Atomistic simulation of laser-pulse surface modification: Predictions of models with various length and time scales

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

Starikov, Sergey V., E-mail: starikov@ihed.ras.ru; Pisarev, Vasily V.; Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412

2015-04-07

In this work, the femtosecond laser pulse modification of surface is studied for aluminium (Al) and gold (Au) by use of two-temperature atomistic simulation. The results are obtained for various atomistic models with different scales: from pseudo-one-dimensional to full-scale three-dimensional simulation. The surface modification after laser irradiation can be caused by ablation and melting. For low energy laser pulses, the nanoscale ripples may be induced on a surface by melting without laser ablation. In this case, nanoscale changes of the surface are due to a splash of molten metal under temperature gradient. Laser ablation occurs at a higher pulse energymore » when a crater is formed on the surface. There are essential differences between Al ablation and Au ablation. In the first step of shock-wave induced ablation, swelling and void formation occur for both metals. However, the simulation of ablation in gold shows an additional athermal type of ablation that is associated with electron pressure relaxation. This type of ablation takes place at the surface layer, at a depth of several nanometers, and does not induce swelling.« less

Analysis of an optimization-based atomistic-to-continuum coupling method for point defects

DOE PAGES

Olson, Derek; Shapeev, Alexander V.; Bochev, Pavel B.; ...

2015-11-16

Here, we formulate and analyze an optimization-based Atomistic-to-Continuum (AtC) coupling method for problems with point defects. Application of a potential-based atomistic model near the defect core enables accurate simulation of the defect. Away from the core, where site energies become nearly independent of the lattice position, the method switches to a more efficient continuum model. The two models are merged by minimizing the mismatch of their states on an overlap region, subject to the atomistic and continuum force balance equations acting independently in their domains. We prove that the optimization problem is well-posed and establish error estimates.

Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

NASA Astrophysics Data System (ADS)

Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

2017-01-01

This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.

First Principles Atomistic Model for Carbon-Doped Boron Suboxide

DTIC Science & Technology

2014-09-01

First Principles Atomistic Model for Carbon-Doped Boron Suboxide by Amol B Rahane, Jennifer S Dunn, and Vijay Kumar ARL-TR-7106...2014 First Principles Atomistic Model for Carbon-Doped Boron Suboxide Amol B Rahane Dr Vijay Kumar Foundation 1969 Sector 4 Gurgaon...5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Amol B Rahane, Jennifer S Dunn, and Vijay Kumar 5d. PROJECT

A multi-scale model of dislocation plasticity in α-Fe: Incorporating temperature, strain rate and non-Schmid effects

DOE PAGES

Lim, H.; Hale, L. M.; Zimmerman, J. A.; ...

2015-01-05

In this study, we develop an atomistically informed crystal plasticity finite element (CP-FE) model for body-centered-cubic (BCC) α-Fe that incorporates non-Schmid stress dependent slip with temperature and strain rate effects. Based on recent insights obtained from atomistic simulations, we propose a new constitutive model that combines a generalized non-Schmid yield law with aspects from a line tension (LT) model for describing activation enthalpy required for the motion of dislocation kinks. Atomistic calculations are conducted to quantify the non-Schmid effects while both experimental data and atomistic simulations are used to assess the temperature and strain rate effects. The parameterized constitutive equationmore » is implemented into a BCC CP-FE model to simulate plastic deformation of single and polycrystalline Fe which is compared with experimental data from the literature. This direct comparison demonstrates that the atomistically informed model accurately captures the effects of crystal orientation, temperature and strain rate on the flow behavior of siangle crystal Fe. Furthermore, our proposed CP-FE model exhibits temperature and strain rate dependent flow and yield surfaces in polycrystalline Fe that deviate from conventional CP-FE models based on Schmid's law.« less

Atomistic Cohesive Zone Models for Interface Decohesion in Metals

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.; Saether, Erik; Glaessgen, Edward H.

2009-01-01

Using a statistical mechanics approach, a cohesive-zone law in the form of a traction-displacement constitutive relationship characterizing the load transfer across the plane of a growing edge crack is extracted from atomistic simulations for use within a continuum finite element model. The methodology for the atomistic derivation of a cohesive-zone law is presented. This procedure can be implemented to build cohesive-zone finite element models for simulating fracture in nanocrystalline or ultrafine grained materials.

Mirrored continuum and molecular scale simulations of the ignition of high-pressure phases of RDX

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

Lee, Kibaek; Stewart, D. Scott, E-mail: santc@illinois.edu, E-mail: dss@illinois.edu; Joshi, Kaushik

2016-05-14

We present a mirrored atomistic and continuum framework that is used to describe the ignition of energetic materials, and a high-pressure phase of RDX in particular. The continuum formulation uses meaningful averages of thermodynamic properties obtained from the atomistic simulation and a simplification of enormously complex reaction kinetics. In particular, components are identified based on molecular weight bin averages and our methodology assumes that both the averaged atomistic and continuum simulations are represented on the same time and length scales. The atomistic simulations of thermally initiated ignition of RDX are performed using reactive molecular dynamics (RMD). The continuum model ismore » based on multi-component thermodynamics and uses a kinetics scheme that describes observed chemical changes of the averaged atomistic simulations. Thus the mirrored continuum simulations mimic the rapid change in pressure, temperature, and average molecular weight of species in the reactive mixture. This mirroring enables a new technique to simplify the chemistry obtained from reactive MD simulations while retaining the observed features and spatial and temporal scales from both the RMD and continuum model. The primary benefit of this approach is a potentially powerful, but familiar way to interpret the atomistic simulations and understand the chemical events and reaction rates. The approach is quite general and thus can provide a way to model chemistry based on atomistic simulations and extend the reach of those simulations.« less

Simulating complex atomistic processes: On-the-fly kinetic Monte Carlo scheme with selective active volumes

NASA Astrophysics Data System (ADS)

Xu, Haixuan; Osetsky, Yury N.; Stoller, Roger E.

2011-10-01

An accelerated atomistic kinetic Monte Carlo (KMC) approach for evolving complex atomistic structures has been developed. The method incorporates on-the-fly calculations of transition states (TSs) with a scheme for defining active volumes (AVs) in an off-lattice (relaxed) system. In contrast to conventional KMC models that require all reactions to be predetermined, this approach is self-evolving and any physically relevant motion or reaction may occur. Application of this self-evolving atomistic kinetic Monte Carlo (SEAK-MC) approach is illustrated by predicting the evolution of a complex defect configuration obtained in a molecular dynamics (MD) simulation of a displacement cascade in Fe. Over much longer times, it was shown that interstitial clusters interacting with other defects may change their structure, e.g., from glissile to sessile configuration. The direct comparison with MD modeling confirms the atomistic fidelity of the approach, while the longer time simulation demonstrates the unique capability of the model.

Fermi-level effects in semiconductor processing: A modeling scheme for atomistic kinetic Monte Carlo simulators

NASA Astrophysics Data System (ADS)

Martin-Bragado, I.; Castrillo, P.; Jaraiz, M.; Pinacho, R.; Rubio, J. E.; Barbolla, J.; Moroz, V.

2005-09-01

Atomistic process simulation is expected to play an important role for the development of next generations of integrated circuits. This work describes an approach for modeling electric charge effects in a three-dimensional atomistic kinetic Monte Carlo process simulator. The proposed model has been applied to the diffusion of electrically active boron and arsenic atoms in silicon. Several key aspects of the underlying physical mechanisms are discussed: (i) the use of the local Debye length to smooth out the atomistic point-charge distribution, (ii) algorithms to correctly update the charge state in a physically accurate and computationally efficient way, and (iii) an efficient implementation of the drift of charged particles in an electric field. High-concentration effects such as band-gap narrowing and degenerate statistics are also taken into account. The efficiency, accuracy, and relevance of the model are discussed.

The notion of a plastic material spin in atomistic simulations

NASA Astrophysics Data System (ADS)

Dickel, D.; Tenev, T. G.; Gullett, P.; Horstemeyer, M. F.

2016-12-01

A kinematic algorithm is proposed to extend existing constructions of strain tensors from atomistic data to decouple elastic and plastic contributions to the strain. Elastic and plastic deformation and ultimately the plastic spin, useful quantities in continuum mechanics and finite element simulations, are computed from the full, discrete deformation gradient and an algorithm for the local elastic deformation gradient. This elastic deformation gradient algorithm identifies a crystal type using bond angle analysis (Ackland and Jones 2006 Phys. Rev. B 73 054104) and further exploits the relationship between bond angles to determine the local deformation from an ideal crystal lattice. Full definitions of plastic deformation follow directly using a multiplicative decomposition of the deformation gradient. The results of molecular dynamics simulations of copper in simple shear and torsion are presented to demonstrate the ability of these new discrete measures to describe plastic material spin in atomistic simulation and to compare them with continuum theory.

Atomistic modeling of BN nanofillers for mechanical and thermal properties: a review.

PubMed

Kumar, Rajesh; Parashar, Avinash

2016-01-07

Due to their exceptional mechanical properties, thermal conductivity and a wide band gap (5-6 eV), boron nitride nanotubes and nanosheets have promising applications in the field of engineering and biomedical science. Accurate modeling of failure or fracture in a nanomaterial inherently involves coupling of atomic domains of cracks and voids as well as a deformation mechanism originating from grain boundaries. This review highlights the recent progress made in the atomistic modeling of boron nitride nanofillers. Continuous improvements in computational power have made it possible to study the structural properties of these nanofillers at the atomistic scale.

An Optimization-based Atomistic-to-Continuum Coupling Method

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

Olson, Derek; Bochev, Pavel B.; Luskin, Mitchell

2014-08-21

In this paper, we present a new optimization-based method for atomistic-to-continuum (AtC) coupling. The main idea is to cast the latter as a constrained optimization problem with virtual Dirichlet controls on the interfaces between the atomistic and continuum subdomains. The optimization objective is to minimize the error between the atomistic and continuum solutions on the overlap between the two subdomains, while the atomistic and continuum force balance equations provide the constraints. Separation, rather then blending of the atomistic and continuum problems, and their subsequent use as constraints in the optimization problem distinguishes our approach from the existing AtC formulations. Finally,more » we present and analyze the method in the context of a one-dimensional chain of atoms modeled using a linearized two-body potential with next-nearest neighbor interactions.« less

Understanding materials behavior from atomistic simulations: Case study of al-containing high entropy alloys and thermally grown aluminum oxide

NASA Astrophysics Data System (ADS)

Yinkai Lei

Atomistic simulation refers to a set of simulation methods that model the materials on the atomistic scale. These simulation methods are faster and cheaper alternative approaches to investigate thermodynamics and kinetics of materials compared to experiments. In this dissertation, atomistic simulation methods have been used to study the thermodynamic and kinetic properties of two material systems, i.e. the entropy of Al-containing high entropy alloys (HEAs) and the vacancy migration energy of thermally grown aluminum oxide. (Abstract shortened by ProQuest.).

