in microprocessor systems has become a popular topic of architecture research.Much work has been done at different levels to accomplish reliability against soft errors, and some fault tolerance architectures have been proposed. But little attention is paid to the thread level superscalar fault tolerance.This letter introduces microthread concept into superscalar processor fault tolerance domain, and puts forward a novel fault tolerance architecture, namely, MicroThread Based (MTB) coarse grained transient fault tolerance superscalar processor architecture, then discusses some detailed implementations.
Flow behavior of coarse-grained slurries in pipes
Vlasák, P.; Chára, Z.; Kysela, B. (Bohuš); Sobota , J.
2011-01-01
The paper describes the experimental investigation of model coarse-grained slurry on a recirculation pipe loop with smooth stainless steel pipes. Graded pebble gravel and glass balls were used as a model for poly-metallic nodules, and very fine glass beads as a model for fine-grained sand. The investigation was focused on evaluating the effect of slurry velocity and particle concentration on pressure drops and the slurry flow behavior in the turbulent regime. Also the effect of fine-grained p...
Realistic coarse-grained cosmic structure from Szekeres models
Sussman, Roberto A
2015-01-01
A systematic self-consistent procedure is provided to describe by means of the Szekeres dust models the evolution of multiple self-gravitating cold dark matter structures (over-densities and density voids), whose spatial location can be prescribed beforehand for all times by suitable initial conditions that define the free parameters of the models. Following this procedure makes it possible to obtain a fully relativistic non-perturbative coarse grained description of actually existing cosmic structure at various scales. We discuss possible astrophysical and cosmological applications.
Neural Adaptive Sequential Monte Carlo
Gu, Shixiang; Ghahramani, Zoubin; Turner, Richard E
2015-01-01
Sequential Monte Carlo (SMC), or particle filtering, is a popular class of methods for sampling from an intractable target distribution using a sequence of simpler intermediate distributions. Like other importance sampling-based methods, performance is critically dependent on the proposal distribution: a bad proposal can lead to arbitrarily inaccurate estimates of the target distribution. This paper presents a new method for automatically adapting the proposal using an approximation of the Ku...
Deformation Behaviour of Coarse Grain Alumina under Shock Loading
Gupta, Satish
2013-06-01
To develop better understanding of the shock wave induced deformation behavior of coarse grain alumina ceramics, and for measurement of its Hugoniot Elastic Limit (HEL), in-situ and recovery gas gun experiments have been carried out on coarse grain alumina (grain size ~ 10 μm), prepared in the form of discs (>99.9% TMD) by pressure-less sintering of alpha alumina powder at 1583 K. The HEL value of 1.9 GPa has been determined from the kink in the pressure history recorded using piezoresistance gauge and also from the free surface velocity history of the sample shocked to 9 GPa. The nano-indentation measurements on the alumina samples shocked to 6.5 GPa showed hardness value 15% lower than 21.3 GPa for unshocked alumina, and strong Indentation Size Effect (ISE); the hardness value was still lower and the ISE was stronger for the sample shocked to 12 GPa. The XRD measurements showed reduced particle size and increased microstrains in the shocked alumina fragments. SEM, FESEM and TEM measurements on shock treated samples showed presence of grain localized micro- and nano-scale deformations, micro-cleavages, grain-boundary microcracks, extensive shear induced deformations, and localized micro-fractures, etc. These observations led to the development of a qualitative model for the damage initiation and its subsequent growth mechanisms in shocked alumina. The work performed in collaboration with K.D. Joshi of BARC and A.K. Mukhopadhyay of CGCRI.
An exactly solvable coarse-grained model for species diversity
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.
Million atom DFT calculations using coarse graining and petascale computing
Nicholson, Don; Odbadrakh, Kh.; Samolyuk, G. D.; Stoller, R. E.; Zhang, X. G.; Stocks, G. M.
2014-03-01
Researchers performing classical Molecular Dynamics (MD) on defect structures often find it necessary to use millions of atoms in their models. It would be useful to perform density functional calculations on these large configurations in order to observe electron-based properties such as local charge and spin and the Helmann-Feynman forces on the atoms. The great number of atoms usually requires that a subset be ``carved'' from the configuration and terminated in a less that satisfactory manner, e.g. free space or inappropriate periodic boundary conditions. Coarse graining based on the Locally Self-consistent Multiple Scattering method (LSMS) and petascale computing can circumvent this problem by treating the whole system but dividing the atoms into two groups. In Coarse Grained LSMS (CG-LSMS) one group of atoms has its charge and scattering determined prescriptively based on neighboring atoms while the remaining group of atoms have their charge and scattering determined according to DFT as implemented in the LSMS. The method will be demonstrated for a one-million-atom model of a displacement cascade in Fe for which 24,130 atoms are treated with full DFT and the remaining atoms are treated prescriptively. Work supported as part of Center for Defect Physics, an Energy Frontier Research Center funded by the U.S. DOE, Office of Science, Basic Energy Sciences, used Oak Ridge Leadership Computing Facility, Oak Ridge National Lab, of DOE Office of Science.
Coarse-grained modeling of RNA 3D structure.
Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M
2016-07-01
Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.
Coarse-grained rigid blob model for soft matter simulations
Chao, Sheng D.; Kress, Joel D.; Redondo, Antonio
2005-06-01
We have developed a coarse-grained multiscale molecular simulation method for soft matter systems that directly incorporates stereochemical information. We divide the material into disjoint groups of atoms or particles that move as separate rigid bodies; we call these groups "rigid blobs," hence the name coarse-grained rigid blob model. The method is enabled by the construction of transferable interblob potentials that approximate the net intermolecular interactions, as obtained from ab initio electronic structure calculations, other all-atom empirical potentials, experimental data, or any combination of the above. We utilize a multipolar expansion to obtain the interblob potential-energy functions. The series, which contains controllable approximations that allow us to estimate the errors, approaches the original intermolecular potential as the number of terms increases. Using a novel numerical algorithm, we can calculate the interblob potentials very efficiently in terms of a few interaction moment tensors. This reduces the labor well beyond what is required in standard molecular-dynamics calculations and allows large-scale simulations for temporal scales commensurate with characteristic times of nano- and mesoscale systems. A detailed derivation of the formulas is presented, followed by illustrative applications to several systems showing that the method can effectively capture realistic microscopic details and can easily extend to large-scale simulations.
Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers
West, Beate; Schmid, Friederike
2008-01-01
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the hydrophobic force and the hydrophobic thickness of the proteins are systematically varied. The results are compared with analytical predictions of two popular analytical theories: The Landau-de Gennes theory and the elastic theory. The elastic theory provides an excellent description of the fluctuation spectra of pure membranes and successfully reproduces the deformation profiles of membranes around single proteins. However, its prediction for the potential of mean force between proteins is not compatible with the simulation data for large distances. The simulations show that the lipid-mediated interactions are governed by five competing factors: Direct interactions, lipid-induced depletion interactions, lipid bridging, lipid packing, and a smooth long-range contribution. The mechan...
DEFF Research Database (Denmark)
Murtola, Teemu; Karttunen, Mikko; Vattulainen, Ilpo
2009-01-01
We present a two-dimensional coarse-grained (CG) model for a lipid membrane composed of phospholipids and cholesterol. The effective CG interactions are determined using radial distribution functions (RDFs) from atom-scale molecular dynamics simulations using the inverse Monte Carlo (IMC) technique...... in the presence of internal states, in general, and present a modified IMC method for their inclusion. The new model agrees with the original models on large-scale structural features such as density fluctuations in pure dipalmitoylphosphocholine and cholesterol domain formation at intermediate concentrations...... and also indicates that ordered and disordered domains form at all cholesterol concentrations, even if the global density remains uniform. The inclusion of ordering also improves transferability of the interactions between different concentrations, but does not eliminate transferability problems completely...
Unconstrained Structure Formation in Coarse-Grained Protein Simulations
Bereau, Tristan
The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid
Coarse-Grained Molecular Simulations of Allosteric Cooperativity
Nandigrami, Prithviraj
2015-01-01
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 calcium 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 is treated implicitly at the mean field level. 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 energy to the open and closed ensembles accurately describe...
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 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...... smaller arrays that can execute threads in parallel. Because the partition can be changed dynamically, this extension provides more flexibility than a multi-core approach. This article presents details of the enhanced architecture and results obtained from an MPEG-2 decoder implementation that exploits...
Irregular Coarse-Grain Data Parallelism under LPARX
Directory of Open Access Journals (Sweden)
Scott R. Kohn
1996-01-01
Full Text Available LPARX is a software development tool for implementing dynamic, irregular scientific applications, such as multilevel finite difference and particle methods, on high-performance multiple instruction multiple data (MIMD parallel architectures. It supports coarse-grain data parallelism and gives the application complete control over specifying arbitrary block decompositions. LPARX provides structural abstraction, representing data decompositions as first-class objects that can be manipulated and modified at runtime. LPARX, implemented as a C++ class library, is currently running on diverse MIMD platforms, including the Intel Paragon, Cray C-90, IBM SP2, and networks of workstations running under PVM. Software may be developed and debugged on a singe-processor workstation.
Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity
Frigori, Rafael B; Alves, Nelson A
2012-01-01
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid $\\beta$-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method (REM) is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid $\\beta$ isoforms and Src SH3 domain indicated that th...
Effective thermostat induced by coarse-graining of SPC water
Eriksson, Anders; Nyström, Johan; Tunstrøm, Kolbjørn
2008-01-01
We investigate how the transport properties of a united atoms fluid with a dissipative particle dynamics thermostat depend on the functional form and magnitude of both the conservative and the stochastic interactions. We demonstrate how the thermostat strongly affects the hydrodynamics, especially diffusion, viscosity, and local escape times. As model system we use SPC water, from which projected trajectories are used to determine the effective interactions in the united atoms model. The simulation results support our argument that the thermostat should be viewed as an integral part of the coarse-grained dynamics, rather than a tool for approaching thermal equilibrium. As our main result we show that the united atoms model with the adjusted effective interactions approximately reproduce the diffusion constant and the viscosity of the underlying detailed SPC water model.
Coarse-grained cellular automaton for traffic systems
Krawczyk, Malgorzata J
2012-01-01
A coarse-grained cellular automaton is proposed to simulate traffic systems. There, cells represent road sections. A cell can be in two states: jammed or passable. Numerical calculations are performed for a piece of square lattice with open boundary conditions, for the same piece with some cells removed and for a map of a small city. The results indicate the presence of a phase transition in the parameter space, between two macroscopic phases: passable and jammed. The results are supplemented by exact calculations of the stationary probabilities of states for the related Kripke structure constructed for the traffic system. There, the symmetry-based reduction of the state space allows to partially reduce the computational limitations of the numerical method.
A Coarse-Grained Model for Simulating Chitosan Hydrogels
Xu, Hongcheng; Matysiak, Silvina
Hydrogels are biologically-derived materials composed of water-filled cross-linking polymer chains. It has widely been used as biodegradable material and has many applications in medical devices. The chitosan hydrogel is stimuli-responsive for undergoing pH-sensitive self-assembly process, allowing programmable tuning of the chitosan deposition through electric pulse. To explore the self-assembly mechanism of chitosan hydroge, we have developed an explicit-solvent coarse-grained chitosan model that has roots in the MARTINI force field, and the pH change is modeled by protonating chitosan chains using the Henderson-Hasselbalch equation. The mechanism of hydrogel network formation will be presented. The self-assembled polymer network qualitatively reproduce many experimental observables such as the pH-dependent strain-stress curve, bulk moduli, and structure factor. Our model is also capable of simulating other similar polyelectrolyte polymer systems.
Coarse-grain parallelism using remote method invocation
International Nuclear Information System (INIS)
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-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)
Directory of Open Access Journals (Sweden)
Souad Oudjemia
2013-01-01
Full Text Available This paper proposes a combined coarse-grained multifractal method to discriminate between distressed and normal foetuses. The coarse-graining operation was performed by means of a coarse-grained procedure and the multifractal operation was based on a structure function. The proposed method was evaluated by one hundred recordings including eighty normal foetuses and twenty distressed foetuses. We found that it was possible to discriminate between distressed and normal foetuses using the Hurst exponent, singularity, and Holder spectra.
Robotic action acquisition with cognitive biases in coarse-grained state space.
Uragami, Daisuke; Kohno, Yu; Takahashi, Tatsuji
2016-07-01
Some of the authors have previously proposed a cognitively inspired reinforcement learning architecture (LS-Q) that mimics cognitive biases in humans. LS-Q adaptively learns under uniform, coarse-grained state division and performs well without parameter tuning in a giant-swing robot task. However, these results were shown only in simulations. In this study, we test the validity of the LS-Q implemented in a robot in a real environment. In addition, we analyze the learning process to elucidate the mechanism by which the LS-Q adaptively learns under the partially observable environment. We argue that the LS-Q may be a versatile reinforcement learning architecture, which is, despite its simplicity, easily applicable and does not require well-prepared settings. PMID:27195484
Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water
DEFF Research Database (Denmark)
Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore;
2010-01-01
We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations of...... the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our...... method in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water....
A Column Arrangement Algorithm for a Coarse-grained Reconfigurable Architecture
Guo, Y.; Hoede, C.; Smit, G.J.M.; Plaks, T.P.; DeMara, R.; Gokhale, M.; Guccione, S.; Platzner, M.; Smit, G.J.M.; Wirthlin, M.
2006-01-01
In a coarse-grained reconfigurable architecture, the functions of resources such as Arithmetic Logic Units (ALUs) can be reconfigured. Unlike the programmability of a general purpose processor, the programmability of a coarse-grained reconfigurable architecture is limited. The limitation might be th
Influence of fines content on the anti-frost properties of coarse-grained soil
Institute of Scientific and Technical Information of China (English)
TianLiang Wang; ZuRun Yue; TieCheng Sun; JinChuang Hua
2015-01-01
This paper aims to determine the optimal fines content of coarse-grained soil required to simultaneously achieve weaker frost susceptibility and better bearing capacity. We studied the frost susceptibility and strength properties of coarse-grained soil by means of frost heaving tests and static triaxial tests, and the results are as follows: (1) the freezing temperature of coarse-grained soil decreased gradually and then leveled off with incremental increases in the percent content of fines; (2) the fines content proved to be an important factor influencing the frost heave susceptibility and strength properties of coarse-grained soil. With incremental increases in the percent content of fines, the frost heave ratio increased gradually and the cohesion function of fines effectively enhanced the shear strength of coarse-grained soil before freeze-thaw, but the frost susceptibility of fines weakened the shear strength of coarse-grained soil after freeze-thaw; (3) with increasing numbers of freeze-thaw cycles, the shear strength of coarse-grained soil decreased and then stabilized after the ninth freeze-thaw cycle, and therefore the mechanical indexes of the ninth freeze-thaw cycle are recommended for the engi-neering design values; and (4) considering frost susceptibility and strength properties as a whole, the optimal fines content of 5% is recommended for railway subgrade coarse-grained soil fillings in frozen regions.
Perspective: Coarse-grained models for biomolecular systems
Noid, W. G.
2013-09-01
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
Entrainment of coarse grains using a discrete particle model
International Nuclear Information System (INIS)
Conventional bedload transport models and incipient motion theories relying on a time-averaged boundary shear stress are incapable of accounting for the effects of fluctuating near-bed velocity in turbulent flow and are therefore prone to significant errors. Impulse, the product of an instantaneous force magnitude and its duration, has been recently proposed as an appropriate criterion for quantifying the effects of flow turbulence in removing coarse grains from the bed surface. Here, a discrete particle model (DPM) is used to examine the effects of impulse, representing a single idealized turbulent event, on particle entrainment. The results are classified according to the degree of grain movement into the following categories: motion prior to entrainment, initial dislodgement, and energetic displacement. The results indicate that in all three cases the degree of particle motion depends on both the force magnitude and the duration of its application and suggest that the effects of turbulence must be adequately accounted for in order to develop a more accurate method of determining incipient motion. DPM is capable of simulating the dynamics of grain entrainment and is an appropriate tool for further study of the fundamental mechanisms of sediment transport
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.
Cellulose microfibril formation within a coarse grained molecular dynamics
Nili, Abdolmadjid; Shklyaev, Oleg; Crespi, Vincent; Zhao, Zhen; Zhong, Linghao; CLSF Collaboration
2014-03-01
Cellulose in biomass is mostly in the form of crystalline microfibrils composed of 18 to 36 parallel chains of polymerized glucose monomers. A single chain is produced by cellular machinery (CesA) located on the preliminary cell wall membrane. Information about the nucleation stage can address important questions about intermediate region between cell wall and the fully formed crystalline microfibrils. Very little is known about the transition from isolated chains to protofibrils up to a full microfibril, in contrast to a large body of studies on both CesA and the final crystalline microfibril. In addition to major experimental challenges in studying this transient regime, the length and time scales of microfibril nucleation are inaccessible to atomistic molecular dynamics. We have developed a novel coarse grained model for cellulose microfibrils which accounts for anisotropic interchain interactions. The model allows us to study nucleation, kinetics, and growth of cellulose chains/protofibrils/microfibrils. This work is supported by the US Department of Energy, Office of Basic Energy Sciences as part of The Center for LignoCellulose Structure and Formation, an Energy Frontier Research Center.
Coarse-grained DNA model capable of simulating ribose flexibility
Kovaleva, Natalya A; Mazo, Mikhail A; Zubova, Elena A
2014-01-01
We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically significant B- and A-DNA forms. The number of degrees of freedom is reduced to six grains per nucleotide. We show that this is the minimal number sufficient for this purpose. The key features of the sugar CG DNA model are: (1) simulation of sugar repuckering between C2'-endo and C3'-endo by the use of one non-harmonic potential and one three-particle potential, (2) explicit representation of sodium counterions and (3) implicit solvent approach. Effects of solvation and of partial charge screening at small distances are taken into account through the shape of potentials of interactions between charged particles. We obtain parameters of the sugar CG DNA model from the all-atom AMBER model. The suggested model allows adequate simulation of the transitions between A- and B-DNA forms, as well as of large deformations of long DNA molecules, for example, in binding with proteins. Small modifications of the model can provide th...
Generic Coarse-Grained Model for Protein Folding and Aggregation
Bereau, Tristan; Deserno, Markus
2009-03-01
The complexity involved in protein structure is not only due to the rich variety of amino acids, but also the inherent weak interactions, comparable to thermal energy, and important cooperative phenomena. This presents a challenge in atomistic simulations, as it is associated with high-dimensionality and ruggedness of the energy landscape as well as long equilibration times. We have recently developed a coarse-grained (CG) implicit solvent peptide model which has been designed to reproduce key consequences of the abovementioned weak interactions. Its intermediate level of resolution, four beads per amino acid, allows for accurate sampling of local conformations by designing a force field that relies on simple interactions. A realistic ratio of α-helix to β-sheet content is achieved by mimicking a nearest-neighbor dipole interaction. We tune the model in order to fold helical proteins while systematically comparing the structure with NMR data. Very good agreement is achieved for proteins that have simple tertiary structures. We further probe the effects of cooperativity between amino acids by looking at peptide aggregation, where hydrophobic peptide fragments cooperatively form large-scale β-sheet structures. The model is able to reproduce features from atomistic simulations on a qualitative basis.
Coarse-Grained Model for Water Involving a Virtual Site.
Deng, Mingsen; Shen, Hujun
2016-02-01
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. PMID:26747089
Efficient Topology-aware Coarse Graining for Synchronization in Directed Networks
Zeng, An
2010-01-01
Coarse graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve the same statistical properties as well as the dynamic behaviors as the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse graining in directed networks lacks of consideration. In this paper, we proposed a Topology-aware Coarse Graining (TCG) method to coarse grain the directed networks. Performing the linear stability analysis of synchronization and numerical simulation of the Kuramoto model on four kinds of directed networks, including tree-like networks and variants of Barab\\'{a}si-Albert networks, Watts-Strogatz networks and Erd\\"{o}s-R\\'{e}nyi networks, we find our method can effectively preserve the network synchronizability.
Development and application of coarse-grained models for lipids
Cui, Qiang
2013-03-01
I'll discuss a number of topics that represent our efforts in developing reliable molecular models for describing chemical and physical processes involving biomembranes. This is an exciting yet challenging research area because of the multiple length and time scales that are present in the relevant problems. Accordingly, we attempt to (1) understand the value and limitation of popular coarse-grained (CG) models for lipid membranes with either a particle or continuum representation; (2) develop new CG models that are appropriate for the particular problem of interest. As specific examples, I'll discuss (1) a comparison of atomistic, MARTINI (a particle based CG model) and continuum descriptions of a membrane fusion pore; (2) the development of a modified MARTINI model (BMW-MARTINI) that features a reliable description of membrane/water interfacial electrostatics and its application to cell-penetration peptides and membrane-bending proteins. Motivated specifically by the recent studies of Wong and co-workers, we compare the self-assembly behaviors of lipids with cationic peptides that include either Arg residues or a combination of Lys and hydrophobic residues; in particular, we attempt to reveal factors that stabilize the cubic ``double diamond'' Pn3m phase over the inverted hexagonal HII phase. For example, to explicitly test the importance of the bidentate hydrogen-bonding capability of Arg to the stabilization of negative Gaussian curvature, we also compare results using variants of the BMW-MARTINI model that treat the side chain of Arg with different levels of details. Collectively, the results suggest that both the bidentate feature of Arg and the overall electrostatic properties of cationic peptides are important to the self-assembly behavior of these peptides with lipids. The results are expected to have general implications to the mechanism of peptides and proteins that stimulate pore formation in biomembranes. Work in collaboration with Zhe Wu, Leili Zhang
STOCK: Structure mapper and online coarse-graining kit for molecular simulations
International Nuclear Information System (INIS)
We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DLCGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si
Coarse graining the distribution function of cold dark matter - II
Henriksen, R. N.
2004-12-01
We study analytically the coarse- and fine-grained distribution function (DF) established by the self-similar infall of collisionless matter. We find this function explicitly for isotropic and spherically symmetric systems in terms of cosmological initial conditions. The coarse-grained function is structureless and steady but the familiar phase-space sheet substructure is recovered in the fine-grained limit. By breaking the self-similarity of the halo infall we are able to argue for a central density flattening. In addition there will be an edge steepening. The best-fitting analytic density function is likely to be provided by a high-order polytrope fit smoothly to an outer power law of index -3 for isolated systems. There may be a transition to a -4 power law in the outer regions of tidally truncated systems. As we find that the central flattening is progressive in time, dynamically young systems such as galaxy clusters may well possess a Navarro, Frenk and White type density profile, while primordial dwarf galaxies, for example, are expected to have cores. This progressive flattening is expected to end either in the non-singular isothermal sphere, or in the non-singular metastable polytropic cores; as the DFs associated with each of these arise naturally in the bulk halo during the infall. We suggest, based on previous studies of the evolution of de-stabilized polytropes, that a collisionless system may pass through a family of polytropes of increasing order, finally approaching the limit of the non-singular isothermal sphere, if the `violent' collective relaxation is frequently re-excited by `merger' events. Thus central dominant (cD) galaxies, and indeed all bright galaxies that have grown in this fashion, should be in polytropic states. Our results suggest that no physics beyond that of wave-particle scattering is necessary to explain the nature of dark matter density profiles. However, this may be assisted by the scattering of particles from the centre of the
Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion
Moore, Timothy C; McCabe, Clare
2015-01-01
A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use of structure-based coarse-graining methods. The model is derived to match the bulk and interfacial properties of liquid water and improves upon previous work that used single state iterative Boltzmann inversion. The model accurately reproduces the density and structural correlations of water at 305 K and 1.0 atm, stability of a liquid droplet at 305 K, and shows little tendency to crystallize at physiological conditions. This work also illustrates several advantages of using multistate iterative Boltzmann inversion for deriving generally applicable coarse-grained forcefields.
Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution.
McCullagh, Peter; Lake, Peter T; McCullagh, Martin
2016-09-13
An analytic method to assign optimal coarse-grained charges based on electrostatic potential matching is presented. This solution is the infinite size and density limit of grid-integration charge-fitting and is computationally more efficient by several orders of magnitude. The solution is also minimized with respect to coarse-grained positions which proves to be an extremely important step in reproducing the all-atom electrostatic potential. The joint optimal-charge optimal-position coarse-graining procedure is applied to a number of aggregating proteins using single-site per amino acid resolution. These models provide a good estimate of both the vacuum and Debye-Hückel screened all-atom electrostatic potentials in the vicinity and in the far-field of the protein. Additionally, these coarse-grained models are shown to approximate the all-atom dimerization electrostatic potential energy of 10 aggregating proteins with good accuracy.
Atomistic description of binary lanthanoid salt solutions: A coarse-graining approach
International Nuclear Information System (INIS)
The experimental difficulties inherent to the solution chemistry of actinoids and lanthanoids have led to the use of a wide variety of models, from the microscopic to the macroscopic scale, in an attempt to represent their solution properties. Molecular dynamics (MD) simulations, with explicit solvents, have been successfully used to describe the structural characteristics, but the limits on the accessible length and time scales do not allow for an equivalent description of the macroscopic properties. In this study, we propose a multi-scale approach, based on MD simulation results, to study the thermodynamic and structural properties of a series of lanthanoid-chloride aqueous solutions. An inversion procedure, based on the approximate hypernetted chain (HNC) closure and the Stillinger-Lovett sum rules for ionic liquids, is used to obtain the effective ion-ion potentials from MD-generated radial distribution functions (RDF). Implicit solvent Monte Carlo (MC) simulations are then performed to compute the osmotic coefficients of the salt solutions. This coarse-grained strategy provides accurate effective pair potentials for the lanthanoid salts, derived from an atomic model. The method presented here is an attempt to bridge the gap between MD and the thermodynamic properties of solutions that are experimentally measured. (authors)
Adapting phase-switch Monte Carlo method for flexible organic molecules
Bridgwater, Sally; Quigley, David
2014-03-01
The role of cholesterol in lipid bilayers has been widely studied via molecular simulation, however, there has been relatively little work on crystalline cholesterol in biological environments. Recent work has linked the crystallisation of cholesterol in the body with heart attacks and strokes. Any attempt to model this process will require new models and advanced sampling methods to capture and quantify the subtle polymorphism of solid cholesterol, in which two crystalline phases are separated by a phase transition close to body temperature. To this end, we have adapted phase-switch Monte Carlo for use with flexible molecules, to calculate the free energy between crystal polymorphs to a high degree of accuracy. The method samples an order parameter , which divides a displacement space for the N molecules, into regions energetically favourable for each polymorph; which is traversed using biased Monte Carlo. Results for a simple model of butane will be presented, demonstrating that conformational flexibility can be correctly incorporated within a phase-switching scheme. Extension to a coarse grained model of cholesterol and the resulting free energies will be discussed.
Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.
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. PMID:26930392
Coarse-graining using the relative entropy and simplex-based optimization methods in VOTCA
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.
Shi, Ya-Zhou; Wu, Yuan-Yan; Tan, Zhi-Jie
2014-01-01
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (less than or equal to 45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 {\\AA} and an overall minimum RMSD of 1.9 {\\AA} from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ~ 1.0 degrees Celsius of melting temperatures, as compared wi...
A pressure-transferable coarse-grained potential for modeling the shock Hugoniot of polyethylene
Agrawal, Vipin; Peralta, Pedro; Li, Yiyang; Oswald, Jay
2016-09-01
We investigate the thermomechanical response of semi-crystalline polyethylene under shock compression by performing molecular dynamics (MD) simulations using a new coarse-graining scheme inspired by the embedded atom method. The coarse-graining scheme combines the iterative Boltzmann inversion method and least squares optimization to parameterize interactions between coarse-grained sites, including a many-body potential energy designed to improve the representability of the model across a wide range of thermodynamic states. We demonstrate that a coarse-grained model of polyethylene, calibrated to match target structural and thermodynamic data generated from isothermal MD simulations at different pressures, can also accurately predict the shock Hugoniot response. Analysis of the rise in temperature along the shock Hugoniot and comparison with analytical predictions from the Mie-Grüneisen equation of state are performed to thoroughly explore the thermodynamic consistency of the model. As the coarse-graining model affords nearly two orders of magnitude reduction in simulation time compared to all-atom MD simulations, the proposed model can help identify how nanoscale structure in semi-crystalline polymers, such as polyethylene, influences mechanical behavior under extreme loading.
A pressure-transferable coarse-grained potential for modeling the shock Hugoniot of polyethylene.
Agrawal, Vipin; Peralta, Pedro; Li, Yiyang; Oswald, Jay
2016-09-14
We investigate the thermomechanical response of semi-crystalline polyethylene under shock compression by performing molecular dynamics (MD) simulations using a new coarse-graining scheme inspired by the embedded atom method. The coarse-graining scheme combines the iterative Boltzmann inversion method and least squares optimization to parameterize interactions between coarse-grained sites, including a many-body potential energy designed to improve the representability of the model across a wide range of thermodynamic states. We demonstrate that a coarse-grained model of polyethylene, calibrated to match target structural and thermodynamic data generated from isothermal MD simulations at different pressures, can also accurately predict the shock Hugoniot response. Analysis of the rise in temperature along the shock Hugoniot and comparison with analytical predictions from the Mie-Grüneisen equation of state are performed to thoroughly explore the thermodynamic consistency of the model. As the coarse-graining model affords nearly two orders of magnitude reduction in simulation time compared to all-atom MD simulations, the proposed model can help identify how nanoscale structure in semi-crystalline polymers, such as polyethylene, influences mechanical behavior under extreme loading. PMID:27634275
Dynamics in coarse-grained models for oligomer-grafted silica nanoparticles
Hong, Bingbing
2012-01-01
Coarse-grained models of poly(ethylene oxide) oligomer-grafted nanoparticles are established by matching their structural distribution functions to atomistic simulation data. Coarse-grained force fields for bulk oligomer chains show excellent transferability with respect to chain lengths and temperature, but structure and dynamics of grafted nanoparticle systems exhibit a strong dependence on the core-core interactions. This leads to poor transferability of the core potential to conditions different from the state point at which the potential was optimized. Remarkably, coarse graining of grafted nanoparticles can either accelerate or slowdown the core motions, depending on the length of the grafted chains. This stands in sharp contrast to linear polymer systems, for which coarse graining always accelerates the dynamics. Diffusivity data suggest that the grafting topology is one cause of slower motions of the cores for short-chain oligomer-grafted nanoparticles; an estimation based on transition-state theory shows the coarse-grained core-core potential also has a slowing-down effect on the nanoparticle organic hybrid materials motions; both effects diminish as grafted chains become longer. © 2012 American Institute of Physics.
Iig, Patrick
2011-01-01
Complex fluids, such as polymers, colloids, liquid-crystals etc., show intriguing viscoelastic properties, due to the complicated interplay between flow-induced structure formation and dynamical behavior. Starting from microscopic models of complex fluids, a systematic coarse-graining method is presented that allows us to derive closed-form and thermodynamically consistent constitutive equations for such fluids. Essential ingredients of the proposed approach are thermodynamically guided simulations within a consistent coarse-graining scheme. In addition to this new type of multiscale simulations, we reconstruct the building blocks that constitute the thermodynamically consistent coarse-grained model. We illustrate the method for low-molecular polymer melts, which are subject to different imposed flow fields like planar shear and different elongational flows. The constitutive equation for general flow conditions we obtain shows rheological behavior including shear thinning, normal stress differences, and elongational viscosities in good agreement with reference results. PMID:21678766
A unified data representation theory for network visualization, ordering and coarse-graining
Kovács, István A.; Mizsei, Réka; Csermely, Péter
2015-09-01
Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form.
An implicit solvent coarse-grained lipid model with correct stress profile
Sodt, Alex J.; Head-Gordon, Teresa
2010-05-01
We develop a coarse-grained parametrization strategy for lipid membranes that we illustrate for a dipalmitoylphosphatidylcholine bilayer. Our coarse-graining approach eliminates the high cost of explicit solvent but maintains more lipid interaction sites. We use a broad attractive tail-tail potential and extract realistic bonded potentials of mean force from all-atom simulations, resulting in a model with a sharp gel to fluid transition, a correct bending modulus, and overall very reasonable dynamics when compared with experiment. We also determine a quantitative stress profile and correct breakdown of contributions from lipid components when compared with detailed all-atom simulation benchmarks, which has been difficult to achieve for implicit membrane models. Such a coarse-grained lipid model will be necessary for efficiently simulating complex constructs of the membrane, such as protein assembly and lipid raft formation, within these nonaqueous chemical environments.
From time series to complex networks: The phase space coarse graining
Wang, Minggang; Tian, Lixin
2016-11-01
In this paper, we present a simple and fast computational method, the phase space coarse graining algorithm that converts a time series into a directed and weighted complex network. The constructed directed and weighted complex network inherits several properties of the series in its structure. Thereby, periodic series convert into regular networks, and random series do so into random networks. Moreover, chaotic series convert into scale-free networks. It is shown that the phase space coarse graining algorithm allows us to distinguish, identify and describe in detail various time series. Finally, we apply the phase space coarse graining algorithm to the practical observations series, international gasoline regular spot price series and identify its dynamic characteristics.
A unified data representation theory for network visualization, ordering and coarse-graining
Kovács, István A; Csermely, Peter
2014-01-01
Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of huge data sets in science, by reve...
Coarse-graining the dynamics of network evolution: the rise and fall of a networked society
International Nuclear Information System (INIS)
We explore a systematic approach to studying the dynamics of evolving networks at a coarse-grained, system level. We emphasize the importance of finding good observables (network properties) in terms of which coarse-grained models can be developed. We illustrate our approach through a particular social network model: the ‘rise and fall’ of a networked society (Marsili M et al 2004 Proc. Natl Acad. Sci. USA 101 1439). We implement our low-dimensional description computationally using the equation-free approach and show how it can be used to (i) accelerate simulations and (ii) extract system-level stability/bifurcation information from the detailed dynamic model. We discuss other system-level tasks that can be enabled through such a computer-assisted coarse-graining approach. (paper)
Effect of coarse-grain contents on strength and fracture toughness of fine-grained graphite
Energy Technology Data Exchange (ETDEWEB)
Takahashi, Tsuneo; Ishihara, Masahiro; Baba, Shinichi; Hayashi, Kimio [Japan Atomic Energy Research Inst., Oarai, Ibaraki (Japan). Oarai Research Establishment; Arai, Taketoshi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Konishi, Takashi [Toyo Tanso Co. Ltd., Osaka (Japan)
2001-03-01
To investigate the effect of the coarse-grain content on strength and fracture toughness of fine-grained graphite, bending and fracture toughness tests were conducted for specimens with different contents of coarse-grains. In the study the standard specimen was made of fine-grained isotropic graphite (IG-11) with a mean grain size of 20 {mu}m, and two kinds of different grain size specimens were prepared by 20 and 40% mixing of coarse-grains with a mean grain size of 125 {mu}m. The bending test revealed a strength increase for the 40% specimen with a small deviation compared with that for the standard specimen. As for the fracture toughness, two kinds of fracture toughnesses were investigated on the basis of the crack initiation load and the maximum applied load. The initiation load based fracture toughness for the 20% and 40% specimens was higher than that for the standard one; however, the difference for the 20% and 40% specimens was not observed clearly. These results suggest that the fracture toughness tends to saturate at a relatively low coarse-grain content, which is below 20% in the present study. On the other hand, the maximum load based fracture toughness increased with increasing coarse-grain content; thus the difference with different coarse-grain contents was observed. Moreover, the present authors applied a probabilistic strength model to the bending test results, using the pore size distributions obtained by image analysis of microstructures observed by optical microscopy. The model had been proposed by Burchell under uniaxial stress conditions, in consideration of pore size distributions. The prediction by the present model indicated a good correlation with the experimental results. (author)
Effect of coarse-grain contents on strength and fracture toughness of fine-grained graphite
International Nuclear Information System (INIS)
To investigate the effect of the coarse-grain content on strength and fracture toughness of fine-grained graphite, bending and fracture toughness tests were conducted for specimens with different contents of coarse-grains. In the study the standard specimen was made of fine-grained isotropic graphite (IG-11) with a mean grain size of 20 μm, and two kinds of different grain size specimens were prepared by 20 and 40% mixing of coarse-grains with a mean grain size of 125 μm. The bending test revealed a strength increase for the 40% specimen with a small deviation compared with that for the standard specimen. As for the fracture toughness, two kinds of fracture toughnesses were investigated on the basis of the crack initiation load and the maximum applied load. The initiation load based fracture toughness for the 20% and 40% specimens was higher than that for the standard one; however, the difference for the 20% and 40% specimens was not observed clearly. These results suggest that the fracture toughness tends to saturate at a relatively low coarse-grain content, which is below 20% in the present study. On the other hand, the maximum load based fracture toughness increased with increasing coarse-grain content; thus the difference with different coarse-grain contents was observed. Moreover, the present authors applied a probabilistic strength model to the bending test results, using the pore size distributions obtained by image analysis of microstructures observed by optical microscopy. The model had been proposed by Burchell under uniaxial stress conditions, in consideration of pore size distributions. The prediction by the present model indicated a good correlation with the experimental results. (author)
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models
Jonikas, Magdalena A; RADMER, RANDALL J.; Altman, Russ B
2009-01-01
Motivation: The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications. Results: We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA ...
Competition of Two Types of Correlations in Coarse-Grained Natural Written Texts
Melnyk, S S; Yampolskii, V A; Golick, V A
2004-01-01
A theory of additive Markov chains with long-range memory is used for a description of correlation properties of literary texts. The coarse-grained naturally written texts are shown to be strongly correlated sequences that possess antipersistent properties at small distances (in the region of grammatical rules action, $L 300$). For some concrete examples of literary texts, a memory function is constructed and its power-law behavior is revealed at long distances. This behavior is shown to be a cause for self-similarity of coarse-grained texts with respect to the decimation procedure.
Lee, Hwankyu; de Vries, Alex H.; Marrink, Siewert-Jan; Pastor, Richard W.
2009-01-01
A coarse-grained (CG) model for polyethylene oxide (PEO) and polyethylene glycol (PEG) developed within the framework of the MARTINI CG force field (FF) using the distributions of bonds, angles, and dihedrals from the CHARMM all-atom FF is presented. Densities of neat low molecular weight PEO agree
Polarizable Water Model for the Coarse-Grained MARTINI Force Field
Yesylevskyy, Semen O.; Schafer, Lars V.; Sengupta, Durba; Marrink, Siewert J.
2010-01-01
Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, whic
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
in the parameterization. We refine the MARTINI procedure by including one additional target property related to the structure of the polymer, namely the radius of gyration. The force-field optimization is mainly based on experimental data. We test our procedure on polystyrene, a standard benchmark for coarse-grained (CG...
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...
Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes
Energy Technology Data Exchange (ETDEWEB)
Holm, Christian [Institut für Computerphysik, Universität Stuttgart, Allmandring 3, 70569 Stuttgart (Germany); Gompper, Gerhard [Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich (Germany); Dill, Ken A. [Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 (United States)
2015-12-28
This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.
Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes.
Holm, Christian; Gompper, Gerhard; Dill, Ken A
2015-12-28
This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.
Path-space variational inference for non-equilibrium coarse-grained systems
Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plecháč, Petr
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.