Folding and insertion thermodynamics of the transmembrane WALP peptide

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

Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de; Bennett, W. F. Drew; Pfaendtner, Jim

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of meanmore » force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.« less

Folding and insertion thermodynamics of the transmembrane WALP peptide

NASA Astrophysics Data System (ADS)

Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

2015-12-01

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

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

NASA Astrophysics Data System (ADS)

Takada, Shoji

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

Effect of alloying on screw dislocation structure in Mo: atomistic modelling approach with ab-initio parametrization

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.

2005-03-01

The plastic deformation in bcc metals is realized by the motion of screw dislocations with a complex star-like non-planar core. In this case, the direct investigation of the solute effect by first principles electronic structure calculations is a challenging problem for which we follow a combined approach that includes atomistic dislocation modelling with ab-initio parametrization of interatomic interactions. The screw dislocation core structure in Mo alloys is described within the model of atomic row displacements along a dislocation line with the interatomic row potential estimated from total energy full-potential linear muffin-tin orbital (FLMTO) calculations with the generalized gradient approximation (GGA) for the exchange-correlation potential. We demonstrate (1) that the solute effect on the dislocation structure is different for ``hard'' and ``easy'' cores and (2) that the softener addition in a ``hard'' core gives rise to a structural transformation into a configuration with a lower energy through an intermediate state. The softener solute is shown to disturb locally the three-fold symmetry of the dislocation core and the dislocation structure tends to the split planar core.

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

Yang, Qingcheng, E-mail: qiy9@pitt.edu; To, Albert C., E-mail: albertto@pitt.edu

Surface effects have been observed to contribute significantly to the mechanical response of nanoscale structures. The newly proposed energy-based coarse-grained atomistic method Multiresolution Molecular Mechanics (MMM) (Yang, To (2015), ) is applied to capture surface effect for nanosized structures by designing a surface summation rule SR{sup S} within the framework of MMM. Combined with previously proposed bulk summation rule SR{sup B}, the MMM summation rule SR{sup MMM} is completed. SR{sup S} and SR{sup B} are consistently formed within SR{sup MMM} for general finite element shape functions. Analogous to quadrature rules in finite element method (FEM), the key idea to themore » good performance of SR{sup MMM} lies in that the order or distribution of energy for coarse-grained atomistic model is mathematically derived such that the number, position and weight of quadrature-type (sampling) atoms can be determined. Mathematically, the derived energy distribution of surface area is different from that of bulk region. Physically, the difference is due to the fact that surface atoms lack neighboring bonding. As such, SR{sup S} and SR{sup B} are employed for surface and bulk domains, respectively. Two- and three-dimensional numerical examples using the respective 4-node bilinear quadrilateral, 8-node quadratic quadrilateral and 8-node hexahedral meshes are employed to verify and validate the proposed approach. It is shown that MMM with SR{sup MMM} accurately captures corner, edge and surface effects with less 0.3% degrees of freedom of the original atomistic system, compared against full atomistic simulation. The effectiveness of SR{sup MMM} with respect to high order element is also demonstrated by employing the 8-node quadratic quadrilateral to solve a beam bending problem considering surface effect. In addition, the introduced sampling error with SR{sup MMM} that is analogous to numerical integration error with quadrature rule in FEM is very small. - Highlights: • Surface effect captured by Multiresolution Molecular Mechanics (MMM) is presented. • A novel surface summation rule within the framework of MMM is proposed. • Surface, corner and edges effects are accuterly captured in two and three dimension. • MMM with less 0.3% degrees of freedom of atomistics reproduces atomistic results.« less

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

PubMed

Abbott, Lauren J; Stevens, Mark J

2015-12-28

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

Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations.

PubMed

Gu, Ruo-Xu; Ingólfsson, Helgi I; de Vries, Alex H; Marrink, Siewert J; Tieleman, D Peter

2017-04-20

Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level.

Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

PubMed Central

2016-01-01

Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level. PMID:27610460

Accelerating molecular Monte Carlo simulations using distance and orientation dependent energy tables: tuning from atomistic accuracy to smoothed “coarse-grained” models

PubMed Central

Lettieri, S.; Zuckerman, D.M.

2011-01-01

Typically, the most time consuming part of any atomistic molecular simulation is due to the repeated calculation of distances, energies and forces between pairs of atoms. However, many molecules contain nearly rigid multi-atom groups such as rings and other conjugated moieties, whose rigidity can be exploited to significantly speed up computations. The availability of GB-scale random-access memory (RAM) offers the possibility of tabulation (pre-calculation) of distance and orientation-dependent interactions among such rigid molecular bodies. Here, we perform an investigation of this energy tabulation approach for a fluid of atomistic – but rigid – benzene molecules at standard temperature and density. In particular, using O(1) GB of RAM, we construct an energy look-up table which encompasses the full range of allowed relative positions and orientations between a pair of whole molecules. We obtain a hardware-dependent speed-up of a factor of 24-50 as compared to an ordinary (“exact”) Monte Carlo simulation and find excellent agreement between energetic and structural properties. Second, we examine the somewhat reduced fidelity of results obtained using energy tables based on much less memory use. Third, the energy table serves as a convenient platform to explore potential energy smoothing techniques, akin to coarse-graining. Simulations with smoothed tables exhibit near atomistic accuracy while increasing diffusivity. The combined speed-up in sampling from tabulation and smoothing exceeds a factor of 100. For future applications greater speed-ups can be expected for larger rigid groups, such as those found in biomolecules. PMID:22120971

Acceleration of saddle-point searches with machine learning.

PubMed

Peterson, Andrew A

2016-08-21

In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the number of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.

Acceleration of saddle-point searches with machine learning

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

Peterson, Andrew A., E-mail: andrew-peterson@brown.edu

In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the numbermore » of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.« less

CG2AA: backmapping protein coarse-grained structures.

PubMed

Lombardi, Leandro E; Martí, Marcelo A; Capece, Luciana

2016-04-15

Coarse grain (CG) models allow long-scale simulations with a much lower computational cost than that of all-atom simulations. However, the absence of atomistic detail impedes the analysis of specific atomic interactions that are determinant in most interesting biomolecular processes. In order to study these phenomena, it is necessary to reconstruct the atomistic structure from the CG representation. This structure can be analyzed by itself or be used as an onset for atomistic molecular dynamics simulations. In this work, we present a computer program that accurately reconstructs the atomistic structure from a CG model for proteins, using a simple geometrical algorithm. The software is free and available online at http://www.ic.fcen.uba.ar/cg2aa/cg2aa.py Supplementary data are available at Bioinformatics online. lula@qi.fcen.uba.ar. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Multiscale Modeling of Damage Processes in fcc Aluminum: From Atoms to Grains

NASA Technical Reports Server (NTRS)

Glaessgen, E. H.; Saether, E.; Yamakov, V.

2008-01-01

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, current analysis is limited to small domains and increasing the size of the MD domain quickly presents intractable computational demands. A preferred approach to surmount this computational limitation has been to combine continuum mechanics-based modeling procedures, such as the finite element method (FEM), with MD analyses thereby reducing the region of atomic scale refinement. Such multiscale modeling strategies can be divided into two broad classifications: concurrent multiscale methods that directly incorporate an atomistic domain within a continuum domain and sequential multiscale methods that extract an averaged response from the atomistic simulation for later use as a constitutive model in a continuum analysis.

Scalable nanohelices for predictive studies and enhanced 3D visualization.

PubMed

Meagher, Kwyn A; Doblack, Benjamin N; Ramirez, Mercedes; Davila, Lilian P

2014-11-12

Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing applications. For predictive simulations, it has become increasingly important to be able to model the structure of nanohelices accurately. To study the effect of local structure on the properties of these complex geometries one must develop realistic models. To date, software packages are rather limited in creating atomistic helical models. This work focuses on producing atomistic models of silica glass (SiO₂) nanoribbons and nanosprings for molecular dynamics (MD) simulations. Using an MD model of "bulk" silica glass, two computational procedures to precisely create the shape of nanoribbons and nanosprings are presented. The first method employs the AWK programming language and open-source software to effectively carve various shapes of silica nanoribbons from the initial bulk model, using desired dimensions and parametric equations to define a helix. With this method, accurate atomistic silica nanoribbons can be generated for a range of pitch values and dimensions. The second method involves a more robust code which allows flexibility in modeling nanohelical structures. This approach utilizes a C++ code particularly written to implement pre-screening methods as well as the mathematical equations for a helix, resulting in greater precision and efficiency when creating nanospring models. Using these codes, well-defined and scalable nanoribbons and nanosprings suited for atomistic simulations can be effectively created. An added value in both open-source codes is that they can be adapted to reproduce different helical structures, independent of material. In addition, a MATLAB graphical user interface (GUI) is used to enhance learning through visualization and interaction for a general user with the atomistic helical structures. One application of these methods is the recent study of nanohelices via MD simulations for mechanical energy harvesting purposes.

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

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

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived frommore » fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.« less

Development of Continuum-Atomistic Approach for Modeling Metal Irradiation by Heavy Ions

NASA Astrophysics Data System (ADS)

Batgerel, Balt; Dimova, Stefka; Puzynin, Igor; Puzynina, Taisia; Hristov, Ivan; Hristova, Radoslava; Tukhliev, Zafar; Sharipov, Zarif

2018-02-01

Over the last several decades active research in the field of materials irradiation by high-energy heavy ions has been worked out. The experiments in this area are labor-consuming and expensive. Therefore the improvement of the existing mathematical models and the development of new ones based on the experimental data of interaction of high-energy heavy ions with materials are of interest. Presently, two approaches are used for studying these processes: a thermal spike model and molecular dynamics methods. The combination of these two approaches - the continuous-atomistic model - will give the opportunity to investigate more thoroughly the processes of irradiation of materials by high-energy heavy ions. To solve the equations of the continuous-atomistic model, a software package was developed and the block of molecular dynamics software was tested on the heterogeneous cluster HybriLIT.