Free-energy coarse-grained potential for C{sub 60}
Energy Technology Data Exchange (ETDEWEB)
Edmunds, D. M., E-mail: david.edmunds09@imperial.ac.uk; Tangney, P.; Vvedensky, D. D.; Foulkes, W. M. C. [Department of Physics, Imperial College London, London SW7 2AZ (United Kingdom)
2015-10-28
We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C{sub 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.
Diffusion-Based Coarse Graining in Hybrid Continuum--Discrete Solvers: Applications in CFD--DEM
Sun, Rui
2014-01-01
In this work, a coarse graining method previously proposed by the authors based on solving diffusion equations is applied to CFD--DEM simulations, where coarse graining is used to obtain solid volume fraction, particle phase velocity, and fluid--particle interaction forces. By examining the conservation requirements, the variables to solve diffusion equations for in CFD--DEM simulations are identified. The algorithm is then implemented to a CFD--DEM solver based on OpenFOAM and LAMMPS, the former being a general-purpose, three-dimensional CFD solver based on unstructured meshes. Numerical simulations are performed for a fluidized bed by using the CFD--DEM solver with the diffusion-based coarse graining algorithm. Converged results are obtained on successively refined meshes, even for meshes with cell sizes comparable to or smaller than the particle diameter. This is a critical advantage of the proposed method over many existing coarse graining methods, and would be particularly valuable when small cells are r...
Coarse-grained simulations of charge, current and flow in heterogeneous media
B. Rotenberg; I. Pagonabarraga; D. Frenkel
2010-01-01
We present a coarse-grained simulation method for complex charged systems. This mesoscopic model couples a hydrodynamic description to a free energy functional accounting for the interactions between solvent(s) and charged solutes. It is implemented in a hybrid lattice-based algorithm, whereby the e
Coarse-grained molecular dynamics simulations of polymer melts in transient and steady shear flow
Padding, J.T.; Briels, W.J.
2003-01-01
By use of nonequilibrium simulations a coarse-grained model of polyethylene, developed in our previous work [J. Chem. Phys. 115, 2846 (2001); 117, 925 (2002)], is subjected to a planar Couette flow. Both transient and steady-state nonlinear flow properties are investigated for shear rates varying fr
Molecular Dynamics Simulation of Coarse-Grain Model of Silicon Functionalized Graphene
Directory of Open Access Journals (Sweden)
Hui Zhixin
2015-01-01
Full Text Available The electronic transport, the storage capacity and the service life of the anode material for lithium ion batteries will be reduced seriously in the event of the material layering or cracking, so the anode material must have strong mechanical reliability. Firstly, in view of the traditional molecular dynamics (MD limited by the geometric scales of the model of Silicon functionalized graphenen (SFG as lithium ion batteries anode material, some full atomic models of SFG were established using Tersoff potential and Lennard-Jones potential, and used to calculate the modulus and the adhesion properties. What’s more, the assertion of mechanical equilibrium condition and energy conservation between full atomic and coarse-grain models through elastic strain energy were enforced to arrive at model parameters. The model of SFG coarse-grain bead-spring elements and its system energy function were obtained via full atomic simulations. Finally, the validity of the SFG coarse-grain model was verified by comparing the tensile property of coarse-grain model with full atoms model.
Coarse-grained molecular dynamics: Nonlinear finite elements and finite temperature
Energy Technology Data Exchange (ETDEWEB)
Rudd, R E; Broughton, J Q
2005-05-30
Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are modeled on a mesh in a formulation that generalizes conventional finite element modeling (FEM) of continuum elasticity. CGMD is derived solely from the MD model, however, and has no continuum parameters. As a result, it provides a coupling that is smooth and provides control of errors that arise at the coupling between the atomistic and coarse-grained regions. In this article, we elaborate on the formulation of CGMD, describing in detail how CGMD is applied to anharmonic solids and finite temperature simulations. As tests of CGMD, we present in detail the calculation of the phonon spectra for solid argon and tantalum in 3D, demonstrating how CGMD provides a better description of the elastic waves than that provided by FEM. We also present elastic wave scattering calculations that show the elastic wave scattering is more benign in CGMD than FEM. We also discuss the dependence of scattering on the properties of the mesh. We introduce a rigid approximation to CGMD that eliminates internal relaxation, similar to the Quasicontinuum technique, and compare it to the full CGMD.
Consistent and transferable coarse-grained model for semidilute polymer solutions in good solvent.
D'Adamo, Giuseppe; Pelissetto, Andrea; Pierleoni, Carlo
2012-07-14
We present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and intermolecular potentials obtained at zero density. We show how this model is able to accurately reproduce the universal properties of the underlying solution of athermal linear chains at various levels of coarse-graining and in a range of chain densities which can be widened by increasing the spatial resolution of the multiblob representation, i.e., the number of blobs per chain. The present model is unique in its ability to quantitatively predict thermodynamic and large scale structural properties of polymer solutions deep in the semidilute regime with a very limited computational effort, overcoming most of the problems related to the simulations of semidilute polymer solutions in good solvent conditions.
Haxton, Thomas K; Zuckermann, Ronald N; Whitelam, Stephen
2014-01-01
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale dynamic processes in biology and materials science, understanding the details of this supramolecular assembly process requires a modeling approach that captures behavior on a wide range of length and time scales, from those on which individual sidechains fluctuate to those on which assemblies of polymers evolve. Here we demonstrate that a new coarse-grained modeling approach is accurate and computationally efficient enough to do so. Our approach uses only a minimal number of coarse-grained sites, but retains independently fluctuating orientational degrees of freedom for each site. These orientational degrees of freedom allow us to accurately parameterize both bonded and nonbonded interactions, and to generate all-atom configurations with sufficient accuracy to perform atomic sca...
Coarse-Grained Molecular Dynamics Simulation of a Red Blood Cell
Jiang, Li-Guo; Wu, Heng-An; Zhou, Xiao-Zhou; Wang, Xiu-Xi
2010-02-01
A worm-like chain model based on a spectrin network is employed to study the biomechanics of red blood cells. Coarse-grained molecular dynamics simulations are performed to obtain a stable configuration free of external loadings. We also discuss the influence of two parameters: the average bending modulus and the persistence length. The change in shape of a malaria-infected red blood cell can contribute to the change in its molecular-based structure. As the persistence length of the membrane network in the infected red blood cell decreases, the deformability decreases and the biconcave shape is destroyed. The numerical results are comparable with previously reported experimental results. The coarse-grained model can be used to study the relationship between macro-mechanical properties and molecular-scale structures of cells.
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. PMID:24718295
Ito, Hiroaki; Shimokawa, Naofumi
2016-01-01
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and morphological dynamics in charged lipid bilayer vesicles. The screened long-range electrostatic repulsion among charged head groups delays or inhibits the lateral phase separation in charged vesicles compared with neutral vesicles, suggesting the transition of the phase-separation mechanism from spinodal decomposition to nucleation or homogeneous dispersion. Moreover, the electrostatic repulsion causes morphological changes, such as pore formation, and further transformations into disk, string, and bicelle structures, which are spatiotemporally coupled to the lateral segregation of charged lipids. Based on our coarse-grained MD simulation, we propose a plausible mechanism of pore formation at the molecular level. The pore formation in a charged-lipid-rich domain is initiated by the p...
Moving beyond Watson-Crick models of coarse grained DNA dynamics
Linak, Margaret C.; Tourdot, Richard; Dorfman, Kevin D.
2011-11-01
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.
Microstructure and Property of Coarse Grain HAZ X80 Pipeline Steel
Institute of Scientific and Technical Information of China (English)
ZHOU Yun; XUE Xiao-huai; QIAN Bai-nian; LI Jing-li; SHAN Yi-Yin; LOU Song-nian
2005-01-01
The coarse grain HAZ microstructure and property of X80 pipeline steel with different carbon content was investigated. The weld thermal simulation test was carried out on Gleeble 1500 thermal mechanical test machine. The Charpy tests were completed at -20 ℃ for evaluating the toughness of coarse grain heat affected zone (CGHAZ). The microstructure was examined by optical microscope (OM) and transmission electron microscopy (TEM), and the austenite constituent was quantified by X-ray diffraction. The results showed that the ultra-low carbon can improve the toughness of CGHAZ by suppressing the formation of carbide, decreasing the martensite austenite (M-A) constituent and increasing the residual austenite in the M-A.
Turbulent channel flow simulations using a coarse-grained extension of the Lattice Boltzmann method
Amati, G; Benzi, R; Amati, Giorgio; Succi, Sauro; Benzi, Roberto
1996-01-01
A coarse-grained version of the Lattice Boltzmann (LB) method is developed with the intent of enhancing its geometrical flexibility so as to be able to tackle a wider class of flows of engineering interest. To this purpose, the original uniform LB technique is combined with standard finite-volume techniques based upon a blend of piecewise constant and piecewise linear interpolation schemes. A series of validation tests for the three dimensional channel flow with one-dimensional (cross-channel) statistical behaviour are presented. The main conclusion is that, although the method does indeed mark a significant stride forward with respect to the original uniform LB scheme, better interpolation schemes should be developed before the coarse-grain LB can become fully competitive with modern CFD schemes.
Folding of small knotted proteins: Insights from a mean field coarse-grained model
Energy Technology Data Exchange (ETDEWEB)
Najafi, Saeed; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)
2015-12-28
A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
Energy Technology Data Exchange (ETDEWEB)
Wei, Zonghui [Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois 60208 (United States); Luijten, Erik, E-mail: luijten@northwestern.edu [Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois 60208 (United States); Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208 (United States); Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208 (United States)
2015-12-28
All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.
Folding of small knotted proteins: Insights from a mean field coarse-grained model
International Nuclear Information System (INIS)
A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations
Tensor network algorithm by coarse-graining tensor renormalization on finite periodic lattices
Zhao, Hui-Hai; Xie, Zhi-Yuan; Xiang, Tao; Imada, Masatoshi
2016-03-01
We develop coarse-graining tensor renormalization group algorithms to compute physical properties of two-dimensional lattice models on finite periodic lattices. Two different coarse-graining strategies, one based on the tensor renormalization group and the other based on the higher-order tensor renormalization group, are introduced. In order to optimize the tensor network model globally, a sweeping scheme is proposed to account for the renormalization effect from the environment tensors under the framework of second renormalization group. We demonstrate the algorithms by the classical Ising model on the square lattice and the Kitaev model on the honeycomb lattice, and show that the finite-size algorithms achieve substantially more accurate results than the corresponding infinite-size ones.
Dalgıçdir, Cahit; Şensoy, Özge; Sayar, Mehmet; Peter, Christine
2013-01-01
A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition Cahit Dalgicdir, Ozge Sensoy, Christine Peter, and Mehmet Sayar Citation: The Journal of Chemical Physics 139, 234115 (2013); doi: 10.1063/1.4848675 View online: http://dx.doi.org/10.1063/1.4848675 View Table of Contents: http://scitation.aip.org/content/aip/journal/jcp/139/23?ver=pdfcov Published by the AIP Publishing Articles you may be interested in...
Schnabel, Stefan; Bachmann, Michael; Janke, Wolfhard
2007-01-01
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a heteropolymer sequence lead to completely different folding behaviors. Studying three exemplified sequences with the same content of hydrophobic and polar residues, we can reproduce within this simple model two-state folding, folding through intermediates, as well ...
Procedures for Residual Stress Analysis in Textured and in Coarse Grained Materials
Reimers, W.; Dupke, R.
1995-01-01
For the investigation of residual stresses by means of X-ray diffraction, special procedures for the registration and evaluation of the experimental strain data are necessary for textured and coarse grained materials. In both cases inhomogeneous diffraction intensity patterns are present which lead to the formation of intensity poles or even to Bragg reflections. Such experimental findings indicate also that the material properties within the investigated gauge volume are anisotropic so that ...
Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers
2015-01-01
Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond time scales, it is essential to develop accurate coarse-grained simulation models that can reach these time scales. Cholesterol has been shown experimentally to thicken the membrane and increase phospholipid tail order between 0 and 40% cholesterol, above which these effects plateau or slightly decrease. Here, we showed that the published MARTINI coarse-grained force-field for phospholipid (POPC) and cholesterol fails to capture these effects. Using reference atomistic simulations, we systematically modified POPC and cholesterol bonded parameters in MARTINI to improve its performance. We showed that the corrections to pseudobond angles between glycerol and the lipid tails and around the oleoyl double bond particle (the “angle-corrected model”) slightly improves the agreement of MARTINI with experimentally measured thermal, elastic, and dynamic properties of POPC membranes. The angle-corrected model improves prediction of the thickening and ordering effects up to 40% cholesterol but overestimates these effects at higher cholesterol concentration. In accordance with prior work that showed the cholesterol rough face methyl groups are important for limiting cholesterol self-association, we revised the coarse-grained representation of these methyl groups to better match cholesterol-cholesterol radial distribution functions from atomistic simulations. In addition, by using a finer-grained representation of the branched cholesterol tail than MARTINI, we improved predictions of lipid tail order and bilayer thickness across a wide range of concentrations. Finally, transferability testing shows that a model incorporating our revised parameters into DOPC outperforms other
Sandim, H.; Raabe, D.
2004-01-01
Orientation effects concerning grain subdivision and further annealing behavior of three neighboring grains were observed in 80% cold-rolled coarse-grained niobium. The present study which was conducted as a cooperation on the basis of DAAD and CAPES funding attempts to clarify the microstructural evolution of deformed niobium and the differences in terms of stored energy (boundary distribution) using high-resolution electron backscattering diffraction (FE-EBSD).
Nguyen, O. T.; Ortiz, M.
2001-01-01
We present two approaches for coarse-graining interplanar potentials and determining the corresponding macroscopic cohesive laws based on energy relaxation and the renormalization group. We analyze the cohesive behavior of a large---but finite---number of interatomic planes and find that the macroscopic cohesive law adopts a universal asymptotic form. The universal form of the macroscopic cohesive law is an attractive fixed point of a suitably-defined renormalization-group transformation.
Coarse-Grained Model for Colloidal Protein Interactions, B22, and Protein Cluster Formation
Blanco, Marco A.; Sahin, Eric; Robinson, Anne S.; Roberts, Christopher J.
2013-01-01
Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semi-quantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as t...
Anomalous g-Factors for Charged Leptons in a Fractional Coarse-Grained Approach
2014-01-01
In this work, we investigate aspects of the electron, muon and tau gyromagnetic ratios (g-factor) in a fractional coarse-grained scenario, by adopting a Modified Riemann-Liouville (MRL) fractional calculus. We point out the possibility of mapping the experimental values of the specie's g-factors into a theoretical parameter which accounts for fractionality, without computing higher-order QED calculations. We wish to understand whether the value of (g-2) may be traced back to a fractionality o...
Coarse-grained simulation of a real-time process control network under peak load
International Nuclear Information System (INIS)
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
Trément, Sébastien; Schnell, Benoît; Petitjean, Laurent; Couty, Marc; Rousseau, Bernard
2014-04-01
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. PMID:24712786
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.
Pairwise energies for polypeptide coarse-grained models derived from atomic force fields
Betancourt, Marcos R.; Omovie, Sheyore J.
2009-05-01
The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.
Model reduction for agent-based social simulation: Coarse-graining a civil violence model
Zou, Yu; Fonoberov, Vladimir A.; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G.
2012-06-01
Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).
Coarse grain deposit feature of Guantao formation in western depression Shuyi area of Liaohe basin
Institute of Scientific and Technical Information of China (English)
GUO Jian-hua; LIU Chen-sheng; ZHU Mei-heng
2005-01-01
The extensive distribution of coarse-grained clastic rock of Guantao formation in Shuyi area of Liaohe basin was considered as a result of fluvial deposit. According to the comprehensive analysis of seism data, well log, core observation and experimental data, this kind of clastic rock is composed of pebblestone-cobblestone, microconglomerate, sand conglomerate, medium-coarse grained sandstone and fine-sandstone. According to the clast composition, sedimentary texture, structure and rock type, 3 kinds of sediment facies can be recognized ie the mixed accumulation-conglomerate dominated debris flow, pebblestone-cobblestone dominated gradient flow and sandstone dominated braided stream. Vertically, the bottom gradient current deposit and top braided stream deposit form fining-upward sediment sequence, and the debris flow deposit distributes in them at random. The sedimentary feature of coarse grain clastic of Guantao formation in Shuyi area is accordant with proximal wet alluvial fan deposited in wet climate at foreland and this kind of alluvial fan is different from the traditional one.
Model reduction for agent-based social simulation: coarse-graining a civil violence model.
Zou, Yu; Fonoberov, Vladimir A; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G
2012-06-01
Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).
Directory of Open Access Journals (Sweden)
Kristian Lindgren
2015-05-01
Full Text Available An information-theoretic perspective on coarse-graining is presented. It starts with an information characterization of configurations at the micro-level using a local information quantity that has a spatial average equal to a microscopic entropy. With a reversible micro dynamics, this entropy is conserved. In the micro-macro transition, it is shown how this local information quantity is transformed into a macroscopic entropy, as the local states are aggregated into macroscopic concentration variables. The information loss in this transition is identified, and the connection to the irreversibility of the macro dynamics and the second law of thermodynamics is discussed. This is then connected to a process of further coarse-graining towards higher characteristic length scales in the context of chemical reaction-diffusion dynamics capable of pattern formation. On these higher levels of coarse-graining, information flows across length scales and across space are defined. These flows obey a continuity equation for information, and they are connected to the thermodynamic constraints of the system, via an outflow of information from macroscopic to microscopic levels in the form of entropy production, as well as an inflow of information, from an external free energy source, if a spatial chemical pattern is to be maintained.
Lyubimov, I. Y.; Guenza, M. G.
2013-03-01
The theory to reconstruct the atomistic-level chain diffusion from the accelerated dynamics that is measured in mesoscale simulations of the coarse-grained system, is applied here to the dynamics of cis-1,4-polybutadiene melts where each chain is described as a soft interacting colloidal particle. The rescaling formalism accounts for the corrections in the dynamics due to the change in entropy and the change in friction that are a consequence of the coarse-graining procedure. By including these two corrections the dynamics is rescaled to reproduce the realistic dynamics of the system described at the atomistic level. The rescaled diffusion coefficient obtained from mesoscale simulations of coarse-grained cis-1,4-polybutadiene melts shows good agreement with data from united atom simulations performed by Tsolou et al. [Macromolecules 38, 1478 (2005)], 10.1021/ma0491210. The derived monomer friction coefficient is used as an input to the theory for cooperative dynamics that describes the internal dynamics of a polymer moving in a transient regions of slow cooperative motion in a liquid of macromolecules. Theoretically predicted time correlation functions show good agreement with simulations in the whole range of length and time scales in which data are available.
Multiscale simulation of thin-film lubrication: Free-energy-corrected coarse graining
Wu, Z.-B.; Zeng, X. C.
2014-09-01
The quasicontinuum method was previously extended to the nonzero temperature conditions by implementing a free-energy correction on non-nodal atoms in coarse-grained solid systems to avoid the dynamical constraint, [Diestler, Wu, and Zeng, J. Chem. Phys. 121, 9279 (2004), 10.1063/1.1806811]. In this paper, we combine the extended quasicontinuum method and an atomistic simulation to treat the monolayer film lubrication with elastic (nonrigid) substrates. It is shown that the multiscale method with the coarse-graining local elements in the merging regions between the atomistic and continuous descriptions of the substrates can reasonably predict the shear stress profile, the mean separation curve, and the transverse stress profile in the fully atomistic simulation for the tribological system. Moreover, when the nonlocal elements are placed in the merging regions, the inhomogeneous solid atoms in the near regions covered by the cut-off circles of the nonlocal elements replace the homogeneous ones at the equilibrium configuration for the free-energy correction on the non-nodal atoms. The treatment can cause an unphysical sliding between the near and far regions of the upper substrate. It is shown that if the free-energy correction on the non-nodal atoms in the coarse-grained merging regions is removed, the multiscale method can still well reproduce the shear stress profile, the mean separation curve, and the transverse stress profile obtained from the fully atomistic simulation for the system.
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.
Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design.
Energy Technology Data Exchange (ETDEWEB)
Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.
2010-09-01
This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and
Vögele, Martin; Holm, Christian; Smiatek, Jens
2015-12-01
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.
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.
Moritsugu, Kei; Smith, Jeremy C
2008-08-01
Coarse graining of protein interactions provides a means of simulating large biological systems. The REACH (Realistic Extension Algorithm via Covariance Hessian) coarse-graining method, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation, involves direct mapping between scales without the need for iterative optimization. Here, the transferability of the REACH force field is examined between protein molecules of different structural classes. As test cases, myoglobin (all alpha), plastocyanin (all beta), and dihydrofolate reductase (alpha/beta) are taken. The force constants derived are found to be closely similar in all three proteins. An MD version of REACH is presented, and low-temperature coarse-grained (CG) REACH MD simulations of the three proteins are compared with atomistic MD results. The mean-square fluctuations of the atomistic MD are well reproduced by the CGMD. Model functions for the CG interactions, derived by averaging over the three proteins, are also shown to produce fluctuations in good agreement with the atomistic MD. The results indicate that, similarly to the use of atomistic force fields, it is now possible to use a single, generic REACH force field for all protein studies, without having first to derive parameters from atomistic MD simulation for each individual system studied. The REACH method is thus likely to be a reliable way of determining spatiotemporal motion of a variety of proteins without the need for expensive computation of long atomistic MD simulations. PMID:18469078
Directory of Open Access Journals (Sweden)
A. V. Milovanov
2000-01-01
Full Text Available The concept of the generalized entropy is analyzed, with the particular attention to the definition postulated by Tsallis [J. Stat. Phys. 52, 479 (1988]. We show that the Tsallis entropy can be rigorously obtained as the solution of a nonlinear functional equation; this equation represents the entropy of a complex system via the partial entropies of the subsystems involved, and includes two principal parts. The first part is linear (additive and leads to the conventional, Boltzmann, definition of entropy as the logarithm of the statistical weight of the system. The second part is multiplicative and contains all sorts of multilinear products of the partial entropies; inclusion of the multiplicative terms is shown to reproduce the generalized entropy exactly in the Tsallis sense. We speculate that the physical background for considering the multiplicative terms is the role of the long-range correlations supporting the "macroscopic" ordering phenomena (e.g., formation of the "coarse-grained" correlated patterns. We prove that the canonical distribution corresponding to the Tsallis definition of entropy, coincides with the so-called "kappa" redistribution which appears in many physical realizations. This has led us to associate the origin of the "kappa" distributions with the "macroscopic" ordering ("coarse-graining" of the system. Our results indicate that an application of the formalism based on the Tsallis notion of entropy might actually have sense only for the systems whose statistical weights, Ω, are relatively small. (For the "coarse-grained" systems, the weight omega could be interpreted as the number of the "grains". For large Ω (i.e., Ω -> ∞, the standard statistical mechanical formalism is advocated, which implies the conventional, Boltzmann definition of entropy as ln Ω.
Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.
Fossépré, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P
2016-09-01
Despite progress in computer modeling, most biological processes are still out of reach when using all-atom (AA) models. Coarse-grained (CG) models allow classical molecular dynamics (MD) simulations to be accelerated. Although simplification of spatial resolution at different levels is often investigated, simplification of the CG potential in itself has been less common. CG potentials are often similar to AA potentials. In this work, we consider the design and reliability of purely mechanical CG models of the μ opioid receptor (μOR), a G protein-coupled receptor (GPCR). In this sense, CG force fields (FF) consist of a set of holonomic constraints guided by an elastic network model (ENM). Even though ENMs are used widely to perform normal mode analysis (NMA), they are not often implemented as a single FF in the context of MD simulations. In this work, various ENM-like potentials were investigated by varying their force constant schemes and connectivity patterns. A method was established to systematically parameterize ENM-like potentials at different spatial resolutions by using AA data. To do so, new descriptors were introduced. The choice of conformation descriptors that also include flexibility information is important for a reliable parameterization of ENMs with different degrees of sensitivity. Hence, ENM-like potentials, with specific parameters, can be sufficient to accurately reproduce AA MD simulations of μOR at highly coarse-grained resolutions. Therefore, the essence of the flexibility properties of μOR can be captured with simple models at different CG spatial resolutions, opening the way to mechanical approaches to understanding GPCR functions. Graphical Abstract All atom structure, residue interaction network and coarse-grained elastic network models of the μ opioid receptor (μOR). PMID:27566318
CG-OoO: Energy-Efficient Coarse-Grain Out-of-Order Execution
Mohammadi, Milad; Aamodt, Tor M.; Dally, William J.
2016-01-01
We introduce the Coarse-Grain Out-of-Order (CG- OoO) general purpose processor designed to achieve close to In-Order processor energy while maintaining Out-of-Order (OoO) performance. CG-OoO is an energy-performance proportional general purpose architecture that scales according to the program load. Block-level code processing is at the heart of the this architecture; CG-OoO speculates, fetches, schedules, and commits code at block-level granularity. It eliminates unnecessary accesses to ener...
Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.
Rzepiela, Andrzej J; Louhivuori, Martti; Peter, Christine; Marrink, Siewert J
2011-06-14
Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1:1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein
Functional RG flow equation: regularization and coarse-graining in phase space
Vacca, G P
2011-01-01
Starting from the basic path integral in phase space we reconsider the functional approach to the RG flow of the one particle irreducible effective average action. On employing a balanced coarse-graining procedure for the canonical variables we obtain a functional integral with a non trivial measure which leads to a modified flow equation. We first address quantum mechanics for boson and fermion degrees of freedom and we then extend the construction to quantum field theories. For this modified flow equation we discuss the reconstruction of the bare action and the implications on the computation of the vacuum energy density.
Directory of Open Access Journals (Sweden)
V.PURUSHOTHAM REDDY
2011-02-01
Full Text Available In computer networks the routing is based on shortest path routing algorithms. Based on its advantages, an alternative method is used known as Genetic Algorithm based routing algorithm, which is highly scalable and insensitive to variations in network topology. Here we propose a coarse-grained parallel genetic algorithm to solve the shortest path routing problem with the primary goal of computation time reduction along with the use of migration scheme. This algorithm is developed and implemented on an MPI cluster. The effects of migration and its performance is studied in this paper.
Towards a unified framework for coarse-graining particle-based simulations.
Energy Technology Data Exchange (ETDEWEB)
Junghans, Christoph [Los Alamos National Laboratory
2012-06-28
Different coarse-graining techniques for soft matter systems have been developed in recent years, however it is often very demanding to find the method most suitable for the problem studied. For this reason we began to develop the VOTCA toolkit to allow for easy comparison of different methods. We have incorporated 6 different techniques into the package and implemented a powerful and parallel analysis framework plus multiple simulation back-ends. We will discuss the specifics of the package by means of various studies, which have been performed with the toolkit and highlight problems we encountered along the way.
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 to...... [001], the boundaries between the bands were parallel to [010] and the neighbouring bands were rotated around [100] with respect to one another. Two slip systems in a critical relationship are equally stressed with a Schmid factor of 0.49 in grains with a [120] orientation, namely (a/2)[011](111) and...
Water hammer in coarse-grained solid-liquid flows in hydraulic hoisting for ocean mining
Institute of Scientific and Technical Information of China (English)
韩文亮; 王光谦; 吴保生; 刘少军; 邹伟生
2002-01-01
The particles of polymetallic nodules in hydraulic hoisting flows that are used for mining in deep sea are rather coarse, therefore their flow velocity is smaller than that of the surrounding water. The characteristics of solid-liquid flows such as their density, concentration, elastic modulus and resistance were discussed. The wave propagation speed and the continuity and momentum equations of water hammer in coarse-grained solid-liquid flows were theoretically derived, and a water hammer model for such flows was developed.
Directory of Open Access Journals (Sweden)
Lee-Wei Yang
2008-01-01
Full Text Available Molecular dynamics (MD simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the a bsence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed.
International Nuclear Information System (INIS)
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
Español, Pep; Donev, Aleksandar
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 simulations as input
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
Coarse-Grained Modeling of Genetic Circuits as a Function of the Inherent Time Scales
Labavic, Darka; Hildegard, Wolfhard Janke; Meyer-Ortmanns,
2012-01-01
From a coarse-grained perspective the motif of a self-activating species, activating a second species which acts as its own repressor, is widely found in biological systems, in particular in genetic systems with inherent oscillatory behavior. Here we consider a specific realization of this motif as a genetic circuit, in which genes are described as directly producing proteins, leaving out the intermediate step of mRNA production. We focus on the effect that inherent time scales on the underlying fine-grained scale can have on the bifurcation patterns on a coarser scale in time. Time scales are set by the binding and unbinding rates of the transcription factors to the promoter regions of the genes. Depending on the ratio of these rates to the decay times of the proteins, the appropriate averaging procedure for obtaining a coarse-grained description changes and leads to sets of deterministic equations, which differ in their bifurcation structure. In particular the desired intermediate range of regular limit cyc...
Thermal and mechanical properties of thermosetting polymers using coarse-grained simulation
Jang, C.; Abrams, C. F.
2016-07-01
We developed coarse-grained (CG) molecular representations of mixtures of diglycidyl ether of bisphenol-A (DGEBA) and poly(oxypropylene) diamine (POP-DA) for use in CG molecular dynamics (MD) simulations. In the CG representation, DGEBA is comprised of three beads of two types and POP-DA also by three beads of two types. Atomistic MD of liquid systems was performed to derive intra- and inter-bead potentials via Boltzmann inversion. While the bonded potentials, composed of bond stretching and angle bending, were parameterized directly from the distribution functions of all atomistic molecular dynamics trajectories, the non-bonded potentials were derived from the iterative Boltzmann Inversion with a given set of coarse-grained interactions. CG systems correctly reproduced liquid and crosslinked densities. Under uniaxial tension, the Young's modulus of the CG systems was much lower than the experimental value, and we show this arises from the assumed form of the extrapolated regions of the CG potentials. By stiffening these regions, we increased the CG Young's modulus of the crosslinked systems without sacrificing the correct prediction of density. This suggests that transferrable CG potentials can be optimized for use in non-equilibrium MD for property estimation.
Deviation of permeable coarse-grained boundary resistance from Nikuradse's observations
Cheng, Nian-Sheng; Liu, Xingnian; Chen, Xingwei; Qiao, Changkai
2016-02-01
Nikuradse's (1933) rough pipe study is enormously influential in the understanding of flow resistance over a sediment bed. However, the rough boundary employed in Nikuradse's study differs from permeable sediment beds in rivers. This implies that the results derived from the rough pipe experiments may not be applicable for flows over a permeable coarse-grained bed. The present study aimed to explore to what extent the flow resistance of a permeable coarse-grained boundary deviates from the Nikuradse's observations. Experiments were conducted with rough pipes, which were prepared by overlaying the inner wall with one to four layers of spherical beads. The single layer roughness resembles the experimental setup reported in Nikuradse's study, while the multilayer of grains allows significant flow to pass through the porous roughness layer. In addition, the ratio of grain diameter, k, to pipe diameter, d, was chosen to be one to two orders greater than the range (0.001 measurements also suggest the existence of a laminar flow regime, in which the friction factor is inversely proportional to the Reynolds number. The observed variations in the flow resistance are attributed to both wall permeability and large-scale roughness.
Macro-micromechanical approaches for non-coaxiality of coarse grained soils
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
For coarse grained soils,their principal stress directions may change when the water level of embankment dam varies instantaneously.In this loading case,the principal directions of stress and strain rate will become non-coaxial.In an effort to model non-coaxial behavior,a modified three-dimensional non-coaxial model is developed in the context of vertex yield(tangent plasticity) theory.Discrete Element Method(PFC) incorporating user-defined interparticle contact models is also employed to gain an insight into microscopic mechanism of non-coaxiality.The analysis focuses on non-coaxial behaviors under simple shear condition.It has been shown that the proposed non-coaxial model gives good predictions for non-coaxiality with reference to microscopic observations while the classical coaxial model fails to simulate the non-coaxial behaviors.In general,non-coaxiality as a result of the rotation of principal stress,is large at a small shear strain,and inclined to become negligible with increasing shear strain.For coarse grained soils,their non-coaxiality tends to largely depend on the initial normal pressure,where a larger degree of non-coaxiality can be observed at a higher pressure.
Path statistics, memory, and coarse-graining of continuous-time random walks on networks
Manhart, Michael; Kion-Crosby, Willow; Morozov, Alexandre V.
2015-12-01
Continuous-time random walks (CTRWs) on discrete state spaces, ranging from regular lattices to complex networks, are ubiquitous across physics, chemistry, and biology. Models with coarse-grained states (for example, those employed in studies of molecular kinetics) or spatial disorder can give rise to memory and non-exponential distributions of waiting times and first-passage statistics. However, existing methods for analyzing CTRWs on complex energy landscapes do not address these effects. Here we use statistical mechanics of the nonequilibrium path ensemble to characterize first-passage CTRWs on networks with arbitrary connectivity, energy landscape, and waiting time distributions. Our approach can be applied to calculating higher moments (beyond the mean) of path length, time, and action, as well as statistics of any conservative or non-conservative force along a path. For homogeneous networks, we derive exact relations between length and time moments, quantifying the validity of approximating a continuous-time process with its discrete-time projection. For more general models, we obtain recursion relations, reminiscent of transfer matrix and exact enumeration techniques, to efficiently calculate path statistics numerically. We have implemented our algorithm in PathMAN (Path Matrix Algorithm for Networks), a Python script that users can apply to their model of choice. We demonstrate the algorithm on a few representative examples which underscore the importance of non-exponential distributions, memory, and coarse-graining in CTRWs.
Coarse-grained molecular dynamics simulations of protein-ligand binding.
Negami, Tatsuki; Shimizu, Kentaro; Terada, Tohru
2014-09-30
Coarse-grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein-ligand binding processes. We chose two protein-ligand systems, the levansucrase-sugar (glucose or sucrose), and LinB-1,2-dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand-binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse-grained (CG) ligand molecules revealed potential ligand-binding sites on the protein surfaces other than the real ligand-binding sites. The ligands bound most strongly to the real ligand-binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase-sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand-binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein-ligand binding processes.
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.
Differences between real and particle-in-cell plasmas: effects of coarse-graining
Melzani, Mickaël; Folini, Doris; Winisdoerffer, Christophe
2013-01-01
The PIC model relies on two building blocks. The first stems from the capability of computers to handle only up to $\\sim10^{10}$ particles, while real plasmas contain from $10^4$ to $10^{20}$ particles per Debye sphere: a coarse-graining step must be used, whereby of the order of $p\\sim10^{10}$ real particles are represented by a single computer superparticle. The second is field storage on a grid with its subsequent finite superparticle size. We introduce the notion of coarse-graining dependent quantities, i.e. physical quantities depending on the number $p$. They all derive from the plasma parameter $\\Lambda$, which we show to be proportional to $1/p$. We explore three examples: the rapid collision- and fluctuation-induced thermalization of plasmas with different temperatures, that scale with the number of superparticles per grid cell and are a factor $p\\sim10^{10}$ faster than in real plasmas; the high level of electrostatic fluctuations in a thermal plasma, with corrections due to the finite superparticle...
Construction of Coarse-Grained Models by Reproducing Equilibrium Probability Density Function
Lu, Shi-Jing; Zhou, Xin
2015-01-01
The present work proposes a novel methodology for constructing coarse-grained (CG) models, which aims at minimizing the difference between CG model and the corresponding original system. The difference is defined as a functional of their equilibrium conformational probability densities, then is estimated from equilibrium averages of many independent physical quantities denoted as basis functions. An orthonormalization strategy is adopted to get the independent basis functions from sufficiently preselected interesting physical quantities of the system. Thus the current method is named as probability density matching coarse-graining (PMCG) scheme, which effectively takes into account the overall characteristics of the original systems to construct CG model, and it is a natural improvement of the usual CG scheme wherein some physical quantities are intuitively chosen without considering their correlations. We verify the general PMCG framework in constructing a one-site CG water model from TIP3P model. Both structure of liquids and pressure of the TIP3P water system are found to be well reproduced at the same time in the constructed CG model.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.
2015-11-01
In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism
Energy Technology Data Exchange (ETDEWEB)
Li, Zhen; Bian, Xin; Karniadakis, George Em, E-mail: george-karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912 (United States); Li, Xiantao [Department of Mathematics, Pennsylvania State University, University Park, Pennsylvania 16802 (United States)
2015-12-28
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism
Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em
2015-12-01
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.
Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em
2015-12-28
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model. PMID:26723613
3d Quantum Gravity: Coarse-Graining and q-Deformation
Livine, Etera R
2016-01-01
The Ponzano-Regge state-sum model provides a quantization of 3d gravity as a spin foam, providing a quantum amplitude to each 3d triangulation defined in terms of the 6j-symbol (from the spin-recoupling theory of SU(2) representations). In this context, the invariance of the 6j-symbol under 4-1 Pachner moves, mathematically defined by the Biedenharn-Elliot identity, can be understood as the invariance of the Ponzano-Regge model under coarse-graining or equivalently as the invariance of the amplitudes under the Hamiltonian constraints. Here we look at length and volume insertions in the Biedenharn-Elliot identity for the 6j-symbol, derived in some sense as higher derivatives of the original formula. This gives the behavior of these geometrical observables under coarse-graining. These new identities turn out to be related to the Biedenharn-Elliot identity for the q-deformed 6j-symbol and highlight that the q-deformation produces a cosmological constant term in the Hamiltonian constraints of 3d quantum gravity.
Simulation of ballistic performance of coarse-grained metals strengthened by nanotwinned regions
Yang, G.; Guo, X.; Weng, G. J.; Zhu, L. L.; Ji, R.
2015-12-01
Coarse-grained (CG) metals strengthened by nanotwinned (NT) regions have both ultrahigh strength and good ductility. The presence of the NT regions contributes to their ultrahigh strength, while their good ductility is attributed to the recrystallized coarse grains. These characteristics make them a potential candidate for bullet-proof material. In this paper, numerical simulations based on the mechanism-based strain gradient plasticity and the Johnson-Cook failure criterion are carried out to investigate the effects of twin spacing and microstructural attributes on the ballistic performance of CG copper strengthened by NT regions. We investigate the performance of fourteen idealized microstructures, and find that smaller twin spacing and regular distribution of NT regions are more conducive to the promotion of the ballistic performance. We also uncover that the role of the shape of NT regions is significantly affected by twin spacing. Furthermore, we make a comparison with its CG counterpart without NTs, and find that microstructures with array arrangement of NT regions have higher limit velocities and smaller relative displacements than the single phase CG structure. This makes them a strong candidate for helmets and other personal protective equipments. It is believed that the simulated results could provide useful insights into the development of this advanced class of metals for ballistic protection.
Coarse-grained simulation of lipid vesicles with ``n-atic'' orientational order
Geng, Jun; Selinger, Jonathan; Selinger, Robin
2012-02-01
We perform coarse-grained simulation studies of fluid lipid vesicles with in-plane ``n-atic'' orientational order associated with the shape of lipid head group, to test the theoretical predictions of Park, Lubensky and MacKintosh [1] for resulting vesicle shape and defect structures. Our simulation model uses a single layer coarse-grained implicit-solvent approach proposed by Yuan et al [2], with addition of an extra vector degree of freedom representing in-plane orientational order. We carry out simulation studies for n=1 to 6, examining in each case the spatial distribution of defects and resulting deformation of the vesicle. An initially spherical vesicle (genus zero) with n-atic order has a ground state with 2n vortices of strength 1/n, as expected, but the observed equilibrium shapes are sometimes quite different from those predicted theoretically. For the n=1 case, we find that the vesicle may become trapped in a disordered, long-lived metastable state with extra +/- defects whose pair-annihilation is inhibited by local changes in membrane curvature, and thus may never reach its predicted ground state. [4pt] [1] J. Park, T. C. Lubensky, and F. C. MacKintosh, Europhys. Lett. 20, 279 (1992)[0pt] [2] H. Yuan, C. Huang, Ju Li, G. Lykotrafitis, and S. Zhang, Phys. Rev. E 82, 011905 (2010)
Conformational Properties of Comb-Like Polyelectrolytes: A Coarse-Grained MD Study.
Ghelichi, Mahdi; Eikerling, Michael H
2016-03-17
This article presents a coarse-grained molecular dynamics study of single comb-like polyelectrolyte or ionomer chains in aqueous solution. The model polymer is comprised of a hydrophobic backbone chain with grafted side chains that terminate in anionic headgroups. The comb-polymer is modeled at a coarse-grained level with implicit treatment of the solvent. The computational study rationalizes conformational properties of the backbone chain and localization of counterions as functions of side chain length, grafting density of side chains, backbone stiffness, and counterion valence. The main interplay that determines the ionomer properties unfolds between electrostatic interactions among charged groups, hydrophobic backbone interactions, and steric effects induced by the pendant side chains. Depending on the density of branching sites, we have found two opposing effects of side chain length on the backbone gyration radius and local persistence length. Variation in comb-polyelectrolyte architecture is shown to have nontrivial effects on the localization of mobile counterions. Changes in Bjerrum length and counterion valence are also shown to alter the strength of Coulomb interactions and emphasize the role of excluded-volume effects on controlling the backbone conformational behavior. The results of simulations are in qualitative agreement with existing experimental and theoretical studies. The comprehensive conformational picture provides a framework for future studies of comb-polyelectrolyte systems. PMID:26910617
A coarse-grained model to study calcium activation of the cardiac thin filament
Zhang, Jing; Schwartz, Steven
2015-03-01
Familial hypertrophic cardiomyopathy (FHC) is one of the most common heart disease caused by genetic mutations. Cardiac muscle contraction and relaxation involve regulation of crossbridge binding to the cardiac thin filament, which regulates actomyosin interactions through calcium-dependent alterations in the dynamics of cardiac troponin (cTn) and tropomyosin (Tm). An atomistic model of cTn complex interacting with Tm has been studied by our group. A more realistic model requires the inclusion of the dynamics of actin filament, which is almost 6 times larger than cTn and Tm in terms of atom numbers, and extensive sampling of the model becomes very resource-demanding. By using physics-based protein united-residue force field, we introduce a coarse-grained model to study the calcium activation of the thin filament resulting from cTn's allosteric regulation of Tm dynamics on actin. The time scale is much longer than that of all-atom molecular dynamics simulation because of the reduction of the degrees of freedom. The coarse-grained model is a good template for studying cardiac thin filament mutations that cause FHC, and reduces the cost of computational resources.
Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu
2011-10-01
A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
International Nuclear Information System (INIS)
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
Xia, Wenjie; Hsu, David; Keten, Sinan
Understanding and predicting the thermomechanical responses of nanoscale polymer systems are very challenging as their responses are greatly influenced by many factors, such as interfacial energy, filler volume fraction and molecule weight, giving rise to the presence of nanoscale interface and free surface. To overcome these issues, here we employ a novel atomistically informed coarse-grained computational technique, called thermomechanically consistent coarse graining (TCCG), to investigate how the nanoscale interface and free surface influence the elastic modulus (E) and glass transition temperature (Tg) of polymer films and nanocomposites. By performing tensile tests and nanoindentation simulations, we are able to predict the size dependent elastic properties of polymer films and quantify the length scale of the local mechanical interphase. Finally, taking cellulose nanocrystal (CNC) and poly(methyl-methacrylate) (PMMA) nanocomposites as a relevant model system, we present a multi-scale framework built upon our CG approach to allow the prediction of Tg of nanocomposite as a function of interfacial energy and filler volume fractions by drawing the analogy between thin film and nanocomposites. Our established multi-scale framework is validated by recent experiments and breaks new ground in predicting, without any empirical parameters, key structure-property relationships for polymer nanomaterials.
An Impulse-C Hardware Accelerator for Packet Classification Based on Fine/Coarse Grain Optimization
Directory of Open Access Journals (Sweden)
O. Ahmed
2013-01-01
Full Text Available Current software-based packet classification algorithms exhibit relatively poor performance, prompting many researchers to concentrate on novel frameworks and architectures that employ both hardware and software components. The Packet Classification with Incremental Update (PCIU algorithm, Ahmed et al. (2010, is a novel and efficient packet classification algorithm with a unique incremental update capability that demonstrated excellent results and was shown to be scalable for many different tasks and clients. While a pure software implementation can generate powerful results on a server machine, an embedded solution may be more desirable for some applications and clients. Embedded, specialized hardware accelerator based solutions are typically much more efficient in speed, cost, and size than solutions that are implemented on general-purpose processor systems. This paper seeks to explore the design space of translating the PCIU algorithm into hardware by utilizing several optimization techniques, ranging from fine grain to coarse grain and parallel coarse grain approaches. The paper presents a detailed implementation of a hardware accelerator of the PCIU based on an Electronic System Level (ESL approach. Results obtained indicate that the hardware accelerator achieves on average 27x speedup over a state-of-the-art Xeon processor.
Path statistics, memory, and coarse-graining of continuous-time random walks on networks.
Manhart, Michael; Kion-Crosby, Willow; Morozov, Alexandre V
2015-12-01
Continuous-time random walks (CTRWs) on discrete state spaces, ranging from regular lattices to complex networks, are ubiquitous across physics, chemistry, and biology. Models with coarse-grained states (for example, those employed in studies of molecular kinetics) or spatial disorder can give rise to memory and non-exponential distributions of waiting times and first-passage statistics. However, existing methods for analyzing CTRWs on complex energy landscapes do not address these effects. Here we use statistical mechanics of the nonequilibrium path ensemble to characterize first-passage CTRWs on networks with arbitrary connectivity, energy landscape, and waiting time distributions. Our approach can be applied to calculating higher moments (beyond the mean) of path length, time, and action, as well as statistics of any conservative or non-conservative force along a path. For homogeneous networks, we derive exact relations between length and time moments, quantifying the validity of approximating a continuous-time process with its discrete-time projection. For more general models, we obtain recursion relations, reminiscent of transfer matrix and exact enumeration techniques, to efficiently calculate path statistics numerically. We have implemented our algorithm in PathMAN (Path Matrix Algorithm for Networks), a Python script that users can apply to their model of choice. We demonstrate the algorithm on a few representative examples which underscore the importance of non-exponential distributions, memory, and coarse-graining in CTRWs.
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.
Baertschiger, T; Joyce, M; Gabrielli, A; Sylos Labini, F
2007-07-01
We study the evolution under their self-gravity of particles evolving from infinite "shuffled lattice" initial conditions. We focus here specifically on the comparison between the evolution of such a system and that of "daughter" coarse-grained particle distributions. These are sparser (i.e., lower density) particle distributions, defined by a simple coarse-graining procedure, which share the same large-scale mass fluctuations. We consider both the case that such coarse-grainings are performed (i) on the initial conditions, and (ii) at a finite time with a specific additional prescription. In numerical simulations we observe that, to a first approximation, these coarse-grainings represent well the evolution of the two-point correlation properties over a significant range of scales. We note, in particular, that the form of the two-point correlation function in the original system, when it is evolving in the asymptotic "self-similar" regime, may be reproduced well in a daughter coarse-grained system in which the dynamics are still dominated by two-body (nearest neighbor) interactions. This provides a simple physical description of the origin of the form of part of the asymptotic nonlinear correlation function. Using analytical results on the early time evolution of these systems, however, we show that small observed differences between the evolved system and its coarse-grainings at the initial time will in fact diverge as the ratio of the coarse-graining scale to the original interparticle distance increases. The second coarse-graining studied, performed at a finite time in a specified manner, circumvents this problem. It also makes it more physically transparent why gravitational dynamics from these initial conditions tends toward a self-similar evolution. We finally discuss the precise definition of a limit in which a continuum (specifically Vlasov-type) description of the observed linear and nonlinear evolution should be applicable. This requires the introduction
Coarse-grained transport of a turbulent flow via moments of the Reynolds-averaged Boltzmann equation
Abramov, Rafail V
2015-01-01
Here we introduce new coarse-grained variables for a turbulent flow in the form of moments of its Reynolds-averaged Boltzmann equation. With the exception of the collision moments, the transport equations for the new variables are identical to the usual moment equations, and thus naturally lend themselves to the variety of already existing closure methods. Under the anelastic turbulence approximation, we derive equations for the Reynolds-averaged turbulent fluctuations around the coarse-grained state. We show that the global relative entropy of the coarse-grained state is bounded from above by the Reynolds average of the fine-grained global relative entropy, and thus obeys the time decay bound of Desvillettes and Villani. This is similar to what is observed in the rarefied gas dynamics, which makes the Grad moment closure a good candidate for truncating the hierarchy of the coarse-grained moment equations. We also show that, under additional assumptions on the form of the coarse-grained collision terms, one a...
Directory of Open Access Journals (Sweden)
Peter Mirau
2015-09-01
Full Text Available Despite enormous efforts, our understanding the structure and dynamics of α-synuclein (ASN, a disordered protein (that plays a key role in neurodegenerative disease is far from complete. In order to better understand sequence-structure-property relationships in α-SYNUCLEIN we have developed a coarse-grained model using knowledge-based residue-residue interactions and used it to study the structure of free ASN as a function of temperature (T with a large-scale Monte Carlo simulation. Snapshots of the simulation and contour contact maps show changes in structure formation due to self-assembly as a function of temperature. Variations in the residue mobility profiles reveal clear distinction among three segments along the protein sequence. The N-terminal (1-60 and C-terminal (96-140 regions contain the least mobile residues, which are separated by the higher mobility non-amyloid component (NAC (61-95. Our analysis of the intra-protein contact profile shows a higher frequency of residue aggregation (clumping in the N-terminal region relative to that in the C-terminal region, with little or no aggregation in the NAC region. The radius of gyration (Rg of ASN decays monotonically with decreasing the temperature, consistent with the finding of Allison et al. (JACS, 2009. Our analysis of the structure function provides an insight into the mass (N distribution of ASN, and the dimensionality (D of the structure as a function of temperature. We find that the globular structure with D ≈ 3 at low T, a random coil, D ≈ 2 at high T and in between (2 ≤ D ≤ 3 at the intermediate temperatures. The magnitudes of D are in agreement with experimental estimates (J. Biological Chem 2002.
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.
International Nuclear Information System (INIS)
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
Static Recrystallized Grain Size of Coarse-Grained Austenite in an API-X70 Pipeline Steel
Sha, Qingyun; Li, Guiyan; Li, Dahang
2013-12-01
The effects of initial grain size and strain on the static recrystallized grain size of coarse-grained austenite in an API-X70 steel microalloyed with Nb, V, and Ti were investigated using a Gleeble-3800 thermomechanical simulator. The results indicate that the static recrystallized grain size of coarse-grained austenite decreases with decreasing initial grain size and increasing applied strain. The addition of microalloying elements can lead to a smaller initial grain size for hot deformation due to the grain growth inhibition during reheating, resulting in decreasing of static recrystallized grain size. Based on the experimental data, an equation for the static recrystallized grain size was derived using the least square method. The grain sizes calculated using this equation fit well with the measured ones compared with the equations for fine-grained austenite and for coarse-grained austenite of Nb-V microalloyed steel.
Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A; Plecháč, Petr
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.
Energy Technology Data Exchange (ETDEWEB)
Markutsya, Sergiy [Ames Laboratory; Lamm, Monica H [Ames Laboratory
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.
Virtual ultrasound sources for inspecting nuclear components of coarse-grained structure
International Nuclear Information System (INIS)
This work describes an ultrasonic inspection procedure designed for verifying coarse-grained structure materials, which are commonly used on nuclear reactors. In this case, conventional phased array techniques cannot be used due to attenuating characteristics and backscattered noise from microstructures inside the material. Thus, synthetic aperture ultrasonic imaging (SAFT) is used for this approach in contact conditions. In order to increase energy transferred to the medium, synthetic transmit aperture is formed by several elements which generate a diverging wavefront equivalent to a virtual ultrasound source behind the transducer. On the other hand, the phase coherence technique has been applied to reduce more structural noise and improve the image quality. The beamforming process has been implemented over a GPU platform to reduce computing time
Tian, Pu
2015-01-01
Free energy is arguably the most important thermodynamic property for physical systems. Despite the fact that free energy is a state function, presently available rigorous methodologies, such as those based on thermodynamic integration (TI) or non-equilibrium work (NEW) analysis, involve energetic calculations on path(s) connecting the starting and the end macrostates. Meanwhile, presently widely utilized approximate end-point free energy methods lack rigorous treatment of conformational variation within end macrostates, and are consequently not sufficiently reliable. Here we present an alternative and rigorous end point free energy calculation formulation based on microscopic configurational space coarse graining, where the configurational space of a high dimensional system is divided into a large number of sufficiently fine and uniform elements, which were termed conformers. It was found that change of free energy is essentially decided by change of the number of conformers, with an error term that accounts...
A coarse-grained simulation for the folding of molybdenum disulphide
International Nuclear Information System (INIS)
We investigate the folding of molybdenum disulphide (MoS2) using coarse-grained (CG) simulations, in which all the parameters are determined analytically from the Stillinger–Weber atomic potential. Owing to its simplicity, the CG model can be used to derive analytic predictions for the relaxed configuration of the folded MoS2 and the resonant frequency for the breathing-like oscillation. We disclose two interesting phenomena for the breathing-like oscillation in the folded MoS2. First, the breathing-like oscillation is self-actuated, since this oscillation can be actuated by intrinsic thermal vibrations without any external actuation force. Second, the resonant frequency of the breathing-like oscillation is insensitive to the adsorption effect. These two features enable practical applications of the folded MoS2 based nanoresonators, where stable resonant oscillations are desirable. (paper)
Macroscopic and large scale phenomena coarse graining, mean field limits and ergodicity
Rademacher, Jens; Zagaris, Antonios
2016-01-01
This book is the offspring of a summer school school “Macroscopic and large scale phenomena: coarse graining, mean field limits and ergodicity”, which was held in 2012 at the University of Twente, the Netherlands. The focus lies on mathematically rigorous methods for multiscale problems of physical origins. Each of the four book chapters is based on a set of lectures delivered at the school, yet all authors have expanded and refined their contributions. Francois Golse delivers a chapter on the dynamics of large particle systems in the mean field limit and surveys the most significant tools and methods to establish such limits with mathematical rigor. Golse discusses in depth a variety of examples, including Vlasov--Poisson and Vlasov--Maxwell systems. Lucia Scardia focuses on the rigorous derivation of macroscopic models using $\\Gamma$-convergence, a more recent variational method, which has proved very powerful for problems in material science. Scardia illustrates this by various basic examples and a mor...
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 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...... in multiple smaller arrays that can execute threads in parallel. Because the partition can be changed dynamically, this extension provides more flexibility than a multi-core approach. This article presents details of the enhanced architecture and results obtained from an MPEG-2 decoder implementation...
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...... a comprehensive analysis on the trade-off between power consumption and available optical capacity, and power consumption and capital expenditure (CAPEX) for three different scenarios, defining the impact of provisioning the network with higher granularity transmission technology. Regarding the available optical......Power consumption is becoming one of the most significant limitations while seeking new solutions to cope with the traffic demand increase. 100 Gbps optical transmission technology has the potential to accommodate upcoming traffic demands with improved figures for W/Gbps compared to previous...
Structural investigation of MscL gating using experimental data and coarse grained MD simulations.
Directory of Open Access Journals (Sweden)
Evelyne Deplazes
Full Text Available The mechanosensitive channel of large conductance (MscL has become a model system in which to understand mechanosensation, a process involved in osmoregulation and many other physiological functions. While a high resolution closed state structure is available, details of the open structure and the gating mechanism remain unknown. In this study we combine coarse grained simulations with restraints from EPR and FRET experiments to study the structural changes involved in gating with much greater level of conformational sampling than has previously been possible. We generated a set of plausible open pore structures that agree well with existing open pore structures and gating models. Most interestingly, we found that membrane thinning induces a kink in the upper part of TM1 that causes an outward motion of the periplasmic loop away from the pore centre. This previously unobserved structural change might present a new mechanism of tension sensing and might be related to a functional role in osmoregulation.
Experimental study on waves propagation over a coarse-grained sloping beach
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
Coarse-grained entropy and causal holographic information in AdS/CFT
Energy Technology Data Exchange (ETDEWEB)
Kelly, William R.; Wall, Aron C. [University of California at Santa Barbara, Santa Barbara, CA 93106 (United States)
2014-03-26
We propose bulk duals for certain coarse-grained entropies of boundary regions. The ‘one-point entropy’ is defined in the conformal field theory by maximizing the entropy in a domain of dependence while fixing the one-point functions. We conjecture that this is dual to the area of the edge of the region causally accessible to the domain of dependence (i.e. the ‘causal holographic information’ of Hubeny and Rangamani). The ‘future one-point entropy’ is defined by generalizing this conjecture to future domains of dependence and their corresponding bulk regions. We show that the future one-point entropy obeys a nontrivial second law. If our conjecture is true, this answers the question “What is the field theory dual of Hawking’s area theorem?”.
Generalization of the DLA process with different immiscible components by time-scale coarse graining
Energy Technology Data Exchange (ETDEWEB)
Postnikov, E B [Kursk State University, Theoretical Physics Department, Radishcheva st, 33, 305000, Kursk (Russian Federation); Ryabov, A B [MV Lomonosov Moscow State University, Physics Faculty, 119992 Moscow (Russian Federation); Loskutov, A [MV Lomonosov Moscow State University, Physics Faculty, 119992 Moscow (Russian Federation)
2007-10-05
In the framework of the mean-field approximation we propose a new approach to the description of the growth of fractal structures which are formed as a result of the process of diffusion limited aggregation. Our approach is based on the coarse graining of the time scale which takes into account the property of discreteness of such structures. The obtained system of partial differential equations allows us to evaluate numerically the fractal dimension and the cluster density depending on the distance from the cluster center. The results are in a quite good agreement with values found by the direct numerical simulations. The proposed approach is generalized for the case of the cluster description with different immiscible particles.
Generalization of the DLA process with different immiscible components by time-scale coarse graining
Postnikov, E. B.; Ryabov, A. B.; Loskutov, A.
2007-10-01
In the framework of the mean-field approximation we propose a new approach to the description of the growth of fractal structures which are formed as a result of the process of diffusion limited aggregation. Our approach is based on the coarse graining of the time scale which takes into account the property of discreteness of such structures. The obtained system of partial differential equations allows us to evaluate numerically the fractal dimension and the cluster density depending on the distance from the cluster center. The results are in a quite good agreement with values found by the direct numerical simulations. The proposed approach is generalized for the case of the cluster description with different immiscible particles.
A Dynamically Reconfigurable Video Compression Scheme Using FPGAs with Coarse-grain Parallelism
Directory of Open Access Journals (Sweden)
S. Ramachandran
2002-01-01
Full Text Available A dynamically reconfigurable scheme for video encoder to switch among many different applications is presented. The scheme is suitable for FPGA implementation and conforms to JPEG, MPEG-1, MPEG-2, and H.263 standards. The scheme has emerged as an efficient and cost-effective solution for video compression as a result of innovative design using well-partitioned algorithms, highly pipelined architecture and coarse-grain parallelism. The reconfiguration time of the video encoder is less than 320 μs while switching from one standard to another. Although the dynamic reconfiguration scheme is presented for a video encoder, the same design methodology may be applied effectively for any other application.
Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model
Sayar, Mehmet; Kabakcioglu, Alkan
2009-01-01
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 depe...
Probing the QCD phase diagram with dileptons - a study using coarse-grained transport dynamics
Endres, Stephan; Bleicher, Marcus
2016-01-01
Dilepton production in heavy-ion collisions at various energies is studied using coarse-grained transport simulations. Microscopic output from the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) model is hereby put on a grid of space-time cells which allows to extract the local temperature and chemical potential in each cell via an equation of state. The dilepton emission is then calculated applying in-medium spectral functions from hadronic many-body theory and partonic production rates based on lattice calculations. The comparison of the resulting spectra with experimental data shows that the dilepton excess beyond the decay contributions from a hadronic cocktail reflects the trajectory of the fireball in the $T-\\mu_{\\mathrm{B}}$ plane of the QCD phase diagram.
A coarse-grain force field for RDX: Density dependent and energy conserving
Moore, Joshua D.; Barnes, Brian C.; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S.; Taylor, DeCarlos E.; Brennan, John K.
2016-03-01
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.
Tunable-slip boundaries for coarse-grained simulations of fluid flow
Smiatek, Jens; Schmid, Friederike
2007-01-01
On the micro- and nanoscale, classical hydrodynamic boundary conditions such as the no-slip condition no longer apply. Instead, the flow profiles exhibit ``slip`` at the surface, which is characterized by a finite slip length (partial slip). We present a new, systematic way of implementing partial-slip boundary conditions with arbitrary slip length in coarse-grained computer simulations. The main idea is to represent the complex microscopic interface structure by a spatially varying effective viscous force. An analytical equation for the resulting slip length can be derived for planar and for curved surfaces. The comparison with computer simulations of a DPD (dissipative particle dynamics) fluid shows that this expression is valid from full-slip to no-slip.
Development of DPD coarse-grained models: From bulk to interfacial properties
Solano Canchaya, José G.; Dequidt, Alain; Goujon, Florent; Malfreyt, Patrice
2016-08-01
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.
A polarizable coarse-grained protein model for dissipative particle dynamics.
Peter, Emanuel K; Lykov, Kirill; Pivkin, Igor V
2015-10-01
We present a new coarse-grained polarizable protein model for dissipative particle dynamics (DPD) method. This method allows large timesteps in particle-based systems and speeds up sampling by many orders of magnitude. Our new model is based on the electrostatic polarization of the protein backbone and a detailed representation of the sidechains in combination with a polarizable water model. We define our model parameters using the experimental structures of two proteins, TrpZip2 and TrpCage. Backmapping and subsequent short replica-exchange molecular dynamics runs verify our approach and show convergence to the experimental structures on the atomistic level. We validate our model on five different proteins: GB1, the WW-domain, the B-domain of Protein A, the peripheral binding subunit and villin headpiece. PMID:26339692
Coarse-grained entropy and causal holographic information in AdS/CFT
International Nuclear Information System (INIS)
We propose bulk duals for certain coarse-grained entropies of boundary regions. The ‘one-point entropy’ is defined in the conformal field theory by maximizing the entropy in a domain of dependence while fixing the one-point functions. We conjecture that this is dual to the area of the edge of the region causally accessible to the domain of dependence (i.e. the ‘causal holographic information’ of Hubeny and Rangamani). The ‘future one-point entropy’ is defined by generalizing this conjecture to future domains of dependence and their corresponding bulk regions. We show that the future one-point entropy obeys a nontrivial second law. If our conjecture is true, this answers the question “What is the field theory dual of Hawking’s area theorem?”
Coarse-grained Dynamic Taint Analysis for Defeating Control and Non-control Data Attacks
Kohli, Pankaj
2009-01-01
Memory corruption attacks remain the primary threat for computer security. Information flow tracking or taint analysis has been proven to be effective against most memory corruption attacks. However, there are two shortcomings with current taint analysis based techniques. First, these techniques cause application slowdown by about 76% thereby limiting their practicality. Second, these techniques cannot handle non-control data attacks i.e., attacks that do not overwrite control data such as return address, but instead overwrite critical application configuration data or user identity data. In this work, to address these problems, we describe a coarse-grained taint analysis technique that uses information flow tracking at the level of application data objects. We propagate a one-bit taint over each application object that is modified by untrusted data thereby reducing the taint management overhead considerably. We performed extensive experimental evaluation of our approach and show that it can detect all critic...
Simulations of room temperature ionic liquids: From polarizable to coarse-grained force fields
Salanne, Mathieu
2015-01-01
Room temperature ionic liquids (RTILs) are solvent with unusual properties, which are difficult to characterize experimentally because of their intrinsic complexity (large number of atoms, strong Coulomb interactions). Molecular simulations have therefore been essential in our understanding of these systems. Depending on the target property and on the necessity to account for fine details of the molecular structure of the ions, a large range of simulation techniques are available. Here I focus on classical molecular dynamics, in which the level of complexity of the simulation, and therefore the computational cost, mostly depends on the force field. Depending on the representation of the ions, these are either classified as all-atom or coarse-grained. In addition, all-atom force fields may account for polarization effects if necessary. The most widely used methods for RTILs are described together with their main achievements and limitations.
A coarse-grained reconfigurable computing architecture with loop self-pipelining
Institute of Scientific and Technical Information of China (English)
DOU Yong; WU GuiMing; XU JinHui; ZHOU XingMing
2009-01-01
Reconfigurable computing tries to achieve the balance between high efficiency of custom computing and flexibility of general-purpose computing. This paper presents the Implementation techniques in LEAP, a coarse-grained reconfigurable array, and proposes a speculative execution mechanism for dynamic loop scheduling with the goal of one iteration per cycle and Implementation techniques to support decoupling synchronization between the token generator and the collector. This paper also in-troduces the techniques of exploiting both data dependences of intra- and inter-Iteration, with the help of two instructions for special data reuses in the loop-carried dependences. The experimental results show that the number of memory accesses reaches on average 3% of an RISC processor simulator with no memory optimization. In a practical Image matching application, LEAP architecture achieves about 34 times of speedup in execution cycles, compared with general-purpose processors.
Investigating bile salt aggregation using coarse-grained molecular dynamics simulations
Vila Verde, Ana; Frenkel, Daan
2010-03-01
Bile salts are necessary for fat digestion due to their unusual surfactant properties: they assemble into small, polydisperse micelles and easily form mixed micelles with poorly soluble amphiphiles. Understanding these properties requires molecular scale information about bile salt micelles, something challenging to obtain experimentally but amenable to computational modeling. To address this issue we build a coarse-grained model of bile salts. We investigate their aggregation behavior through molecular dynamics simulations in a grand-canonical parallel tempering scheme. We validate our model against available solubility and light scattering data. Our results indicate that at physiological bile salt and counter ion concentrations, bile salts pack in many different orientations in pure bile micelles, contrary to standard surfactants. This feature may be physiologically relevant, allowing bile salts to solubilize the heterogeneous blends of fats typical of digestion.
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 simulation reveals key features of HIV-1 capsid self-assembly
Grime, John M. A.; Dama, James F.; Ganser-Pornillos, Barbie K.; Woodward, Cora L.; Jensen, Grant J.; Yeager, Mark; Voth, Gregory A.
2016-05-01
The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej
2013-01-01
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
Šulc, Petr; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A
2012-01-01
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively along a track of single-stranded stators. We demonstrate that the model is able to simulate such a system, and investigate the sensitivity of the stepping process to the spatial separation of stators, finding that an increased distance can suppress successful steps due to the build up of unfavourable tension. The mechanism of suppression suggests that varying the distance between stators could be used as a method for improving signal-to-noise ratios for motors that are required to make a decision at a junction of stators.
Anomalous g-Factors for Charged Leptons in a Fractional Coarse-Grained Approach
International Nuclear Information System (INIS)
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
Rudzinski, Joseph F
2016-01-01
The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG representation usually results in faster, albeit inconsistent, dynamics. In this work, we rely on Markov state models to simultaneously characterize the static and kinetic properties of two CG peptide force fields---one top-down and one bottom-up. Instead of a rigorous evolution of CG dynamics (e.g., using a generalized Langevin equation), we attempt to improve the description of kinetics by simply altering the existing CG models, which employ standard Langevin dynamics. By varying masses and relevant force-field parameters, we can improve the timescale separation of the slow kinetic processes, achieve a more consistent ratio of mean-first-passage times between metastable states, and refine the relative free-energies between these states. Importantly, we show that the incorporation of kinetic information into a structure-based parametriz...
Energy Technology Data Exchange (ETDEWEB)
Ruff, Kiersten M. [Computational and Systems Biology Program and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899 (United States); Harmon, Tyler S. [Department of Physics and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899 (United States); Pappu, Rohit V., E-mail: pappu@wustl.edu [Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, CB 1097, St. Louis, Missouri 63130-4899 (United States)
2015-12-28
We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.
Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.
2015-12-01
We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.
International Nuclear Information System (INIS)
We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences
Energy Technology Data Exchange (ETDEWEB)
Shendruk, Tyler N., E-mail: tyler.shendruk@physics.ox.ac.uk [The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Bertrand, Martin; Harden, James L.; Slater, Gary W. [Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario K1N 6N5 (Canada); Haan, Hendrick W. de [Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St. North, Oshawa, Ontario L1H 7K4 (Canada)
2014-12-28
Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics (MD) simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (Weeks-Chandler-Andersen (WCA)) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer. It is found that the depletion-induced well depth for the combinatorial-WCA model is significantly deeper than the shifted-WCA model because the resulting overlap of the colloids yields extra accessible volume for depletants. For both shifted- and combinatorial-WCA simulations, the second virial coefficients and pair potentials between colloids are demonstrated to be well approximated by the Morphometric Thermodynamics (MT) model. This agreement suggests that the presence of depletants can be accurately modelled in MD simulations by implicitly including them through simple, analytical MT forms for depletion-induced interactions. Although both WCA potentials are found to be effective generic coarse-grained simulation approaches for studying depletion effects in complicated soft matter systems, combinatorial-WCA is the more efficient approach as depletion effects are enhanced at lower depletant densities. The findings indicate that for soft matter systems that are better modelled by potentials with some compressibility, predictions from hard-sphere systems could greatly underestimate the magnitude of depletion effects at a given depletant density.
Thermal dileptons from coarse-grained transport as fireball probes at SIS energies
Energy Technology Data Exchange (ETDEWEB)
Galatyuk, Tetyana; Seck, Florian [Technische Universitaet Darmstadt, Darmstadt (Germany); GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany); Hohler, Paul M.; Rapp, Ralf [Texas A and M University, College Station, TX (United States); Stroth, Joachim [Texas A and M University, College Station, TX (United States); GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany)
2016-05-15
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{sup 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.)
Hydrogen accumulation in nanostructured as compared to the coarse-grained tungsten
Energy Technology Data Exchange (ETDEWEB)
Gonzalez-Arrabal, R., E-mail: raquel.gonzalez.arrabal@upm.es [Instituto de Fusión Nuclear, ETSI de Industriales, Universidad Politécnica de Madrid, C/José Gutierrez Abascal, 2, E-28006 Madrid (Spain); Panizo-Laiz, M. [Instituto de Fusión Nuclear, ETSI de Industriales, Universidad Politécnica de Madrid, C/José Gutierrez Abascal, 2, E-28006 Madrid (Spain); Gordillo, N. [Instituto de Fusión Nuclear, ETSI de Industriales, Universidad Politécnica de Madrid, C/José Gutierrez Abascal, 2, E-28006 Madrid (Spain); CEI Campus Moncloa, UCM-UPM, Madrid (Spain); Tejado, E. [Departamento de Ciencia de Materiales, ETSI Caminos, Canales y Puertos, Universidad Politécnica de Madrid, E-28040 Madrid (Spain); Centro Nacional de Investigaciones Metalurgicas (C.S.I.C.), Ave. de Gregorio del Amo 8, E-28040 Madrid (Spain); Munnik, F. [Helmholtz-Zentrum Dresden-Rossendorf, PO Box 10119, D-01314 Dresden (Germany); Rivera, A.; Perlado, J.M. [Instituto de Fusión Nuclear, ETSI de Industriales, Universidad Politécnica de Madrid, C/José Gutierrez Abascal, 2, E-28006 Madrid (Spain)
2014-10-15
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{sup 20} m{sup −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.
Coarse-graining to the meso and continuum scales with molecular-dynamics-like models
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.
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.
Grünberger, Alexander; Lai, Pin-Kuang; Blanco, Marco A; Roberts, Christopher J
2013-01-24
A series of coarse-grained models, with different levels of structural resolution, were tested to calculate the steric contributions to protein osmotic second virial coefficients (B(22,S)) for proteins ranging from small single-domain molecules to large multidomain molecules, using the recently developed Mayer sampling method. B(22,S) was compared for different levels of coarse-graining: four-beads-per-amino-acid (4bAA), one-bead-per-amino-acid (1bAA), one-sphere-per-domain (1sD), and one-sphere-per-protein (1sP). Values for the 1bAA and 4bAA models were quantitatively indistinguishable for both spherical and nonspherical proteins, and the agreement with values from all-atom models improved with increasing protein size, making the CG approach attractive for large proteins of biotechnological interest. Interestingly, in the absence of detailed structural information, the hydrodynamic radius (R(h)) along with a simple 1sP approximation provided reasonably accurate values for B(22,S) for both globular and highly asymmetric protein structures, while other 1sP approximations gave poorer agreement; this helps to justify the currently empirical practice of estimating B(22,S) from R(h) for large proteins such as antibodies. The results also indicate that either 1bAA or 4bAA CG models may be good starting points for incorporating short-range attractions. Comparison of gD-crystallin B(22) values including both sterics and short-range attractions shows that 1bAA and 4bAA models give equivalent results when properly scaled to account for differences in the number of surface beads in the two CG descriptions. This provides a basis for future work that will also incorporate long-ranged electrostatic attractions and repulsions. PMID:23245189
Polarizable water model for the coarse-grained MARTINI force field.
Directory of Open Access Journals (Sweden)
Semen O Yesylevskyy
2010-06-01
Full Text Available Coarse-grained (CG simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models.
On the second law of thermodynamics: The significance of coarse-graining and the role of decoherence
Energy Technology Data Exchange (ETDEWEB)
Noorbala, Mahdiyar, E-mail: mnoorbala@ut.ac.ir
2014-12-15
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.
Terzi, Sofiane; Couturier, Raphael; Guétaz, Laure; Viguier, Bernard
2008-01-01
The study of creep deformation in a coarse-grained Udimet 720 superalloy obtained by powder-metallurgy reveals a good resistance associated to a dislocational deformation mechanism. A model is proposed for simulating creep and tensile curves. This model is used to understand the effect of microstructural changes on the deformation mechanisms.
Grahnen, Johan A; Kubelka, Jan; Liberles, David A
2011-08-01
For high-throughput structural genomic and evolutionary bioinformatics approaches, there is a clear need for fast methods to evaluate substitutions structurally. Coarse-grained methods are both powerful and fast, and a coarse-grained approach to position the substituted side chains is presented. Through the application of a coarse-grained method, a speed-up on the single- residue replacement, of at least sevenfold is achieved compared with modern all-atom approaches. At the same time, this approach maintains a small median RMSD from the leading all-atom approach (as measured in coarse-grained space), and predicts the conformation of point mutants with similar accuracy and generates biologically realistic side chain angles. This method is also substantially more predictable in its run time, making it useful for high-throughput studies of protein structural evolution. To demonstrate the utility of this method, it has been implemented in a forward simulation of sequences threaded through the SH2 domains, with selective pressures to fold and bind specifically. The relative substitution rates across the protein structure and at the binding interface are reflective of those observed in SH2 domain evolution. The algorithm has been implemented in C++, with the source code and binaries (currently supported for Linux systems) freely available as SARA at http://www.wyomingbioinformatics.org/LiberlesGroup/SARA .
DEFF Research Database (Denmark)
Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit;
2012-01-01
in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable...
Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers
Energy Technology Data Exchange (ETDEWEB)
Daily, Michael D.; Olsen, Brett N.; Schlesinger, Paul H.; Ory, Daniel S.; Baker, Nathan A.
2014-03-24
In mammalian cells cholesterol is essential for membrane function, but in excess can be cytototoxic. The cellular response to acute cholesterol loading involves biophysical-based mechanisms that regulate cholesterol levels, through modulation of the “activity” or accessibility of cholesterol to extra-membrane acceptors. Experiments and united atom (UA) simulations show that at high concentrations of cholesterol, lipid bilayers thin significantly and cholesterol availability to external acceptors increases substantially. Such cholesterol activation is critical to its trafficking within cells. Here we aim to reduce the computational cost to enable simulation of large and complex systems involved in cholesterol regulation, such as those including oxysterols and cholesterol-sensing proteins. To accomplish this, we have modified the published MARTINI coarse-grained force field to improve its predictions of cholesterol-induced changes in both macroscopic and microscopic properties of membranes. Most notably, MARTINI fails to capture both the (macroscopic) area condensation and membrane thickening seen at less than 30% cholesterol and the thinning seen above 40% cholesterol. The thinning at high concentration is critical to cholesterol activation. Microscopic properties of interest include cholesterol-cholesterol radial distribution functions (RDFs), tilt angle, and accessible surface area. First, we develop an “angle-corrected” model wherein we modify the coarse-grained bond angle potentials based on atomistic simulations. This modification significantly improves prediction of macroscopic properties, most notably the thickening/thinning behavior, and also slightly improves microscopic property prediction relative to MARTINI. Second, we add to the angle correction a “volume correction” by also adjusting phospholipid bond lengths to achieve a more accurate volume per molecule. The angle + volume correction substantially further improves the quantitative
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
Computer simulation of strength and ductility of nanotwin-strengthened coarse-grained metals
Guo, X.; Ji, R.; Weng, G. J.; Zhu, L. L.; Lu, J.
2014-10-01
The superior strength-ductility combination in nanotwin (NT)-strengthened metals has provided a new potential for optimizing the mechanical properties of coarse-grained (CG) metals. In this paper computer simulations based on the mechanism-based strain gradient plasticity and the Johnson-Cook failure criterion have been carried out to uncover the critical factors that serve to provide this dual function. Our results indicate that both the distribution characteristics of the NT regions and the constitutive relations of the NT phase can have a significant impact on the strength and ductility of the CG Cu strengthened by the NT regions. In particular, twin spacing, distribution characteristics such as arrangement, shape and orientation, together with volume fraction of the NT regions, can all have significant effects. Along the way, we also discovered that microcrack initiation, coalescence and deflection constituted the entire failure process. Significant insights into the morphology of NT regions that could deliver superior strength and ductility combination for CG metals have been established.
Synthetic Aperture Focusing Technique in Ultrasonic Inspection of Coarse Grained Materials
International Nuclear Information System (INIS)
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
Universal and non-universal features in coarse-grained models of flow in disordered solids.
Nicolas, Alexandre; Martens, Kirsten; Bocquet, Lydéric; Barrat, Jean-Louis
2014-07-14
We study the two-dimensional (2D) shear flow of amorphous solids within variants of an elastoplastic model, paying particular attention to spatial correlations and time fluctuations of, e.g., local stresses. The model is based on the local alternation between an elastic regime and plastic events during which the local stress is redistributed. The importance of a fully tensorial description of the stress and of the inclusion of (coarse-grained) convection in the model is investigated; scalar and tensorial models yield similar results, while convection enhances fluctuations and breaks the spurious symmetry between the flow and velocity gradient directions, for instance when shear localisation is observed. Besides, correlation lengths measured with diverse protocols are discussed. One class of such correlation lengths simply scale with the spacing between homogeneously distributed, simultaneous plastic events. This leads to a scaling of the correlation length with the shear rate as γ̇(-1/2) in 2D in the athermal regime, regardless of the details of the model. The radius of the cooperative disk, defined as the near-field region in which plastic events induce a stress redistribution that is not amenable to a mean-field treatment, notably follows this scaling. On the other hand, the cooperative volume measured from the four-point stress susceptibility and its dependence on the system size and the shear rate are model-dependent.