Atomistic Conversion Reaction Mechanism of WO 3 in Secondary Ion Batteries of Li, Na, and Ca

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

He, Yang; Gu, Meng; Xiao, Haiyan

2016-04-13

Reversible insertion and extraction of ionic species into a host lattice governs the basic operating principle for both rechargeable battery (such as lithium batteries) and electrochromic devices (such as ANA Boeing 787-8 Dreamliner electrochromic window). Intercalation and/or conversion are two fundamental chemical processes for some materials in response to the ion insertion. The interplay between these two chemical processes has never been established. It is speculated that the conversion reaction is initiated by ion intercalation. However, experimental evidence of intercalation and subsequent conversion remains unexplored. Here, using in situ HRTEM and spectroscopy, we captured the atomistic conversion reaction processes duringmore » lithium, sodium and calcium ion insertion into tungsten trioxide (WO3) single crystal model electrodes. An intercalation step right prior to conversion is explicitly revealed at atomic scale for the first time for these three ion species. Combining nanoscale diffraction and ab initio molecular dynamics simulations, it is found that, beyond intercalation, the inserted ion-oxygen bonding formation destabilized the transition-metal framework which gradually shrunk, distorted and finally collapsed to a pseudo-amorphous structure. This study provides a full atomistic picture on the transition from intercalation to conversion, which is of essential for material applications in both secondary ion batteries and electrochromic devices.« less

A Model for Predicting Thermoelectric Properties of Bi2Te3

NASA Technical Reports Server (NTRS)

Lee, Seungwon; VonAllmen, Paul

2009-01-01

A parameterized orthogonal tight-binding mathematical model of the quantum electronic structure of the bismuth telluride molecule has been devised for use in conjunction with a semiclassical transport model in predicting the thermoelectric properties of doped bismuth telluride. This model is expected to be useful in designing and analyzing Bi2Te3 thermoelectric devices, including ones that contain such nano - structures as quantum wells and wires. In addition, the understanding gained in the use of this model can be expected to lead to the development of better models that could be useful for developing other thermoelectric materials and devices having enhanced thermoelectric properties. Bi2Te3 is one of the best bulk thermoelectric materials and is widely used in commercial thermoelectric devices. Most prior theoretical studies of the thermoelectric properties of Bi2Te3 have involved either continuum models or ab-initio models. Continuum models are computationally very efficient, but do not account for atomic-level effects. Ab-initio models are atomistic by definition, but do not scale well in that computation times increase excessively with increasing numbers of atoms. The present tight-binding model bridges the gap between the well-scalable but non-atomistic continuum models and the atomistic but poorly scalable ab-initio models: The present tight-binding model is atomistic, yet also computationally efficient because of the reduced (relative to an ab-initio model) number of basis orbitals and flexible parameterization of the Hamiltonian.

The Quasicontinuum Method: Overview, applications and current directions

NASA Astrophysics Data System (ADS)

Miller, Ronald E.; Tadmor, E. B.

2002-10-01

The Quasicontinuum (QC) Method, originally conceived and developed by Tadmor, Ortiz and Phillips [1] in 1996, has since seen a great deal of development and application by a number of researchers. The idea of the method is a relatively simple one. With the goal of modeling an atomistic system without explicitly treating every atom in the problem, the QC provides a framework whereby degrees of freedom are judiciously eliminated and force/energy calculations are expedited. This is combined with adaptive model refinement to ensure that full atomistic detail is retained in regions of the problem where it is required while continuum assumptions reduce the computational demand elsewhere. This article provides a review of the method, from its original motivations and formulation to recent improvements and developments. A summary of the important mechanics of materials results that have been obtained using the QC approach is presented. Finally, several related modeling techniques from the literature are briefly discussed. As an accompaniment to this paper, a website designed to serve as a clearinghouse for information on the QC method has been established at www.qcmethod.com. The site includes information on QC research, links to researchers, downloadable QC code and documentation.

Atomistic modeling trap-assisted tunneling in hole tunnel field effect transistors

NASA Astrophysics Data System (ADS)

Long, Pengyu; Huang, Jun Z.; Povolotskyi, Michael; Sarangapani, Prasad; Valencia-Zapata, Gustavo A.; Kubis, Tillmann; Rodwell, Mark J. W.; Klimeck, Gerhard

2018-05-01

Tunnel Field Effect Transistors (FETs) have the potential to achieve steep Subthreshold Swing (S.S.) below 60 mV/dec, but their S.S. could be limited by trap-assisted tunneling (TAT) due to interface traps. In this paper, the effect of trap energy and location on OFF-current (IOFF) of tunnel FETs is evaluated systematically using an atomistic trap level representation in a full quantum transport simulation. Trap energy levels close to band edges cause the highest leakage. Wave function penetration into the surrounding oxide increases the TAT current. To estimate the effects of multiple traps, we assume that the traps themselves do not interact with each other and as a whole do not modify the electrostatic potential dramatically. Within that model limitation, this numerical metrology study points to the critical importance of TAT in the IOFF in tunnel FETs. The model shows that for Dit higher than 1012/(cm2 eV) IO F F is critically increased with a degraded IO N/IO F F ratio of the tunnel FET. In order to have an IO N/IO F F ratio higher than 104, the acceptable Dit near Ev should be controlled to no larger than 1012/(cm2 eV) .

Effect of Single-Electron Interface Trapping in Decanano MOSFETs: A 3D Atomistic Simulation Study

NASA Technical Reports Server (NTRS)

Asenov, Asen; Balasubramaniam, R.; Brown, A. R.; Davies, J. H.

2000-01-01

We study the effect of trapping/detrapping of a single-electron in interface states in the channel of n-type MOSFETs with decanano dimensions using 3D atomistic simulation techniques. In order to highlight the basic dependencies, the simulations are carried out initially assuming continuous doping charge, and discrete localized charge only for the trapped electron. The dependence of the random telegraph signal (RTS) amplitudes on the device dimensions and on the position of the trapped charge in the channel are studied in detail. Later, in full-scale, atomistic simulations assuming discrete charge for both randomly placed dopants and the trapped electron, we highlight the importance of current percolation and of traps with strategic position where the trapped electron blocks a dominant current path.

An Embedded Statistical Method for Coupling Molecular Dynamics and Finite Element Analyses

NASA Technical Reports Server (NTRS)

Saether, E.; Glaessgen, E.H.; Yamakov, V.

2008-01-01

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

A New Concurrent Multiscale Methodology for Coupling Molecular Dynamics and Finite Element Analyses

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin; Saether, Erik; Glaessgen, Edward H/.

2008-01-01

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Two-electron states of a group-V donor in silicon from atomistic full configuration interactions

NASA Astrophysics Data System (ADS)

Tankasala, Archana; Salfi, Joseph; Bocquel, Juanita; Voisin, Benoit; Usman, Muhammad; Klimeck, Gerhard; Simmons, Michelle Y.; Hollenberg, Lloyd C. L.; Rogge, Sven; Rahman, Rajib

2018-05-01

Two-electron states bound to donors in silicon are important for both two-qubit gates and spin readout. We present a full configuration interaction technique in the atomistic tight-binding basis to capture multielectron exchange and correlation effects taking into account the full band structure of silicon and the atomic-scale granularity of a nanoscale device. Excited s -like states of A1 symmetry are found to strongly influence the charging energy of a negative donor center. We apply the technique on subsurface dopants subjected to gate electric fields and show that bound triplet states appear in the spectrum as a result of decreased charging energy. The exchange energy, obtained for the two-electron states in various confinement regimes, may enable engineering electrical control of spins in donor-dot hybrid qubits.

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

NASA Astrophysics Data System (ADS)

Farrell, Kathryn; Oden, J. Tinsley; Faghihi, Danial

2015-08-01

A general adaptive modeling algorithm for selection and validation of coarse-grained models of atomistic systems is presented. A Bayesian framework is developed to address uncertainties in parameters, data, and model selection. Algorithms for computing output sensitivities to parameter variances, model evidence and posterior model plausibilities for given data, and for computing what are referred to as Occam Categories in reference to a rough measure of model simplicity, make up components of the overall approach. Computational results are provided for representative applications.

Multiresolution molecular mechanics: Surface effects in nanoscale materials

NASA Astrophysics Data System (ADS)

Yang, Qingcheng; To, Albert C.

2017-05-01

Surface effects have been observed to contribute significantly to the mechanical response of nanoscale structures. The newly proposed energy-based coarse-grained atomistic method Multiresolution Molecular Mechanics (MMM) (Yang, To (2015), [57]) is applied to capture surface effect for nanosized structures by designing a surface summation rule SRS within the framework of MMM. Combined with previously proposed bulk summation rule SRB, the MMM summation rule SRMMM is completed. SRS and SRB are consistently formed within SRMMM for general finite element shape functions. Analogous to quadrature rules in finite element method (FEM), the key idea to the good performance of SRMMM lies in that the order or distribution of energy for coarse-grained atomistic model is mathematically derived such that the number, position and weight of quadrature-type (sampling) atoms can be determined. Mathematically, the derived energy distribution of surface area is different from that of bulk region. Physically, the difference is due to the fact that surface atoms lack neighboring bonding. As such, SRS and SRB are employed for surface and bulk domains, respectively. Two- and three-dimensional numerical examples using the respective 4-node bilinear quadrilateral, 8-node quadratic quadrilateral and 8-node hexahedral meshes are employed to verify and validate the proposed approach. It is shown that MMM with SRMMM accurately captures corner, edge and surface effects with less 0.3% degrees of freedom of the original atomistic system, compared against full atomistic simulation. The effectiveness of SRMMM with respect to high order element is also demonstrated by employing the 8-node quadratic quadrilateral to solve a beam bending problem considering surface effect. In addition, the introduced sampling error with SRMMM that is analogous to numerical integration error with quadrature rule in FEM is very small.

Atomistic to continuum modeling of solidification microstructures

DOE PAGES

Karma, Alain; Tourret, Damien

2015-09-26

We summarize recent advances in modeling of solidification microstructures using computational methods that bridge atomistic to continuum scales. We first discuss progress in atomistic modeling of equilibrium and non-equilibrium solid–liquid interface properties influencing microstructure formation, as well as interface coalescence phenomena influencing the late stages of solidification. The latter is relevant in the context of hot tearing reviewed in the article by M. Rappaz in this issue. We then discuss progress to model microstructures on a continuum scale using phase-field methods. We focus on selected examples in which modeling of 3D cellular and dendritic microstructures has been directly linked tomore » experimental observations. Finally, we discuss a recently introduced coarse-grained dendritic needle network approach to simulate the formation of well-developed dendritic microstructures. The approach reliably bridges the well-separated scales traditionally simulated by phase-field and grain structure models, hence opening new avenues for quantitative modeling of complex intra- and inter-grain dynamical interactions on a grain scale.« less

A Configurational-Bias-Monte-Carlo Back-Mapping Algorithm for Efficient and Rapid Conversion of Coarse-Grained Water Structures Into Atomistic Models.

PubMed

Loeffler, Troy David; Chan, Henry; Narayanan, Badri; Cherukara, Mathew J; Gray, Stephen K; Sankaranarayanan, Subramanian K R S

2018-06-20

Coarse-grained molecular dynamics (MD) simulations represent a powerful approach to simulate longer time scale and larger length scale phenomena than those accessible to all-atom models. The gain in efficiency, however, comes at the cost of atomistic details. The reverse transformation, also known as back-mapping, of coarse grained beads into their atomistic constituents represents a major challenge. Most existing approaches are limited to specific molecules or specific force-fields and often rely on running a long time atomistic MD of the back-mapped configuration to arrive at an optimal solution. Such approaches are problematic when dealing with systems with high diffusion barriers. Here, we introduce a new extension of the configurational-bias-Monte-Carlo (CBMC) algorithm, which we term the crystalline-configurational-bias-Monte-Carlo (C-CBMC) algortihm, that allows rapid and efficient conversion of a coarse-grained model back into its atomistic representation. Although the method is generic, we use a coarse-grained water model as a representative example and demonstrate the back-mapping or reverse transformation for model systems ranging from the ice-liquid water interface to amorphous and crystalline ice configurations. A series of simulations using the TIP4P/Ice model are performed to compare the new CBMC method to several other standard Monte Carlo and Molecular Dynamics based back-mapping techniques. In all the cases, the C-CBMC algorithm is able to find optimal hydrogen bonded configuration many thousand evaluations/steps sooner than the other methods compared within this paper. For crystalline ice structures such as a hexagonal, cubic, and cubic-hexagonal stacking disorder structures, the C-CBMC was able to find structures that were between 0.05 and 0.1 eV/water molecule lower in energy than the ground state energies predicted by the other methods. Detailed analysis of the atomistic structures show a significantly better global hydrogen positioning when contrasted with the existing simpler back-mapping methods. Our results demonstrate the efficiency and efficacy of our new back-mapping approach, especially for crystalline systems where simple force-field based relaxations have a tendency to get trapped in local minima.