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.
Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H; Elsener, Andreas; Marrink, Siewert J; van Gunsteren, Wilfred F
2007-02-19
Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.
Comparing allosteric transitions in the domains of calmodulin through coarse-grained simulations
Nandigrami, Prithviraj
2015-01-01
Calmodulin (CaM) is a ubiquitous calcium binding protein consisting of two structurally similar domains with distinct stabilities, binding affinities, and flexibilities. We present coarse grained simulations that suggest the mechanism for the domain's allosteric transitions between the open and closed conformations depend on subtle differences in the folded state topology of the two domains. Throughout a wide temperature range, the simulated transition mechanism of the N-terminal domain (nCaM) follows a two-state transition mechanism while domain opening in the C-terminal domain (cCaM) involves unfolding and refolding of the tertiary structure. The appearance of the unfolded intermediate occurs at a higher temperature in nCaM than it does in cCaM. That is, we find that cCaM unfolds more readily along the transition route than nCaM. Furthermore, unfolding and refolding of the domain significantly slows the domain opening and closing rates of cCaM, a distinct scenario which can potentially influence the mechani...
Couillard: Parallel Programming via Coarse-Grained Data-Flow Compilation
Marzulo, Leandro A J; França, Felipe M G; Costa, Vítor Santos
2011-01-01
Data-flow is a natural approach to parallelism. However, describing dependencies and control between fine-grained data-flow tasks can be complex and present unwanted overheads. TALM (TALM is an Architecture and Language for Multi-threading) introduces a user-defined coarse-grained parallel data-flow model, where programmers identify code blocks, called super-instructions, to be run in parallel and connect them in a data-flow graph. TALM has been implemented as a hybrid Von Neumann/data-flow execution system: the \\emph{Trebuchet}. We have observed that TALM's usefulness largely depends on how programmers specify and connect super-instructions. Thus, we present \\emph{Couillard}, a full compiler that creates, based on an annotated C-program, a data-flow graph and C-code corresponding to each super-instruction. We show that our toolchain allows one to benefit from data-flow execution and explore sophisticated parallel programming techniques, with small effort. To evaluate our system we have executed a set of real...
Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik
2016-08-01
Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.
Spreading of a Unilamellar Liposome on Charged Substrates: A Coarse-Grained Molecular Simulation.
Kong, Xian; Lu, Diannan; Wu, Jianzhong; Liu, Zheng
2016-04-19
Supported lipid bilayers (SLBs) are able to accommodate membrane proteins useful for diverse biomimetic applications. Although liposome spreading represents a common procedure for preparation of SLBs, the underlying mechanism is not yet fully understood, particularly from a molecular perspective. The present study examines the effects of the substrate charge on unilamellar liposome spreading on the basis of molecular dynamics simulations for a coarse-grained model of the solvent and lipid molecules. Liposome transformation into a lipid bilayer of different microscopic structures suggests three types of kinetic pathways depending on the substrate charge density, that is, top-receding, parachute, and parachute with wormholes. Each pathway leads to a unique distribution of the lipid molecules and thereby distinctive properties of SLBs. An increase of the substrate charge density results in a magnified asymmetry of the SLBs in terms of the ratio of charged lipids, parallel surface movements, and the distribution of lipid molecules. While the lipid mobility in the proximal layer is strongly correlated with the substrate potential, the dynamics of lipid molecules in the distal monolayer is similar to that of a freestanding lipid bilayer. For liposome spreading on a highly charged surface, wormhole formation promotes lipid exchange between the SLB monolayers thus reduces the asymmetry on the number density of lipid molecules, the lipid order parameter, and the monolayer thickness. The simulation results reveal the important regulatory role of electrostatic interactions on liposome spreading and the properties of SLBs. PMID:27019394
Indian Academy of Sciences (India)
A Ciampalini; M Firpo
2015-12-01
This study aims to develop a better understanding of the stratigraphy of the southern side of the Maritime Alps and of the Ligurian Sea during the Plio-Pleistocene. Five stratigraphic sections were measured and studied in the Segno River valley (Liguria, Italy). These sections are composed of Lower to Middle Pleistocene marine and continental deposits. Based on detailed mapping and sedimentological analysis, 12 marine and deltaic facies were identified. These facies were grouped into facies associations. Two allostratigraphic units were recognized, namely U1 and U2 from oldest to youngest. The lower unit (U1) represents the evolution of a coarse-grained delta developed in a valley or embayment. Within the deltaic sequence, transgressive and highstand systems tracts were recognized. The coarsening/shallowing upward trend observed within the sections suggests that the delta prograded rapidly in the landward portion of the canyon adjacent to the paleo-river outlet. The upper boundary of U1 is represented by a subaerial unconformity overlain by U2, which is composed of sediments deposited by several alluvial fan systems.
Coarse-graining polymer solutions: A critical appraisal of single- and multi-site models
D'Adamo, G.; Menichetti, R.; Pelissetto, A.; Pierleoni, C.
2015-09-01
We critically discuss and review the general ideas behind single- and multi-site coarse-grained (CG) models as applied to macromolecular solutions in the dilute and semi-dilute regime. We first consider single-site models with zero-density and density-dependent pair potentials. We highlight advantages and limitations of each option in reproducing the thermodynamic behavior and the large-scale structure of the underlying reference model. As a case study we consider solutions of linear homopolymers in a solvent of variable quality. Secondly, we extend the discussion to multi-component systems presenting, as a test case, results for mixtures of colloids and polymers. Specifically, we found the CG model with zero-density potentials to be unable to predict fluid-fluid demixing in a reasonable range of densities for mixtures of colloids and polymers of equal size. For larger colloids, the polymer volume fractions at which phase separation occurs are largely overestimated. CG models with density-dependent potentials are somewhat less accurate than models with zero-density potentials in reproducing the thermodynamics of the system and, although they present a phase separation, they significantly underestimate the polymer volume fractions along the binodal. Finally, we discuss a general multi-site strategy, which is thermodynamically consistent and fully transferable with the number of sites, and that allows us to overcome most of the limitations discussed for single-site models.
Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V.
2016-01-01
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.
International Nuclear Information System (INIS)
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
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.
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.
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.
A coarse-grained model for the simulations of biomolecular interactions in cellular environments
Energy Technology Data Exchange (ETDEWEB)
Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao, E-mail: yinghao.wu@einstein.yu.edu [Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461 (United States)
2014-02-07
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.
Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation.
Villa, Alessandra; Peter, Christine; van der Vegt, Nico F A
2009-03-28
We discuss the development of a coarse-grained (CG) model for molecular dynamics (MD) simulation of a hydrophobic dipeptide, diphenylalanine, in aqueous solution. The peptide backbone is described with two CG beads per amino acid, the side groups and charged end groups are each described with one CG bead. In the derivation of interaction functions between CG beads we follow a bottom-up strategy where we devise potentials such that the resulting CG simulation reproduces the conformational sampling and the intermolecular interactions observed in an atomistic simulation of the same peptide. In the CG model, conformational flexibility of the peptide is accounted for through a set of intra-molecular (bonded) potentials. The approach followed to obtain the bonded potentials is discussed in detail. The CG potentials for nonbonded interactions are based on potentials of mean force obtained by atomistic simulations in aqueous solution. Following this approach, solvent mediation effects are included in the effective bead-bead nonbonded interactions and computationally very efficient (solvent-free) simulations of self-assembly processes can be performed. We show that the conformational properties of the all-atom dipeptide in explicit solvent can be accurately reproduced with the CG model. Moreover, preliminary simulations of peptide self-assembly performed with the CG model illustrate good agreement with results obtained from all-atom, explicit solvent simulations. PMID:19280018
Protein secondary-structure description with a coarse-grained model.
Kneller, Gerald R; Hinsen, Konrad
2015-07-01
A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using the ASTRAL subset of the SCOPe database of protein structures, thresholds are derived for the screw parameters of secondary-structure elements and demonstrate that the latter can be reliably assigned on the basis of a C(α) model. For this purpose, a comparative study with the widely used DSSP (Define Secondary Structure of Proteins) algorithm was performed and it was shown that the parameter distribution corresponding to the ensemble of all pure C(α) structures in the RCSB Protein Data Bank matches that of the ASTRAL database. It is expected that this approach will be useful in the development of structure-refinement techniques for low-resolution data. PMID:26143913
Anomalous g-Factors for Charged Leptons in a Fractional Coarse-Grained Approach
Weberszpil, J
2013-01-01
In this work, we investigate aspects of the electron, muon and tau gyromagnetic ratios (g-factor) in a fractional coarse-grained scenario, by adopting a Modified Riemann-Liouville (MRL) fractional calculus. We point out the possibility of mapping the experimental values of the specie's g-factors into a theoretical parameter which accounts for fractionality, without computing higher-order QED calculations. We wish to understand whether the value of (g-2) may be traced back to a fractionality of space-time.The justification for the difference between the experimental and the theoretical value g=2 stemming from the Dirac equation is given in the terms of the complexity of the interactions of the charged leptons, considered as pseudo-particles and "dressed" by the interactions and the medium. Stepwise, we build up a fractional Dirac equation from the fractional Weyl equation that, on the other hand, was formulated exclusively in terms of the helicity operator. From the fractional angular momentum algebra, in a co...
Coarse-graining the distribution function of cold dark matter II
Henriksen, R N
2004-01-01
We study analytically the coarse and fine-grained distribution function established by the self-similar infall of collisionless matter. We find this function explicitly for isotropic and spherically symmetric systems in terms of cosmological initial conditions. The coarse-grained function is structureless and steady but the familiar phase space sheet sub-structure is recovered in the fine-grained limit. By breaking the self-similarity of the halo infall we are able to argue for a central density flattening. In addition there will be an edge steepening. The best fitting analytic density function is likely to be provided by a high order polytrope fit smoothly to an outer power law of index -3 for isolated systems. There may be a transition to a -4 power law in the outer regions of tidally truncated systems. We find a progressive central flattening that is expected to end either in the non-singular isothermal sphere, or in non-singular metastable polytropic cores. Therefore a collisionless system may pass throug...
Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei
2016-02-01
In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths. PMID:26717419
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V
2016-01-01
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments. PMID:26747818
Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane
Energy Technology Data Exchange (ETDEWEB)
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V., E-mail: aneimark@rutgers.edu [Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854-8058 (United States)
2016-01-07
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.
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.
Thermal Dileptons from Coarse-Grained Transport as Fireball Probes at SIS Energies
Galatyuk, Tetyana; Rapp, Ralf; Seck, Florian; Stroth, Joachim
2015-01-01
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 $\\rho$ spectral function that describes available spectra at ultrarelativistic collision energies. In particular, we analyze in 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 evolutio...
van den Wildenberg, Siet; Tourin, Arnaud; Jia, Xiaoping
2016-08-01
We measure the consequences of elastic heterogeneities in confined granular layers using long-wavelength sound velocity determination. By progressively decreasing the coarse-graining length w, which is determined here by the sample size L, we measure the standard deviation of the longitudinal sound velocity δ VL and the packing density ϕ, normalized by their ensemble-averaged values. We find that the relative fluctuations in V L and ϕ increase when w is decreased. Importantly, we observe that decreasing the confining pressure P or using nonspherical particles leads to an important increase of the fluctuations in δ V_L/\\bar{V_L} . We conduct simulations of sound propagation in 2D hexagonal packings with contact-stiffness disorder to mimic the inhomogeneous contact networks. The sound velocity fluctuations of coherent longitudinal waves increase either with decreasing the sample size or with increasing the elastic disorder related to confining pressure, in consistency with the experiments. Our experimental observations thus support the scenario of a pressure-dependent mesoscopic length ξ∼10d (at P∼200 \\text{kPa} ), below which the continuum elasticity breaks down, likely due to the large spatial fluctuation of the shear modulus δ G/\\bar{G} ∼ 5δ V_L/\\bar{V_L}>20% .
Application-specific coarse-grained reconfigurable array: architecture and design methodology
Zhou, Li; Liu, Dongpei; Zhang, Jianfeng; Liu, Hengzhu
2015-06-01
Coarse-grained reconfigurable arrays (CGRAs) have shown potential for application in embedded systems in recent years. Numerous reconfigurable processing elements (PEs) in CGRAs provide flexibility while maintaining high performance by exploring different levels of parallelism. However, a difference remains between the CGRA and the application-specific integrated circuit (ASIC). Some application domains, such as software-defined radios (SDRs), require flexibility with performance demand increases. More effective CGRA architectures are expected to be developed. Customisation of a CGRA according to its application can improve performance and efficiency. This study proposes an application-specific CGRA architecture template composed of generic PEs (GPEs) and special PEs (SPEs). The hardware of the SPE can be customised to accelerate specific computational patterns. An automatic design methodology that includes pattern identification and application-specific function unit generation is also presented. A mapping algorithm based on ant colony optimisation is provided. Experimental results on the SDR target domain show that compared with other ordinary and application-specific reconfigurable architectures, the CGRA generated by the proposed method performs more efficiently for given applications.
Effect of forming conditions on the softening behavior in coarse grained structures
Energy Technology Data Exchange (ETDEWEB)
Rehrl, C., E-mail: christian.rehrl@oeaw.ac.at [Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Jahnstr. 12, 8700 Leoben (Austria); Kleber, S. [Boehler Edelstahl GmbH, Kapfenberg, Mariazeller Str. 25, 8605 Kapfenberg (Austria); Renk, O.; Pippan, R. [Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Jahnstr. 12, 8700 Leoben (Austria)
2011-07-25
Highlights: {yields} Unexpected warm forming behavior of coarse grained pure Ni. {yields} Coarsening in starting microstructure leads to a higher flow stress and higher hardening rate. {yields} Grain boundary movement is strongly dependent on the initial grain size. {yields} Discontinuous dynamic recrystallization (DDRX) is retarded by coarsening of initial grain size. {yields} DDRX generates a metastable grain size finer than the steady state grain size. - Abstract: Polycrystalline nickel with a purity of 99.99 wt% and different starting grain sizes of 240 {mu}m and 770 {mu}m has been investigated. The effects of the initial grain size on the hot deformation behavior were studied by compression tests at various forming conditions. The microstructure was captured after deformation, using electron back scatter diffraction technique (EBSD). A variation of the initial grain size has unexpected effects on the acting softening mechanisms. A coarsening in the starting microstructure leads to a higher flow stress and a remarkable higher hardening at elevated temperatures. Furthermore, the nucleation of dynamic recrystallized grains is enormously retarded due to the less pronounced grain boundary bulging in a coarser grained microstructure compared to a finer one. As a consequence, discontinuous dynamic recrystallization generates a metastable grain size, that is finer than the steady state grain size.
A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics.
Masella, Michel; Borgis, Daniel; Cuniasse, Philippe
2013-05-15
A multiscale coarse-grained approach able to handle efficiently the solvation of microscopic solutes in extended chemical environment is described. That approach is able to compute readily and efficiently very long-range solute/solvent electrostatic microscopic interactions, up to the 1-μm scale, by considering a reduced amount of computational resources. All the required parameters are assigned to reproduce available data concerning the solvation of single ions. Such a strategy makes it possible to reproduce with good accuracy the solvation properties concerning simple ion pairs in solution (in particular, the asymptotic behavior of the ion pair potentials of mean force). This new method represents an extension of the polarizable pseudoparticle solvent model, which has been recently improved to account for the main features of hydrophobic effects in liquid water (Masella et al., J. Comput. Chem. 2011, 32, 2664). This multiscale approach is well suited to be used for computing the impact of charge changes in free energy computations, in terms of both accuracy and efficiency. PMID:23382002
A Coarse Grained Model for Methylcellulose: Spontaneous Ring Formation at Elevated Temperature
Huang, Wenjun; Larson, Ronald
Methylcellulose (MC) is widely used as food additives and pharma applications, where its thermo-reversible gelation behavior plays an important role. To date the gelation mechanism is not well understood, and therefore attracts great research interest. In this study, we adopted coarse-grained (CG) molecular dynamics simulations to model the MC chains, including the homopolymers and random copolymers that models commercial METHOCEL A, in an implicit water environment, where each MC monomer modeled with a single bead. The simulations are carried using a LAMMPS program. We parameterized our CG model using the radial distribution functions from atomistic simulations of short MC oligomers, extrapolating the results to long chains. We used dissociation free energy to validate our CG model against the atomistic model. The CG model captured the effects of monomer substitution type and temperature from the atomistic simulations. We applied this CG model to simulate single chains up to 1000 monomers long and obtained persistence lengths that are close to those determined from experiment. We observed the chain collapse transition for random copolymer at 600 monomers long at 50C. The chain collapsed into a stable ring structure with outer diameter around 14nm, which appears to be a precursor to the fibril structure observed in the methylcellulose gel observed by Lodge et al. in the recent studies. Our CG model can be extended to other MC derivatives for studying the interaction between these polymers and small molecules, such as hydrophobic drugs.
Extension of 239+240Pu sediment geochronology to coarse-grained marine sediments
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.
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.
Equation of state for a coarse-grained DPPC monolayer at the air/water interface
Adhangale, Parag S.; Gaver, Donald P., III
Pulmonary surfactant, a complex mixture of phospholipids and proteins, secreted by the type II epithelial cells in the lungs, is crucial to reducing the effort required for breathing. A lack of adequate amounts of pulmonary surfactant in underdeveloped lungs of premature infants results in infant respiratory distress syndrome (RDS). Surfactant replacement therapy (SRT) is the approved method of mitigating the effects of RDS. The development of new SRT regimens requires a fundamental understanding of the links between surfactant biochemistry and functionality. We use a coarse-grained (CG) model to predict the surface pressure-surface concentration relationship (equation of state) for pure DPPC, which is a major component of endogenous and synthetic pulmonary surfactant mixtures. We show that the model can be efficiently used to predict the equation of state in excellent agreement with experimental results. We also study the structure of the monolayer as a function of the surface tension of the system. We show that a decrease in the applied surface tension results in an increase in order in the head group region and a decrease in order in the tail region of DPPC. This technique may be useful in the prediction of equations of state for surfactant replacements.
The impact of resolution upon entropy and information in coarse-grained models
Energy Technology Data Exchange (ETDEWEB)
Foley, Thomas T. [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Shell, M. Scott, E-mail: shell@engineering.ucsb.edu [Department of Chemical Engineering, University of California, Santa Barbara, California 93106 (United States); Noid, W. G., E-mail: wnoid@chem.psu.edu [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)
2015-12-28
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously facilitate numerical calculations and theoretical analyses of complex phenomena. However, their success critically depends upon the representation of the system and the effective potential that governs the CG degrees of freedom. This work investigates the relationship between the CG representation and the many-body potential of mean force (PMF), W, which is the appropriate effective potential for a CG model that exactly preserves the structural and thermodynamic properties of a given high resolution model. In particular, we investigate the entropic component of the PMF and its dependence upon the CG resolution. This entropic component, S{sub W}, is a configuration-dependent relative entropy that determines the temperature dependence of W. As a direct consequence of eliminating high resolution details from the CG model, the coarsening process transfers configurational entropy and information from the configuration space into S{sub W}. In order to further investigate these general results, we consider the popular Gaussian Network Model (GNM) for protein conformational fluctuations. We analytically derive the exact PMF for the GNM as a function of the CG representation. In the case of the GNM, −TS{sub W} is a positive, configuration-independent term that depends upon the temperature, the complexity of the protein interaction network, and the details of the CG representation. This entropic term demonstrates similar behavior for seven model proteins and also suggests, in each case, that certain resolutions provide a more efficient description of protein fluctuations. These results may provide general insight into the role of resolution for determining the information content, thermodynamic properties, and transferability of CG models. Ultimately, they may lead to a rigorous and systematic framework for optimizing the representation of CG models.
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.
Experimental deformation of coarse-grained rock salt to high strain
Linckens, J.; Zulauf, G.; Hammer, J.
2016-08-01
The processes and deformation mechanisms (e.g., dislocation creep, pressure solution, grain boundary sliding, and recrystallization) of rock salt are still a matter of debate. In order to fill this gap, high strain constriction experiments at 345°C, atmospheric pressure and a strain rate of 10-7 s-1 have been conducted on natural halite cuboids (60 × 60 × 45 mm) from the Morsleben mine of Northern Germany. Most samples were almost single crystals and contain a small amount of smaller grains (10-26%). The grain boundaries are decorated with fluid inclusions. The experiments were stopped at different final strains (ɛy = z of 10, 20, 30, and 40%) corresponding to a maximum strain (ɛx) range of 20-170%. The halite is deformed by dislocation creep, and the size of developed subgrains corresponds to the applied stress. The combined Schmid factor and subgrain boundary analysis indicate that slip was largely accommodated by the {110} slip systems, with possible minor contribution by slip on the {100} slip systems. Some of the deformed samples show evidence of grain boundary migration. In addition, subgrains with small misorientations form that result in large cumulative misorientations within a single grain (>40°). However, no subgrain rotation recrystallization is observed (i.e., misorientation angles are <10°). All the experiments show strain hardening, suggesting that recrystallization by grain boundary migration was not extensive and did not reset the microstructure. The experiments show that high finite strain in coarse-grained relatively dry rock salt can be accommodated by dislocation creep, without extensive dynamic recrystallization.
Freeman, Gordon Samuel
DNA is of central importance in biology as it is responsible for carrying, copying, and translating the genetic code into the building blocks that comprise life. In order to accomplish these tasks, the DNA molecule must be versatile and robust. Indeed, the underlying molecular interactions that allow DNA to execute these tasks are complex and their origins are only beginning to be understood. While experiments are able to elucidate many key biophysical phenomena, there remain many unanswered questions. Molecular simulation is able to shed light on phenomena at the molecular scale and provide information that is missing from experimental views of DNA behavior. In this dissertation I use state-of-the-art coarse-grained DNA models to address two key problems. In the first, metadynamics calculations are employed to uncover the free energy surface of two complimentary DNA strands. This free energy surface takes on the appearance of a hybridization funnel and reveals candidates for intermediate states in the hybridization of short DNA oligomers. Such short oligomers are important building blocks for DNA-driven self-assembly and the mechanism of hybridization in this regime is not well understood. The second problem is that of nucleosome formation. Nucleosomes are the fundamental subunit of genome compaction in the nucleus of a cell. As such, nucleosomes are a key epigenetic factor and affect gene expression and the ability of DNA-binding proteins to locate and bind to the appropriate position in the genome. However, the factors that drive nucleosome positioning are not well understood. While DNA sequence is known to affect nucleosome formation, the mechanism by which it does so has not been established and a number of hypotheses explaining this sequence-dependence exist in the literature. I demonstrate that DNA shape dominates this process with contributions arising from both intrinsic DNA curvature as well as DNA-protein interactions driven by sequence
Hu, Hongda; Shu, Hong
2015-05-01
Heavy computation limits the use of Kriging interpolation methods in many real-time applications, especially with the ever-increasing problem size. Many researchers have realized that parallel processing techniques are critical to fully exploit computational resources and feasibly solve computation-intensive problems like Kriging. Much research has addressed the parallelization of traditional approach to Kriging, but this computation-intensive procedure may not be suitable for high-resolution interpolation of spatial data. On the basis of a more effective serial approach, we propose an improved coarse-grained parallel algorithm to accelerate ordinary Kriging interpolation. In particular, the interpolation task of each unobserved point is considered as a basic parallel unit. To reduce time complexity and memory consumption, the large right hand side matrix in the Kriging linear system is transformed and fixed at only two columns and therefore no longer directly relevant to the number of unobserved points. The MPI (Message Passing Interface) model is employed to implement our parallel programs in a homogeneous distributed memory system. Experimentally, the improved parallel algorithm performs better than the traditional one in spatial interpolation of annual average precipitation in Victoria, Australia. For example, when the number of processors is 24, the improved algorithm keeps speed-up at 20.8 while the speed-up of the traditional algorithm only reaches 9.3. Likewise, the weak scaling efficiency of the improved algorithm is nearly 90% while that of the traditional algorithm almost drops to 40% with 16 processors. Experimental results also demonstrate that the performance of the improved algorithm is enhanced by increasing the problem size.
Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array
Energy Technology Data Exchange (ETDEWEB)
Van Essen, B; Panda, R; Wood, A; Ebeling, C; Hauck, S
2010-12-01
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
Global- and local-scale characterisation of bed surface structure in coarse-grained alluvial rivers
Powell, Mark; Ockelford, Annie; Nguyen, Thao; Wood, Jo; Rice, Steve; Reid, Ian; Tate, Nick
2013-04-01
It is widely recognised that adjustments in bed surface grain size (texture) and grain arrangement (structure) exert significant controls on the stability of coarse-grained alluvial rivers. Modifications to bed surface texture and structure occur during active sediment transport and are mediated by the process of mobile armouring which concentrates coarser-than-average particles on the surface and organises them into a variety of grain- and bedform-scale configurations. Textural aspects of surface armouring are well understood to the extent that sediment transport models can be used to predict the size distribution of armours that develop under different sediment supply regimes and shear stresses. Research has also found that the adjustment of bed surface grain size is often patchy and that the development of finer-grained and coarser-grained areas of the bed has important implications for both the rate and grain size of transported sediment. The structural aspects of stream-bed armouring, however, are less well understood, largely because of the difficulty of recognising and characterising bedforms and bed-structures that have dimensions similar to their constituent particles. Moreover, bed structure is generally parameterised using global scale descriptors of the bed surface such that information on the spatial heterogeneity of the structure is lost. The aim of this poster is to characterise the structural characteristics of water-worked river gravels, paying particular attention to quantifying the spatial heterogeneity of those characteristics using local scale descriptors. Results reported from a number of flume experiments designed to simulate the spatio-temporal evolution of bed configurations (surface texture and structure) as the system adjusts to a condition of equilibrium transport are used to evaluate the spatial variability of bed surface structure and explore its significance for modelling sediment transport rates in gravel-bed rivers. Keywords: bed
Probing the structural dynamics of the SNARE recycling machine based on coarse-grained modeling.
Zheng, Wenjun
2016-08-01
Membrane fusion in eukaryotes is driven by the formation of a four-helix bundle by three SNARE proteins. To recycle the SNARE proteins, they must be disassembled by the ATPase NSF and four SNAP proteins which together form a 20S supercomplex. Recently, the first high-resolution structures of the NSF (in both ATP and ADP state) and 20S (in four distinct states termed I, II, IIIa, and IIIb) were solved by cryo-electron microscopy (cryo-EM), which have paved the way for structure-driven studies of the SNARE recycling mechanism. To probe the structural dynamics of SNARE disassembly at amino-acid level of details, a systematic coarse-grained modeling based on an elastic network model and related analyses were performed. Our normal mode analysis of NSF, SNARE, and 20S predicted key modes of collective motions that partially account for the observed structural changes, and illuminated how the SNARE complex can be effectively destabilized by untwisting and bending motions of the SNARE complex driven by the amino-terminal domains of NSF in state II. Our flexibility analysis identified regions with high/low flexibility that coincide with key functional sites (such as the NSF-SNAPs-SNARE binding sites). A subset of hotspot residues that control the above collective motions, which will make promising targets for future mutagenesis studies were also identified. Finally, the conformational changes in 20S as induced by the transition of NSF from ATP to ADP state were modeled, and a concerted untwisting motion of SNARE/SNAPs and a sideway flip of two amino-terminal domains were observed. In sum, the findings have offered new structural and dynamic details relevant to the SNARE disassembly mechanism, and will guide future functional studies of the SNARE recycling machinery. Proteins 2016; 84:1055-1066. © 2016 Wiley Periodicals, Inc. PMID:27090373
Coarse-Grained Molecular Dynamics for Computer Modeling of Nanomechanical Systems
Energy Technology Data Exchange (ETDEWEB)
Rudd, R E
2003-11-02
Unique challenges for computer modeling and simulation arise in the course of the development and design of nanoscale mechanical systems. Materials often exhibit unconventional behavior at the nanoscale that can affect device operation and failure. This uncertainty poses a problem because of the limited experimental characterization at these ultra-small length scales. In this Article we give an overview of how we have used concurrent multiscale modeling techniques to address some of these issues. Of particular interest are the dynamic and temperature-dependent processes found in nanomechanical systems. We focus on the behavior of sub-micron mechanical components of Micro-Electro-Mechanical Systems (MEMS) and Nano-Electro-Mechanical Systems (NEMS), especially flexural-mode resonators. The concurrent multiscale methodology we have developed for NEMS employs an atomistic description of millions of atoms in relatively small but key regions of the system, coupled to, and run concurrently with, a generalized finite element model of the periphery. We describe two such techniques. The more precise model, Coarse-Grained Molecular Dynamics (CGMD), describes the dynamics on a mesh of elements, but the equations of motion are built up from the underlying atomistic physics to ensure a smooth coupling between regions governed by different length scales. In many cases the degrees of smoothness of the coupling provided by CGMD is not necessary. The hybrid Coupling of Length Scales (CLS) methodology, combining molecular dynamics with conventional finite element modeling, provides a suitable technique for these cases at a greatly reduced computation expense. We review these models and some of the results we have obtained regarding size effects in the elasticity and dissipation of nanomechanical systems.
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.
Energy Technology Data Exchange (ETDEWEB)
Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)
2015-12-28
The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.
Energy Technology Data Exchange (ETDEWEB)
Poursina, Mohammad [Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ 85721 (United States); Anderson, Kurt S. [Department of Mechanical, Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute (RPI), Troy, NY 12180 (United States)
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.
Mechanism of the formation of peripheral coarse grain structure in hot extrusion of Al-4.5Zn-1Mg
Eivani, A. R.; Zhou, J.; Duszczyk, J.
2016-04-01
Microstructural evolution leading to peripheral coarse grain (PCG) structure in hot extruded Al-4.5Zn-1Mg rods is investigated. The extent of dynamic recrystallization (DRX) in the as-extruded product falls not in line with the basis over which the existing mechanisms for interpretation of PCG formation are built. A new mechanism is therefore proposed based on partial DRX during extrusion and nucleation and abnormal growth of statically recrsystallised grains.
Dunn, Nicholas J. H.; Noid, W. G.
2015-12-01
The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.
YAMAZAKI, Tamio
2011-01-01
To evaluate shear viscosity of ethylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded interactions among CG particles. Our parameterization procedure consists of three steps: 1) determination of bonded potentials, 2) scaling for time and solvent diffusivity, and 3) optimization of Lennard-Jones parameters to reproduce experimental self-diffusion coef...
Xiaoxu Li; Lianghui Gao; Weihai Fang
2016-01-01
In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divided into types distinguished by charge type, polarizability, and hydrogen-bonding capacity. First, we derive the relationship between the DPD repulsive force and Flory-Huggins χ-parameters based on...
Capdevila, Carlos; Miller, U; Jelenak, H; Bhadeshia, H. K. D. H.
2001-01-01
Mechanically alloyed iron-based ODS alloys have the potential for application in heat exchangers for biomass processing, with gas operating temperatures and pressures of approximately 1100°C and 15–30 bar. The yttria dispersion in such alloys improves the high-temperature creep and stress rupture life. The elevated temperature strength is enhanced by the development of a coarse-grained microstructure during recrystallisation. Factors controlling the evolution of this desirable micros...
Chu, Jhih-Wei; Voth, Gregory A.
2007-01-01
In this work, a double-well network model (DWNM) is presented for generating a coarse-grained free energy function that can be used to study the transition between reference conformational states of a protein molecule. Compared to earlier work that uses a single, multidimensional double-well potential to connect two conformational states, the DWNM uses a set of interconnected double-well potentials for this purpose. The DWNM free energy function has multiple intermediate states and saddle poi...
Li, Zhen; Bian, Xin; Yang, Xiu; Karniadakis, George Em
2016-07-01
We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.
Majumder, Manoj K; S, Ramkumar; Mahajan, Dhiraj K; Basu, Sumit
2010-01-01
Simulation of the deformation of polymers below their glass transition through molecular dynamics provides an useful route to correlate their molecular architecture to deformation behavior. However, present computational capabilities severely restrict the time and length scales that can be simulated when detailed models of these macromolecules are used. Coarse-graining techniques for macromolecular structures intend to make bigger and longer simulations possible by grouping atoms into superatoms and devising ways of determining reasonable force fields for the superatoms in a manner that retains essential macromolecular features relevant to the process under study but jettisons unnecessary details. In this work we systematically develop a coarse-graining scheme aimed at simulating uniaxial stress-strain behavior of polymers below their glass transition. The scheme involves a two step process of obtaining the coarse grained force field parameters above glass transition. This seems to be enough to obtain "faithful" stress-strain responses after quenching to below the glass transition temperature. We apply the scheme developed to a commercially important polymer polystyrene, derive its complete force field parameters and thus demonstrate the effectiveness of the technique.
Sanyal, Tanmoy; Shell, M. Scott
2016-07-01
Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.
Rui, Sun
2014-01-01
Coarse graining is an important ingredient in many multi-scale continuum-discrete solvers such as CFD--DEM (computational fluid dynamics--discrete element method) solvers for dense particle-laden flows. Although CFD--DEM solvers have become a mature technique that is widely used in multiphase flow research and industrial flow simulations, a flexible and easy-to-implement coarse graining algorithm that can work with CFD solvers of arbitrary meshes is still lacking. In this work, we proposed a new coarse graining algorithm for continuum--discrete solvers for dense particle-laden flows based on solving a transient diffusion equation. Via theoretical analysis we demonstrated that the proposed method is equivalent to the statistical kernel method with a Gaussian kernel, but the current method is much more straightforward to implement in CFD--DEM solvers. A priori numerical tests were performed to obtain the solid volume fraction fields based on given particle distributions, the results obtained by using the propos...
Sellers, Michael; Lisal, Martin; Schweigert, Igor; Larentzos, James; Brennan, John
2015-06-01
In discrete particle simulations, when an atomistic model is coarse-grained, a trade-off is made: a boost in computational speed for a reduction in accuracy. Dissipative Particle Dynamics (DPD) methods help to recover accuracy in viscous and thermal properties, while giving back a small amount of computational speed. One of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. Today, pairing the current evolution of DPD-RX with a coarse-grained potential and its chemical decomposition reactions allows for the simulation of the shock behavior of energetic materials at a timescale faster than an atomistic counterpart. In 2007, Maillet et al. introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We have recently extended the DPD-RX method and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its tranition to hot product gases within DPD-RX will be presented. Additionally, examples of the effect of microstructure on shock behavior will be shown. Approved for public release. Distribution is unlimited.
Adaptive Monte Carlo on multivariate binary sampling spaces
Schäfer, Christian
2010-01-01
A Monte Carlo algorithm is said to be adaptive if it can adjust automatically its current proposal distribution, using past simulations. The choice of the parametric family that defines the set of proposal distributions is critical for a good performance. We treat the problem of constructing such parametric families for adaptive sampling on multivariate binary spaces. A practical motivation for this problem is variable selection in a linear regression context, where we need to either find the best model, with respect to some criterion, or to sample from a Bayesian posterior distribution on the model space. In terms of adaptive algorithms, we focus on the Cross-Entropy (CE) method for optimisation, and the Sequential Monte Carlo (SMC) methods for sampling. Raw versions of both SMC and CE algorithms are easily implemented using binary vectors with independent components. However, for high-dimensional model choice problems, these straightforward proposals do not yields satisfactory results. The key to advanced a...
Derivation of free energy expressions for tube models from coarse-grained slip-link models
Steenbakkers, Rudi J. A.; Schieber, Jay D.
2012-07-01
We present the free energy of a single-chain mean-field model for polymer melt dynamics, which uses a continuous (tube-like) approximation to the discrete entanglements with surrounding chains, but, in contrast to previous tube models, includes fluctuations in the number density of Kuhn steps along the primitive path and in the degree of entanglement. The free energy is obtained from that of the slip-link model with fluctuating entanglement positions [J. D. Schieber and K. Horio, J. Chem. Phys. 132, 074905 (2010)], 10.1063/1.3314727 by taking the continuous limit of (functions of) the discrete Kuhn-step numbers and end-to-end vectors of the strands between entanglements. This coarse-graining from a more-detailed level of description has the advantage that no ad hoc arguments need to be introduced. Moreover, the thermodynamic consistency of the slip-link model [J. D. Schieber, J. Non-Equilib. Thermodyn. 28, 179 (2003)], 10.1515/JNETDY.2003.010 can be preserved. Fluctuations in the positions of entanglements lead to a harmonic bending term in the free energy of the continuous chain, similar to that derived by Read et al. [Macromolecules 41, 6843 (2008)], 10.1021/ma8009855 starting from a modified GLaMM model [R. S. Graham, A. E. Likhtman, T. C. B. McLeish, and S. T. Milner, J. Rheol. 47, 1171 (2003)], 10.1122/1.1595099. If these fluctuations are set to zero, the free energy becomes purely Gaussian and corresponds to the continuous limit of the original slip-link model, with affinely moving entanglements [J. D. Schieber, J. Chem. Phys. 118, 5162 (2003)], 10.1063/1.1553764. The free energy reduces to that of Read et al. under their assumptions of a homogeneous Kuhn-step number density and a constant degree of entanglement. Finally, we show how a transformation of the primitive-path coordinate can be applied to make the degree of entanglement an outcome of the model instead of a variable. In summary, this paper constitutes a first step towards a unified mathematical
Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation.
Blanco, Marco A; Sahin, Erinc; Robinson, Anne S; Roberts, Christopher J
2013-12-19
Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semiquantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work (Grüenberger et al., J. Phys. Chem. B 2013, 117, 763), this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental value of B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-Crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependence on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.
Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo
2015-12-15
Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to
Temperature-sensitive nanogels in the presence of salt: Explicit coarse-grained simulations
Quesada-Pérez, Manuel; Ahualli, Silvia; Martín-Molina, Alberto
2014-09-01
In this work, coarse-grained simulations of two charged thermo-shrinking nanogels (with degrees of ionization of 0.125 and 0.250) in the presence of 1:1 and 3:1 electrolytes have been explicitly performed through the bead-spring model of polyelectrolyte. In a first set of simulations, salt concentrations for 1:1 and 3:1 electrolytes ranged from 1 to 100 mM and from 0.167 to 16.7 mM, respectively, whereas temperature remained fixed at a value for which hydrophobic forces were negligible in our case (288 K). The sizes of swollen nanogels are smaller when trivalent cations are present, but they do not change significantly in the range of concentrations of 3:1 electrolyte studied here. It should be also stressed that trivalent cations neutralize the nanogel charge more efficiently. According to these results the electrostatic repulsion plays an important role. In a second set of simulations, the temperature varied from 288 to 333 K to study the effect of salt on the thermal response when hydrophobic forces are not negligible. For the nanogels with the lowest degree of ionization, the behavior of the radius with increasing the temperature can be described by a sigmoid function, which shifts towards lower temperatures in the presence of salt. This shift is more clearly observed for trivalent cations, even at low concentrations. For the nanogels with the highest degree of ionization, the effect of additional electrolyte is also noticeable. In this case, hydrophobic forces are not the only responsible for their shrinkage in the presence of trivalent cations. The surface electrostatic potential and the concentration of salt cations inside the nanogel have been computed from simulations and a modified Poisson-Boltzmann (PB) cell model. The thermosensitivity in size have certain influence on the sensitivity of these properties to temperature changes. The rich behavior of the surface electrostatic potential and the uptake of salt cations are successfully predicted by the
Odoh, S.; Saylor, J. E.; Higuera-Diaz, C.; Lapen, T. J.; Copeland, P.
2015-12-01
Progradation of coarse clastic material into distal foreland basins has been attributed to both 1) enhanced sediment production during rapid tectonic exhumation and 2) sediment reworking during tectonic quiescence. The Floresta and Medina basins in the Eastern Cordillera record deposition of alternating coarse- and fine-grained clastic strata in medial and distal (respectively) Cenozoic foreland basins. The Medina Basin records the continued eastward progradation of the deformation front in the Neogene. We use detrital zircon U-Pb (ZPb) and (U-Th)/He (ZHe) analyses from the Paleogene Floresta Basin and the entire Cenozoic Medina Basin record to evaluate the effects of episodic thrust-belt exhumation and wide-spread deposition of coarse-grained sediments in the adjacent foreland basin. Both ZPb and ZHe systems are applied to individual grains (double dating) to constrain source area and up-section variations in exhumation rates. Changes in exhumation rate or introduction of new sediment sources are recorded as changes in lag time (ZHe age - depositional age). Analysis of 6 samples from the Floresta Basin shows a decrease in lag time during deposition of the coarse-grained middle Eocene Picacho Formation and upper Paleocene Socha Sandstone suggesting that Paleogene deposition of coarse-grained intervals in this medial location corresponds to an increase in exhumation rate. However, initial results from the Medina basin are less clear as there is evidence for Paleocene volcanic input but no clear evidence for thrust-belt related sediment until the Oligocene-early Miocene. We interpret the evidence for different sediment sources for Eocene strata in the axial Eastern Cordillera (Floresta) versus the Eastern foothills (Medina) as indicative of separation of these two regions by an emergent forebulge. Exhumation rate and granularity appear to be inversely correlated in post-Oligocene strata, though confirmation of initial interpretations awaits larger samples sizes
Rojas, Ana; Liwo, Adam; Browne, Dana; Scheraga, Harold A.
2010-01-01
The mechanism of growth of fibrils of the β-amyloid peptide (Aβ) was studied by means of a physics-based coarse-grained united-residue (UNRES) model and molecular dynamics (MD) simulations. To identify the mechanism of monomer addition to an Aβ1–40 fibril, an unstructured monomer was placed at a 20 Å distance from a fibril template, and allowed to interact freely with it. The monomer was not biased towards the fibril conformation, by either the force field or the MD algorithm. By using a coar...
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
Large-diameter (4 to 6 m) monopiles are often used as foundations for offshore wind turbines. The monopiles are subjected to large horizontal forces and overturning moments and they are traditionally designed based on the p-y curve method. The p-y curves recommended in offshore design regulations...... 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...
Implementation and analysis of an adaptive multilevel Monte Carlo algorithm
Hoel, Hakon
2014-01-01
We present an adaptive multilevel Monte Carlo (MLMC) method for weak approximations of solutions to Itô stochastic dierential equations (SDE). The work [11] proposed and analyzed an MLMC method based on a hierarchy of uniform time discretizations and control variates to reduce the computational effort required by a single level Euler-Maruyama Monte Carlo method from O(TOL-3) to O(TOL-2 log(TOL-1)2) for a mean square error of O(TOL2). Later, the work [17] presented an MLMC method using a hierarchy of adaptively re ned, non-uniform time discretizations, and, as such, it may be considered a generalization of the uniform time discretizationMLMC method. This work improves the adaptiveMLMC algorithms presented in [17] and it also provides mathematical analysis of the improved algorithms. In particular, we show that under some assumptions our adaptive MLMC algorithms are asymptotically accurate and essentially have the correct complexity but with improved control of the complexity constant factor in the asymptotic analysis. Numerical tests include one case with singular drift and one with stopped diusion, where the complexity of a uniform single level method is O(TOL-4). For both these cases the results con rm the theory, exhibiting savings in the computational cost for achieving the accuracy O(TOL) from O(TOL-3) for the adaptive single level algorithm to essentially O(TOL-2 log(TOL-1)2) for the adaptive MLMC algorithm. © 2014 by Walter de Gruyter Berlin/Boston 2014.
Endres, Stephan; Weil, Janus; Bleicher, Marcus
2015-01-01
Dilepton invariant-mass spectra for heavy-ion collisions at SIS 18 and BEVALAC energies are calculated using a coarse-grained time evolution from the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) model. The coarse-graining of the microscopic simulations enables to calculate thermal dilepton emission rates by application of in-medium spectral functions from equilibrium quantum-field theoretical calculations. The results show that extremely high baryon chemical potentials dominate the evolution of the created hot and dense fireball. Consequently, a significant modification of the $\\rho$ spectral shape becomes visible in the dilepton invariant-mass spectrum, resulting in an enhancement in the low-mass region $M_{ee} = 200$ to 600 MeV/$c^{2}$. This enhancement, mainly caused by baryonic effects on the $\\rho$ spectral shape, can fully describe the experimentally observed excess above the hadronic cocktail contributions in Ar+KCl ($E_{\\mathrm{lab}}=1.76$ $A$GeV) reactions as measured by the HADES collaborat...
Nozaki, Daijiro; Bustos-Marún, Raul; Cattena, Carlos J.; Cuniberti, Gianaurelio; Pastawski, Horacio M.
2016-04-01
Dephasing effects in electron transport in molecular systems connected between contacts average out the quantum characteristics of the system, forming a bridge to the classical behavior as the size of the system increases. For the evaluation of the conductance of the molecular systems which have sizes within this boundary domain, it is necessary to include these dephasing effects. These effects can be calculated by using the D'Amato-Pastawski model. However, this method is computationally demanding for large molecular systems since transmission functions for all pairs of atomic orbitals need to be calculated. To overcome this difficulty, we develop an efficient coarse-grained model for the calculation of conductance of molecular junctions including decoherence. By analyzing the relationship between chemical potential and inter-molecular coupling, we find that the chemical potential drops stepwise in the systems with weaker inter-unit coupling. Using this property, an efficient coarse-grained algorithm which can reduce computational costs considerably without losing the accuracy is derived and applied to one-dimensional organic systems as a demonstration. This model can be used for the study of the orientation dependence of conductivity in various phases (amorphous, crystals, and polymers) of large molecular systems such as organic semiconducting materials.
Non-Markovian coarse-grained modeling of polymeric fluids based on the Mori-Zwanzig formalism
Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables based on the Mori-Zwanzig formalism. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons on both static and dynamic properties between the CG models with Markovian and non-Markovian approximations will be presented. Supported by the DOE Center on Mathematics for Mesoscopic Modeling of Materials (CM4) and an INCITE grant.
Endres, Stephan; van Hees, Hendrik; Bleicher, Marcus
2016-08-01
Dilepton production in heavy-ion collisions at collider energies—i.e., for the Relativistic Heavy Ion Collider (RHIC) and the Large Hadron Collider (LHC)—is studied within an approach that uses coarse-grained transport simulations to calculate thermal dilepton emission applying in-medium spectral functions from hadronic many-body theory and partonic production rates based on lattice calculations. The microscopic output from the Ultrarelativistic Quantum Molecular Dynamics (UrQMD) model is hereby put on a grid of space-time cells, which makes it possible to extract the local temperature and chemical potential in each cell via an equation of state. The resulting dilepton spectra are in good agreement with the experimental results for the range of energies available at RHIC, √{sN N}=19.6 -200 GeV . The comparison of the data with the outcome from the coarse-grained UrQMD simulations shows that the newest measurements by the PHENIX and STAR Collaborations are consistent and that the low-mass spectra can be described by a cocktail of hadronic decay contributions together with thermal emission from broadened vector-meson spectral functions and from the quark-gluon plasma phase. Predictions for dilepton results at LHC energies show no significant change of the spectra as compared to RHIC, but a higher fraction of thermal contribution and harder slopes of the transverse-momentum distributions owing to the higher temperatures and flow obtained.
Vries, de R.
2011-01-01
A large literature exists on modeling the influence of sequence-specific DNA-binding proteins on the shape of the DNA double helix in terms of one or a few fixed constraints. This approach is inadequate for the many proteins that bind DNA sequence independently, and that are present in very large qu
Kim, J.; Chang, T.; Yi, S.; Hong, S.
2012-12-01
We tested the applicability of optically stimulated luminescence (OSL) dating to fine- and coarse-grained quartz from the western coastal sediments of the Korean Peninsula. Twenty six samples were collected from 43-m-long core sediments, which contain two tidal deposits stratigraphically separated by a yellow, semi-consolidated mud layer and a gravel layer. A single aliquot regenerative dose (SAR) procedure was applied to chemically purified quartz grains of different grain sizes (4-11 and 90-212 μm diameter). The fine grain (4-11μm) OSL shows much higher saturation characteristic doses than those of the coarse grain (90-212 μm) OSL. The growth curves of the fine grain OSL show linear growth with dose up to ~800 Gy, whereas the those of the coarse grain OSL show an early saturated growth curve pattern (below 300 Gy). The OSL signal from the fine grain shows a quartz-dominated signal. On the other hand, OSL signals from coarse grain still contain a contribution from feldspars even after repeated chemical treatments. The De values are in agreement between the fine- and coarse-grained OSL in the upper part (0-15 m depth), but those of the lower part (>15 m) sediments are not. In the lower part, the De values of the fine grain are much higher (>400 Gy) than those from the coarse grain (part, but for the lower core samples ages based on fine grain OSL become progressively larger than those based on coarse grain. The fine grain ages are considered to be more accurate than the coarse grain ages, because they are not affected by signal saturation in this age range. Also, feldspar contamination may give rise to underestimation of the ages from the coarse grain OSL. Our results indicate that the ages obtained using fine-grained quartz can be old back to the Eemian. The major parts containing two tidal deposits have been deposited during the Holocene and MIS 5, with a limited sediment record during the last glacial period (MIS 2-4).
Camadas de tempestito grosso (coarse grained storm beds: exemplos do Permiano da bacia do Paraná
Directory of Open Access Journals (Sweden)
Joel C. de Castro
2001-07-01
Full Text Available Tempestitos grossos constituem camadas delgadas de conglomerado gradando a arenito, com estratificação cruzada seguida de laminação ondulada truncante a simétrica e de drape/flaser de siltito/folhelho. Cinco exemplos extraídos do Permiano da bacia do Paraná ilustram esse tipo de depósito: três deles são de rochas siliciclásticas, contendo bioclastos de bivalves e vertebrados (Formação Rio Bonito-Membro Triunfo e Formação Palermo, enquanto os outros dois são de rochas carbonática e fosfática (respectivamente, formações Teresina e Corumbataí do Grupo Passa Dois. O componente tracional da base do tempestito grosso apresenta-se como arenite quartzoso/lítico ou grainstone oolítico com cimento calcífero preenchendo poros (casos das formações Palermo e Teresina. Em sua maioria, os tempestitos grossos constituem pavimentos transgressivos intercalados em folhelhos ou tempestitos finos (arenitos muito finos a folhelhos com estratificação ondulada truncante-hummocky. Em outro caso, extraído de subsuperfície, o pavimento transgressivo ocorre na base de uma sucessão progradante de barra de plataforma. O tempestito grosso da Formação Teresina constitui um evento transgressivo sobreposto a depósitos de barra de plataforma.Coarse-grained storm beds are formed by cross-bedded to symmetrically-rippled conglomerate and sandstone, followed by drape or flaser of siltstone/shale. Five examples from the Permian of Paraná Basin illustrate this type of deposit: three of them are bioclast-bearing siliciclastic rocks of Rio Bonito (Triunfo Member and Palermo formations, while the other two are carbonate and phosphate rocks of Teresina and Corumbataí formations. The traction component at the base of coarse-grained storm beds is represented by quartzose arenite or oolitic grainstone with cavity-filling calcite cement (Palermo and Teresina formations. Most of the coarse-grained storm beds are transgressive lags intercalated in shales and
Korotin, D M; Bartkowski, S; Kurmaev, E Z; Borchers, C; Müller, M; Neumann, M; Gunderov, D V; Valiev, R Z; Cholakh, S O
2012-10-01
XPS measurements of coarse-grained and nanostructured nitinol (Ni(50.2)Ti(49.8)) before and after chemical treatment in hydrofluoric acid (40% HF, 1 min) are presented. The nanostructured state, providing the excellent mechanical properties of nitinol, is achieved by severe plastic deformation. The near-surface layers of nitinol were studied by XPS depth profiling. According to the obtained results, a chemical treatment in hydrofluoric acid reduces the thickness of the protective TiO(2) oxide layer and induces a nickel release from the nitinol surface and an arsenic contamination, and can therefore not be recommended as conditioning to increase the roughness of NiTi-implants. A detailed evaluation of the resulting toxicological risks is given.
Haxton, Thomas K; Zuckermann, Ronald N; Whitelam, Stephen
2016-01-12
Peptoid polymers form extended two-dimensional nanostructures via an interface-mediated assembly process: the amphiphilic peptoids first adsorb to an air-water interface as a monolayer, then buckle and collapse into free-floating bilayer nanosheets when the interface is compressed. Here, we investigate the molecular mechanism of monolayer buckling by developing a method for incorporating interface fluctuations into an implicit-solvent coarse-grained model. Representing the interface with a triangular mesh controlled by surface tension and surfactant adsorption, we predict the direction of buckling for peptoids with a segregated arrangement of charged side chains and predict that peptoids with with an alternating charge pattern should buckle less easily than peptoids with a segregated charge pattern. PMID:26647143
Yamazaki, Tamio
2011-01-01
To evaluate shear viscosity of ehylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded interactions among CG particles. Our parameterization procedure consists of three steps: 1)determination of bonded potentials, 2)scaling for time and solvent diffusivity, and 3)optimization of Lennard-Jones parameters to reproduce experimental self-diffusion coefficient data. With the determined parameters and the scaling relations, we evaluated shear viscosities of EGO/water binary mixtures, which are in close agreement with the experimental data, without any further fitting procedure. The largest simulation in this article corresponds to a 1.2 microseconds atomistic simulation for 100,000 atoms. Our CG model with the parameterization scheme for CG particles may be useful to study the dynamic properties of a liquid which contains relatively low molecular weight polymers or oligomers...
Li, Xiaoxu; Gao, Lianghui; Fang, Weihai
2016-01-01
In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divided into types distinguished by charge type, polarizability, and hydrogen-bonding capacity. First, we derive the relationship between the DPD repulsive force and Flory-Huggins χ-parameters based on this four-to-one CG mapping scheme. Then, we optimize the DPD force parameters for phospholipids. The feasibility of this model is demonstrated by simulating the structural and thermodynamic properties of lipid bilayer membranes, including the membrane thickness, the area per lipid, the lipid tail orientation, the bending rigidity, the rupture behavior, and the potential of mean force for lipid flip-flop. PMID:27137463
Directory of Open Access Journals (Sweden)
Xiaoxu Li
Full Text Available In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD force field is developed for phospholipids. The coarse-grained (CG models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divided into types distinguished by charge type, polarizability, and hydrogen-bonding capacity. First, we derive the relationship between the DPD repulsive force and Flory-Huggins χ-parameters based on this four-to-one CG mapping scheme. Then, we optimize the DPD force parameters for phospholipids. The feasibility of this model is demonstrated by simulating the structural and thermodynamic properties of lipid bilayer membranes, including the membrane thickness, the area per lipid, the lipid tail orientation, the bending rigidity, the rupture behavior, and the potential of mean force for lipid flip-flop.
Institute of Scientific and Technical Information of China (English)
LI Xing-mei; ZHANG Li-hui; QI Jian-xun; ZHANG Su-fang
2008-01-01
In order to study the problem that particle swarm optimization (PSO) algorithm can easily trap into local mechanism when analyzing the high dimensional complex optimization problems, the optimization calculation using the information in the iterative process of more particles was analyzed and the optimal system of particle swarm algorithm was improved. The extended particle swarm optimization algorithm (EPSO) was proposed. The coarse-grained and free-grained criteria that can control the selection were given to ensure the convergence of the algorithm. The two criteria considered the parameter selection mechanism under the situation of random probability. By adopting MATLAB7.1, the extended particle swarm optimization algorithm was demonstrated in the resource leveling of power project scheduling. EPSO was compared with genetic algorithm (GA) and common PSO, the result indicates that the variance of the objective function of resource leveling is decreased by 7.9%, 18.2%, respectively, certifying thee effectiveness and stronger global convergence ability of the EPSO.
Institute of Scientific and Technical Information of China (English)
Gui-long Xie; Yong-hong Zhang; Shi-ping Huang
2012-01-01
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.
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.
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
Okazaki, Kei-ichi; Sato, Takato; Takano, Mitsunori
2012-05-30
Association of protein molecules constitutes the basis for the interaction network in a cell. Despite its fundamental importance, the thermodynamic aspect of protein-protein binding, particularly the issues relating to the entropy change upon binding, remains elusive. The binding of actin and myosin, which are vital proteins in motility, is a typical example, in which two different binding mechanisms have been argued: the binding affinity increases with increasing temperature and with decreasing salt-concentration, indicating the entropy-driven binding and the enthalpy-driven binding, respectively. How can these thermodynamically different binding mechanisms coexist? To address this question, which is of general importance in understanding protein-protein bindings, we conducted an in silico titration of the actin-myosin system by molecular dynamics simulation using a residue-level coarse-grained model, with particular focus on the role of the electrostatic interaction. We found a good agreement between in silico and in vitro experiments on the salt-concentration dependence and the temperature dependence of the binding affinity. We then figured out how the two binding mechanisms can coexist: the enthalpy (due to electrostatic interaction between actin and myosin) provides the basal binding affinity, and the entropy (due to the orientational disorder of water molecules) enhances it at higher temperatures. In addition, we analyzed the actin-myosin complex structures observed during the simulation and obtained a variety of weak-binding complex structures, among which were found an unusual binding mode suggested by an earlier experiment and precursor structures of the strong-binding complex proposed by electron microscopy. These results collectively indicate the potential capability of a residue-level coarse-grained model to simulate the association-dissociation dynamics (particularly for transient weak-bindings) exhibited by larger and more complicated systems, as in a
Coarse-grained and fine-grained parallel optimization for real-time en-face OCT imaging
Kapinchev, Konstantin; Bradu, Adrian; Barnes, Frederick; Podoleanu, Adrian
2016-03-01
This paper presents parallel optimizations in the en-face (C-scan) optical coherence tomography (OCT) display. Compared with the cross-sectional (B-scan) imagery, the production of en-face images is more computationally demanding, due to the increased size of the data handled by the digital signal processing (DSP) algorithms. A sequential implementation of the DSP leads to a limited number of real-time generated en-face images. There are OCT applications, where simultaneous production of large number of en-face images from multiple depths is required, such as real-time diagnostics and monitoring of surgery and ablation. In sequential computing, this requirement leads to a significant increase of the time to process the data and to generate the images. As a result, the processing time exceeds the acquisition time and the image generation is not in real-time. In these cases, not producing en-face images in real-time makes the OCT system ineffective. Parallel optimization of the DSP algorithms provides a solution to this problem. Coarse-grained central processing unit (CPU) based and fine-grained graphics processing unit (GPU) based parallel implementations of the conventional Fourier domain (CFD) OCT method and the Master-Slave Interferometry (MSI) OCT method are studied. In the coarse-grained CPU implementation, each parallel thread processes the whole OCT frame and generates a single en-face image. The corresponding fine-grained GPU implementation launches one parallel thread for every data point from the OCT frame and thus achieves maximum parallelism. The performance and scalability of the CPU-based and GPU-based parallel approaches are analyzed and compared. The quality and the resolution of the images generated by the CFD method and the MSI method are also discussed and compared.
Dudarev, E. F.; Pochivalova, G. P.; Kolobov, Yu. R.; Bakach, G. P.; Skosyrskii, A. B.; Zhorovkov, M. F.; Goraynov, А. А.
2013-10-01
The results of an experimental investigation of the effect of mechanical-thermal treatment of submicrocrystalline and coarse-grained titanium on the deformation behavior in the stage of microplastic deformation at room and elevated temperatures are reported. The structural factors giving rise to the flowstress changes in the stage of microplastic deformation as a result of mechanical-thermal treatment are discussed. The general tendencies and special features of the effect of annealing and testing temperatures on the deformation behavior and flow stress in the first and second stages of microplastic deformation of submicrocrystalline and coarse-grained titanium subjected to large plastic deformation at 295 K are clarified.
Directory of Open Access Journals (Sweden)
Eisuke Chikayama
Full Text Available 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
Rojas, Ana; Liwo, Adam; Browne, Dana; Scheraga, Harold A
2010-12-01
The growth mechanism of β-amyloid (Aβ) peptide fibrils was studied by a physics-based coarse-grained united-residue model and molecular dynamics (MD) simulations. To identify the mechanism of monomer addition to an Aβ(1-40) fibril, we placed an unstructured monomer at a distance of 20 Å from a fibril template and allowed it to interact freely with the latter. The monomer was not biased towards fibril conformation by either the force field or the MD algorithm. With the use of a coarse-grained model with replica-exchange molecular dynamics, a longer timescale was accessible, making it possible to observe how the monomers probe different binding modes during their search for the fibril conformation. Although different assembly pathways were seen, they all follow a dock-lock mechanism with two distinct locking stages, consistent with experimental data on fibril elongation. Whereas these experiments have not been able to characterize the conformations populating the different stages, we have been able to describe these different stages explicitly by following free monomers as they dock onto a fibril template and to adopt the fibril conformation (i.e., we describe fibril elongation step by step at the molecular level). During the first stage of the assembly ("docking"), the monomer tries different conformations. After docking, the monomer is locked into the fibril through two different locking stages. In the first stage, the monomer forms hydrogen bonds with the fibril template along one of the strands in a two-stranded β-hairpin; in the second stage, hydrogen bonds are formed along the second strand, locking the monomer into the fibril structure. The data reveal a free-energy barrier separating the two locking stages. The importance of hydrophobic interactions and hydrogen bonds in the stability of the Aβ fibril structure was examined by carrying out additional canonical MD simulations of oligomers with different numbers of chains (4-16 chains), with the fibril
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
基于状态参数的筑坝粗粒土本构模型%Constitutive model for coarse-grained dam materials considering state parameter
Institute of Scientific and Technical Information of China (English)
魏匡民; 陈生水; 李国英; 傅中志
2016-01-01
Thestress-strain relationship of coarse-grained soils is closely related to soil density. The regularconstitutive model cannot consider the effect of initialvoid ratio on mechanical behaviors of coarse-grained soils. In this paper, a two-yield-surface modelis proposed for coarse-grained soils based on triaxial tests. The two-yield-surface model using a stateparameter so that can reflect the influence of soil density on the peak stress ratio, dilatancy rule, strain hardening or softening rule in shearing of coarse-grained soils. The stress-strain expressions of this model were also deduced. Several kind of coarse-grained soils test results were used to verify theadaptability of the proposed model, results showed that the model predictions are consistent with test results.%粗粒土的应力应变关系与其密实度有着密切的关系。当前常用的粗粒土本构模型无法考虑密实度对其力学行为的影响，在粗粒土三轴试验基础上建议了一个基于状态参数的粗粒土双屈服面模型，推导了其应力应变表达式。该模型能够反映不同初始孔隙比条件下粗粒土的峰值强度、剪胀性、应变硬化或软化规律。通过与多组粗粒土三轴试验结果比较，验证了模型的适应性。
International Nuclear Information System (INIS)
We investigate the volumetric glass transition temperature Tg 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 Tg increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition Tg 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 Tg 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
Langeloth, Michael; Sugii, Taisuke; Böhm, Michael C.; Müller-Plathe, Florian
2015-12-01
We investigate the volumetric glass transition temperature Tg 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 Tg increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition Tg 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 Tg 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.
Zaccone, A; Terentjev, I; Herling, T W; Knowles, T P J; Aleksandrova, A; Terentjev, E M
2016-09-14
While a significant body of investigations have been focused on the process of protein self-assembly, much less is understood about the reverse process of a filament breaking due to thermal motion into smaller fragments, or depolymerization of subunits from the filament ends. Indirect evidence for actin and amyloid filament fragmentation has been reported, although the phenomenon has never been directly observed either experimentally or in simulations. Here we report the direct observation of filament depolymerization and breakup in a minimal, calibrated model of coarse-grained molecular simulation. We quantify the orders of magnitude by which the depolymerization rate from the filament ends koff is larger than fragmentation rate k- and establish the law koff/k- = exp[(ε‖ - ε⊥)/kBT] = exp[0.5ε/kBT], which accounts for the topology and energy of bonds holding the filament together. This mechanism and the order-of-magnitude predictions are well supported by direct experimental measurements of depolymerization of insulin amyloid filaments. PMID:27634278
Energy Technology Data Exchange (ETDEWEB)
Kawamoto, Shuhei; Shinoda, Wataru, E-mail: w.shinoda@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603 (Japan); Klein, Michael L. [Institute for Computational Molecular Science, Temple University, SERC Building 1925 North 12th Street, Philadelphia, Pennsylvania 19122 (United States)
2015-12-28
The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle–vesicle, vesicle–planar, and planar–planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion.
Reasor, Daniel; Clausen, Jonathan; Aidun, Cyrus
2010-11-01
In small vessels, the cellular nature of blood is of utmost importance. The investigation of the non-Newtonian effects of blood for a complete range of hematocrit values and shear rates requires the direct numerical simulation (DNS) of individual red blood cells (RBCs) immersed in Newtonian blood plasma with hemoglobin within. Consequently, a coarse-grained spectrin-link (SL) RBC membrane model is coupled with a highly scalable lattice-Boltzmann (LB) flow solver to capture RBC dynamics in isolation and in dense suspensions of O(1,000) RBCs at realistic hematocrit values. Validation results include experimental comparisons with results for isolated RBCs tumbling, tank-treading, deforming in the wheel configuration, and parachuting in a microvessel-sized rigid tube. The rheology of blood is analyzed via LB-SL simulations of RBC suspensions at physiological concentrations. The results characterize the effect of the RBC deformation on the viscosity, normal stress differences, and particle pressure. Also, a demonstration of the Fahraeus effect is included which correlates the cell-depleted wall layer thickness with tube diameter for a variety of rigid microvessel-sized tube sizes. Lastly, the Fahraeus--Lindqvist effect is demonstrated using the apparent viscosity obtained from these simulations.
Institute of Scientific and Technical Information of China (English)
ZHANG Ying-qiao; ZHANG Han-qian; LI Jin-fu; LIU Wei-ming
2009-01-01
The influence of Nb on microstructure, mechanical property and the transformation kinetics of the coarse grain heat affected zone (CGHAZ) in HSLA steels for different heat inputs, has been investigated. When welded at higher heat inputs (100-60 kJ/cm), impact toughness values of the steel without Nb are much higher than those of the steel with Nb, and the lowest span is 153 J at 60 kJ/cm. But only a little higher values are observed at lower heat inputs (40-30 kJ/cm), and the highest span is 68 J at 30 kJ/cm. Dilatation studies indicate that continuous cooling transformation starting temperatures (Ts) of CGHAZ for the steel with Nb are approximately 15-30 ℃ which are lower than those of the steel without Nb at all heat inputs. For higher heat inputs, Nb in solid solution suppresses ferrite transformation and promotes the formation of granular bainite which has detrimental effect on impact tough-ness. For lower heat inputs higher Charpy impact energy values in the steel with Nb are associated with the formation of low carbon self-tempered martensite.
International Nuclear Information System (INIS)
The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle–vesicle, vesicle–planar, and planar–planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion
Directory of Open Access Journals (Sweden)
Artturi Koivuniemi
2012-01-01
Full Text Available 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 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 through its charged and tryptophan residues. Upon binding, CETP rapidly (in about 10 ns induced the formation of a small hydrophobic patch to the phospholipid surface of the droplet, opening a route from the core of the lipid droplet to the binding pocket of CETP. This was followed by a conformational change of helix X of CETP to an open state, in which we found the accessibility of cholesteryl esters to the C-terminal tunnel opening of CETP to increase. Furthermore, in the absence of helix X, cholesteryl esters rapidly diffused into CETP through the C-terminal opening. The results provide compelling 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.
Cipcigan, Flaviu S; 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 was recognised early-on and described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082-1086]. However, dispersion forces are still 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]. A way of treating both polarisation and dispersion on an equal basis is to coarse grain the electrons a molecular moiety to a single quantum harmonic oscillator, as suggested as early as the 1960s by Hirschfelder, Curtiss and Bird [The Molecular Theory of Gases and Liquids (1954)]. This treatment, when solved in the strong coupling ...
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.
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.
Masella, Michel; Borgis, Daniel; Cuniasse, Philippe
2011-09-01
A revised and improved version of our efficient polarizable force-field/coarse grained solvent combined approach (Masella, Borgis, and Cuniasse, J. Comput. Chem. 2008, 29, 1707) is described. The polarizable pseudo-particle solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile pseudo-particles. In this study, we propose a new formulation of the energy term handling the nonelectrostatic interactions among the pseudo-particles. This term is now able to reproduce the energetic and structural response of liquid water due to the presence of a hydrophobic spherical cavity. Accordingly, the parameters of the energy term handling the nonpolar solute/solvent interactions have been refined to reproduce the free-solvation energy of small solutes, based on a standard thermodynamic integration scheme. The reliability of this new approach has been checked for the properties of solvated methane and of the solvated methane dimer, as well as by performing 10 × 20 ns molecular dynamics (MD) trajectories for three solvated proteins. A long-time stability of the protein structures along the trajectories is observed. Moreover, our method still provides a measure of the protein solvation thermodynamic at the same accuracy as standard Poisson-Boltzman continuum methods. These results show the relevance of our approach and its applicability to massively coupled MD schemes to accurately and intensively explore solvated macromolecule potential energy surfaces. PMID:21647929
Zaccone, A; Herling, T W; Knowles, T P J; Aleksandrova, A; Terentjev, E M
2016-01-01
While a significant body of investigations have been focused on the process of protein self-assembly, much less is understood about the reverse process of a filament breaking due to thermal motion into smaller fragments, or depolymerization of subunits from the filament ends. Indirect evidence for actin and amyloid filament fragmentation has been reported, although the phenomenon has never been directly observed either experimentally or in simulations. Here we report the direct observation of filament depolymerization and breakup in a minimal, calibrated model of coarse-grained molecular simulation. We quantify the orders of magnitude by which the depolymerization rate from the filament ends $k_\\mathrm{off}$ is larger than fragmentation rate $k_{-}$ and establish the law $k_\\mathrm{off}/k_- = \\exp [( \\varepsilon_\\| - \\varepsilon_\\bot) / k_\\mathrm{B}T ] = \\exp [0.5 \\varepsilon / k_\\mathrm{B}T ]$, which accounts for the topology and energy of bonds holding the filament together. This mechanism and the order-of-...
Xie, Jinchuan; Lin, Jianfeng; Wang, Yu; Li, Mei; Zhang, Jihong; Zhou, Xiaohua; He, Yifeng
2015-01-01
The fate and transport of colloidal contaminants in natural media are complicated by physicochemical properties of the contaminants and heterogeneous characteristics of the media. Size and charge exclusion are two key microscopic mechanisms dominating macroscopic transport velocities. Faster velocities of colloid-associated actinides than that of 3H2O were consistently indicated in many studies. However, dissociation/dissolution of these sorbed actinides (e.g., Pu and Np), caused by their redox reactions on mineral surfaces, possibly occurred under certain chemical conditions. How this dissolution is related to transport velocities remains unanswered. In this study, aging of the colloid-associated Pu (pseudo-colloid) at room temperature and transport through the saturated coarse-grained granites were performed to study whether Pu could exhibit slower velocity than that of 3H2O (UPu/UT oxidative dissolution of Pu(IV) associated with the surfaces of colloidal granite particles took place during the aging period. The relative velocity of UPu/UT declined from 1.06 (unaged) to 0.745 (135 d) over time. Size exclusion limited to the uncharged nano-sized particles could not explain such observed UPu/UT oxidative dissolution of colloid-associated Pu(IV) was observed in the aged suspensions.
High-temperature creep in a coarse-grained oxide-dispersion strengthened Ni{sub 3}Al alloy
Energy Technology Data Exchange (ETDEWEB)
Klotz, U.E. [Eidgenoessische Technische Hochschule, Zurich (Switzerland). Inst. fuer Metallforschung; Mason, R.P. [Metal Matrix Cast Composites, Unit 1, 101 Clematis Ave, Waltham, MA 02154 (United States); Goehring, E. [Max-Planck-Institut fuer Metallforschung, Stuttgart (Germany). Inst. fuer Werkstoffwissenschaft]|[Stuttgart Univ. (Germany). Inst. fuer Metallkunde; Arzt, E. [Max-Planck-Institut fuer Metallforschung, Stuttgart (Germany). Inst. fuer Werkstoffwissenschaft]|[Stuttgart Univ. (Germany). Inst. fuer Metallkunde
1997-07-15
An oxide-dispersion strengthened (ODS) Ni{sub 3}Al(B)-alloy containing 5 at.% chromium, produced by powder metallurgy, was zone-annealed to produce a coarse-grained microstructure. The creep properties were then investigated between 1000 and 1200 C at creep rates from 10{sup -7} to 10{sup -3} s{sup -1} and the resulting experimental data were compared with several models of creep deformation. As expected, the Roesler and Arzt model for the detachment of single dislocations from the dispersoids did not satisfactorily explain the measured data. The model of Goehring and Arzt, which considers superdislocations, as present in ordered Ni{sub 3}Al, provided a much better correlation. The measured creep strengths were approximately five to ten times higher than those of fine-grained ODS-Ni{sub 3}Al; however, they were about 1000 times lower than those of commercial Ni-based alloys such as MA 6000. Suggestions for further development and experiments are made. (orig.)
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.
MacDermaid, Christopher M.; Kashyap, Hemant K.; DeVane, Russell H.; Shinoda, Wataru; Klauda, Jeffery B.; Klein, Michael L.; Fiorin, Giacomo
2015-12-01
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.
Isasti, N.; Jorge-Badiola, D.; Taheri, M. L.; López, B.; Uranga, P.
2011-12-01
Thermomechanical processing of microalloyed steels containing niobium can be performed to obtain deformed austenite prior to transformation. Accelerated cooling can be employed to refine the final microstructure and, consequently, to improve both strength and toughness. This general rule is fulfilled if the transformation occurs on a quite homogeneous austenite microstructure. Nevertheless, the presence of coarse austenite grains before transformation in different industrial processes is a usual source of concern, and regarding toughness, the coarsest high-angle boundary units would determine its final value. Sets of deformation dilatometry tests were carried out using three 0.06 pct Nb microalloyed steels to evaluate the effect of Mo alloying additions (0, 0.16, and 0.31 pct Mo) on final transformation from both recrystallized and unrecrystallized coarse-grained austenite. Continuous cooling transformation (CCT) diagrams were created, and detailed microstructural characterization was achieved through the use of optical microscopy (OM), field emission gun scanning electron microscopy (FEGSEM), and electron backscattered diffraction (EBSD). The resultant microstructures ranged from polygonal ferrite (PF) and pearlite (P) at slow cooling ranges to bainitic ferrite (BF) accompanied by martensite (M) for fast cooling rates. Plastic deformation of the parent austenite accelerated both ferrite and bainite transformation, moving the CCT curves to higher temperatures and shorter times. However, an increase in the final heterogeneity was observed when BF packets were formed, creating coarse high-angle grain boundary units.
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.
Directory of Open Access Journals (Sweden)
Samia Aci-Sèche
Full Text Available The cancer associated class 3 semaphorins require direct binding to neuropilins and association to plexins to trigger cell signaling. Here, we address the role of the transmembrane domains of neuropilin 1 and plexin A1 for the dimerization of the two receptors by characterizing the assembly in lipid bilayers using coarse-grained molecular dynamics simulations. From experimental evidence using a two-hybrid system showing the biochemical association of the two receptors transmembrane domains, we performed molecular simulations in DOPC and POPC demonstrating spontaneously assembly to form homodimers and heterodimers with a very high propensity for right-handed packing of the helices. Inversely, left-handed packing was observed with a very low propensity. This mode of packing was observed uniquely when the plexin A1 transmembrane domain was involved in association. Potential of mean force calculations were used to predict a hierarchy of self-association for the monomers: the two neuropilin 1 transmembrane domains strongly associated, neuropilin 1 and plexin A1 transmembrane domains associated less and the two plexin A1 transmembrane domains weakly but significantly associated. We demonstrated that homodimerization and heterodimerization are driven by GxxxG motifs, and that the sequence context modulates the packing mode of the plexin A1 transmembrane domains. This work presents major advances towards our understanding of membrane signaling platforms assembly through membrane domains and provides exquisite information for the design of antagonist drugs defining a novel class of therapeutic agents.
Directory of Open Access Journals (Sweden)
Qingzhen Hou
Full Text Available Large-scale identification of native binding orientations is crucial for understanding the role of protein-protein interactions in their biological context. Measuring binding free energy is the method of choice to estimate binding strength and reveal the relevance of particular conformations in which proteins interact. In a recent study, we successfully applied coarse-grained molecular dynamics simulations to measure binding free energy for two protein complexes with similar accuracy to full-atomistic simulation, but 500-fold less time consuming. Here, we investigate the efficacy of this approach as a scoring method to identify stable binding conformations from thousands of docking decoys produced by protein docking programs. To test our method, we first applied it to calculate binding free energies of all protein conformations in a CAPRI (Critical Assessment of PRedicted Interactions benchmark dataset, which included over 19000 protein docking solutions for 15 benchmark targets. Based on the binding free energies, we ranked all docking solutions to select the near-native binding modes under the assumption that the native-solutions have lowest binding free energies. In our top 100 ranked structures, for the 'easy' targets that have many near-native conformations, we obtain a strong enrichment of acceptable or better quality structures; for the 'hard' targets without near-native decoys, our method is still able to retain structures which have native binding contacts. Moreover, in our top 10 selections, CLUB-MARTINI shows a comparable performance when compared with other state-of-the-art docking scoring functions. As a proof of concept, CLUB-MARTINI performs remarkably well for many targets and is able to pinpoint near-native binding modes in the top selections. To the best of our knowledge, this is the first time interaction free energy calculated from MD simulations have been used to rank docking solutions at a large scale.
Breitsprecher, Konrad; Košovan, Peter; Holm, Christian
2014-07-16
We introduce a hierarchy of generic coarse-grained models of ionic liquids of increasing complexity. We use them in molecular dynamics simulations to study the differential capacitance of a capacitor consisting of an ionic liquid between two planar electrodes. The primary goal is to explain the complex dependence of the differential capacitance Cd on the electrode potential U in simple terms, e.g. in terms of the size and valency of the ions. For this purpose we introduce the symmetric model A, which qualitatively reproduces the Cd(U) dependence predicted by the mean-field theory but also reveals strong quantitative deviations. We further introduce size asymmetry in model A by increasing the cation size. In model B we vary the cation valency, keeping the sizes of both ions constant. We show that simultaneous increases in size and valency may compensate for each other, leading to a Cd(U) very similar to that for the symmetric case. We interpret distinct features in Cd(U) on the basis of the density profiles of the ions and charge density profiles. We focus on the first two ion layers at the electrode, and demonstrate that the polarization of the ionic liquid proceeds through replacement of one ion type by the other, in contrast to the simple increase in ion concentrations typical for dilute systems. The understanding gained for the simple models serves as a reference for interpretation of complex effects of ion size, valency and shape. This is carried through in part II (a separate article) where we show how the planar shape of ions in model C brings new features to the Cd(U) curve and also to the polarization mechanism.