Phase transformations at interfaces: Observations from atomistic modeling

DOE PAGES

Frolov, T.; Asta, M.; Mishin, Y.

2016-10-01

Here, we review the recent progress in theoretical understanding and atomistic computer simulations of phase transformations in materials interfaces, focusing on grain boundaries (GBs) in metallic systems. Recently developed simulation approaches enable the search and structural characterization of GB phases in single-component metals and binary alloys, calculation of thermodynamic properties of individual GB phases, and modeling of the effect of the GB phase transformations on GB kinetics. Atomistic simulations demonstrate that the GB transformations can be induced by varying the temperature, loading the GB with point defects, or varying the amount of solute segregation. The atomic-level understanding obtained from suchmore » simulations can provide input for further development of thermodynamics theories and continuous models of interface phase transformations while simultaneously serving as a testing ground for validation of theories and models. They can also help interpret and guide experimental work in this field.« less

Molecular Modeling for Calculation of Mechanical Properties of Epoxies with Moisture Ingress

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Frankland, Sarah J.; Hinkley, J. A.; Gates, T. S.

2009-01-01

Atomistic models of epoxy structures were built in order to assess the effect of crosslink degree, moisture content and temperature on the calculated properties of a typical representative generic epoxy. Each atomistic model had approximately 7000 atoms and was contained within a periodic boundary condition cell with edge lengths of about 4 nm. Four atomistic models were built with a range of crosslink degree and moisture content. Each of these structures was simulated at three temperatures: 300 K, 350 K, and 400 K. Elastic constants were calculated for these structures by monitoring the stress tensor as a function of applied strain deformations to the periodic boundary conditions. The mechanical properties showed reasonably consistent behavior with respect to these parameters. The moduli decreased with decreasing crosslink degree with increasing temperature. The moduli generally decreased with increasing moisture content, although this effect was not as consistent as that seen for temperature and crosslink degree.

Coarse-grained modeling of polyethylene melts: Effect on dynamics

DOE PAGES

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

2017-05-23

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

Coarse-grained modeling of polyethylene melts: Effect on dynamics

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

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

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

Multiscale Modeling of Stiffness, Friction and Adhesion in Mechanical Contacts

DTIC Science & Technology

2012-02-29

over a lateral length l scales as a power law: h  lH, where H is called the Hurst exponent . For typical experimental surfaces, H ranges from 0.5 to 0.8...surfaces with a wide range of Hurst exponents using fully atomistic calculations and the Green’s function method. A simple relation like Eq. (2...described above to explore a full range of parameter space with different rms roughness h0, rms slope h’0, Hurst exponent H, adhesion energy

An atomistic simulation scheme for modeling crystal formation from solution.

PubMed

Kawska, Agnieszka; Brickmann, Jürgen; Kniep, Rüdiger; Hochrein, Oliver; Zahn, Dirk

2006-01-14

We present an atomistic simulation scheme for investigating crystal growth from solution. Molecular-dynamics simulation studies of such processes typically suffer from considerable limitations concerning both system size and simulation times. In our method this time-length scale problem is circumvented by an iterative scheme which combines a Monte Carlo-type approach for the identification of ion adsorption sites and, after each growth step, structural optimization of the ion cluster and the solvent by means of molecular-dynamics simulation runs. An important approximation of our method is based on assuming full structural relaxation of the aggregates between each of the growth steps. This concept only holds for compounds of low solubility. To illustrate our method we studied CaF2 aggregate growth from aqueous solution, which may be taken as prototypes for compounds of very low solubility. The limitations of our simulation scheme are illustrated by the example of NaCl aggregation from aqueous solution, which corresponds to a solute/solvent combination of very high salt solubility.

Literature review report on atomistic modeling tools for FeCrAl alloys

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

Zhang, Yongfeng; Schwen, Daniel; Martinez, Enrique

2015-12-01

This reports summarizes the literature review results on atomistic tools, particularly interatomic potentials used in molecular dynamics simulations, for FeCrAl ternary alloys. FeCrAl has recently been identified as a possible cladding concept for accident tolerant fuels for its superior corrosion resistance. Along with several other concepts, an initial evaluation and recommendation are desired for FeCrAl before it’s used in realistic fuels. For this purpose, sufficient understanding on the in-reactor behavior of FeCrAl needs to be grained in a relatively short timeframe, and multiscale modeling and simulations have been selected as an efficient measure to supplement experiments and in-reactor testing formore » better understanding on FeCrAl. For the limited knowledge on FeCrAl alloys, the multiscale modeling approach relies on atomistic simulations to obtain the missing material parameters and properties. As a first step, atomistic tools have to be identified and this is the purpose of the present report. It was noticed during the literature survey that no interatomic potentials currently available for FeCrAl. Here, we summarize the interatomic potentials available for FeCr alloys for possible molecular dynamics studies using FeCr as surrogate materials. Other atomistic methods such as lattice kinetic Monte Carlo are also included in this report. A couple of research topics at the atomic scale are suggested based on the literature survey.« less

Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

NASA Astrophysics Data System (ADS)

Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kibaek

2017-01-01

We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link.

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

PubMed

Rapaport, D C

2009-04-01

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

Coarse-Grained Molecular Models of Water: A Review

PubMed Central

Hadley, Kevin R.; McCabe, Clare

2012-01-01

Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regards to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. Finally, how the models are parameterized depends on their application, so, while some are fitted to experimental properties such as surface tension and density, others are fitted to radial distribution functions extracted from atomistic simulations. PMID:22904601

Hierarchical lattice models of hydrogen-bond networks in water

NASA Astrophysics Data System (ADS)

Dandekar, Rahul; Hassanali, Ali A.

2018-06-01

We develop a graph-based model of the hydrogen-bond network in water, with a view toward quantitatively modeling the molecular-level correlational structure of the network. The networks formed are studied by the constructing the model on two infinite-dimensional lattices. Our models are built bottom up, based on microscopic information coming from atomistic simulations, and we show that the predictions of the model are consistent with known results from ab initio simulations of liquid water. We show that simple entropic models can predict the correlations and clustering of local-coordination defects around tetrahedral waters observed in the atomistic simulations. We also find that orientational correlations between bonds are longer ranged than density correlations, determine the directional correlations within closed loops, and show that the patterns of water wires within these structures are also consistent with previous atomistic simulations. Our models show the existence of density and compressibility anomalies, as seen in the real liquid, and the phase diagram of these models is consistent with the singularity-free scenario previously proposed by Sastry and coworkers [Phys. Rev. E 53, 6144 (1996), 10.1103/PhysRevE.53.6144].

Modelling irradiation-induced softening in BCC iron by crystal plasticity approach

NASA Astrophysics Data System (ADS)

Xiao, Xiazi; Terentyev, Dmitry; Yu, Long; Song, Dingkun; Bakaev, A.; Duan, Huiling

2015-11-01

Crystal plasticity model (CPM) for BCC iron to account for radiation-induced strain softening is proposed. CPM is based on the plastically-driven and thermally-activated removal of dislocation loops. Atomistic simulations are applied to parameterize dislocation-defect interactions. Combining experimental microstructures, defect-hardening/absorption rules from atomistic simulations, and CPM fitted to properties of non-irradiated iron, the model achieves a good agreement with experimental data regarding radiation-induced strain softening and flow stress increase under neutron irradiation.

Atomistic and coarse-grained computer simulations of raft-like lipid mixtures.

PubMed

Pandit, Sagar A; Scott, H Larry

2007-01-01

Computer modeling can provide insights into the existence, structure, size, and thermodynamic stability of localized raft-like regions in membranes. However, the challenges in the construction and simulation of accurate models of heterogeneous membranes are great. The primary obstacle in modeling the lateral organization within a membrane is the relatively slow lateral diffusion rate for lipid molecules. Microsecond or longer time-scales are needed to fully model the formation and stability of a raft in a membra ne. Atomistic simulations currently are not able to reach this scale, but they do provide quantitative information on the intermolecular forces and correlations that are involved in lateral organization. In this chapter, the steps needed to carry out and analyze atomistic simulations of hydrated lipid bilayers having heterogeneous composition are outlined. It is then shown how the data from a molecular dynamics simulation can be used to construct a coarse-grained model for the heterogeneous bilayer that can predict the lateral organization and stability of rafts at up to millisecond time-scales.

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

NASA Technical Reports Server (NTRS)

Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

2009-01-01

Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

A kinetic Monte Carlo simulation method of van der Waals epitaxy for atomistic nucleation-growth processes of transition metal dichalcogenides.

PubMed

Nie, Yifan; Liang, Chaoping; Cha, Pil-Ryung; Colombo, Luigi; Wallace, Robert M; Cho, Kyeongjae

2017-06-07

Controlled growth of crystalline solids is critical for device applications, and atomistic modeling methods have been developed for bulk crystalline solids. Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW) heterostructures has not yet been developed. Specifically, the growth of single-layered transition metal dichalcogenides (TMDs) is currently facing tremendous challenges, and a detailed understanding based on KMC simulations would provide critical guidance to enable controlled growth of vdW heterostructures. In this work, a KMC simulation method is developed for the growth modeling on the vdW epitaxy of TMDs. The KMC method has introduced full material parameters for TMDs in bottom-up synthesis: metal and chalcogen adsorption/desorption/diffusion on substrate and grown TMD surface, TMD stacking sequence, chalcogen/metal ratio, flake edge diffusion and vacancy diffusion. The KMC processes result in multiple kinetic behaviors associated with various growth behaviors observed in experiments. Different phenomena observed during vdW epitaxy process are analysed in terms of complex competitions among multiple kinetic processes. The KMC method is used in the investigation and prediction of growth mechanisms, which provide qualitative suggestions to guide experimental study.

A Method for Combining Experimentation and Molecular Dynamics Simulation to Improve Cohesive Zone Models for Metallic Microstructures

NASA Technical Reports Server (NTRS)

Hochhalter, J. D.; Glaessgen, E. H.; Ingraffea, A. R.; Aquino, W. A.

2009-01-01

Fracture processes within a material begin at the nanometer length scale at which the formation, propagation, and interaction of fundamental damage mechanisms occur. Physics-based modeling of these atomic processes quickly becomes computationally intractable as the system size increases. Thus, a multiscale modeling method, based on the aggregation of fundamental damage processes occurring at the nanoscale within a cohesive zone model, is under development and will enable computationally feasible and physically meaningful microscale fracture simulation in polycrystalline metals. This method employs atomistic simulation to provide an optimization loop with an initial prediction of a cohesive zone model (CZM). This initial CZM is then applied at the crack front region within a finite element model. The optimization procedure iterates upon the CZM until the finite element model acceptably reproduces the near-crack-front displacement fields obtained from experimental observation. With this approach, a comparison can be made between the original CZM predicted by atomistic simulation and the converged CZM that is based on experimental observation. Comparison of the two CZMs gives insight into how atomistic simulation scales.