Zhang, Peng; Gao, Chao; Zhang, Na; Slepian, Marvin J.; Deng, Yuefan; Bluestein, Danny
2014-01-01
We developed a multiscale particle-based model of platelets, to study the transport dynamics of shear stresses between the surrounding fluid and the platelet membrane. This model facilitates a more accurate prediction of the activation potential of platelets by viscous shear stresses - one of the major mechanisms leading to thrombus formation in cardiovascular diseases and in prosthetic cardiovascular devices. The interface of the model couples coarse-grained molecular dynamics (CGMD) with dissipative particle dynamics (DPD). The CGMD handles individual platelets while the DPD models the macroscopic transport of blood plasma in vessels. A hybrid force field is formulated for establishing a functional interface between the platelet membrane and the surrounding fluid, in which the microstructural changes of platelets may respond to the extracellular viscous shear stresses transferred to them. The interaction between the two systems preserves dynamic properties of the flowing platelets, such as the flipping motion. Using this multiscale particle-based approach, we have further studied the effects of the platelet elastic modulus by comparing the action of the flow-induced shear stresses on rigid and deformable platelet models. The results indicate that neglecting the platelet deformability may overestimate the stress on the platelet membrane, which in turn may lead to erroneous predictions of the platelet activation under viscous shear flow conditions. This particle-based fluid-structure interaction multiscale model offers for the first time a computationally feasible approach for simulating deformable platelets interacting with viscous blood flow, aimed at predicting flow induced platelet activation by using a highly resolved mapping of the stress distribution on the platelet membrane under dynamic flow conditions. PMID:25530818
International Nuclear Information System (INIS)
An important step in the simulation of a membrane protein in a phospholipid bilayer is the correct immersion of the protein in the bilayer. Crystal structures are determined without the bilayer. Particularly for proteins with monotopic domains, it can be unclear how deeply and in which orientation the protein is being inserted in the membrane. We have previously developed a procedure combining coarse-grain (CG) with all-atom (AA) molecular dynamics (MD) simulations to insert and simulate a cytochrome P450 (CYP) possessing an N-terminal transmembrane helix connected by a flexible linker region to a globular domain that dips into the membrane. The CG simulations provide a computationally efficient means to explore different orientations and conformations of the CYP in the membrane. Converged configurations obtained in the CG simulations are then refined in AA simulations. Here, we tested different variants of the MARTINI CG model, differing in the water model, the treatment of long-range non-bonded interactions, and the implementation (GROMACS 4.5.5 vs 5.0.4), for this purpose. We examined the behavior of the models for simulating a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in water and for the immersion of CYP3A4 in a POPC bilayer, and compared the CG-MD results with the previously reported experimental and simulation results. We also tested the methodology on a set of four other CYPs. Finally, we propose an optimized protocol for modeling such protein-membrane systems that provides the most plausible configurations and is computationally efficient; this incorporates the standard non-polar water model and the GROMACS 5.0.4 implementation with a reaction field treatment of long-range interactions
Energy Technology Data Exchange (ETDEWEB)
Mustafa, Ghulam, E-mail: Ghulam.Mustafa@h-its.org, E-mail: rebecca.wade@h-its.org; Nandekar, Prajwal P.; Yu, Xiaofeng [Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg (Germany); Wade, Rebecca C., E-mail: Ghulam.Mustafa@h-its.org, E-mail: rebecca.wade@h-its.org [Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg (Germany); Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120 Heidelberg (Germany); Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, INF 368, 69120 Heidelberg (Germany)
2015-12-28
An important step in the simulation of a membrane protein in a phospholipid bilayer is the correct immersion of the protein in the bilayer. Crystal structures are determined without the bilayer. Particularly for proteins with monotopic domains, it can be unclear how deeply and in which orientation the protein is being inserted in the membrane. We have previously developed a procedure combining coarse-grain (CG) with all-atom (AA) molecular dynamics (MD) simulations to insert and simulate a cytochrome P450 (CYP) possessing an N-terminal transmembrane helix connected by a flexible linker region to a globular domain that dips into the membrane. The CG simulations provide a computationally efficient means to explore different orientations and conformations of the CYP in the membrane. Converged configurations obtained in the CG simulations are then refined in AA simulations. Here, we tested different variants of the MARTINI CG model, differing in the water model, the treatment of long-range non-bonded interactions, and the implementation (GROMACS 4.5.5 vs 5.0.4), for this purpose. We examined the behavior of the models for simulating a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in water and for the immersion of CYP3A4 in a POPC bilayer, and compared the CG-MD results with the previously reported experimental and simulation results. We also tested the methodology on a set of four other CYPs. Finally, we propose an optimized protocol for modeling such protein-membrane systems that provides the most plausible configurations and is computationally efficient; this incorporates the standard non-polar water model and the GROMACS 5.0.4 implementation with a reaction field treatment of long-range interactions.
International Nuclear Information System (INIS)
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
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.
de Oliveira, Tiago E; Netz, Paulo A; Kremer, Kurt; Junghans, Christoph; Mukherji, Debashish
2016-05-01
We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C-IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. Additionally, we observe much faster convergence within C-IBI compared to IBI. To validate the robustness, we apply C-IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.
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.
Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Panahi, Afra; Feig, Michael
2014-01-01
An extension of the recently developed PRIMO coarse-grained force field to membrane environments, PRIMO-M, is described. The membrane environment is modeled with the heterogeneous dielectric generalized Born (HDGB) methodology that simply replaces the standard generalized Born model in PRIMO without further parametrization. The resulting model was validated by comparing amino acid insertion free energy profiles and application in molecular dynamics simulations of membrane proteins and membran...
Cao, R.; Li, J.; Liu, D. S.; Ma, J. Y.; Chen, J. H.
2015-07-01
This paper analyzes the micromechanism of decrease of impact toughness with increasing the welding heat input in coarse-grain heat-affected zone (CGHAZ) of a low-alloy high-strength ship-building steel plate. By comparing the microstructures, measuring the extending length of the fibrous crack, identifying the critical event of cleavage fracture, measuring the critical length, and calculating the local cleavage fracture stress σ f, and then using the basic principles of the micromechanism of cleavage fracture, this work reveals the essential causes of deteriorated toughness in the CGHAZ of high-strength steel welded joints.
粗粒土三轴试验的细观模拟%Meso-mechanics Simulation Triaxial Test of Coarse-grained Soil
Institute of Scientific and Technical Information of China (English)
耿丽; 黄志强; 苗雨
2011-01-01
对排土场粗粒土进行室内三轴固结排水试验,以此试验结果为基础,基于三维离散元颗粒流理论,从细观角度出发,以PFC3D为工具,通过自编程序并引入接触黏结模型,得到按级配生成的粗粒土三轴试验三维颗粒流模型.对比了不同围压下颗粒流模型与三轴试验的应力应变关系.分析了颗粒细观参数对粗粒土强度的影响.结果表明:按级配曲线得到的PFC数值模型的应力应变曲线的变化趋势与试验值一致,但强度值略低于试验值.粗粒土强度随颗粒间摩擦系数、接触处黏结强度的增大而提高；颗粒形状对材料的抗剪强度影响显著.研究意义在于从细观角度揭示影响粗粒土强度的因素,突破了常规三轴试验的局限性.%Consolidated-drained triaxial test is conducted for coarse-grained soil, based on the values of this test and three dimension particle flow code theory, the numerical model of triaxial test for graded coarse-grained soil is obtained by programming PFC3D (particle flow code of three dimension)from the view of microscopic scale. Stress-strain relationship of particle flow model and triaxial test are compared under different confining pressure. The influence of micro-properties on coarse-grained soil strength is analysed. The numerical results show that the strength of PFC model is lower than that of test, the increasing of friction coefficient between particles and bonded strength in contact result in higher strength of model. The particle shape has significant effects on the shear strength of numerical model. The research found the effect on coarse-grained soil strength from the view of microscopic scale and the results overcome the limits of real lab tests.
On adaptive resampling strategies for sequential Monte Carlo methods
Del Moral, Pierre; Jasra, Ajay; 10.3150/10-BEJ335
2012-01-01
Sequential Monte Carlo (SMC) methods are a class of techniques to sample approximately from any sequence of probability distributions using a combination of importance sampling and resampling steps. This paper is concerned with the convergence analysis of a class of SMC methods where the times at which resampling occurs are computed online using criteria such as the effective sample size. This is a popular approach amongst practitioners but there are very few convergence results available for these methods. By combining semigroup techniques with an original coupling argument, we obtain functional central limit theorems and uniform exponential concentration estimates for these algorithms.
International Nuclear Information System (INIS)
Graphical abstract: EBSD results showing the inhomogeneous recrystallization behavior in FSS-A after final recrystallization annealing: (a) orientation map; (b) pole figures corresponding to partial-recrystallized region 1; (c and d) ODFs (φ2-constant sections) corresponding to distinct recrystallized regions 2 and 3, respectively and (e) pole figures corresponding to recovered region 4. . Research highlights: → Recrystallization of coarse-grained Nb-bearing ferritic stainless steels → important orientation and composition effects during primary recrystallization → distinct recrystallization textures depending on the chemical composition. - Abstract: Composition and orientation effects on the final recrystallization texture of three coarse-grained Nb-containing AISI 430 ferritic stainless steels (FSSs) were investigated. Hot-bands of steels containing distinct amounts of niobium, carbon and nitrogen were annealed at 1250 deg. C for 2 h to promote grain growth. In particular, the amounts of Nb in solid solution vary from one grade to another. For purposes of comparison, the texture evolution of a hot-band sheet annealed at 1030 deg. C for 1 min (finer grain structure) was also investigated. Subsequently, the four sheets were cold rolled up to 80% reduction and then annealed at 800 deg. C for 15 min. Texture was determined using X-ray diffraction and electron backscatter diffraction (EBSD). Noticeable differences regarding the final recrystallization texture and microstructure were observed in the four investigated grades. Results suggest that distinct nucleation mechanisms take place within these large grains leading to the development of different final recrystallization textures.
Energy Technology Data Exchange (ETDEWEB)
Siqueira, R.P. [Departamento de Engenharia de Materiais, Escola de Engenharia de Lorena, University of Sao Paulo, 12600-970, Lorena-SP (Brazil); Sandim, H.R.Z., E-mail: hsandim@demar.eel.usp.br [Departamento de Engenharia de Materiais, Escola de Engenharia de Lorena, University of Sao Paulo, 12600-970, Lorena-SP (Brazil); Oliveira, T.R. [Centro de Pesquisa da ArcelorMittal Inox Brasil S.A., 35180-000, Timoteo-MG (Brazil); Raabe, D. [Max-Planck Institut fuer Eisenforschung, D-40237, Duesseldorf (Germany)
2011-04-15
Graphical abstract: EBSD results showing the inhomogeneous recrystallization behavior in FSS-A after final recrystallization annealing: (a) orientation map; (b) pole figures corresponding to partial-recrystallized region 1; (c and d) ODFs ({phi}{sub 2}-constant sections) corresponding to distinct recrystallized regions 2 and 3, respectively and (e) pole figures corresponding to recovered region 4. . Research highlights: {yields} Recrystallization of coarse-grained Nb-bearing ferritic stainless steels {yields} important orientation and composition effects during primary recrystallization {yields} distinct recrystallization textures depending on the chemical composition. - Abstract: Composition and orientation effects on the final recrystallization texture of three coarse-grained Nb-containing AISI 430 ferritic stainless steels (FSSs) were investigated. Hot-bands of steels containing distinct amounts of niobium, carbon and nitrogen were annealed at 1250 deg. C for 2 h to promote grain growth. In particular, the amounts of Nb in solid solution vary from one grade to another. For purposes of comparison, the texture evolution of a hot-band sheet annealed at 1030 deg. C for 1 min (finer grain structure) was also investigated. Subsequently, the four sheets were cold rolled up to 80% reduction and then annealed at 800 deg. C for 15 min. Texture was determined using X-ray diffraction and electron backscatter diffraction (EBSD). Noticeable differences regarding the final recrystallization texture and microstructure were observed in the four investigated grades. Results suggest that distinct nucleation mechanisms take place within these large grains leading to the development of different final recrystallization textures.
Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue
2016-05-01
Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program.
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.
Directory of Open Access Journals (Sweden)
Hiroto eKubo
2015-06-01
Full Text Available The characteristics of a coarse-grained high-remanence magnetite obtained from shocked Vredefort granite were investigated by X-ray magnetic circular dichroism (XMCD analysis and X-ray absorption spectroscopy (XAS. The study utilized a spectroscopic photoelectron low-energy electron emission microscope (SPELEEM and was conducted in the SPring-8 large-synchrotron radiation facility. It is generally believed that the strong and stable bulk remanence of Vredefort granites is due to the presence of minerals that have been strongly magnetized by either an impact-generated magnetic field or terrestrial lightning strikes. Although coarse-grained magnetite is traditionally characterized by weak coercivity and remanence, the specimen used in the present study exhibited high coercivity and an intense remanent magnetization. The presence of hematite lamellae observed on the partially oxidized magnetite specimen indicated an array of striped domains, intensifying a remanence and coercivity. We also conducted XAS and XMCD analyses on a natural lodestone permanent magnet produced by lightning strikes; while maghemite was found to be present, no magnetic domain structures were observed. Considering that the nucleation of hematite lamellae on magnetite/maghemite grains is due to high-temperature oxidation, we attribute the intense remanent magnetization and magnetic hardening of Vredefort granites to post-impact hydrothermal activity.
Braun, Daniel; Boresch, Stefan; Steinhauser, Othmar
2014-02-01
Long-term molecular dynamics simulations are used to compare the single particle dipole reorientation time, the diffusion constant, the viscosity, and the frequency-dependent dielectric constant of the coarse-grained big multipole water (BMW) model to two common atomistic three-point water models, SPC/E and TIP3P. In particular, the agreement between the calculated viscosity of BMW and the experimental viscosity of water is satisfactory. We also discuss contradictory values for the static dielectric properties reported in the literature. Employing molecular hydrodynamics, we show that the viscosity can be computed from single particle dynamics, circumventing the slow convergence of the standard approaches. Furthermore, our data indicate that the Kivelson relation connecting single particle and collective reorientation time holds true for all systems investigated. Since simulations with coarse-grained force fields often employ extremely large time steps, we also investigate the influence of time step on dynamical properties. We observe a systematic acceleration of system dynamics when increasing the time step. Carefully monitoring energy/temperature conservation is found to be a sufficient criterion for the reliable calculation of dynamical properties. By contrast, recommended criteria based on the ratio of fluctuations of total vs. kinetic energy are not sensitive enough.
The information-based complexity of approximation problem by adaptive Monte Carlo methods
Institute of Scientific and Technical Information of China (English)
2008-01-01
In this paper, we study the complexity of information of approximation problem on the multivariate Sobolev space with bounded mixed derivative MWpr,α(Td), 1 < p < ∞, in the norm of Lq(Td), 1 < q < ∞, by adaptive Monte Carlo methods. Applying the discretization technique and some properties of pseudo-s-scale, we determine the exact asymptotic orders of this problem.
Energy Technology Data Exchange (ETDEWEB)
Frusawa, Hiroshi, E-mail: frusawa.hiroshi@kochi-tech.ac.jp
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 ϕ{sub 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{sub c} and the jamming limit in the car parking problem.
Preparation of Nutritional Coarse Grain Powder by Twin-Screw Extrusion%膨化营养杂粮粉的挤压制备工艺研究
Institute of Scientific and Technical Information of China (English)
郑志; 王丽娟; 杨雪飞; 祁斌; 赖华楠; 姜绍通
2012-01-01
分别以80目玉米粉、糙米粉、燕麦粉、麦麸粉作为营养杂粮粉生产原料，研究物料含水量、螺杆转速、机筒温度对产品品质指标径向膨化度、糊化度和吸水性指数的影响，在此基础上设计正交试验，确定挤压技术制备膨化营养杂粮粉的最佳工艺参数为物料含水量15％、螺杆转速130r／min、机筒温度160℃，此时产品径向膨化度为3．26，糊化度为91．87％，吸水性指数为491．8％。%Nutritional coarse grain powder was developed using twin-screw extrusion technology with mixed powder of corn, unpolished rice, oat and wheat bran. The effects of water content in raw materials, screw speed and barrel temperature on quality indices including radial expansion degree, gelatinizafion degree and water-absorbing capacity of extruded powder were investigated. An orthogonal array design was used to determine the optimal process parameters for the preparation of nutritional coarse grain powder as follows: water content in raw materials of 15%, screw speed of 130 r/min, and barrel temperature of 160 ℃. The radial expansion degree, gelatinization degree and water-absorbing capacity of the obtained product were 3.26, 91.87 % and 491.8 %, respectively.
Reigada, Ramon; Buceta, Javier; Gómez, Jordi; Sagués, Francesc; Lindenberg, Katja
2008-01-14
Preferential affinity of cholesterol for saturated rather than unsaturated lipids underlies the thermodynamic process of the formation of lipid nanostructures in cell membranes, that is, of rafts. In this context, phase segregation of two-dimensional ternary lipid mixtures is formally studied from two different perspectives. The simplest approach is based on Monte Carlo simulations of an Ising model corresponding to two interconnected lattices, from which the basic features of the phenomenon are investigated. Then, the coarse-graining mean field procedure of the discrete Hamiltonian is adapted and a Ginzburg-Landau-like free energy expression is obtained. From this latter description, we construct kinetic equations that enable us to perform numerical simulations and to establish analytical phase separation criteria. Application of our formalism in the biological context is also discussed.
Lafitte, Thomas; Avendaño, Carlos; Papaioannou, Vasileios; Galindo, Amparo; Adjiman, Claire S.; Jackson, George; Müller, Erich A.
2012-06-01
In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C.S. Adjiman, G. Jackson, and E.A. Müller, J. Phys. Chem. B 115, 11154 (2011)] our methodology for the development of accurate coarse-grained (CG) SAFT-γ force fields for the computer simulation of molecular fluids was introduced with carbon dioxide as a particular case study. The procedure involves the use of a molecular-based equation of state to obtain effective intermolecular parameters (from experimental fluid phase equilibrium data) appropriate for molecular simulation over a wide range of fluid conditions. We now extend the methodology to develop coarse-grained models for benzene (C6H6) that can be used in fluid phase simulations. Our SAFT-γ CG force fields for benzene consist of a simple single-segment spherical model, and a rigid three-segment ring structure of tangent spherical groups interacting via Mie (generalized Lennard-Jones) segment-segment interactions. The description of the fluid phase behaviour of benzene with our simplified CG force fields is found to be comparable to that obtained with the more sophisticated models commonly used in the field; a marked improvement is seen with our SAFT-γ models for the vapour pressure, particularly at lower temperatures. These models of benzene together with the previously developed SAFT-γ three-segment chain model of n-decane are used to develop hetero-group force fields for n-decylbenzene, in the spirit of a group contribution methodology. In our approach, the parameters of the phenyl and n-decyl groups are obtained transferably from the individual models of benzene and n-decane, respectively, and the unlike energetic parameters between the phenyl and decyl segments can be obtained from vapour-liquid equilibria data for n-decylbenzene using the SAFT-γ equation of state. The resulting CG hetero-group models are found to describe the fluid properties of n-decylbenzene over a wide range of conditions, exemplifying how our approach
Romans, B.W.; Normark, W.R.; McGann, M.M.; Covault, J.A.; Graham, S.A.
2009-01-01
Utilizing accumulations of coarse-grained terrigenous sediment from deep-marine basins to evaluate the relative contributions of and history of controls on sediment flux through a source-to-sink system has been difficult as a result of limited knowledge of event timing. In this study, six new radiocarbon (14C) dates are integrated with five previously published dates that have been recalibrated from a 12.5-m-thick turbidite section from Ocean Drilling Program (ODP) Site 1015 in Santa Monica Basin, offshore California. This borehole is tied to high-resolution seismic-reflection profiles that cover an 1100 km2 area of the middle and lower Hueneme submarine fan and most of the basin plain. The resulting stratigraphic framework provides the highest temporal resolution for a thick-bedded Holocene turbidite succession to date, permitting an evaluation of source-to-sink controls at millennial (1000 yr) scales. The depositional history from 7 ka to present indicates that the recurrence interval for large turbidity-current events is relatively constant (300-360 yr), but the volume of sediment deposited on the fan and in the basin plain has increased by a factor of 2 over this period. Moreover, the amount of sand per event on the basin plain during the same interval has increased by a factor of 7. Maps of sediment distribution derived from correlation of seismic-reflection profiles indicate that this trend cannot be attributed exclusively to autogenic processes (e.g., progradation of depocenters). The observed variability in sediment accumulation rates is thus largely controlled by allogenic factors, including: (1) increased discharge of Santa Clara River as a result of increased magnitude and frequency of El Ni??o-Southern Oscillation (ENSO) events from ca. 2 ka to present, (2) an apparent change in routing of coarse-grained sediment within the staging area at ca. 3 ka (i.e., from direct river input to indirect, littoral cell input into Hueneme submarine canyon), and (3
Meyer, Sam
2014-01-01
The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unkown despite a growing structural knowledge of the complex. Here, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We apply the procedure on a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at the sites of histone-DNA contact, the DNA base-pairs are locally shifted outwards, consistent with locally repulsive forces exerted by the histones. In a second step, we show that the various force profiles of the analyzed structures derive locally from a unique, sequence-independent, quadratic repulsive force field, while the sequence preferences are entirely due to the internal DNA mechanics. We thus obtain the first knowledge-derived nanosca...
Energy Technology Data Exchange (ETDEWEB)
Zhu, Zhixiong, E-mail: zhixiongzhu@gmail.com [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Kuzmikova, Lenka; Li, Huijun [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Barbaro, Frank [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); CBMM Technology Suisse, 14, Rue du Rhone, Geneva 1204 (Switzerland)
2014-05-01
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.
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.
Dunn, Nicholas J. H.; Noid, W. G.
2016-05-01
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.
Dai, Xingxing; Yin, Qianqian; Wan, Guang; Wang, Ran; Shi, Xinyuan; Qiao, Yanjiang
2016-01-01
Borneol is a natural permeation enhancer that is effective in drugs used in traditional clinical practices as well as in modern scientific research. However, its molecular mechanism is not fully understood. In this study, a mixed coarse-grained model of stratum corneum (SC) lipid bilayer comprised of Ceramide-N-sphingosine (CER NS) 24:0, cholesterol (CHOL) and free fatty acids (FFA) 24:0 (2:2:1) was used to examine the permeation enhancing mechanism of borneol on the model drug osthole. We found two different mechanisms that were dependent on concentrations levels of borneol. At low concentrations, the lipid system maintained a bilayer structure. The addition of borneol made the lipid bilayer loosen and improved drug permeation. The "pull" effect of borneol also improved drug permeation. However, for a strongly hydrophobic drug like osthole, the permeation enhancement of borneol was limited. When most borneol molecules permeated into bilayers and were located at the hydrophobic tail region, the spatial competition effect inhibited drug molecules from permeating deeper into the bilayer. At high concentrations, borneol led to the formation of water pores and long-lived reversed micelles. This improved the permeation of osthole and possibly other hydrophobic or hydrophilic drugs through the SC. Our simulation results were supported by Franz diffusion tests and transmission electron microscope (TEM) experiments. PMID:27548141
Schindler, Tanja; Kröner, Dietmar; Steinhauser, Martin O
2016-09-01
We present a molecular dynamics simulation study of the self-assembly of coarse-grained lipid molecules from unbiased random initial configurations. Our lipid model is based on a well-tried CG polymer model with an additional potential that mimics the hydrophobic properties of lipid tails. We find that several stages of self-organization of lipid clusters are involved in the dynamics of bilayer formation and that the resulting equilibrium structures sensitively depend on the strength of hydrophobic interactions hc of the lipid tails and on temperature T. The obtained stable lipid membranes are quantitatively analyzed with respect to their local structure and their degree of order. At equilibrium, we obtain self-stabilizing bilayer membrane structures that exhibit a bending stiffness κB and compression modulus KC comparable to experimental measurements under physiological conditions. We present a phase diagram of our lipid model which covers a sol-gel transition, a liquid (or gel-like) phase including stable bilayer structures and vesicle formation, as well as a quasi-crystalline phase. We also determine the exact conditions for temperature T and degree of hydrophobicity hc for stable bilayer formation including closed vesicles. PMID:27216316
Directory of Open Access Journals (Sweden)
Xingxing Dai
2016-08-01
Full Text Available Borneol is a natural permeation enhancer that is effective in drugs used in traditional clinical practices as well as in modern scientific research. However, its molecular mechanism is not fully understood. In this study, a mixed coarse-grained model of stratum corneum (SC lipid bilayer comprised of Ceramide-N-sphingosine (CER NS 24:0, cholesterol (CHOL and free fatty acids (FFA 24:0 (2:2:1 was used to examine the permeation enhancing mechanism of borneol on the model drug osthole. We found two different mechanisms that were dependent on concentrations levels of borneol. At low concentrations, the lipid system maintained a bilayer structure. The addition of borneol made the lipid bilayer loosen and improved drug permeation. The “pull” effect of borneol also improved drug permeation. However, for a strongly hydrophobic drug like osthole, the permeation enhancement of borneol was limited. When most borneol molecules permeated into bilayers and were located at the hydrophobic tail region, the spatial competition effect inhibited drug molecules from permeating deeper into the bilayer. At high concentrations, borneol led to the formation of water pores and long-lived reversed micelles. This improved the permeation of osthole and possibly other hydrophobic or hydrophilic drugs through the SC. Our simulation results were supported by Franz diffusion tests and transmission electron microscope (TEM experiments.
International Nuclear Information System (INIS)
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
Energy Technology Data Exchange (ETDEWEB)
Khodabakhshi, F.; Kazeminezhad, M., E-mail: mkazemi@sharif.edu; Kokabi, A.H.
2015-06-18
We studied the microstructure and mechanical characteristics of spot welded specimens, fabricated from low carbon steel sheets with different microstructures. Both ultra-fine grained (UFG) steel sheet and coarse grained (CG) steel sheet were used. The refined microstructure of the UFG steel has been produced by severe plastic deformation (SPD) using the constrained groove pressing (CGP) method. The grain size of the base metals was approximately 260 nm and 30 µm in diameter, respectively, in the UFG and CG steels. Examining the microstructure of a cross section cut through the spot weld reveals a similar grain size and phase distribution in the nugget on both the sides of the initial interface between sheets. Some recrystallization is observed in the heat affected zone on the UFG side as previously reported after the welding of symmetrical UFG–UFG spot welded specimens. The same energy deposit produces larger nuggets after the spot welding of UFG steels. Moreover, the hardness distribution across the nugget changes after welding on both sides of the initial (UFG/CG) interface. This effect is presently attributed to a change in the solidification, cooling rate and tempering after welding, likely because the higher resistance of UFG steel sheets increases the heat release by the Joule effect during spot welding. These changes in the mechanical behavior modify the transition between the interfacial failure (IF) and pull out failure (PF) mode with respect to energy deposit.
Institute of Scientific and Technical Information of China (English)
Y.T. Chen; X. Chen; Q.F. Ding; J. Zeng
2005-01-01
The microstructure and the characteristics of the inclusions embedded in ferrite matrix in simu lated coarse-grain heat affected zone (CGHAZ) of a Ti-Zr-treated high strength low alloy (HSLA) steel have been investigated. The microstructure of the simulated CGHAZ dominantly consisted of intragranular acicular ferrite (IAF) combining with a small amount of polygonal ferrite (PF), widmanstatten ferrite (WF), bainite ferrite (BF), pearlite and martensite-austenite (M-A) islands. The PF, WF and BF were generally observed at the prior austenite grain boundaries and the interlocking acicular ferrite was usually found intragranularly. It was found that the inclusions were composed of Ti2O3, ZrO2 Al2O3 locating at the center of the particles and MnS lying on the surface layer of the inclusions. The intragranular complex inclusions prornoted the acicular ferrite formation and the refinement of microstructure whilst those at prior austenite grain boundaries caused PF formation on the inclusions. The simulated CGHAZ con sisting of such complicated microstructure exhibited desired mechanical properties.
Mohseni, Peyman; Solberg, Jan Ketil; Karlsen, Morten; Akselsen, Odd Magne; Østby, Erling
2014-01-01
Local brittle zones, i.e., martensite-austenite (M-A) islands, are formed within the coarse-grained heat-affected zone (CGHAZ) and the intercritically reheated CGHAZ (ICCGHAZ) during welding of many HSLA steels. In the current study, the M-A constituents in the microstructure of simulated ICCGHAZ of an API X80 pipeline steel were investigated using transmission electron microscopy and scanning electron microscopy. The focused ion beam technique was applied to make TEM specimens of M-A constituents that were located in the initiation sites of cleavage cracks. The main purpose of the study was to identify crack-initiation sites of cleavage fracture in ICCGHAZ and to prove the presence of M-A constituents in such initiation sites. Twinned martensite was detected in all local brittle zones that were investigated in the current study, demonstrating that they are M-A constituents. It was also demonstrated that the fracture initiation occurred preferentially at M-A constituents by a debonding mechanism rather than cracking of the M-A constituents.
Energy Technology Data Exchange (ETDEWEB)
Zhang, Y.Q. [Department of Materials Science and Engineering, Shanghai Jiaotong University, Shanghai 200030 (China)], E-mail: yingqiaozhang@yahoo.com.cn; Zhang, H.Q. [Department of Materials Science and Engineering, Shanghai Jiaotong University, Shanghai 200030 (China); Research Institute for Advanced Structural Steel, R and D Center, Baoshan Iron and Steel Limited Company, Shanghai 201900 (China); Liu, W.M. [Department of Materials Science and Engineering, Shanghai Jiaotong University, Shanghai 200030 (China); Hou, H. [Research Institute for Advanced Structural Steel, R and D Center, Baoshan Iron and Steel Limited Company, Shanghai 201900 (China)
2009-01-15
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, transformation start temperature is decreased by 20 K approximately in the steel with Nb compared with that without Nb. Ferrite nucleation at prior austenite grain boundaries is suppressed and the cooling rate region for granular bainite transformation is broadened. 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.
Yu, S. F.; Yan, N.; Chen, Y.
2016-06-01
In high heat-input multi-pass twin-wire submerged-arc welding, weld metal of previous pass will be affected by the heat input of subsequent one and form coarse-grained heat-affected zone (CGHAZ). This study focused on the effects of welding thermal cycle on the inclusions and microstructure of Ce-alloyed weld metal CGHAZ. According to the study of inclusions and microstructure of weld metal CGHAZ, it was found that the composition and type of the inclusions did not change under the effect of welding thermal cycle. Although the inclusions were coarsened slightly, the promoting ability to acicular ferrite (AF) was not deprived after thermal cycling. There are three types of AF in weld metal CGHAZ, which include oxy-sulfides of Ce inclusions-promoted AF, home-position-precipitated AF, and sympathetic AF. Results showed more than 80% of microstructure was AF, which greatly benefited the mechanical properties of weld metal CGHAZ, even though granular bainite and M-A constituents were generated.
Nagarajan, Anu; Andersen, Jens Peter; Woolf, Thomas B
2012-09-28
SERCA is a membrane transport protein that has been extensively studied. There are a large number of highly resolved X-ray structures and several hundred mutations that have been characterized functionally. Despite this, the molecular details of the catalytic cycle, a cycle that includes large conformational changes, is not fully understood. In this computational study, we provide molecular dynamics descriptions of conformational changes during the E2→E1 transitions. The motivating point for these calculations was a series of insertion mutants in the A-M3 linker region that led to significant shifts in measured rates between the E2 and E1 states, as shown by experimental characterization. Using coarse-grained dynamic importance sampling within the context of a population shift framework, we sample on the intermediates along the transition pathway to address the mechanism for the conformational changes and the effects of the insertion mutations on the kinetics of the transition. The calculations define an approximation for the relative changes in entropy and enthalpy along the transition. These are found to be important for understanding the experimentally observed differences in rates. In particular, the interactions between cytoplasmic domains, water interactions, and the shifts in protein degrees of freedom with the insertion mutations show mutual compensation for the E2→E1 transitions in wild-type and mutant systems.
Energy Technology Data Exchange (ETDEWEB)
Ardham, Vikram Reddy; Leroy, Frédéric, E-mail: vandervegt@csi.tu-darmstadt.de, E-mail: f.leroy@theo.chemie.tu-darmstadt.de [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt (Germany); Deichmann, Gregor; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de, E-mail: f.leroy@theo.chemie.tu-darmstadt.de [Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt (Germany)
2015-12-28
We address the question of how reducing the number of degrees of freedom modifies the interfacial thermodynamic properties of heterogeneous solid-liquid systems. We consider the example of n-hexane interacting with multi-layer graphene which we model both with fully atomistic and coarse-grained (CG) models. The CG models are obtained by means of the conditional reversible work (CRW) method. The interfacial thermodynamics of these models is characterized by the solid-liquid work of adhesion W{sub SL} calculated by means of the dry-surface methodology through molecular dynamics simulations. We find that the CRW potentials lead to values of W{sub SL} that are larger than the atomistic ones. Clear understanding of the relationship between the structure of n-hexane in the vicinity of the surface and W{sub SL} is elucidated through a detailed study of the energy and entropy components of W{sub SL}. We highlight the crucial role played by the solid-liquid energy fluctuations. Our approach suggests that CG potentials should be designed in such a way that they preserve the range of solid-liquid interaction energies, but also their fluctuations in order to preserve the reference atomistic value of W{sub SL}. Our study thus opens perspectives into deriving CG interaction potentials that preserve the thermodynamics of solid-liquid contacts and will find application in studies that intend to address materials driven by interfaces.
Petkevičiūtė, D; Pasi, M; Gonzalez, O; Maddocks, J H
2014-11-10
cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated free energy minimizer, i.e. the relative positions and orientations of each base, along with a stiffness matrix, which together govern differences in free energies. The model predicts non-local (i.e. beyond base-pair step) sequence dependence of the free energy minimizer. Configurations can be input or output in either the Curves+ definition of the usual helical DNA structural variables, or as a PDB file of coordinates of base atoms. We illustrate the cgDNA package by comparing predictions of free energy minimizers from (a) the cgDNA model, (b) time-averaged atomistic molecular dynamics (or MD) simulations, and (c) NMR or X-ray experimental observation, for (i) the Dickerson-Drew dodecamer and (ii) three oligomers containing A-tracts. The cgDNA predictions are rather close to those of the MD simulations, but many orders of magnitude faster to compute. Both the cgDNA and MD predictions are in reasonable agreement with the available experimental data. Our conclusion is that cgDNA can serve as a highly efficient tool for studying structural variations in B-form DNA over a wide range of sequences.
Dai, Xingxing; Yin, Qianqian; Wan, Guang; Wang, Ran; Shi, Xinyuan; Qiao, Yanjiang
2016-01-01
Borneol is a natural permeation enhancer that is effective in drugs used in traditional clinical practices as well as in modern scientific research. However, its molecular mechanism is not fully understood. In this study, a mixed coarse-grained model of stratum corneum (SC) lipid bilayer comprised of Ceramide-N-sphingosine (CER NS) 24:0, cholesterol (CHOL) and free fatty acids (FFA) 24:0 (2:2:1) was used to examine the permeation enhancing mechanism of borneol on the model drug osthole. We found two different mechanisms that were dependent on concentrations levels of borneol. At low concentrations, the lipid system maintained a bilayer structure. The addition of borneol made the lipid bilayer loosen and improved drug permeation. The “pull” effect of borneol also improved drug permeation. However, for a strongly hydrophobic drug like osthole, the permeation enhancement of borneol was limited. When most borneol molecules permeated into bilayers and were located at the hydrophobic tail region, the spatial competition effect inhibited drug molecules from permeating deeper into the bilayer. At high concentrations, borneol led to the formation of water pores and long-lived reversed micelles. This improved the permeation of osthole and possibly other hydrophobic or hydrophilic drugs through the SC. Our simulation results were supported by Franz diffusion tests and transmission electron microscope (TEM) experiments. PMID:27548141
Institute of Scientific and Technical Information of China (English)
Xiang-liang Wan; Kai-ming Wu; Gang Huang; Ran Wei; Lin Cheng
2014-01-01
The austenite grain growth behavior in a simulated coarse-grained heat-affected zone during thermal cycling was investigated via in situ observation. Austenite grains nucleated at ferrite grain boundaries and then grew in different directions through movement of grain boundaries into the ferrite phase. Subsequently, the adjacent austenite grains impinged against each other during theα→γtransformation. After theα→γtransformation, austenite grains coarsened via the coalescence of small grains and via boundary migration between grains. The growth process of austenite grains was a continuous process during heating, isothermal holding, and cooling in simulated thermal cy-cling. Abundant finely dispersed nanoscale TiN particles in a steel specimen containing 0.012wt%Ti effectively retarded the grain boundary migration, which resulted in refined austenite grains. When the Ti concentration in the steel was increased, the number of TiN particles de-creased and their size coarsened. The big particles were not effective in pinning the austenite grain boundary movement and resulted in coarse austenite grains.
International Nuclear Information System (INIS)
We address the question of how reducing the number of degrees of freedom modifies the interfacial thermodynamic properties of heterogeneous solid-liquid systems. We consider the example of n-hexane interacting with multi-layer graphene which we model both with fully atomistic and coarse-grained (CG) models. The CG models are obtained by means of the conditional reversible work (CRW) method. The interfacial thermodynamics of these models is characterized by the solid-liquid work of adhesion WSL calculated by means of the dry-surface methodology through molecular dynamics simulations. We find that the CRW potentials lead to values of WSL that are larger than the atomistic ones. Clear understanding of the relationship between the structure of n-hexane in the vicinity of the surface and WSL is elucidated through a detailed study of the energy and entropy components of WSL. We highlight the crucial role played by the solid-liquid energy fluctuations. Our approach suggests that CG potentials should be designed in such a way that they preserve the range of solid-liquid interaction energies, but also their fluctuations in order to preserve the reference atomistic value of WSL. Our study thus opens perspectives into deriving CG interaction potentials that preserve the thermodynamics of solid-liquid contacts and will find application in studies that intend to address materials driven by interfaces
Ardham, Vikram Reddy; Deichmann, Gregor; van der Vegt, Nico F A; Leroy, Frédéric
2015-12-28
We address the question of how reducing the number of degrees of freedom modifies the interfacial thermodynamic properties of heterogeneous solid-liquid systems. We consider the example of n-hexane interacting with multi-layer graphene which we model both with fully atomistic and coarse-grained (CG) models. The CG models are obtained by means of the conditional reversible work (CRW) method. The interfacial thermodynamics of these models is characterized by the solid-liquid work of adhesion WSL calculated by means of the dry-surface methodology through molecular dynamics simulations. We find that the CRW potentials lead to values of WSL that are larger than the atomistic ones. Clear understanding of the relationship between the structure of n-hexane in the vicinity of the surface and WSL is elucidated through a detailed study of the energy and entropy components of WSL. We highlight the crucial role played by the solid-liquid energy fluctuations. Our approach suggests that CG potentials should be designed in such a way that they preserve the range of solid-liquid interaction energies, but also their fluctuations in order to preserve the reference atomistic value of WSL. Our study thus opens perspectives into deriving CG interaction potentials that preserve the thermodynamics of solid-liquid contacts and will find application in studies that intend to address materials driven by interfaces.