Crystalline cellulose elastic modulus predicted by atomistic models of uniform deformation and nanoscale indentation

Treesearch

Xiawa Wu; Robert J. Moon; Ashlie Martini

2013-01-01

The elastic modulus of cellulose Iß in the axial and transverse directions was obtained from atomistic simulations using both the standard uniform deformation approach and a complementary approach based on nanoscale indentation. This allowed comparisons between the methods and closer connectivity to experimental measurement techniques. A reactive...

Random Dopant Induced Threshold Voltage Lowering and Fluctuations in Sub-0.1 (micron)meter MOSFET's: A 3-D 'Atomistic' Simulation Study

NASA Technical Reports Server (NTRS)

Asenov, Asen

1998-01-01

A three-dimensional (3-D) "atomistic" simulation study of random dopant induced threshold voltage lowering and fluctuations in sub-0.1 microns MOSFET's is presented. For the first time a systematic analysis of random dopant effects down to an individual dopant level was carried out in 3-D on a scale sufficient to provide quantitative statistical predictions. Efficient algorithms based on a single multigrid solution of the Poisson equation followed by the solution of a simplified current continuity equation are used in the simulations. The effects of various MOSFET design parameters, including the channel length and width, oxide thickness and channel doping, on the threshold voltage lowering and fluctuations are studied using typical samples of 200 atomistically different MOSFET's. The atomistic results for the threshold voltage fluctuations were compared with two analytical models based on dopant number fluctuations. Although the analytical models predict the general trends in the threshold voltage fluctuations, they fail to describe quantitatively the magnitude of the fluctuations. The distribution of the atomistically calculated threshold voltage and its correlation with the number of dopants in the channel of the MOSFET's was analyzed based on a sample of 2500 microscopically different devices. The detailed analysis shows that the threshold voltage fluctuations are determined not only by the fluctuation in the dopant number, but also in the dopant position.

Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

DOE PAGES

Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; ...

2015-02-09

Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the average distance between branches of type 2 or 3 aggregates. Furthermore, this direct comparison of X-ray scattering data to the atomistic MD simulations is a substantive step toward providing a comprehensive, predictive model for ionomer morphology, gives substantial support for this atomistic MD model, and provides new credibility to the presence of stringy, branched, and percolated ionic aggregates in precise ionomer melts.« less

Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal.

PubMed

Huang, Liangliang; Seredych, Mykola; Bandosz, Teresa J; van Duin, Adri C T; Lu, Xiaohua; Gubbins, Keith E

2013-11-21

The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O∕H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O∕H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.

Atomistic modeling of water diffusion in hydrolytic biomaterials.

PubMed

Gautieri, Alfonso; Mezzanzanica, Andrea; Motta, Alberto; Redealli, Alberto; Vesentini, Simone

2012-04-01

One of the most promising applications of hydrolytically degrading biomaterials is their use as drug release carriers. These uses, however, require that the degradation and diffusion of drug are reliably predicted, which is complex to achieve through present experimental methods. Atomistic modeling can help in the knowledge-based design of degrading biomaterials with tuned drug delivery properties, giving insights on the small molecules diffusivity at intermediate states of the degradation process. We present here an atomistic-based approach to investigate the diffusion of water (through which hydrolytic degradation occurs) in degrading bulk models of poly(lactic acid) or PLA. We determine the water diffusion coefficient for different swelling states of the polymeric matrix (from almost dry to pure water) and for different degrees of degradation. We show that water diffusivity is highly influenced by the swelling degree, while little or not influenced by the degradation state. This approach, giving water diffusivity for different states of the matrix, can be combined with diffusion-reaction analytical methods in order to predict the degradation path on longer time scales. Furthermore, atomistic approach can be used to investigate diffusion of other relevant small molecules, eventually leading to the a priori knowledge of degradable biomaterials transport properties, helping the design of the drug delivery systems.

Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations.

PubMed

Numazawa, Satoshi; Smith, Roger

2011-10-01

Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

Atomistic modeling for interfacial properties of Ni-Al-V ternary system

NASA Astrophysics Data System (ADS)

Dong, Wei-ping; Lee, Byeong-Joo; Chen, Zheng

2014-05-01

Interatomic potentials for Ni-Al-V ternary systems have been developed based on the second-nearest-neighbor modified embedded-atom method potential formalism. The potentials can describe various fundamental physical properties of the relevant materials in good agreement with experimental information. The potential is utilized for an atomistic computation of interfacial properties of Ni-Al-V alloys. It is found that vanadium atoms segregate on the γ-fcc/L12 interface and this segregation affects the interfacial properties. The applicability of the atomistic approach to an elaborate alloy design of advanced Ni-based superalloys through the investigation of the effect of alloying elements on interfacial properties is discussed.

Thin films structural properties: results of the full-atomistic supercomputer simulation

NASA Astrophysics Data System (ADS)

Grigoriev, F. V.; Sulimov, V. B.; Tikhonravov, A. V.

2017-12-01

The previously developed full-atomistic approach to the thin film growth simulation is applied for the investigation of the dependence of silicon dioxide films properties on deposition conditions. It is shown that the surface roughness and porosity are essentially reduced with the growth of energy of deposited silicon atoms. The growth of energy from 0.1 eV to 10 eV results in the increase of the film density for 0.2 - 0.4 g/cm3 and of the refractive index for 0.04-0.08. The compressive stress in films structures is observed for all deposition conditions. Absolute values of the stress tensor components increase with the growth of e energy of deposited atoms. The increase of the substrate temperature results in smoothing of the density profiles of the deposited films.

Coarse-Grained Models for Protein-Cell Membrane Interactions

PubMed Central

Bradley, Ryan; Radhakrishnan, Ravi

2015-01-01

The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes. PMID:26613047

Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

DTIC Science & Technology

2014-10-01

the angles and dihedrals that are truly unique will be indicated by the user by editing NewAngleTypesDump and NewDihedralTypesDump. The program ...Atomistic Molecular Simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Robert M Elder, Timothy W Sirk, and...Antechamber program in Assisted Model Building with Energy Refinement (AMBER) Tools to assign partial charges (using the Austin Model 1 [AM1]-bond charge

Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

NASA Technical Reports Server (NTRS)

Asenov, Asen; Brown, Andrew R.; Davies, John H.; Saini, Subhash

1999-01-01

We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

Multiscale Modeling of Grain-Boundary Fracture: Cohesive Zone Models Parameterized From Atomistic Simulations

NASA Technical Reports Server (NTRS)

Glaessgen, Edward H.; Saether, Erik; Phillips, Dawn R.; Yamakov, Vesselin

2006-01-01

A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.

PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

PubMed

Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

2015-10-01

There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps

PubMed Central

Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

2015-01-01

There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF2 fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF2 fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

Tightly Coupled Mechanistic Study of Materials in the Extreme Space Environment

DTIC Science & Technology

2016-10-11

to examine spacecraft contamination issues from the perspective of non- equilibrium gas dynamics (Levin), material response at the atomistic level...Space Environment Group has worked to examine spacecraft contamination issues from the perspective of non- equilibrium gas dynamics (Levin...material response at the atomistic level (Rajan), high fidelity gas -surface chemistry models (van Duin), and experiments to characterize and test

Validation of the Concurrent Atomistic-Continuum Method on Screw Dislocation/Stacking Fault Interactions

DOE PAGES

Xu, Shuozhi; Xiong, Liming; Chen, Youping; ...

2017-04-26

Dislocation/stacking fault interactions play an important role in the plastic deformation of metallic nanocrystals and polycrystals. These interactions have been explored in atomistic models, which are limited in scale length by high computational cost. In contrast, multiscale material modeling approaches have the potential to simulate the same systems at a fraction of the computational cost. In this paper, we validate the concurrent atomistic-continuum (CAC) method on the interactions between a lattice screw dislocation and a stacking fault (SF) in three face-centered cubic metallic materials—Ni, Al, and Ag. Two types of SFs are considered: intrinsic SF (ISF) and extrinsic SF (ESF).more » For the three materials at different strain levels, two screw dislocation/ISF interaction modes (annihilation of the ISF and transmission of the dislocation across the ISF) and three screw dislocation/ESF interaction modes (transformation of the ESF into a three-layer twin, transformation of the ESF into an ISF, and transmission of the dislocation across the ESF) are identified. Here, our results show that CAC is capable of accurately predicting the dislocation/SF interaction modes with greatly reduced DOFs compared to fully-resolved atomistic simulations.« less

Validation of the Concurrent Atomistic-Continuum Method on Screw Dislocation/Stacking Fault Interactions

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

Xu, Shuozhi; Xiong, Liming; Chen, Youping

Dislocation/stacking fault interactions play an important role in the plastic deformation of metallic nanocrystals and polycrystals. These interactions have been explored in atomistic models, which are limited in scale length by high computational cost. In contrast, multiscale material modeling approaches have the potential to simulate the same systems at a fraction of the computational cost. In this paper, we validate the concurrent atomistic-continuum (CAC) method on the interactions between a lattice screw dislocation and a stacking fault (SF) in three face-centered cubic metallic materials—Ni, Al, and Ag. Two types of SFs are considered: intrinsic SF (ISF) and extrinsic SF (ESF).more » For the three materials at different strain levels, two screw dislocation/ISF interaction modes (annihilation of the ISF and transmission of the dislocation across the ISF) and three screw dislocation/ESF interaction modes (transformation of the ESF into a three-layer twin, transformation of the ESF into an ISF, and transmission of the dislocation across the ESF) are identified. Here, our results show that CAC is capable of accurately predicting the dislocation/SF interaction modes with greatly reduced DOFs compared to fully-resolved atomistic simulations.« less

Atomistic modeling of carbon Cottrell atmospheres in bcc iron

NASA Astrophysics Data System (ADS)

Veiga, R. G. A.; Perez, M.; Becquart, C. S.; Domain, C.

2013-01-01

Atomistic simulations with an EAM interatomic potential were used to evaluate carbon-dislocation binding energies in bcc iron. These binding energies were then used to calculate the occupation probability of interstitial sites in the vicinity of an edge and a screw dislocation. The saturation concentration due to carbon-carbon interactions was also estimated by atomistic simulations in the dislocation core and taken as an upper limit for carbon concentration in a Cottrell atmosphere. We obtained a maximum concentration of 10 ± 1 at.% C at T = 0 K within a radius of 1 nm from the dislocation lines. The spatial carbon distributions around the line defects revealed that the Cottrell atmosphere associated with an edge dislocation is denser than that around a screw dislocation, in contrast with the predictions of the classical model of Cochardt and colleagues. Moreover, the present Cottrell atmosphere model is in reasonable quantitative accord with the three-dimensional atom probe data available in the literature.

Langevin Equation for DNA Dynamics

NASA Astrophysics Data System (ADS)

Grych, David; Copperman, Jeremy; Guenza, Marina

Under physiological conditions, DNA oligomers can contain well-ordered helical regions and also flexible single-stranded regions. We describe the site-specific motion of DNA with a modified Rouse-Zimm Langevin equation formalism that describes DNA as a coarse-grained polymeric chain with global structure and local flexibility. The approach has successfully described the protein dynamics in solution and has been extended to nucleic acids. Our approach provides diffusive mode analytical solutions for the dynamics of global rotational diffusion and internal motion. The internal DNA dynamics present a rich energy landscape that accounts for an interior where hydrogen bonds and base-stacking determine structure and experience limited solvent exposure. We have implemented several models incorporating different coarse-grained sites with anisotropic rotation, energy barrier crossing, and local friction coefficients that include a unique internal viscosity and our models reproduce dynamics predicted by atomistic simulations. The models reproduce bond autocorrelation along the sequence as compared to that directly calculated from atomistic molecular dynamics simulations. The Langevin equation approach captures the essence of DNA dynamics without a cumbersome atomistic representation.

Multiscale Modeling of UHTC: Thermal Conductivity

NASA Technical Reports Server (NTRS)

Lawson, John W.; Murry, Daw; Squire, Thomas; Bauschlicher, Charles W.

2012-01-01

We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.

Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies

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

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

2016-02-05

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

Multiscale Modeling of Carbon/Phenolic Composite Thermal Protection Materials: Atomistic to Effective Properties

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Murthy, Pappu L.; Bednarcyk, Brett A.; Lawson, John W.; Monk, Joshua D.; Bauschlicher, Charles W., Jr.

2016-01-01

Next generation ablative thermal protection systems are expected to consist of 3D woven composite architectures. It is well known that composites can be tailored to achieve desired mechanical and thermal properties in various directions and thus can be made fit-for-purpose if the proper combination of constituent materials and microstructures can be realized. In the present work, the first, multiscale, atomistically-informed, computational analysis of mechanical and thermal properties of a present day - Carbon/Phenolic composite Thermal Protection System (TPS) material is conducted. Model results are compared to measured in-plane and out-of-plane mechanical and thermal properties to validate the computational approach. Results indicate that given sufficient microstructural fidelity, along with lowerscale, constituent properties derived from molecular dynamics simulations, accurate composite level (effective) thermo-elastic properties can be obtained. This suggests that next generation TPS properties can be accurately estimated via atomistically informed multiscale analysis.

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

PubMed Central

Mariani, Simona; Dell'Orco, Daniele; Felline, Angelo; Raimondi, Francesco; Fanelli, Francesca

2013-01-01

A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions. PMID:24009494

Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique

NASA Astrophysics Data System (ADS)

Shadrack Jabes, B.; Krekeler, C.; Klein, R.; Delle Site, L.

2018-05-01

We employ the Grand Canonical Adaptive Resolution Simulation (GC-AdResS) molecular dynamics technique to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS, atomistic details are kept only in an open sub-region of the system while the environment is treated at coarse-grained level; thus, if spatial quantities calculated in such a sub-region agree with the equivalent quantities calculated in a full atomistic simulation, then the atomistic degrees of freedom outside the sub-region play a negligible role. The size of the sub-region fixes the degree of spatial locality of a certain quantity. We show that even for sub-regions whose radius corresponds to the size of a few molecules, spatial properties are reasonably reproduced thus suggesting a higher degree of spatial locality, a hypothesis put forward also by other researchers and that seems to play an important role for the characterization of fundamental properties of a large class of ionic liquids.

Continuous description of a grain boundary in olivine from atomic scale simulations: the role of disclinations

NASA Astrophysics Data System (ADS)

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

2015-12-01

A crossover between atomistic description and continuous representation of grain boundaries in polycrystals is set-up to model the periodic arrays of structural units by using dislocation and disclination dipole arrays along grain boundaries. Continuous modeling of the boundary is built by bottom-up processing, meaning that the strain, rotation, curvature, disclination and dislocation density fields are calculated by using the discrete atomic positions generated by molecular dynamics simulations. Continuous modeling of a 18.9° symmetric tilt boundary in copper [1] is conducted as a benchmark case. Its accuracy is validated by comparison with a similar recent technique [2]. Then, results on the 60.8° Mg2SiO4 tilt boundary [3-4] are presented. By linking the atomistic description with continuum mechanics representations, they provide new insights into the structure of the grain boundary. [1] Fressengeas, C., Taupin, V., Capolungo, L., 2014. Continuous modelling of the structure of symmetric tilt boundaries. Int. J. Solids Struct. 51, 1434-1441. [2] Zimmerman, J.A., Bammann, D.J., Gao, H., 2009. Deformation gradients for continuum mechanical analysis of atomistic simulations. Int. J. Solids Struct. 46, 238-253. [3] Cordier, P., Demouchy, S., Beausir, B., Taupin, V., Barou, F., Fressengeas, C., 2014. Disclinations provide the missing mechanism for deforming olivine-rich rocks in the mantle. Nature 507, 51-56. [4] Adjaoud, O., Marquardt, K., Jahn, S., 2012. Atomic structures and energies of grain boundaries in Mg2SiO4 forsterite from atomistic modeling. Phys. Chem. Miner. 39, 749-760.

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

Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.

Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the average distance between branches of type 2 or 3 aggregates. Furthermore, this direct comparison of X-ray scattering data to the atomistic MD simulations is a substantive step toward providing a comprehensive, predictive model for ionomer morphology, gives substantial support for this atomistic MD model, and provides new credibility to the presence of stringy, branched, and percolated ionic aggregates in precise ionomer melts.« less

All-atomistic molecular dynamics (AA-MD) studies and pharmacokinetic performance of PAMAM-dendrimer-furosemide delivery systems.

PubMed

Otto, Daniel P; de Villiers, Melgardt M

2018-06-13

Improvement of problematic dissolution and solubility properties of a model drug, furosemide, was investigated for poly(amidoamine) (PAMAM) dendrimer complexes of the drug. Full and half generation dendrimers with amino and ester terminals respectively, were studied. In vitro release performance of these complexes was investigated at drug loads ranging 5-60% using simulated gastric fluids. Full generation dendrimers accommodated higher drug loads, outperformed half-generation complexes, and free drug. Pharmacokinetic studies in rats indicated that the dendrimer complexes markedly improved in the bioavailability of the drug compared to the unformulated drug. The G3.0-PAMAM dendrimer complex showed a two-fold increase in C max and a 1.75-fold increase in AUC over the free drug. Additionally, T max was shortened from approximately 25 to 20 min. One of the first all-atomistic molecular dynamics (AA-MD) simulation studies was performed to evaluate low-generation dendrimer-drug complexes as well as its pharmacokinetic performance. AA-MD provided insight into the intermolecular interactions that take place between the dendrimer and drug. It is suggested that the dendrimer not only encapsulates the drug, but can also orientate the drug in stabilized dispersion to prevent drug clustering which could impact release and bioavailability negatively. AA-MD can be a useful tool to develop dendrimer-based drug delivery systems. Copyright © 2018. Published by Elsevier B.V.

A method for generating reliable atomistic models of amorphous polymers based on a random search of energy minima

NASA Astrophysics Data System (ADS)

Curcó, David; Casanovas, Jordi; Roca, Marc; Alemán, Carlos

2005-07-01

A method for generating atomistic models of dense amorphous polymers is presented. The method is organized in a two-steps procedure. First, structures are generated using an algorithm that minimizes the torsional strain. After this, a relaxation algorithm is applied to minimize the non-bonding interactions. Two alternative relaxation methods, which are based simple minimization and Concerted Rotation techniques, have been implemented. The performance of the method has been checked by simulating polyethylene, polypropylene, nylon 6, poly(L,D-lactic acid) and polyglycolic acid.

Predicting the Macroscopic Fracture Energy of Epoxy Resins from Atomistic Molecular Simulations

DOE PAGES

Meng, Zhaoxu; Bessa, Miguel A.; Xia, Wenjie; ...

2016-12-06

Predicting the macroscopic fracture energy of highly crosslinked glassy polymers from atomistic simulations is challenging due to the size of the process zone being large in these systems. Here, we present a scale-bridging approach that links atomistic molecular dynamics simulations to macroscopic fracture properties on the basis of a continuum fracture mechanics model for two different epoxy materials. Our approach reveals that the fracture energy of epoxy resins strongly depends on the functionality of epoxy resin and the component ratio between the curing agent (amine) and epoxide. The most intriguing part of our study is that we demonstrate that themore » fracture energy exhibits a maximum value within the range of conversion degrees considered (from 65% to 95%), which can be attributed to the combined effects of structural rigidity and post-yield deformability. Our study provides physical insight into the molecular mechanisms that govern the fracture characteristics of epoxy resins and demonstrates the success of utilizing atomistic molecular simulations towards predicting macroscopic material properties.« less

Elastic dipoles of point defects from atomistic simulations

NASA Astrophysics Data System (ADS)

Varvenne, Céline; Clouet, Emmanuel

2017-12-01

The interaction of point defects with an external stress field or with other structural defects is usually well described within continuum elasticity by the elastic dipole approximation. Extraction of the elastic dipoles from atomistic simulations is therefore a fundamental step to connect an atomistic description of the defect with continuum models. This can be done either by a fitting of the point-defect displacement field, by a summation of the Kanzaki forces, or by a linking equation to the residual stress. We perform here a detailed comparison of these different available methods to extract elastic dipoles, and show that they all lead to the same values when the supercell of the atomistic simulations is large enough and when the anharmonic region around the point defect is correctly handled. But, for small simulation cells compatible with ab initio calculations, only the definition through the residual stress appears tractable. The approach is illustrated by considering various point defects (vacancy, self-interstitial, and hydrogen solute atom) in zirconium, using both empirical potentials and ab initio calculations.

Predicting the Macroscopic Fracture Energy of Epoxy Resins from Atomistic Molecular Simulations

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

Meng, Zhaoxu; Bessa, Miguel A.; Xia, Wenjie

Predicting the macroscopic fracture energy of highly crosslinked glassy polymers from atomistic simulations is challenging due to the size of the process zone being large in these systems. Here, we present a scale-bridging approach that links atomistic molecular dynamics simulations to macroscopic fracture properties on the basis of a continuum fracture mechanics model for two different epoxy materials. Our approach reveals that the fracture energy of epoxy resins strongly depends on the functionality of epoxy resin and the component ratio between the curing agent (amine) and epoxide. The most intriguing part of our study is that we demonstrate that themore » fracture energy exhibits a maximum value within the range of conversion degrees considered (from 65% to 95%), which can be attributed to the combined effects of structural rigidity and post-yield deformability. Our study provides physical insight into the molecular mechanisms that govern the fracture characteristics of epoxy resins and demonstrates the success of utilizing atomistic molecular simulations towards predicting macroscopic material properties.« less

Modeling the elastic energy of alloys: Potential pitfalls of continuum treatments.