Directory of Open Access Journals (Sweden)
Alessandro Marchiori
Full Text Available Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs. The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC and propylthiouracil (PROP. We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.
Joyeux, Marc
2014-01-01
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes, the precise structure of complexes of DNA and H-NS proteins is still not well understood. In particular, it is not clear whether the structure of DNA/H-NS complexes in the living cell is similar to that of complexes deposited on mica surfaces, which may be observed by AFM microscopy. A coarse-grained model, which helps getting more insight into this question, is described and analyzed in the present paper. This model is able of describing both the bridging of bacterial DNA by H-NS in the bulk and the deposition and equilibration of the complex on a charged surface. Simulations performed with the model reveal that a slight attraction between DNA and the charged surface is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar plasmids bridged by H-NS protei...
Markegard, Cade B; Gallivan, Cameron P; Cheng, Darrell D; Nguyen, Hung D
2016-08-18
A newly developed coarse-grained model called BioModi is utilized to elucidate the effects of temperature and concentration on DNA hybridization in self-assembly. Large-scale simulations demonstrate that complementary strands of either the tetrablock sequence or randomized sequence with equivalent number of cytosine or guanine nucleotides can form completely hybridized double helices. Even though the end states are the same for the two sequences, there exist multiple kinetic pathways that are populated with a wider range of transient aggregates of different sizes in the system of random sequences compared to that of the tetrablock sequence. The ability of these aggregates to undergo the strand displacement mechanism to form only double helices depends upon the temperature and DNA concentration. On one hand, low temperatures and high concentrations drive the formation and enhance stability of large aggregating species. On the other hand, high temperatures destabilize base-pair interactions and large aggregates. There exists an optimal range of moderate temperatures and low concentrations that allow minimization of large aggregate formation and maximization of fully hybridized dimers. Such investigation on structural dynamics of aggregating species by two closely related sequences during the self-assembly process demonstrates the importance of sequence design in avoiding the formation of metastable species. Finally, from kinetic modeling of self-assembly dynamics, the activation energy for the formation of double helices was found to be in agreement with experimental results. The framework developed in this work can be applied to the future design of DNA nanostructures in both fields of structural DNA nanotechnology and dynamic DNA nanotechnology wherein equilibrium end states and nonequilibrium dynamics are equally important requiring investigation in cooperation. PMID:27447850
Directory of Open Access Journals (Sweden)
Vincent Frappier
2014-04-01
Full Text Available Normal mode analysis (NMA methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.
Directory of Open Access Journals (Sweden)
Andrea N Kravats
2016-01-01
Full Text Available Clp ATPases are powerful ring shaped nanomachines which participate in the degradation pathway of the protein quality control system, coupling the energy from ATP hydrolysis to threading substrate proteins (SP through their narrow central pore. Repetitive cycles of sequential intra-ring ATP hydrolysis events induce axial excursions of diaphragm-forming central pore loops that effect the application of mechanical forces onto SPs to promote unfolding and translocation. We perform Langevin dynamics simulations of a coarse-grained model of the ClpY ATPase-SP system to elucidate the molecular details of unfolding and translocation of an α/β model protein. We contrast this mechanism with our previous studies which used an all-α SP. We find conserved aspects of unfolding and translocation mechanisms by allosteric ClpY, including unfolding initiated at the tagged C-terminus and translocation via a power stroke mechanism. Topology-specific aspects include the time scales, the rate limiting steps in the degradation pathway, the effect of force directionality, and the translocase efficacy. Mechanisms of ClpY-assisted unfolding and translocation are distinct from those resulting from non-allosteric mechanical pulling. Bulk unfolding simulations, which mimic Atomic Force Microscopy-type pulling, reveal multiple unfolding pathways initiated at the C-terminus, N-terminus, or simultaneously from both termini. In a non-allosteric ClpY ATPase pore, mechanical pulling with constant velocity yields larger effective forces for SP unfolding, while pulling with constant force results in simultaneous unfolding and translocation.
Directory of Open Access Journals (Sweden)
Yanping Fan
Full Text Available In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear array of nucleosome core particles (NCPs. The NCP is a well-defined complex of 147 bp DNA with an octamer of histones. Interactions between NCPs are of paramount importance for higher levels of chromatin compaction. The polyelectrolyte nature of the NCP implies that nucleosome-nucleosome interactions must exhibit a great influence from both the ionic environment as well as the positively charged and highly flexible N-terminal histone tails, protruding out from the NCP. The large size of the system precludes a modelling analysis of chromatin at an all-atom level and calls for coarse-grained approximations. Here, a model of the NCP that include the globular histone core and the flexible histone tails described by one particle per each amino acid and taking into account their net charge is proposed. DNA wrapped around the histone core was approximated at the level of two base pairs represented by one bead (bases and sugar plus four beads of charged phosphate groups. Computer simulations, using a Langevin thermostat, in a dielectric continuum with explicit monovalent (K(+, divalent (Mg(2+ or trivalent (Co(NH(3(6 (3+ cations were performed for systems with one or ten NCPs. Increase of the counterion charge results in a switch from repulsive NCP-NCP interaction in the presence of K(+, to partial aggregation with Mg(2+ and to strong mutual attraction of all 10 NCPs in the presence of CoHex(3+. The new model reproduced experimental results and the structure of the NCP-NCP contacts is in agreement with available data. Cation screening, ion-ion correlations and tail bridging contribute to the NCP-NCP attraction and the new NCP model accounts for these interactions.
Fan, Yanping; Korolev, Nikolay; Lyubartsev, Alexander P; Nordenskiöld, Lars
2013-01-01
In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear array of nucleosome core particles (NCPs). The NCP is a well-defined complex of 147 bp DNA with an octamer of histones. Interactions between NCPs are of paramount importance for higher levels of chromatin compaction. The polyelectrolyte nature of the NCP implies that nucleosome-nucleosome interactions must exhibit a great influence from both the ionic environment as well as the positively charged and highly flexible N-terminal histone tails, protruding out from the NCP. The large size of the system precludes a modelling analysis of chromatin at an all-atom level and calls for coarse-grained approximations. Here, a model of the NCP that include the globular histone core and the flexible histone tails described by one particle per each amino acid and taking into account their net charge is proposed. DNA wrapped around the histone core was approximated at the level of two base pairs represented by one bead (bases and sugar) plus four beads of charged phosphate groups. Computer simulations, using a Langevin thermostat, in a dielectric continuum with explicit monovalent (K(+)), divalent (Mg(2+)) or trivalent (Co(NH(3))(6) (3+)) cations were performed for systems with one or ten NCPs. Increase of the counterion charge results in a switch from repulsive NCP-NCP interaction in the presence of K(+), to partial aggregation with Mg(2+) and to strong mutual attraction of all 10 NCPs in the presence of CoHex(3+). The new model reproduced experimental results and the structure of the NCP-NCP contacts is in agreement with available data. Cation screening, ion-ion correlations and tail bridging contribute to the NCP-NCP attraction and the new NCP model accounts for these interactions.
Sergi, Danilo; Ortona, Alberto
2012-01-01
We report on a molecular dynamics investigation of the wetting properties of graphitic surfaces by various solutions at concentrations 1-8 wt% of commercially available non-ionic surfactants with long hydrophilic chains, linear or T-shaped. These are surfactants of length up to 160 [\\AA]. It turns out that molecular dynamics simulations of such systems ask for a number of solvent particles that can be reached without seriously compromising computational efficiency only by employing a coarse-grained model. The MARTINI force field with polarizable water offers a framework particularly suited for our problem. In general, its advantages over other coarse-grained models are the possibility to explore faster long time scales and the wider range of applicability. Although the accuracy is sometimes put under question, the results for the wetting properties by pure water are in good agreement with those for the corresponding atomistic systems and theoretical predictions. On the other hand, the bulk properties of vario...
Multidimensional stochastic approximation Monte Carlo.
Zablotskiy, Sergey V; Ivanov, Victor A; Paul, Wolfgang
2016-06-01
Stochastic Approximation Monte Carlo (SAMC) has been established as a mathematically founded powerful flat-histogram Monte Carlo method, used to determine the density of states, g(E), of a model system. We show here how it can be generalized for the determination of multidimensional probability distributions (or equivalently densities of states) of macroscopic or mesoscopic variables defined on the space of microstates of a statistical mechanical system. This establishes this method as a systematic way for coarse graining a model system, or, in other words, for performing a renormalization group step on a model. We discuss the formulation of the Kadanoff block spin transformation and the coarse-graining procedure for polymer models in this language. We also apply it to a standard case in the literature of two-dimensional densities of states, where two competing energetic effects are present g(E_{1},E_{2}). We show when and why care has to be exercised when obtaining the microcanonical density of states g(E_{1}+E_{2}) from g(E_{1},E_{2}). PMID:27415383
Energy Technology Data Exchange (ETDEWEB)
Vrugt, Jasper A [Los Alamos National Laboratory; Hyman, James M [Los Alamos National Laboratory; Robinson, Bruce A [Los Alamos National Laboratory; Higdon, Dave [Los Alamos National Laboratory; Ter Braak, Cajo J F [NETHERLANDS; Diks, Cees G H [UNIV OF AMSTERDAM
2008-01-01
Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.
Foam Multi-Dimensional General Purpose Monte Carlo Generator With Self-Adapting Symplectic Grid
Jadach, Stanislaw
2000-01-01
A new general purpose Monte Carlo event generator with self-adapting grid consisting of simplices is described. In the process of initialization, the simplex-shaped cells divide into daughter subcells in such a way that: (a) cell density is biggest in areas where integrand is peaked, (b) cells elongate themselves along hyperspaces where integrand is enhanced/singular. The grid is anisotropic, i.e. memory of the axes directions of the primary reference frame is lost. In particular, the algorithm is capable of dealing with distributions featuring strong correlation among variables (like ridge along diagonal). The presented algorithm is complementary to others known and commonly used in the Monte Carlo event generators. It is, in principle, more effective then any other one for distributions with very complicated patterns of singularities - the price to pay is that it is memory-hungry. It is therefore aimed at a small number of integration dimensions (<10). It should be combined with other methods for higher ...
Iterative Monte Carlo with bead-adapted sampling for complex-time correlation functions
Jadhao, Vikram; Makri, Nancy
2010-03-01
In a recent communication [V. Jadhao and N. Makri, J. Chem. Phys. 129, 161102 (2008)], we introduced an iterative Monte Carlo (IMC) path integral methodology for calculating complex-time correlation functions. This method constitutes a stepwise evaluation of the path integral on a grid selected by a Monte Carlo procedure, circumventing the exponential growth of statistical error with increasing propagation time, while realizing the advantageous scaling of importance sampling in the grid selection and integral evaluation. In the present paper, we present an improved formulation of IMC, which is based on a bead-adapted sampling procedure; thus leading to grid point distributions that closely resemble the absolute value of the integrand at each iteration. We show that the statistical error of IMC does not grow upon repeated iteration, in sharp contrast to the performance of the conventional path integral approach which leads to exponential increase in statistical uncertainty. Numerical results on systems with up to 13 degrees of freedom and propagation up to 30 times the "thermal" time ℏβ /2 illustrate these features.
Niccolini, G.; Alcolea, J.
Solving the radiative transfer problem is a common problematic to may fields in astrophysics. With the increasing angular resolution of spatial or ground-based telescopes (VLTI, HST) but also with the next decade instruments (NGST, ALMA, ...), astrophysical objects reveal and will certainly reveal complex spatial structures. Consequently, it is necessary to develop numerical tools being able to solve the radiative transfer equation in three dimensions in order to model and interpret these observations. I present a 3D radiative transfer program, using a new method for the construction of an adaptive spatial grid, based on the Monte Claro method. With the help of this tools, one can solve the continuum radiative transfer problem (e.g. a dusty medium), computes the temperature structure of the considered medium and obtain the flux of the object (SED and images).
Qian, Guangqiang; Yang, Zhuanling; Dong, Zhibao; Luo, Wanyin; Zhang, Zhengcai; Lu, Junfeng
2016-04-01
The aeolian process over fine to medium sand beds has been thoroughly discussed based on short-term, in-situ observations and wind tunnel tests. However, little is known about the long period variation of aeolian sediment transport as well as the geomorphological significance of saltating process, in particular, on the coarse-grained surface. By means of a segmented, eight-directional sand trap (SEDST) designed by the authors, the aeolian sediment transport on zibar surface was measured in the Kumtagh Desert of NW China. The SEDST has eight sub-traps faced to eight directions, each sub-trap contains a vertical array of samplers with four openings at 0 - 0.1 m, 0.1 - 0.2 m, 0.2 - 0.4 m and 0.4 - 1.0 m, respectively. Each opening is connected with an underground sand chamber. During the 1-yr field observation since May 2014, sediments were collected for six times with an interval of 1 to 3 months depending on the wind strength. The total weight of the captured sediments is 314.76 kg and most of them (54%) were transported within 0.1 m above the ground. The sediment transport rate ranges from 0.43 to 64.47 g/m.min for the six runs, the maximum transport rate occurred during the period of Aug to Oct 2014 with sediments from the north direction. The annual mean transport rate changes between 11.81 and 28.49 g/m.min and the sediments are mainly blown from the N, NE and NW directions. The resultant sediment transport direction (net transport) is SSE (172.92°), which implies the major sediment source direction. The sediment flux profiles can be fitted with the exponential decay function for six runs and all directions. Three groups can be identified from the gradients of the fitting curves, i.e. the N, NE and NW cluster, the S and SE cluster, as well as the E, SE and W cluster. Each cluster represents a particular combination of sediment source features and geomorphological settings that may significantly affect the formation process of zibars. The sediment transport
Avendaño, Carlos; Lafitte, Thomas; Adjiman, Claire S; Galindo, Amparo; Müller, Erich A; Jackson, George
2013-03-01
In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, and E. A. Müller, J. Phys. Chem. B2011, 115, 11154] we introduced the SAFT-γ force field for molecular simulation of fluids. In our approach, a molecular-based equation of state (EoS) is used to obtain coarse-grained (CG) intermolecular potentials that can then be employed in molecular simulation over a wide range of thermodynamic conditions of the fluid. The macroscopic experimental data for the vapor-liquid equilibria (saturated liquid density and vapor pressure) of a given system are represented with the SAFT-VR Mie EoS and used to estimate effective intermolecular parameters that provide a good description of the thermodynamic properties by exploring a wide parameter space for models based on the Mie (generalized Lennard-Jones) potential. This methodology was first used to develop a simple single-segment CG Mie model of carbon dioxide (CO2) which allows for a reliable representation of the fluid-phase equilibria (for which the model was parametrized), as well as an accurate prediction of other properties such as the enthalpy of vaporization, interfacial tension, supercritical density, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thomson coefficient, and speed of sound). In our current paper, the methodology is further applied and extended to develop effective SAFT-γ CG Mie force fields for some important greenhouse gases including carbon tetrafluoride (CF4) and sulfur hexafluoride (SF6), modeled as simple spherical molecules, and for long linear alkanes including n-decane (n-C10H22) and n-eicosane (n-C20H42), modeled as homonuclear chains of spherical Mie segments. We also apply the SAFT-γ methodology to obtain a CG homonuclear two-segment Mie intermolecular potential for the more challenging polar and asymmetric compound 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), a novel replacement
Leray, Aymeric; Trinel, Dave; Spriet, Corentin; Usson, Yves; Heliot, Laurent
2011-07-01
Fluorescence Lifetime Imaging Microscopy (FLIM) is a powerful technique which gives access to the local environment of fluorophores in living cells. However, to correctly estimate all lifetime parameters, time domain FLIM imaging requires a high number of photons and consequently a long laser exposure time which is not compatible with the observation of dynamic molecular events and which induces cellular stress phenomena. For reducing this exposure time, we have developed an original approach to statistically inflate the number of collected photon. This approach called Adaptive Monte Carlo Data Inflation (AMDI) combines the well-known bootstrap technique with an adaptive Parzen kernel. We have evaluated its potential on experimental FLIM data in vivo. We have demonstrated that our robust method allows estimating precisely fluorescence lifetime with exposure time reduced up to 50 times for mono-exponential (corresponding to a minimum of 20 photons/pixel) and 10 times for bi-exponential decays (corresponding to a minimum of 5000 photons/pixel) in comparison with the standard fitting method. Furthermore, thanks to AMDI, we demonstrate that it becomes possible to estimate accurately all fitting parameters in FRET experiments without constraining any parameter. An additional benefit of our technique is that it improves the spatial resolution of the FLIM images by reducing the commonly used spatial binning factor.
Adaptive multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model
Navarro, Cristóbal A.; Huang, Wei; Deng, Youjin
2016-08-01
This work presents an adaptive multi-GPU Exchange Monte Carlo approach for the simulation of the 3D Random Field Ising Model (RFIM). The design is based on a two-level parallelization. The first level, spin-level parallelism, maps the parallel computation as optimal 3D thread-blocks that simulate blocks of spins in shared memory with minimal halo surface, assuming a constant block volume. The second level, replica-level parallelism, uses multi-GPU computation to handle the simulation of an ensemble of replicas. CUDA's concurrent kernel execution feature is used in order to fill the occupancy of each GPU with many replicas, providing a performance boost that is more notorious at the smallest values of L. In addition to the two-level parallel design, the work proposes an adaptive multi-GPU approach that dynamically builds a proper temperature set free of exchange bottlenecks. The strategy is based on mid-point insertions at the temperature gaps where the exchange rate is most compromised. The extra work generated by the insertions is balanced across the GPUs independently of where the mid-point insertions were performed. Performance results show that spin-level performance is approximately two orders of magnitude faster than a single-core CPU version and one order of magnitude faster than a parallel multi-core CPU version running on 16-cores. Multi-GPU performance is highly convenient under a weak scaling setting, reaching up to 99 % efficiency as long as the number of GPUs and L increase together. The combination of the adaptive approach with the parallel multi-GPU design has extended our possibilities of simulation to sizes of L = 32 , 64 for a workstation with two GPUs. Sizes beyond L = 64 can eventually be studied using larger multi-GPU systems.
Kink, Dimitri; Bast, Alexander; Meyer, Christine; Meier, Wolfgang; Egli, Markus; Gärtner, Holger
2014-05-01
. In order to confirm this assumption and possibly find more important root properties which have an influence on soil stabilization, the root systems of seven trees (three grey alder, four mountain maple) were excavated and analyzed. The study site is a catchment, where shallow landslides are common. It is located in the Prättigau valley in the Eastern Swiss Alps and was eco-engineered in 1997. The substrate is coarse-grained morainic material, mean annual air temperature reaches 4.64°C, average precipitation is 1170 mm, and the altitude is about 1000 m a.s.l.. The root system of each tree was uncovered carefully by hand to keep the roots undamaged, before removal it was photographed in situ to document the root distribution. The root systems were then cut into single root pieces of about 20 cm length and the position of each sample was documented. The root samples were then hierarchically classified in several root classes. The tensile strength of more than 500 samples was determined. In addition, the values for age, diameter, and root moisture were ascertained. Since it was assumed, that the cellular structure of the roots has an influence on the tensile strength, two microscopic thin-sections were prepared from all successfully tested root samples. The microscopic analysis focused on anatomical parameters such as the size and number of vessels, their distribution as well as their conductivity. The results for the final correlation between the anatomical characteristics and the root's tensile strength are presented for both tree species.
Institute of Scientific and Technical Information of China (English)
刘志伟; 程东幸; 张希宏
2012-01-01
在新疆大规模的开发建设中,大量的工程场地将遇到粗颗粒盐渍土。因厂址区附近建筑材料缺乏,外运距离远,场地回填及地基换填料同时成为工程面临的难题。本文遵循就地取材的原则,开展了粗颗粒盐渍土现场回填碾压试验和专题研究,确定了粗颗粒盐渍土作为回填料的适宜性及相关设计施工参数。试验研究表明：当粗颗粒盐渍土易溶盐含量不是很高,具轻微溶陷性,并不考虑盐胀时,场地料重新回填可消除原有的溶陷性,且地基承载力可达170kPa,通过级配改良,混合料回填碾压后地基承载力可达300kPa,有了较大提高。其成果的获得,具有明显的工程效益。%In the large-scale development and construction in Xinjiang Uygur Autonomous Region, the most engineering site will encounter the coarse-grained salty soil. Due to the lack of building materials near the site and the long-distance transport, the materials for the back filling and soil replacement are facing the engineering problems. Following the principle to obtain raw material locally, the backfill compaction tests with coarse-grained salty soil and the special study in the field are carried out, and the suitability of the coarse-grained salty soil as backfill material and the relative design and construction parameters are determined. When the easy resolving salt content in coarse-grained salty soil is not very high, and with slight thaw collapsibility, without considering the expansion of salts, the experimental study shows that the thaw collapsibility has been eliminated after the back filling and rolling compaction with the site soil, and the bearing capacity can reach 170kPa. Through improving the gradation, the strength of the compacted backfill has been greatly improved; the bearing capacity of the mixed material can reach 300kPa, which obtain the favorable engineering benefit.
International Nuclear Information System (INIS)
The mechanical properties of the coarse grained (CG) Ni-18.75 at.% Fe alloy (the average grain size is 35 mkm) were studied in uniaxial compression with a constant rate in the temperature range 4.2-350 K. The temperature dependence of yield stress was measured, and the shape of the stress-strain curves was analyzed. The temperature dependences of flow stress, strain rate sensitivity of flow stress and activation volume of plastic deformation were measured for plastic strain of 2 %. The thermal activation analysis of the experimental data was carried out. It is shown that the plastic deformation of coarse grained alloy in the temperature range 35-350 K has a thermally activated type and it is controlled by the single deformation mechanism. Empirical estimates of the parameters of dislocation interaction with local barriers and the values of effective and internal stresses were obtained. The comparable analysis was carried out of the regularities of the low-temperature thermally activated plastic deformation of the alloy in CG and nanocrystalline (NC) states. It is concluded that the microscopic barriers, controlling the thermally activated plastic flow, are different in NC and CG states. The range of local barriers, which can determine the thermally activated dis-location plasticity in NC and CG states, is discussed.
Adaptive resolution simulation of an atomistic protein in MARTINI water
Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej
2014-01-01
We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coa
Zavadlav, Julija; Marrink, Siewert J; Praprotnik, Matej
2016-01-01
The adaptive resolution scheme (AdResS) is a multiscale molecular dynamics simulation approach that can concurrently couple atomistic (AT) and coarse-grained (CG) resolution regions, i.e., the molecules can freely adapt their resolution according to their current position in the system. Coupling to
Institute of Scientific and Technical Information of China (English)
惠治鑫; 贺鹏飞; 戴瑛; 吴艾辉
2015-01-01
The electronic transport, the storage capacity, and the service life of the anode material for lithium ion batteries will be reduced seriously in the event of the material layering or cracking, so the anode material must have strong mechanical reliability. Firstly, in view of the traditional molecular dynamics limited by the geometric scales of the model of silicon functionalized graphenen (SFG) as lithium ion battery anode material, some full atomic models of SFG are established by using Tersoff potential and Lennard-Jones potential, and used to calculate the modulus and the adhesion properties. What is more, according to the mechanical equilibrium condition and energy conservation and by combining with calculations from full atomic model through adopting the bead-spring structure, the SFG coarse-grain model and its system energy reservation equation are established. Finally, the validity of the SFG coarse-grain model is verified by comparing the tensile property of coarse-grain model with full atoms model.%硅功能化石墨烯(硅化烯)作为锂离子电池的负极材料，一旦发生分层或粉化等损伤现象，会严重地降低材料的电子输运能力和储锂容量，减少电池的使用寿命，因此要求负极材料具有较强的力学可靠性。考虑到传统分子动力学方法的模拟尺度很难达到硅化烯负极材料的真实尺度，首先采用Tersoff 势函数和Lennard-Jones 势函数建立了多种硅化烯的全原子数值模型，计算材料的各种弹性模量和吸附能；然后采用珠子-弹簧结构，根据力学平衡条件和能量守恒定律，结合全原子模型的计算结果，建立了硅化烯粗粒模型及其系统的能量方程；最后，通过对比石墨烯粗粒模型与其全原子模型的拉伸性能，验证了硅化烯粗粒模型的有效性。
Basden, Alastair
2015-01-01
The performance of a wide-field adaptive optics system depends on input design parameters. Here we investigate the performance of a multi-conjugate adaptive optics system design for the European Extremely Large Telescope, using an end-to-end Monte-Carlo adaptive optics simulation tool, DASP. We consider parameters such as the number of laser guide stars, sodium layer depth, wavefront sensor pixel scale, number of deformable mirrors, mirror conjugation and actuator pitch. We provide potential areas where costs savings can be made, and investigate trade-offs between performance and cost. We conclude that a 6 laser guide star system using 3 DMs seems to be a sweet spot for performance and cost compromise.
Ismail, A E; Rutledge, G C; Ismail, Ahmed E.; Stephanopoulos, George; Rutledge, Gregory C.
2003-01-01
In this paper, we extend our analysis of lattice systems using the wavelet transform to systems for which exact enumeration is impractical. For such systems, we illustrate a wavelet-accelerated Monte Carlo (WAMC) algorithm, which hierarchically coarse-grains a lattice model by computing the probability distribution for successively larger block spins. We demonstrate that although the method perturbs the system by changing its Hamiltonian and by allowing block spins to take on values not permitted for individual spins, the results obtained agree with the analytical results in the preceding paper, and ``converge'' to exact results obtained in the absence of coarse-graining. Additionally, we show that the decorrelation time for the WAMC is no worse than that of Metropolis Monte Carlo (MMC), and that scaling laws can be constructed from data performed in several short simulations to estimate the results that would be obtained from the original simulation. Although the algorithm is not asymptotically faster than t...
Kroonblawd, Matthew P; Sewell, Thomas D; Maillet, Jean-Bernard
2016-02-14
In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.
Energy Technology Data Exchange (ETDEWEB)
Kroonblawd, Matthew P.; Sewell, Thomas D., E-mail: sewellt@missouri.edu [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211-7600 (United States); Maillet, Jean-Bernard, E-mail: jean-bernard.maillet@cea.fr [CEA, DAM, DIF, F-91297 Arpajon (France)
2016-02-14
In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.
Kroonblawd, Matthew P.; Sewell, Thomas D.; Maillet, Jean-Bernard
2016-02-01
In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.
Kroonblawd, Matthew P; Sewell, Thomas D; Maillet, Jean-Bernard
2016-02-14
In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock. PMID:26874491
堆石粗粒土多级加荷三轴试验分析%MULTI-STAGE LOADING TRIAXIAL TEST ANALYSIS OF ROCK-FILL COARSE GRAINED SOIL
Institute of Scientific and Technical Information of China (English)
李远贤; 梁军
2001-01-01
通过分析堆石粗粒土一个试样多级加荷三轴试验方法，将其分为不固结类的连续与固结类的不连续加荷。前者仅适用于σ3≤1.2MPa的低围压，后者必须考虑固结排水引起的应力回弹量。不连续加荷的固结方式对强度指标的影响仅限于C值，内摩擦角Φ值基本保持不变。建议对土工试验规程中有关粗粒土的多级加荷三轴试验作重新修订。%On the basis of one sample multi-stage loading triaxial testanalysis of rock-fill coarse grained soil, the loading is divided into unconsolidated type continuous loading and consolidated type discontinuous loading. The former only applies to low wallrock pressure of σ3≤1.2 MPa, and the latter must consider rebound quantity induced by consolidation and drain. The strength index effect of consolidation style of discontinuous loading is only limited to the value of C, while the angle of internal friction Φ is kept basically the same. It is suggested that the rules for coarse grained soil multi-stage loading triaxial tests be revised.
Wetting of polymer liquids: Monte Carlo simulations and self-consistent field calculations
Müller, M
2003-01-01
Using Monte Carlo simulations and self-consistent field (SCF) theory we study the surface and interface properties of a coarse grained off-lattice model. In the simulations we employ the grand canonical ensemble together with a reweighting scheme in order to measure surface and interface free energies and discuss various methods for accurately locating the wetting transition. In the SCF theory, we use a partial enumeration scheme to incorporate single-chain properties on all length scales and use a weighted density functional for the excess free energy. The results of various forms of the density functional are compared quantitatively to the simulation results. For the theory to be accurate, it is important to decompose the free energy functional into a repulsive and an attractive part, with different approximations for the two parts. Measuring the effective interface potential for our coarse grained model we explore routes for controlling the equilibrium wetting properties. (i) Coating of the substrate by an...
Basden, A. G.; Morris, T. J.
2016-09-01
The performance of a wide-field adaptive optics system depends on input design parameters. Here we investigate the performance of a multi-object adaptive optics system design for the European Extremely Large Telescope, using an end-to-end Monte-Carlo adaptive optics simulation tool, DASP, with relevance for proposed instruments such as MOSAIC. We consider parameters such as the number of laser guide stars, sodium layer depth, wavefront sensor pixel scale, actuator pitch and natural guide star availability. We provide potential areas where costs savings can be made, and investigate trade-offs between performance and cost, and provide solutions that would enable such an instrument to be built with currently available technology. Our key recommendations include a trade-off for laser guide star wavefront sensor pixel scale of about 0.7 arcseconds per pixel, and a field of view of at least 7 arcseconds, that EMCCD technology should be used for natural guide star wavefront sensors even if reduced frame rate is necessary, and that sky coverage can be improved by a slight reduction in natural guide star sub-aperture count without significantly affecting tomographic performance. We find that adaptive optics correction can be maintained across a wide field of view, up to 7 arcminutes in diameter. We also recommend the use of at least 4 laser guide stars, and include ground-layer and multi-object adaptive optics performance estimates.
Monte Carlo simulations of charge transport in heterogeneous organic semiconductors
Aung, Pyie Phyo; Khanal, Kiran; Luettmer-Strathmann, Jutta
2015-03-01
The efficiency of organic solar cells depends on the morphology and electronic properties of the active layer. Research teams have been experimenting with different conducting materials to achieve more efficient solar panels. In this work, we perform Monte Carlo simulations to study charge transport in heterogeneous materials. We have developed a coarse-grained lattice model of polymeric photovoltaics and use it to generate active layers with ordered and disordered regions. We determine carrier mobilities for a range of conditions to investigate the effect of the morphology on charge transport.
Rached, Nadhir B.
2013-12-01
The Monte Carlo forward Euler method with uniform time stepping is the standard technique to compute an approximation of the expected payoff of a solution of an Itô SDE. For a given accuracy requirement TOL, the complexity of this technique for well behaved problems, that is the amount of computational work to solve the problem, is O(TOL-3). A new hybrid adaptive Monte Carlo forward Euler algorithm for SDEs with non-smooth coefficients and low regular observables is developed in this thesis. This adaptive method is based on the derivation of a new error expansion with computable leading-order terms. The basic idea of the new expansion is the use of a mixture of prior information to determine the weight functions and posterior information to compute the local error. In a number of numerical examples the superior efficiency of the hybrid adaptive algorithm over the standard uniform time stepping technique is verified. When a non-smooth binary payoff with either GBM or drift singularity type of SDEs is considered, the new adaptive method achieves the same complexity as the uniform discretization with smooth problems. Moreover, the new developed algorithm is extended to the MLMC forward Euler setting which reduces the complexity from O(TOL-3) to O(TOL-2(log(TOL))2). For the binary option case with the same type of Itô SDEs, the hybrid adaptive MLMC forward Euler recovers the standard multilevel computational cost O(TOL-2(log(TOL))2). When considering a higher order Milstein scheme, a similar complexity result was obtained by Giles using the uniform time stepping for one dimensional SDEs. The difficulty to extend Giles\\' Milstein MLMC method to the multidimensional case is an argument for the flexibility of our new constructed adaptive MLMC forward Euler method which can be easily adapted to this setting. Similarly, the expected complexity O(TOL-2(log(TOL))2) is reached for the multidimensional case and verified numerically.
Institute of Scientific and Technical Information of China (English)
褚福永; 朱俊高; 贾华; 安淑红
2012-01-01
The test results of three different coarse-grained soils are obtained with conventional triaxial cyclic loading test. Based on these results, some useful conclusions are drawn from the discussion and analysis of the phenomenon of volume-contraction in unloading of coarse-grained soils: The phenomenon of the volume-contraction in unloading of coarse-grained soil is more obvious with the increasing of stress level and with the decreasing of confining pressure. According to the test data, a relationship formula among volume contraction in unloading and stress level and confining pressure is obtained. Rebound modulus presents the curve of hump shape with the increasing of stress level and the maximum is obtained when stress level is 0.7. The ratio of average rebound modulus and initial elastic modulus with monotonic loading present decrease of a power function, this ratio of soil material whose mother rock is high hardness is larger and the ratio of soil material whose mother rock is soft is smaller. The general relationship between kur and nur which is obtained from rebound in unloading and k and n which is obtained from monotonic loading is that kur is approximately from 2.46 times to 4.60 times of k and nur is approximately from 0.540 times to 0.885 times of n respectively.%进行了3种不同粗粒土的常规三轴加载-卸载-再加载的剪切试验,对粗粒土的卸载-再加载的力学特性进行了分析.结果表明:粗粒土存在卸载体缩现象,且随着应力水平的增加,卸载体缩量增加；随着围压的增加,卸载体缩量减小.根据试验数据总结了卸载体缩量与应力水平、围压之间关系式.回弹模量随应力水平的增加呈驼峰型曲线,即应力水平在0.7左右时最大,小于或大于0.7时的弹性模量均较小.平均回弹模量与单调加载时的初始弹性模量的比值随围压呈幂函数降低,母岩硬度大的土料,该比值较大,相反,母岩较软的土料,该比值较小.由单调加
Basden, Alastair
2016-01-01
The performance of a wide-field adaptive optics system depends on input design parameters. Here we investigate the performance of a multi-object adaptive optics system design for the European Extremely Large Telescope, using an end-to-end Monte-Carlo adaptive optics simulation tool, DASP, with relevance for proposed instruments such as MOSAIC. We consider parameters such as the number of laser guide stars, sodium layer depth, wavefront sensor pixel scale, actuator pitch and natural guide star availability. We provide potential areas where costs savings can be made, and investigate trade-offs between performance and cost, and provide solutions that would enable such an instrument to be built with currently available technology. Our key recommendations include a trade-off for laser guide star wavefront sensor pixel scale of about 0.7 arcseconds per pixel, and a field of view of at least 7 arcseconds, that EMCCD technology should be used for natural guide star wavefront sensors even if reduced frame rate is nece...
Andolfatto, Loïc; Lavernhe, Sylvain; 10.1016/j.ijmachtools.2011.03.006
2011-01-01
Knowledge of a machine tool axis to axis location errors allows compensation and correcting actions to be taken to enhance its volumetric accuracy. Several procedures exist, involving either lengthy individual test for each geometric error or faster single tests to identify all errors at once. This study focuses on the closed kinematic Cartesian chain method which uses a single setup test to identify the eight link errors of a five axis machine tool. The identification is based on volumetric error measurements for different poses with a non-contact measuring instrument called CapBall, developed in house. In order to evaluate the uncertainty on each identified error, a multi-output Monte Carlo approach is implemented. Uncertainty sources in the measurement and identification chain - such as sensors output, machine drift and frame transformation uncertainties - can be included in the model and propagated to the identified errors. The estimated uncertainties are finally compared to experimental results to assess...
Liwo, Adam; Ołdziej, Stanisław; Czaplewski, Cezary; Kleinerman, Dana S; Blood, Philip; Scheraga, Harold A
2010-03-01
We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures. In addition to coarse-grained parallelism already implemented in our previous work, in which each conformation was treated by a different task, we introduce a fine-grained level in which energy and gradient evaluation are split between several tasks. The Message Passing Interface (MPI) libraries have been utilized to construct the parallel code. The parallel performance of the code has been tested on a professional Beowulf cluster (Xeon Quad Core), a Cray XT3 supercomputer, and two IBM BlueGene/P supercomputers with canonical and replica-exchange molecular dynamics. With IBM BlueGene/P, about 50 % efficiency and 120-fold speed-up of the fine-grained part was achieved for a single trajectory of a 767-residue protein with use of 256 processors/trajectory. Because of averaging over the fast degrees of freedom, UNRES provides an effective 1000-fold speed-up compared to the experimental time scale and, therefore, enables us to effectively carry out millisecond-scale simulations of proteins with 500 and more amino-acid residues in days of wall-clock time.
A Coarse-Grained Clustering Unit Based Parallel Algorithm for Big Data Set%一种面向大数据集的粗粒度并行聚类算法研究
Institute of Scientific and Technical Information of China (English)
向尧; 袁景凌; 钟珞; 赵彦鹏
2014-01-01
随着大数据时代的到来,面对数据量剧增,传统的聚类算法将面临极大的挑战.为了提高聚类算法的效率,本文基于Hadoop平台设计与实现了并行化的Partitioning Around Medoid聚类算法,并从优化聚类单元和聚类中心的角度,结合视觉聚类的核心思想提出了粗粒度聚类单元策略(Coarse-Grained Clustering Unit Strategy).通过多组实验比较,结果表明,在粗粒度聚类单元策略的优化下算法在运行效率,计算能力等方面提高6％以上,所实现的并行算法具有良好的加速比,扩展比和伸缩率.研究结果为以后的大数据集下的聚类分析奠定了基础.
Directory of Open Access Journals (Sweden)
J. A. Vrugt
2011-04-01
Full Text Available Formal and informal Bayesian approaches are increasingly being used to treat forcing, model structural, parameter and calibration data uncertainty, and summarize hydrologic prediction uncertainty. This requires posterior sampling methods that approximate the (evolving posterior distribution. We recently introduced the DiffeRential Evolution Adaptive Metropolis (DREAM algorithm, an adaptive Markov Chain Monte Carlo (MCMC method that is especially designed to solve complex, high-dimensional and multimodal posterior probability density functions. The method runs multiple chains in parallel, and maintains detailed balance and ergodicity. Here, I present the latest algorithmic developments, and introduce a discrete sampling variant of DREAM that samples the parameter space at fixed points. The development of this new code, DREAM(D, has been inspired by the existing class of integer optimization problems, and emerging class of experimental design problems. Such non-continuous parameter estimation problems are of considerable theoretical and practical interest. The theory developed herein is applicable to DREAM(ZS (Vrugt et al., 2011 and MT-DREAM(ZS (Laloy and Vrugt, 2011 as well. Two case studies involving a sudoku puzzle and rainfall – runoff model calibration problem are used to illustrate DREAM(D.
Towards coarse-grained modelling of proteins
Directory of Open Access Journals (Sweden)
M.Stepanova
2007-09-01
Full Text Available This paper introduces a basic theoretical background to the description of conformational dynamics of proteins through a system of interacting domains. The essential collective degrees of freedom derived by principal component analysis of a molecular dynamics trajectory are used as dynamic variables defining the projection operator technique that underlies the formalism suggested. The explicit form of the corresponding projection operator is obtained, and the projection method is employed to derive systems of coupled generalized Langevin equations for both individual atomic degrees of freedom and essential collective degrees of freedom in a protein. A definition of correlated domains in proteins is introduced based on the analysis of the essential dynamics. Examples of identification of such domains are presented. A system of coupled generalized Langevin equations is derived representing the protein through a few interacting domains embedded into a dissipative medium. Further developments and potential applications of the formalism are outlined.
Systematic Coarse-Graining in Nucleation Theory
Schweizer, Marco
2015-01-01
We present a novel approach to nucleation processes based one the GENERIC framework (general equation for the nonequilibrium reversible-irreversible coupling). Solely based on the GENERIC structure of time-evolution equations and thermodynamic consistency arguments of exchange processes between a metastable phase and a nucleating phase, we derive the fundamental dynamics for this phenomenon, based on continuous Fokker-Planck equations. We are readily able to treat non-isothermal nucleation even when the nucleating cores cannot be attributed intensive thermodynamic properties. In addition, we capture the dynamics of the time-dependent metastable phase being continuously expelled from the nucleating phase, and keep rigorous track of the volume corrections to the dynamics. Within our framework the definition of a thermodynamic nuclei temperature is manifest. For the special case of nucleation of a gas phase towards its vapor-liquid coexistence, we illustrate that our approach is capable of reproducing recent lit...
Directory of Open Access Journals (Sweden)
Giorgia Cazzolli
2013-11-01
Full Text Available Euplotes nobilii and Euplotes raikovi are phylogenetically closely allied species of marine ciliates, living in polar and temperate waters, respectively. Their evolutional relation and the sharply different temperatures of their natural environments make them ideal organisms to investigate thermal-adaptation. We perform a comparative study of the thermal unfolding of disulfide-rich protein pheromones produced by these ciliates. Recent circular dichroism (CD measurements have shown that the two psychrophilic (E. nobilii and mesophilic (E. raikovi protein families are characterized by very different melting temperatures, despite their close structural homology. The enhanced thermal stability of the E. raikovi pheromones is realized notwithstanding the fact that these proteins form, as a rule, a smaller number of disulfide bonds. We perform Monte Carlo (MC simulations in a structure-based coarse-grained (CG model to show that the higher stability of the E. raikovi pheromones is due to the lower locality of the disulfide bonds, which yields a lower entropy increase in the unfolding process. Our study suggests that the higher stability of the mesophilic E. raikovi phermones is not mainly due to the presence of a strongly hydrophobic core, as it was proposed in the literature. In addition, we argue that the molecular adaptation of these ciliates may have occurred from cold to warm, and not from warm to cold. To provide a testable prediction, we identify a point-mutation of an E. nobilii pheromone that should lead to an unfolding temperature typical of that of E. raikovi pheromones.
基于PFC方法的粗粒土三轴试验尺寸效应研究%Research on Size Effects of Coarse-grained Soils Triaxial Tests Based on PFC
Institute of Scientific and Technical Information of China (English)
王飞; 徐佩华; 高井望; 卢丙清
2014-01-01
粗粒土是工程建设过程中经常遇到的一类土，由于室内仪器限制，通常将其按一定条件缩尺后进行室内大三轴试验，进而推算原级配土的强度特性。缩尺后替代级配与原级配存在着缩尺条件、尺寸效应等问题。在某高速公路大三轴试验数据基础上，运用 PFC2D 软件，将600×300 mm 样本经等质量替代法缩尺，比较了缩尺后不同尺寸样本的应力-应变曲线。结果表明：PFC2D可以很好的模拟三轴试验；缩尺后的样本应变模量降低，且随着样本尺寸的增大而增大，样本的抗剪强度也存在差异；等质量替代法对缩尺后样本的尺寸大小有限制；当样本颗粒级配相同时，不同尺寸样本在峰前阶段的尺寸效应不明显。%Coarse-grained soils are the soils that always are encountered in the process of engineer-ing construction.Due to indoor instrument limitations,Triaxial tests were performed under certain scale conditions and then the paper calculate the strength properties of original soil gradation.There are prob-lems of size effects and scale conditions between natural gradation and substitute gradation.According to the triaxial test data of some highway ,the sample of 600 ×300 mm will be scaled and the paper will com-pare stress-strain curves of samples of different sizes.The conclusions are as follows:PFC2D can simu-late triaxial tests accurately;Strain modulus decrease in the scale samples,and increase with the increas-ing of sample size;Shear strength of samples are different;the method of equal-weight replacement is limited to the size of the scaled samples;when the particles’size distribution is same ,different samples haven’t obvious size effects.In coarse-grained soil sample preparation process.
The relative entropy is fundamental to adaptive resolution simulations
Kreis, Karsten; Potestio, Raffaello
2016-07-01
Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy with respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner.
Monte Carlo simulation on kinetics of batch and semi-batch free radical polymerization
Shao, Jing
2015-10-27
Based on Monte Carlo simulation technology, we proposed a hybrid routine which combines reaction mechanism together with coarse-grained molecular simulation to study the kinetics of free radical polymerization. By comparing with previous experimental and simulation studies, we showed the capability of our Monte Carlo scheme on representing polymerization kinetics in batch and semi-batch processes. Various kinetics information, such as instant monomer conversion, molecular weight, and polydispersity etc. are readily calculated from Monte Carlo simulation. The kinetic constants such as polymerization rate k p is determined in the simulation without of “steady-state” hypothesis. We explored the mechanism for the variation of polymerization kinetics those observed in previous studies, as well as polymerization-induced phase separation. Our Monte Carlo simulation scheme is versatile on studying polymerization kinetics in batch and semi-batch processes.
Un roman pour la génération dot.com?: Le comte de Monte-Christo dans l'adaptation de Stephen Fry
Directory of Open Access Journals (Sweden)
Katarina Marinčič
2010-12-01
Full Text Available En 2000, le romancier britannique Stephen Fry publie The Starsʹ Tennis Balls, une adaptation modernisante du roman Le Comte de Monte-Cristo dʹAlexandre Dumas. Lʹobjectif de la présente contribution est dʹanalyser les techniques narratives des deux romanciers. Extrêmement fidèle au roman de Dumas au niveau de lʹintrigue, Stephen Fry sʹéloigne de son modèle au niveau stylistique, ce qui produit un effet de modernité qui ne sʹapparente pourtant pas à celui des adaptations cinématographiques.
Institute of Scientific and Technical Information of China (English)
李韬; 孙志刚
2011-01-01
Aimed at the limitation of ILP exploitation and the fixed topology of control-flow NP, a novel scheme of coarse-grained dataflow NP architecture-DynaNP is presented in this paper. DynaNP not only improves the programmability of the NP by the control-flow structure of Processing Elements (Pes), but also effectively exploits the task-level parallelism by introducing a data-flow model into the packet processing. Moreover,to further improve the system throughput of DynaNP, a mechanism of hy brid custom hardware acceleration is proposed taking consideration of the multi-core and dataflow char acteristics of DynaNP. Moreover, some key techniques of implementing the hybrid custom hardware ac celerating unit are also addressed. The mechanism provides a unified interface for two kinds of hardware acceleration of custom instructions and coprocessors.%本文针对控制流网络处理器固定拓扑结构的限制及指令集并行性开发的不足,将粗粒度数据流设计思想引入到网络处理器体系结构设计中,提出了一种新型粗粒度数据流网络处理器体系结构一DynaNP.DynaNP利用处理引擎(PE)内控制流执行方式获得较高的可编程性,还利用PE间数据流执行方式开发了报文处理中的任务级并行性.为了进一步提高DynaNP的系统流量,面向DynaNP的多核及数据流特性,设计了混合定制硬件加速机制,并详细介绍了实现混合定制硬件加速的关键技术,通过提供统一的混合定制硬件加速接口,可以支持定制指令和协处理器两种典型硬件加速器.
Burkatzki, M.; Filippi, Claudia; Dolg, M.
2008-01-01
We extend our recently published set of energy-consistent scalar-relativistic Hartree–Fock pseudopotentials by the 3d-transition metal elements, scandium through zinc. The pseudopotentials do not exhibit a singularity at the nucleus and are therefore suitable for quantum Monte Carlo (QMC) calculatio
Johan Parent; Katja Verbeeck; Jan Lemeire; Ann Nowe; Kris Steenhaut; Erik Dirkx
2004-01-01
We report on the improvements that can be achieved by applying machine learning techniques, in particular reinforcement learning, for the dynamic load balancing of parallel applications. The applications being considered in this paper are coarse grain data intensive applications. Such applications put high pressure on the interconnect of the hardware. Synchronization and load balancing in complex, heterogeneous networks need fast, flexible, adaptive load balancing algorithms. Viewing a parall...
自适应拟蒙特卡罗多极值优化方法%Adaptive Quasi-Monte Carlo Method for Multiple-Extrema Optimization
Institute of Scientific and Technical Information of China (English)
雷桂嫒
2002-01-01
Quasi-Monte Carlo random search is useful in nondifferentiable optimization. By borrowing the ideas of population from genetic algorithms, we introduce an adaptive random search in quasi-Monte Carlo method(AQMC) for global optimization. The adaptive search technique enables local search to head for local extuema quickly. The low discrepancy of quasirandom sequence ensures that the function field be searched evenly and various local extrema including global extremum be found.%拟蒙特卡罗搜索方法能用来有效地解决不可微优化问题.借用遗传算法中种群的概念,介绍了一种解全局优化的拟蒙特卡罗自适应搜索算法.由于应用了自适应搜索技术,局部搜索能够快速找到局部极值.同时,拟随机序列的低偏差性保证了函数定义域能够被均匀地搜索,为找到多个局部极值包括全局极值提供了保证.
Energy Technology Data Exchange (ETDEWEB)
Heidary, Saeed, E-mail: saeedheidary@aut.ac.ir; Setayeshi, Saeed, E-mail: setayesh@aut.ac.ir
2015-01-11
This work presents a simulation based study by Monte Carlo which uses two adaptive neuro-fuzzy inference systems (ANFIS) for cross talk compensation of simultaneous {sup 99m}Tc/{sup 201}Tl dual-radioisotope SPECT imaging. We have compared two neuro-fuzzy systems based on fuzzy c-means (FCM) and subtractive (SUB) clustering. Our approach incorporates eight energy-windows image acquisition from 28 keV to 156 keV and two main photo peaks of {sup 201}Tl (77±10% keV) and {sup 99m}Tc (140±10% keV). The Geant4 application in emission tomography (GATE) is used as a Monte Carlo simulator for three cylindrical and a NURBS Based Cardiac Torso (NCAT) phantom study. Three separate acquisitions including two single-isotopes and one dual isotope were performed in this study. Cross talk and scatter corrected projections are reconstructed by an iterative ordered subsets expectation maximization (OSEM) algorithm which models the non-uniform attenuation in the projection/back-projection. ANFIS-FCM/SUB structures are tuned to create three to sixteen fuzzy rules for modeling the photon cross-talk of the two radioisotopes. Applying seven to nine fuzzy rules leads to a total improvement of the contrast and the bias comparatively. It is found that there is an out performance for the ANFIS-FCM due to its acceleration and accurate results.
Heidary, Saeed; Setayeshi, Saeed
2015-01-01
This work presents a simulation based study by Monte Carlo which uses two adaptive neuro-fuzzy inference systems (ANFIS) for cross talk compensation of simultaneous 99mTc/201Tl dual-radioisotope SPECT imaging. We have compared two neuro-fuzzy systems based on fuzzy c-means (FCM) and subtractive (SUB) clustering. Our approach incorporates eight energy-windows image acquisition from 28 keV to 156 keV and two main photo peaks of 201Tl (77±10% keV) and 99mTc (140±10% keV). The Geant4 application in emission tomography (GATE) is used as a Monte Carlo simulator for three cylindrical and a NURBS Based Cardiac Torso (NCAT) phantom study. Three separate acquisitions including two single-isotopes and one dual isotope were performed in this study. Cross talk and scatter corrected projections are reconstructed by an iterative ordered subsets expectation maximization (OSEM) algorithm which models the non-uniform attenuation in the projection/back-projection. ANFIS-FCM/SUB structures are tuned to create three to sixteen fuzzy rules for modeling the photon cross-talk of the two radioisotopes. Applying seven to nine fuzzy rules leads to a total improvement of the contrast and the bias comparatively. It is found that there is an out performance for the ANFIS-FCM due to its acceleration and accurate results.
Directory of Open Access Journals (Sweden)
Teresa C. T. Pissarra
2013-04-01
Full Text Available The aim of this study was to define the photographic patterns that represent the use and occupation of the landcover of the "spring" of the Rico Stream subbasin, located at Monte Alto, state of São Paulo (SP, Brazil, for environmental adaptation regarding the Brazilian Forest Law. The mapping was performed using remote sensing techniques and visual interpretation of the World View image, followed by the digitalization of the net of drainage and vegetation (natural and agricultural at the AutoCad software with documents and field work. The study area has 2141.53 ha and the results demonstrated that the main crop is sugarcane with 546.34 ha, followed by 251.22 ha of pastures, 191.71 ha of perennial crops, 57.31 ha of Eucalyptus and 49.52 ha of onion, confirming the advance of sugarcane culture in the region. The region has 375.04 ha of areas of permanent preservation (APPs, and of this area it was found that only 72.17 ha (19.24% has arboreal vegetation or natural forest, and 302.87 ha of these areas need to be enriched and reforested with native vegetation from the region, according to the current legislation. The data of the area enable future proposals of models for environmental adaptation to the microbasin according to the current environmental legislation.Este trabalho teve como principal objetivo definir padrões fotográficos que representem o uso e a ocupação do solo da "cabeceira" de drenagem do Córrego Rico, localizada no Município de Monte Alto, Estado de São Paulo, para fins de adequação ambiental no que tange à legislação florestal brasileira. O mapeamento foi realizado utilizando técnicas de sensoriamento remoto e interpretação visual da imagem World View, seguida da digitalização da rede de drenagem e vegetações (naturais e agrícolas no AutoCad, com auxílio de documentos e trabalho de campo. A área de estudo apresenta uma superfície de 2.141,53 ha, e os resultados permitiram constatar que a principal cultura
Application of an adapted Fano cavity test for Monte Carlo simulations in the presence of B-fields
International Nuclear Information System (INIS)
With the advent of MR guided radiotherapy the relevance of Monte Carlo radiation transport simulations in the presence of strong magnetic fields (B-fields) is increasing. While new tests are available to benchmark these simulation algorithms for internal consistency, their application to known codes such as EGSnrc, PENELOPE, and GEANT4 is yet to be provided. In this paper a method is provided to apply the Fano cavity test as a benchmark for a generic implementation of B-field effects in PENELOPE. In addition, it is investigated whether violation of the conditions for the Fano test can partially explain the change in the response of ionization chambers in the presence of strong B-fields.In the present paper it is shown that the condition of isotropy of the secondary particle field (Charged Particle Isotropy, CPI) is an essential requirement to apply the Fano test in the presence of B-fields. Simulations in PENELOPE are performed with (B = 0.0 T) and (B = 1.5 T) for cylindrical cavity geometry. The secondary particle field consists of electrons generated from a mono-energetic source (E = 0.5–4.0 MeV) with a uniform source density and different angular distributions; isotropic, mono-directional, and Compton. In realistic photon fields the secondary radiation field has a non-isotropic angular distribution due to the Compton process. Based on the simulations for the Compton angular distribution (non-CPI), the response change of the cavity model in a uniform radiation field in the presence of B-fields is investigated.For the angular distributions that violate the CPI condition and B = 1.5 T, the deviations from 1 are considerable, which emphasizes the requirement of CPI. For the isotropic angular distributions obeying this requirement, both the results for B = 0.0 T and B = 1.5 T shows deviations from the predictions for E ⩾ 1.5 MeV with values up to 1.0% for E = 4.0 MeV. Nevertheless
Monte Carlo simulations of the phase separation of a copolymer blend in a thin film
Wang, Zhexiao
2014-12-11
Monte Carlo simulations were carried out to study the phase separation of a copolymer blend comprising an alternating copolymer and/or block copolymer in a thin film, and a phase diagram was constructed with a series of composed recipes. The effects of composition and segregation strength on phase separation were discussed in detail. The chain conformation of the block copolymer and alternating copolymer were investigated with changes of the segregation strength. Our simulations revealed that the segment distribution along the copolymer chain and the segregation strength between coarse-grained beads are two important parameters controlling phase separation and chain conformation in thin films of a copolymer blend. A well-controlled phase separation in the copolymer blend can be used to fabricate novel nanostructures.
de Vries, R.
2004-02-01
Electrostatic complexation of flexible polyanions with the whey proteins α-lactalbumin and β-lactoglobulin is studied using Monte Carlo simulations. The proteins are considered at their respective isoelectric points. Discrete charges on the model polyelectrolytes and proteins interact through Debye-Hückel potentials. Protein excluded volume is taken into account through a coarse-grained model of the protein shape. Consistent with experimental results, it is found that α-lactalbumin complexes much more strongly than β-lactoglobulin. For α-lactalbumin, strong complexation is due to localized binding to a single large positive "charge patch," whereas for β-lactoglobulin, weak complexation is due to diffuse binding to multiple smaller charge patches.
Bargatze, L. F.
2015-12-01
Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted
Geometry and Coarse-Grained Representations of Landscapes
DEFF Research Database (Denmark)
Qin, Jing; Stadler, Peter; Klemm, Konstantin
2014-01-01
Recent Advances in the Theory and Application of Fitness Landscapes Emergence, Complexity and ComputationVolume 6, 2014, pp 153-176......Recent Advances in the Theory and Application of Fitness Landscapes Emergence, Complexity and ComputationVolume 6, 2014, pp 153-176...
Coarse-grained sensitivity for multiscale data assimilation
Sugiura, Nozomi
2015-01-01
We show that the effective average action and its gradient are useful for solving multiscale data assimilation problems. We also present a procedure for numerically evaluating the gradient of the effective average action, and demonstrate that the variational problem for slow degrees of freedom can be solved properly using the "effective gradient."
Dynamic coarse-graining approach to quantum field theory
Öttinger, Hans Christian
2010-01-01
We build quantum field theory on the thermodynamic master equation for dissipative quantum systems. The vacuum is represented by a thermodynamic equilibrium state; even in the low-temperature limit, the population and evolution of excited states matter. All regularization is consistently provided by a friction mechanism; with decreasing friction parameter, only shorter and shorter scales are damped out of a quantum field theory. No divergent integrals need to be manipulated, no counterterms need to be invented. Relativistic covariance is recovered in the final results. We illustrate the proposed thermodynamic approach to quantum fields for the phi^4 theory.
Constrained Systems in a Coarse-Grained Scenario
Godinho, Cresus F L; Neto, J A Helayël
2012-01-01
Nowadays, a number of new approaches based on fractional calculus have been presented and discussed in the literature, with the purpose of finding out different perspectives and describing particular phenomena in connection with field theory and gravity at a more fundamental level. On the other hand, procedures related to canonical quantization are really essential in field theory. More recently, the investigation of a wide category of new classical field-theoretic models as well as their respective quantized counterparts have been pursued which yield a very rich scenario, which enables us to connect different areas of physics. For instance, it is not fairly well-known how to deal with dissipative or nonlinear systems; there are many paths of investigation in the literature and none of them present a systematic and general procedure to tackle the problem. Today, it is widely accepted that the fractional formalism may be viewed as a powerful alternative to study dissipative systems. In our present contribution...
CRASIC: Customisation of Coarse Grain Recon gurable Architectures
Azad Payandeh, Siavoosh
2012-01-01
The gap between CGRAs and ASIC designs is a major issue for all digital designers. The main objective of the following thesis is developing a method to customize the design according to the application to increase performance and decrease the area of the chip. although there are commercial high level synthesis tools which are able to synthesis an algorithmic level description of an application to ASIC, how ever they are not able to generate recon gurable hardware operating as multi-mode ASIC....
Coarse-grained description of cosmic structure from Szekeres models
Sussman, Roberto A.; Delgado Gaspar, I.; Hidalgo, Juan Carlos
2016-03-01
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.
Coarse Graining and Localized Plasticity between Sliding Nanocrystalline Metals
Romero, Pedro A.; Järvi, Tommi T.; Beckmann, Nils; Mrovec, Matous; Moseler, Michael
2014-07-01
Tribological shearing of polycrystalline metals typically leads to grain refinement at the sliding interface. This study, however, shows that nanocrystalline metals exhibit qualitatively different behavior. Using large-scale atomistic simulations, we demonstrate that during sliding, contact interface nanocrystalline grains self-organize through extensive grain coarsening and lattice rotation until the optimal plastic slip orientation is established. Subsequently, plastic deformation is frequently confined to localized nanoshear bands aligned with the shearing direction and emanating from voids and other defects in the vicinity of the sliding interface.
Membrane pore formation in atomistic and coarse-grained simulations.
Kirsch, Sonja A; Böckmann, Rainer A
2016-10-01
Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26748016
Schriber, Jeffrey B.; Evangelista, Francesco A.
2016-04-01
We introduce a new procedure for iterative selection of determinant spaces capable of describing highly correlated systems. This adaptive configuration interaction (ACI) determines an optimal basis by an iterative procedure in which the determinant space is expanded and coarse grained until self-consistency. Two importance criteria control the selection process and tune the ACI to a user-defined level of accuracy. The ACI is shown to yield potential energy curves of N2 with nearly constant errors, and it predicts singlet-triplet splittings of acenes up to decacene that are in good agreement with the density matrix renormalization group.
Schriber, Jeffrey B
2016-01-01
We introduce a new procedure for iterative selection of determinant spaces capable of describing highly correlated systems. This adaptive configuration interaction (ACI) determines an optimal basis by an iterative procedure in which the determinant space is expanded and coarse grained until self consistency. Two importance criteria control the selection process and tune the ACI to a user-defined level of accuracy. The ACI is shown to yield potential energy curves of N$_2$ with nearly constant errors, and it predicts singlet-triplet splittings of acenes up to decacene that are in good agreement with the density matrix renormalization group.
Monte Carlo simulation algorithm for B-DNA.
Howell, Steven C; Qiu, Xiangyun; Curtis, Joseph E
2016-11-01
Understanding the structure-function relationship of biomolecules containing DNA has motivated experiments aimed at determining molecular structure using methods such as small-angle X-ray and neutron scattering (SAXS and SANS). SAXS and SANS are useful for determining macromolecular shape in solution, a process which benefits by using atomistic models that reproduce the scattering data. The variety of algorithms available for creating and modifying model DNA structures lack the ability to rapidly modify all-atom models to generate structure ensembles. This article describes a Monte Carlo algorithm for simulating DNA, not with the goal of predicting an equilibrium structure, but rather to generate an ensemble of plausible structures which can be filtered using experimental results to identify a sub-ensemble of conformations that reproduce the solution scattering of DNA macromolecules. The algorithm generates an ensemble of atomic structures through an iterative cycle in which B-DNA is represented using a wormlike bead-rod model, new configurations are generated by sampling bend and twist moves, then atomic detail is recovered by back mapping from the final coarse-grained configuration. Using this algorithm on commodity computing hardware, one can rapidly generate an ensemble of atomic level models, each model representing a physically realistic configuration that could be further studied using molecular dynamics. © 2016 Wiley Periodicals, Inc. PMID:27671358
Adaptive Mesh Refinement for Characteristic Grids
Thornburg, Jonathan
2009-01-01
I consider techniques for Berger-Oliger adaptive mesh refinement (AMR) when numerically solving partial differential equations with wave-like solutions, using characteristic (double-null) grids. Such AMR algorithms are naturally recursive, and the best-known past Berger-Oliger characteristic AMR algorithm, that of Pretorius & Lehner (J. Comp. Phys. 198 (2004), 10), recurses on individual "diamond" characteristic grid cells. This leads to the use of fine-grained memory management, with individual grid cells kept in 2-dimensional linked lists at each refinement level. This complicates the implementation and adds overhead in both space and time. Here I describe a Berger-Oliger characteristic AMR algorithm which instead recurses on null \\emph{slices}. This algorithm is very similar to the usual Cauchy Berger-Oliger algorithm, and uses relatively coarse-grained memory management, allowing entire null slices to be stored stored in contiguous arrays in memory. The algorithm is very efficient in both space and ti...
Energy Technology Data Exchange (ETDEWEB)
Armas-Pérez, Julio C.; Londono-Hurtado, Alejandro [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Guzmán, Orlando [Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, DF 09340, México (Mexico); Hernández-Ortiz, Juan P. [Departamento de Materiales y Minerales, Universidad Nacional de Colombia, Sede Medellín, Medellín (Colombia); Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Pablo, Juan J. de, E-mail: depablo@uchicago.edu [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)
2015-07-28
A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.
Energy Technology Data Exchange (ETDEWEB)
Armas-Perez, Julio C.; Londono-Hurtado, Alejandro; Guzman, Orlando; Hernandez-Ortiz, Juan P.; de Pablo, Juan J.
2015-07-27
A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.
Mean field simulation for Monte Carlo integration
Del Moral, Pierre
2013-01-01
In the last three decades, there has been a dramatic increase in the use of interacting particle methods as a powerful tool in real-world applications of Monte Carlo simulation in computational physics, population biology, computer sciences, and statistical machine learning. Ideally suited to parallel and distributed computation, these advanced particle algorithms include nonlinear interacting jump diffusions; quantum, diffusion, and resampled Monte Carlo methods; Feynman-Kac particle models; genetic and evolutionary algorithms; sequential Monte Carlo methods; adaptive and interacting Marko
Yashina, Tatjana
2011-01-01
Climate change is increasingly recognized as the driver of biodiversity change. In recent years, the issues related to climate change have left the purely scientific realm and got on the agenda of many international organizations, programmes, conventions and initiatives seeking ways to mitigate and adapt to this phenomenon. Protected areas and biosphere reserves (BRs) in particular, focused as they are on the conservation of ecosystem services and on fostering sustainable regional development...
Institute of Scientific and Technical Information of China (English)
徐肖峰; 魏厚振; 孟庆山; 韦昌富; 李永和
2013-01-01
Mechanical behaves of coarse grained soil is greatly influenced by the content of coarse gravels. The shear characteristics of four groups of strong weathered basalt coarse grained soils are investigated under different coarse gravel contents on large-scale direct shear apparatus to obtain the strength and deformation parameters in this paper. Based on the theory of discrete element method (DEM) ,four direct shear samples under vertical pressure of l00kPa are carried out using the parallel bond model ( PBM) with multiplicity coarse gravel content. The parameters are calibrated. Then we simulate the relationship among shear stress, shear deformation and vertical deformation. The simulation also simultaneously analyzes the particle movement and force in order to settle the mechanism for the fact that coarse content affects shearing properties. Results show that the inherence for shear strength increasing with the increase of coarse gravel content at the same vertical stress is due to the increase of particle stiffness and the increase of friction coefficient. The peak of stress-strain curve can be well simulated by the PBM. But the soften segment cannot be well fitted. Simulation of shear-vertical displacement curve does not fit perfectly to the testing value. The effects of coarse particles on the peak force chains were significantly evident than those of fine particles during the shearing process. It is considered that the vortex area is the thickness of shear band, approximately 1/3 -1/5 of the height of shear box.%粗粒含量对砾类土的工程力学特性具有重要的影响.本文对4组不同粗粒含量的强风化玄武岩砾类土进行了大型直剪试验,并获取相关的强度与变形参数,基于离散单元法颗粒流理论,采用粒间作用为平行黏结模型的圆球模拟土颗粒,建立了4种不同粗粒含量砾类土直剪的离散单元模拟的计算模型,并进一步校正了颗粒单元细观参数,模拟
Institute of Scientific and Technical Information of China (English)
马刚; 周伟; 常晓林; 周创兵
2012-01-01
Three-dimensional deformable discrete element method is an appropriate numerical method for studying mechanical behavior of discontinues geo-material. The ability of automatic contact detection and discretization of particle and structure by finite difference grids, makes it had inherent advantages in simulation discrete-continuum coupling problem. The deformable discrete element method is employed to study the mechanical behavior of soil-structure interaction problem, in which the coarse-grained soil is modeled by random simulation technique. The mechanical behavior of interface between soil-structure is compared under direct shear and simple shear conditions. The numerical simulation results are investigated from macroscopic and mesoscopic levels, respectively. The results show that the numerical simulation can reflect the mechanical behavior of soil-structure interface; the curves of shear stress-relative shear displacement have a good agreement with the experimental results; the interface roughness has a great impact on the strength and deformation properties, due to the disturbance of particle induced by shear. The shear stress-relative shear displacement relationships of simple shear and direct shear are both hyperbolic. The initial stiffness of simple shear is smaller than that of direct shear; and the shear strength of two are similar.%三维变形体离散元法能够自动检索接触关系,并对具有不规则形状的粗粒土颗粒和结构物进行有限差分网格离散,因此,具有模拟离散-连续耦合问题的先天优势.采用随机模拟技术生成粗粒土三维数值试样,基于变形体离散元进行粗粒土与结构接触面特性的数值试验,研究了不同接触面粗糙程度的接触面力学特性,对比了粗粒土与结构物在单剪和直剪状态下的接触面力学特性,从宏观和细观两个层面分析了数值试验结果.结果表明,数值试验能较好地反映粗粒土与结构接触面的力学特性,
Directory of Open Access Journals (Sweden)
C. J. F. Ter Braak
2011-12-01
Full Text Available Formal and informal Bayesian approaches have found widespread implementation and use in environmental modeling to summarize parameter and predictive uncertainty. Successful implementation of these methods relies heavily on the availability of efficient sampling methods that approximate, as closely and consistently as possible the (evolving posterior target distribution. Much of this work has focused on continuous variables that can take on any value within their prior defined ranges. Here, we introduce theory and concepts of a discrete sampling method that resolves the parameter space at fixed points. This new code, entitled DREAM(D uses the recently developed DREAM algorithm (Vrugt et al., 2008, 2009a, b as its main building block but implements two novel proposal distributions to help solve discrete and combinatorial optimization problems. This novel MCMC sampler maintains detailed balance and ergodicity, and is especially designed to resolve the emerging class of optimal experimental design problems. Three different case studies involving a Sudoku puzzle, soil water retention curve, and rainfall – runoff model calibration problem are used to benchmark the performance of DREAM(D. The theory and concepts developed herein can be easily integrated into other (adaptive MCMC algorithms.
Adsorption thermodynamics of two-domain antifreeze proteins: theory and Monte Carlo simulations.
Narambuena, Claudio F; Sanchez Varretti, Fabricio O; Ramirez-Pastor, Antonio J
2016-09-21
In this paper we develop the statistical thermodynamics of two-domain antifreeze proteins adsorbed on ice. We use a coarse-grained model and a lattice network in order to represent the protein and ice, respectively. The theory is obtained by combining the exact analytical expression for the partition function of non-interacting linear k-mers adsorbed in one dimension, and its extension to higher dimensions. The total and partial adsorption isotherms, and the coverage and temperature dependence of the Helmholtz free energy and configurational entropy are given. The formalism reproduces the classical Langmuir equation, leads to the exact statistical thermodynamics of molecules adsorbed in one dimension, and provides a close approximation for two-dimensional systems. Comparisons with analytical data obtained using the modified Langmuir model (MLM) and Monte Carlo simulations in the grand canonical ensemble were performed in order to test the validity of the theoretical predictions. In the MC calculations, the different mechanisms proposed in the literature to describe the adsorption of two-domain antifreeze proteins on ice were analyzed. Indistinguishable results were obtained in all cases, which verifies the thermodynamic equivalence of these mechanisms and allows the choice of the most suitable mechanism for theoretical studies of equilibrium properties. Even though a good qualitative agreement is obtained between MLM and MC data, it is found that the new theoretical framework offers a more accurate description of the phenomenon of adsorption of two-domain antifreeze proteins. PMID:27539563
Energy Technology Data Exchange (ETDEWEB)
Mazurier, J
1999-05-28
This thesis has been performed in the framework of national reference setting-up for absorbed dose in water and high energy photon beam provided with the SATURNE-43 medical accelerator of the BNM-LPRI (acronym for National Bureau of Metrology and Primary standard laboratory of ionising radiation). The aim of this work has been to develop and validate different user codes, based on PENELOPE Monte Carlo code system, to determine the photon beam characteristics and calculate the correction factors of reference dosimeters such as Fricke dosimeters and graphite calorimeter. In the first step, the developed user codes have permitted the influence study of different components constituting the irradiation head. Variance reduction techniques have been used to reduce the calculation time. The phase space has been calculated for 6, 12 and 25 MV at the output surface level of the accelerator head, then used for calculating energy spectra and dose distributions in the reference water phantom. Results obtained have been compared with experimental measurements. The second step has been devoted to develop an user code allowing calculation correction factors associated with both BNM-LPRI's graphite and Fricke dosimeters thanks to a correlated sampling method starting with energy spectra obtained in the first step. Then the calculated correction factors have been compared with experimental and calculated results obtained with the Monte Carlo EGS4 code system. The good agreement, between experimental and calculated results, leads to validate simulations performed with the PENELOPE code system. (author)
Modeling epidemics on adaptively evolving networks: A data-mining perspective.
Kattis, Assimakis A; Holiday, Alexander; Stoica, Ana-Andreea; Kevrekidis, Ioannis G
2016-01-01
The exploration of epidemic dynamics on dynamically evolving ("adaptive") networks poses nontrivial challenges to the modeler, such as the determination of a small number of informative statistics of the detailed network state (that is, a few "good observables") that usefully summarize the overall (macroscopic, systems-level) behavior. Obtaining reduced, small size accurate models in terms of these few statistical observables--that is, trying to coarse-grain the full network epidemic model to a small but useful macroscopic one--is even more daunting. Here we describe a data-based approach to solving the first challenge: the detection of a few informative collective observables of the detailed epidemic dynamics. This is accomplished through Diffusion Maps (DMAPS), a recently developed data-mining technique. We illustrate the approach through simulations of a simple mathematical model of epidemics on a network: a model known to exhibit complex temporal dynamics. We discuss potential extensions of the approach, as well as possible shortcomings.
Directory of Open Access Journals (Sweden)
Johan Parent
2004-01-01
Full Text Available We report on the improvements that can be achieved by applying machine learning techniques, in particular reinforcement learning, for the dynamic load balancing of parallel applications. The applications being considered in this paper are coarse grain data intensive applications. Such applications put high pressure on the interconnect of the hardware. Synchronization and load balancing in complex, heterogeneous networks need fast, flexible, adaptive load balancing algorithms. Viewing a parallel application as a one-state coordination game in the framework of multi-agent reinforcement learning, and by using a recently introduced multi-agent exploration technique, we are able to improve upon the classic job farming approach. The improvements are achieved with limited computation and communication overhead.
Dunn, William L
2012-01-01
Exploring Monte Carlo Methods is a basic text that describes the numerical methods that have come to be known as "Monte Carlo." The book treats the subject generically through the first eight chapters and, thus, should be of use to anyone who wants to learn to use Monte Carlo. The next two chapters focus on applications in nuclear engineering, which are illustrative of uses in other fields. Five appendices are included, which provide useful information on probability distributions, general-purpose Monte Carlo codes for radiation transport, and other matters. The famous "Buffon's needle proble
Energy Technology Data Exchange (ETDEWEB)
Castin, N., E-mail: ncastin@sckcen.be [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium); Pascuet, M.I., E-mail: pascuet@cnea.gov.ar [Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires (Argentina); Malerba, L. [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium)
2012-10-15
The formation of Cu-rich precipitates under irradiation is a major cause for changes in the mechanical response to load of reactor pressure vessel steels. In previous works, it has been shown that the mechanism under which precipitation occurs is governed by diffusion of vacancy-copper (VCu) complexes, also in the absence of irradiation. Coarse-grained computer models (such as object kinetic Monte Carlo) aimed at simulating irradiation processes in model alloys or steels should therefore explicitly include the mobility of Cu precipitates, as a consequence of vacancy hops at their surface. For this purpose, in this work we calculate diffusion coefficients and lifetimes for a large variety of VCu complexes. We use an innovative atomistic model, where vacancy migration energies are calculated with little approximations, taking into account all effects of static relaxation and long-range chemical interaction as predicted by an interatomic potential. Our results show that, contrary to what intuition might suggest, saturation in vacancies tend to slow down the transport of Cu atoms.
Adaptive user displays for intelligent tutoring software.
Beal, Carole R
2004-12-01
Intelligent tutoring software (ITS) holds great promise for K-12 instruction. Yet it is difficult to obtain rich information about users that can be used in realistic educational delivery settings--public school classrooms--in which eye tracking and other user sensing technologies are not suitable. We are pursuing three "cheap and cheerful" strategies to meet this challenge in the context of an ITS for high school math instruction. First, we use detailed representations of student cognitive skills, including tasks to assess individual users' proficiency with abstract reasoning, proficiency with simple math facts and computational skill, and spatial ability. Second, we are using data mining and machine learning algorithms to identify instructional sequences that have been effective with previous students, and to use these patterns to make decisions about current students. Third, we are integrating a simple focus-of-attention tracking system into the software, using inexpensive, web cameras. This coarse-grained information can be used to time the display of multimedia hints, explanations, and examples when the user is actually looking at the screen, and to diagnose causes of problem-solving errors. The ultimate goal is to create non-intrusive software that can adapt the display of instructional information in real time to the user's cognitive strengths, motivation, and attention. PMID:15687804
Agarwal, Animesh
2015-01-01
Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however computationally this technique is very demanding. The abovementioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One possible solution to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this ...
Directory of Open Access Journals (Sweden)
Michael Polacek
2008-12-01
Full Text Available In this paper we propose two cooperation schemes to compose new parallel variants of the Variable Neighborhood Search (VNS. On the one hand, a coarse-grained cooperation scheme is introduced which is well suited for being enhanced with a solution warehouse to store and manage the so far best found solutions and a self-adapting mechanism for the most important search parameters. This makes an a priori parameter tuning obsolete. On the other hand, a fine-grained scheme was designed to reproduce the successful properties of the sequential VNS. In combination with the use of parallel exploration threads all of the best solutions and 11 out of 20 new best solutions for the Multi Depot Vehicle Routing Problem with Time Windows were found.
CosmoPMC: Cosmology Population Monte Carlo
Kilbinger, Martin; Cappe, Olivier; Cardoso, Jean-Francois; Fort, Gersende; Prunet, Simon; Robert, Christian P; Wraith, Darren
2011-01-01
We present the public release of the Bayesian sampling algorithm for cosmology, CosmoPMC (Cosmology Population Monte Carlo). CosmoPMC explores the parameter space of various cosmological probes, and also provides a robust estimate of the Bayesian evidence. CosmoPMC is based on an adaptive importance sampling method called Population Monte Carlo (PMC). Various cosmology likelihood modules are implemented, and new modules can be added easily. The importance-sampling algorithm is written in C, and fully parallelised using the Message Passing Interface (MPI). Due to very little overhead, the wall-clock time required for sampling scales approximately with the number of CPUs. The CosmoPMC package contains post-processing and plotting programs, and in addition a Monte-Carlo Markov chain (MCMC) algorithm. The sampling engine is implemented in the library pmclib, and can be used independently. The software is available for download at http://www.cosmopmc.info.
Monte Carlo Radiative Transfer
Whitney, Barbara A
2011-01-01
I outline methods for calculating the solution of Monte Carlo Radiative Transfer (MCRT) in scattering, absorption and emission processes of dust and gas, including polarization. I provide a bibliography of relevant papers on methods with astrophysical applications.