PubMed

Baskaran, Arvind; Ratsch, Christian; Smereka, Peter

2015-12-01

Some issues that arise when modeling elastic energy for binary alloys are discussed within the context of a Keating model and density-functional calculations. The Keating model is a simplified atomistic formulation based on modeling elastic interactions of a binary alloy with harmonic springs whose equilibrium length is species dependent. It is demonstrated that the continuum limit for the strain field are the usual equations of linear elasticity for alloys and that they correctly capture the coarse-grained behavior of the displacement field. In addition, it is established that Euler-Lagrange equation of the continuum limit of the elastic energy will yield the same strain field equation. This is the same energy functional that is often used to model elastic effects in binary alloys. However, a direct calculation of the elastic energy atomistic model reveals that the continuum expression for the elastic energy is both qualitatively and quantitatively incorrect. This is because it does not take atomistic scale compositional nonuniformity into account. Importantly, this result also shows that finely mixed alloys tend to have more elastic energy than segregated systems, which is the exact opposite of predictions made by some continuum theories. It is also shown that for strained thin films the traditionally used effective misfit for alloys systematically underestimate the strain energy. In some models, this drawback is handled by including an elastic contribution to the enthalpy of mixing, which is characterized in terms of the continuum concentration. The direct calculation of the atomistic model reveals that this approach suffers serious difficulties. It is demonstrated that elastic contribution to the enthalpy of mixing is nonisotropic and scale dependent. It is also shown that such effects are present in density-functional theory calculations for the Si-Ge system. This work demonstrates that it is critical to include the microscopic arrangements in any elastic model to achieve even qualitatively correct behavior.

Dynamics in entangled polyethylene melts using coarse-grained models

NASA Astrophysics Data System (ADS)

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

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

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

Fogarty, Aoife C., E-mail: fogarty@mpip-mainz.mpg.de; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de; Kremer, Kurt, E-mail: kremer@mpip-mainz.mpg.de

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydrationmore » shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.« less

Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Multiscale Modeling of Damage Processes in Aluminum Alloys: Grain-Scale Mechanisms

NASA Technical Reports Server (NTRS)

Hochhalter, J. D.; Veilleux, M. G.; Bozek, J. E.; Glaessgen, E. H.; Ingraffea, A. R.

2008-01-01

This paper has two goals related to the development of a physically-grounded methodology for modeling the initial stages of fatigue crack growth in an aluminum alloy. The aluminum alloy, AA 7075-T651, is susceptible to fatigue cracking that nucleates from cracked second phase iron-bearing particles. Thus, the first goal of the paper is to validate an existing framework for the prediction of the conditions under which the particles crack. The observed statistics of particle cracking (defined as incubation for this alloy) must be accurately predicted to simulate the stochastic nature of microstructurally small fatigue crack (MSFC) formation. Also, only by simulating incubation of damage in a statistically accurate manner can subsequent stages of crack growth be accurately predicted. To maintain fidelity and computational efficiency, a filtering procedure was developed to eliminate particles that were unlikely to crack. The particle filter considers the distributions of particle sizes and shapes, grain texture, and the configuration of the surrounding grains. This filter helps substantially reduce the number of particles that need to be included in the microstructural models and forms the basis of the future work on the subsequent stages of MSFC, crack nucleation and microstructurally small crack propagation. A physics-based approach to simulating fracture should ultimately begin at nanometer length scale, in which atomistic simulation is used to predict the fundamental damage mechanisms of MSFC. These mechanisms include dislocation formation and interaction, interstitial void formation, and atomic diffusion. However, atomistic simulations quickly become computationally intractable as the system size increases, especially when directly linking to the already large microstructural models. Therefore, the second goal of this paper is to propose a method that will incorporate atomistic simulation and small-scale experimental characterization into the existing multiscale framework. At the microscale, the nanoscale mechanics are represented within cohesive zones where appropriate, i.e. where the mechanics observed at the nanoscale can be represented as occurring on a plane such as at grain boundaries or slip planes at a crack front. Important advancements that are yet to be made include: 1. an increased fidelity in cohesive zone modeling; 2. a means to understand how atomistic simulation scales with time; 3. a new experimental methodology for generating empirical models for CZMs and emerging materials; and 4. a validation of simulations of the damage processes at the nano-micro scale. With ever-increasing computer power, the long-term ability to employ atomistic simulation for the prognosis of structural components will not be limited by computation power, but by our lack of knowledge in incorporating atomistic models into simulations of MSFC into a multiscale framework.

Computational modeling and simulation of spall fracture in polycrystalline solids by an atomistic-based interfacial zone model

PubMed Central

Lin, Liqiang; Zeng, Xiaowei

2015-01-01

The focus of this work is to investigate spall fracture in polycrystalline materials under high-speed impact loading by using an atomistic-based interfacial zone model. We illustrate that for polycrystalline materials, increases in the potential energy ratio between grain boundaries and grains could cause a fracture transition from intergranular to transgranular mode. We also found out that the spall strength increases when there is a fracture transition from intergranular to transgranular. In addition, analysis of grain size, crystal lattice orientation and impact speed reveals that the spall strength increases as grain size or impact speed increases. PMID:26435546

Extending atomistic simulation timescale in solid/liquid systems: crystal growth from solution by a parallel-replica dynamics and continuum hybrid method.

PubMed

Lu, Chun-Yaung; Voter, Arthur F; Perez, Danny

2014-01-28

Deposition of solid material from solution is ubiquitous in nature. However, due to the inherent complexity of such systems, this process is comparatively much less understood than deposition from a gas or vacuum. Further, the accurate atomistic modeling of such systems is computationally expensive, therefore leaving many intriguing long-timescale phenomena out of reach. We present an atomistic/continuum hybrid method for extending the simulation timescales of dynamics at solid/liquid interfaces. We demonstrate the method by simulating the deposition of Ag on Ag (001) from solution with a significant speedup over standard MD. The results reveal specific features of diffusive deposition dynamics, such as a dramatic increase in the roughness of the film.

Multiscale Modeling of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2: Application to Lattice Thermal Conductivity

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Squire, Thomas H.; Bauschlicher, Charles W.

2012-01-01

We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.

Adaptive resolution simulation of an atomistic protein in MARTINI water

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

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

2014-02-07

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

Adaptive resolution simulation of an atomistic protein in MARTINI water.

PubMed

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

2014-02-07

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

Atomistically determined phase-field modeling of dislocation dissociation, stacking fault formation, dislocation slip, and reactions in fcc systems

NASA Astrophysics Data System (ADS)

Rezaei Mianroodi, Jaber; Svendsen, Bob

2015-04-01

The purpose of the current work is the development of a phase field model for dislocation dissociation, slip and stacking fault formation in single crystals amenable to determination via atomistic or ab initio methods in the spirit of computational material design. The current approach is based in particular on periodic microelasticity (Wang and Jin, 2001; Bulatov and Cai, 2006; Wang and Li, 2010) to model the strongly non-local elastic interaction of dislocation lines via their (residual) strain fields. These strain fields depend in turn on phase fields which are used to parameterize the energy stored in dislocation lines and stacking faults. This energy storage is modeled here with the help of the "interface" energy concept and model of Cahn and Hilliard (1958) (see also Allen and Cahn, 1979; Wang and Li, 2010). In particular, the "homogeneous" part of this energy is related to the "rigid" (i.e., purely translational) part of the displacement of atoms across the slip plane, while the "gradient" part accounts for energy storage in those regions near the slip plane where atomic displacements deviate from being rigid, e.g., in the dislocation core. Via the attendant global energy scaling, the interface energy model facilitates an atomistic determination of the entire phase field energy as an optimal approximation of the (exact) atomistic energy; no adjustable parameters remain. For simplicity, an interatomic potential and molecular statics are employed for this purpose here; alternatively, ab initio (i.e., DFT-based) methods can be used. To illustrate the current approach, it is applied to determine the phase field free energy for fcc aluminum and copper. The identified models are then applied to modeling of dislocation dissociation, stacking fault formation, glide and dislocation reactions in these materials. As well, the tensile loading of a dislocation loop is considered. In the process, the current thermodynamic picture is compared with the classical mechanical one as based on the Peach-Köhler force.

Atomistic Modeling of RuAl and (RuNi) Al Alloys

NASA Technical Reports Server (NTRS)

Gargano, Pablo; Mosca, Hugo; Bozzolo, Guillermo; Noebe, Ronald D.; Gray, Hugh R. (Technical Monitor)

2002-01-01

Atomistic modeling of RuAl and RuAlNi alloys, using the BFS (Bozzolo-Ferrante-Smith) method for alloys is performed. The lattice parameter and energy of formation of B2 RuAl as a function of stoichiometry and the lattice parameter of (Ru(sub 50-x)Ni(sub x)Al(sub 50)) alloys as a function of Ni concentration are computed. BFS based Monte Carlo simulations indicate that compositions close to Ru25Ni25Al50 are single phase with no obvious evidence of a miscibility gap and separation of the individual B2 phases.

Atomistic simulation of the coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface

NASA Astrophysics Data System (ADS)

Xiao, HuiFang; Huang, Bin; Yao, Ge; Kang, WenBin; Gong, Sheng; Pan, Hai; Cao, Yi; Wang, Jun; Zhang, Jian; Wang, Wei

2018-03-01

Understanding the processes of protein adsorption/desorption on nanoparticles' surfaces is important for the development of new nanotechnology involving biomaterials; however, an atomistic resolution picture for these processes and for the simultaneous protein conformational change is missing. Here, we report the adsorption of protein GB1 on a polystyrene nanoparticle surface using atomistic molecular dynamic simulations. Enabled by metadynamics, we explored the relevant phase space and identified three protein states, each involving both the adsorbed and desorbed modes. We also studied the change of the secondary and tertiary structures of GB1 during adsorption and the dominant interactions between the protein and surface in different adsorption stages. The results we obtained from simulation were found to be more adequate and complete than the previous one. We believe the model presented in this paper, in comparison with the previous ones, is a better theoretical model to understand and explain the experimental results.

New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

NASA Technical Reports Server (NTRS)

Saether, E.; Yamakov, V.; Glaessgen, E.

2008-01-01

A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

Gaussian approximation potential modeling of lithium intercalation in carbon nanostructures

NASA Astrophysics Data System (ADS)

Fujikake, So; Deringer, Volker L.; Lee, Tae Hoon; Krynski, Marcin; Elliott, Stephen R.; Csányi, Gábor

2018-06-01

We demonstrate how machine-learning based interatomic potentials can be used to model guest atoms in host structures. Specifically, we generate Gaussian approximation potential (GAP) models for the interaction of lithium atoms with graphene, graphite, and disordered carbon nanostructures, based on reference density functional theory data. Rather than treating the full Li-C system, we demonstrate how the energy and force differences arising from Li intercalation can be modeled and then added to a (prexisting and unmodified) GAP model of pure elemental carbon. Furthermore, we show the benefit of using an explicit pair potential fit to capture "effective" Li-Li interactions and to improve the performance of the GAP model. This provides proof-of-concept for modeling guest atoms in host frameworks with machine-learning based potentials and in the longer run is promising for carrying out detailed atomistic studies of battery materials.

Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids

NASA Astrophysics Data System (ADS)

Dykeman, Eric C.; Sankey, Otto F.

2010-02-01

We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (˜10) low-frequency modes that are global and cooperative.

Tunnel Field-Effect Transistors in 2-D Transition Metal Dichalcogenide Materials

NASA Astrophysics Data System (ADS)

Ilatikhameneh, Hesameddin; Tan, Yaohua; Novakovic, Bozidar; Klimeck, Gerhard; Rahman, Rajib; Appenzeller, Joerg

2015-12-01

In this work, the performance of Tunnel Field-Effect Transistors (TFETs) based on two-dimensional Transition Metal Dichalcogenide (TMD) materials is investigated by atomistic quantum transport simulations. One of the major challenges of TFETs is their low ON-currents. 2D material based TFETs can have tight gate control and high electric fields at the tunnel junction, and can in principle generate high ON-currents along with a sub-threshold swing smaller than 60 mV/dec. Our simulations reveal that high performance TMD TFETs, not only require good gate control, but also rely on the choice of the right channel material with optimum band gap, effective mass and source/drain doping level. Unlike previous works, a full band atomistic tight binding method is used self-consistently with 3D Poisson equation to simulate ballistic quantum transport in these devices. The effect of the choice of TMD material on the performance of the device and its transfer characteristics are discussed. Moreover, the criteria for high ON-currents are explained with a simple analytic model, showing the related fundamental factors. Finally, the subthreshold swing and energy-delay of these TFETs are compared with conventional CMOS devices.

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

Grain-Boundary Resistance in Copper Interconnects: From an Atomistic Model to a Neural Network

NASA Astrophysics Data System (ADS)

Valencia, Daniel; Wilson, Evan; Jiang, Zhengping; Valencia-Zapata, Gustavo A.; Wang, Kuang-Chung; Klimeck, Gerhard; Povolotskyi, Michael

2018-04-01

Orientation effects on the specific resistance of copper grain boundaries are studied systematically with two different atomistic tight-binding methods. A methodology is developed to model the specific resistance of grain boundaries in the ballistic limit using the embedded atom model, tight- binding methods, and nonequilibrium Green's functions. The methodology is validated against first-principles calculations for thin films with a single coincident grain boundary, with 6.4% deviation in the specific resistance. A statistical ensemble of 600 large, random structures with grains is studied. For structures with three grains, it is found that the distribution of specific resistances is close to normal. Finally, a compact model for grain-boundary-specific resistance is constructed based on a neural network.

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS.

PubMed

Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector; Rissanen, Sami; Lolicato, Fabio; Róg, Tomasz; Vattulainen, Ilpo

2017-10-23

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS.

How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

PubMed

Šponer, Jiří; Krepl, Miroslav; Banáš, Pavel; Kührová, Petra; Zgarbová, Marie; Jurečka, Petr; Havrila, Marek; Otyepka, Michal

2017-05-01

We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems. Fundamental limitations are the short physical time-scale of simulations, which can be partially alleviated by enhanced-sampling techniques, and the highly approximate atomistic force fields describing the simulated molecules. The applicability and present limitations of MD are demonstrated on studies of tetranucleotides, tetraloops, ribozymes, riboswitches and protein/RNA complexes. Wisely applied simulations respecting the approximations of the model can successfully complement structural and biochemical experiments. WIREs RNA 2017, 8:e1405. doi: 10.1002/wrna.1405 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

PubMed

Riniker, Sereina; van Gunsteren, Wilfred F

2011-02-28

The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostatic interactions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and all-atom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectric permittivity were chosen as primary target properties. The model properties are compared with those obtained from experiment, from clusters of simple-point-charge water molecules of appropriate size in the liquid phase, and for other CG water models if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine-grained atomistic water models.

Multiscale modeling for ferroelectric materials: identification of the phase-field model’s free energy for PZT from atomistic simulations

NASA Astrophysics Data System (ADS)

Völker, Benjamin; Landis, Chad M.; Kamlah, Marc

2012-03-01

Within a knowledge-based multiscale simulation approach for ferroelectric materials, the atomic level can be linked to the mesoscale by transferring results from first-principles calculations into a phase-field model. A recently presented routine (Völker et al 2011 Contin. Mech. Thermodyn. 23 435-51) for adjusting the Helmholtz free energy coefficients to intrinsic and extrinsic ferroelectric material properties obtained by DFT calculations and atomistic simulations was subject to certain limitations: caused by too small available degrees of freedom, an independent adjustment of the spontaneous strains and piezoelectric coefficients was not possible, and the elastic properties could only be considered in cubic instead of tetragonal symmetry. In this work we overcome such restrictions by expanding the formulation of the free energy function, i.e. by motivating and introducing new higher-order terms that have not appeared in the literature before. Subsequently we present an improved version of the adjustment procedure for the free energy coefficients that is solely based on input parameters from first-principles calculations performed by Marton and Elsässer, as documented in Völker et al (2011 Contin. Mech. Thermodyn. 23 435-51). Full sets of adjusted free energy coefficients for PbTiO3 and tetragonal Pb(Zr,Ti)O3 are presented, and the benefits of the newly introduced higher-order free energy terms are discussed.

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

NASA Astrophysics Data System (ADS)

Fogarty, Aoife C.; Potestio, Raffaello; Kremer, Kurt

2015-05-01

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

Sequential slip transfer of mixed-character dislocations across Σ3 coherent twin boundary in FCC metals: a concurrent atomistic-continuum study

DOE PAGES

Xu, Shuozhi; Xiong, Liming; Chen, Youping; ...

2016-01-29

Sequential slip transfer across grain boundaries (GB) has an important role in size-dependent propagation of plastic deformation in polycrystalline metals. For example, the Hall–Petch effect, which states that a smaller average grain size results in a higher yield stress, can be rationalised in terms of dislocation pile-ups against GBs. In spite of extensive studies in modelling individual phases and grains using atomistic simulations, well-accepted criteria of slip transfer across GBs are still lacking, as well as models of predicting irreversible GB structure evolution. Slip transfer is inherently multiscale since both the atomic structure of the boundary and the long-range fieldsmore » of the dislocation pile-up come into play. In this work, concurrent atomistic-continuum simulations are performed to study sequential slip transfer of a series of curved dislocations from a given pile-up on Σ3 coherent twin boundary (CTB) in Cu and Al, with dominant leading screw character at the site of interaction. A Frank-Read source is employed to nucleate dislocations continuously. It is found that subject to a shear stress of 1.2 GPa, screw dislocations transfer into the twinned grain in Cu, but glide on the twin boundary plane in Al. Moreover, four dislocation/CTB interaction modes are identified in Al, which are affected by (1) applied shear stress, (2) dislocation line length, and (3) dislocation line curvature. Our results elucidate the discrepancies between atomistic simulations and experimental observations of dislocation-GB reactions and highlight the importance of directly modeling sequential dislocation slip transfer reactions using fully 3D models.« less

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

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

Perkins, Stephen J.; Wright, David W.; Zhang, Hailiang

2016-10-14

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-artmore » molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in whichGenAppprovides the deployment infrastructure for running applications on both standard and high-performance computing hardware, andSASSIEprovides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data.GenAppproduces the accessible web-based front end termedSASSIE-web, andGenAppandSASSIEalso make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.« less

Sequential slip transfer of mixed-character dislocations across Σ3 coherent twin boundary in FCC metals: a concurrent atomistic-continuum study

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

Xu, Shuozhi; Xiong, Liming; Chen, Youping

Sequential slip transfer across grain boundaries (GB) has an important role in size-dependent propagation of plastic deformation in polycrystalline metals. For example, the Hall–Petch effect, which states that a smaller average grain size results in a higher yield stress, can be rationalised in terms of dislocation pile-ups against GBs. In spite of extensive studies in modelling individual phases and grains using atomistic simulations, well-accepted criteria of slip transfer across GBs are still lacking, as well as models of predicting irreversible GB structure evolution. Slip transfer is inherently multiscale since both the atomic structure of the boundary and the long-range fieldsmore » of the dislocation pile-up come into play. In this work, concurrent atomistic-continuum simulations are performed to study sequential slip transfer of a series of curved dislocations from a given pile-up on Σ3 coherent twin boundary (CTB) in Cu and Al, with dominant leading screw character at the site of interaction. A Frank-Read source is employed to nucleate dislocations continuously. It is found that subject to a shear stress of 1.2 GPa, screw dislocations transfer into the twinned grain in Cu, but glide on the twin boundary plane in Al. Moreover, four dislocation/CTB interaction modes are identified in Al, which are affected by (1) applied shear stress, (2) dislocation line length, and (3) dislocation line curvature. Our results elucidate the discrepancies between atomistic simulations and experimental observations of dislocation-GB reactions and highlight the importance of directly modeling sequential dislocation slip transfer reactions using fully 3D models.« less

Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

PubMed

Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

2015-04-14

We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

PubMed

Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

2016-12-01

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web , and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

A Coarse Grained Model for Methylcellulose: Spontaneous Ring Formation at Elevated Temperature

NASA Astrophysics Data System (ADS)

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.

Evaluation of Alternative Atomistic Models for the Incipient Growth of ZnO by Atomic Layer Deposition

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

Chu, Manh-Hung; Tian, Liang; Chaker, Ahmad

ZnO thin films are interesting for applications in several technological fields, including optoelectronics and renewable energies. Nanodevice applications require controlled synthesis of ZnO structures at nanometer scale, which can be achieved via atomic layer deposition (ALD). However, the mechanisms governing the initial stages of ALD had not been addressed until very recently. Investigations into the initial nucleation and growth as well as the atomic structure of the heterointerface are crucial to optimize the ALD process and understand the structure-property relationships for ZnO. We have used a complementary suite of in situ synchrotron x-ray techniques to investigate both the structural andmore » chemical evolution during ZnO growth by ALD on two different substrates, i.e., SiO2 and Al2O3, which led us to formulate an atomistic model of the incipient growth of ZnO. The model relies on the formation of nanoscale islands of different size and aspect ratio and consequent disorder induced in the Zn neighbors' distribution. However, endorsement of our model requires testing and discussion of possible alternative models which could account for the experimental results. In this work, we review, test, and rule out several alternative models; the results confirm our view of the atomistic mechanisms at play, which influence the overall microstructure and resulting properties of the final thin film.« less

Directional pair distribution function for diffraction line profile analysis of atomistic models

PubMed Central

Leonardi, Alberto; Leoni, Matteo; Scardi, Paolo

2013-01-01

The concept of the directional pair distribution function is proposed to describe line broadening effects in powder patterns calculated from atomistic models of nano-polycrystalline microstructures. The approach provides at the same time a description of the size effect for domains of any shape and a detailed explanation of the strain effect caused by the local atomic displacement. The latter is discussed in terms of different strain types, also accounting for strain field anisotropy and grain boundary effects. The results can in addition be directly read in terms of traditional line profile analysis, such as that based on the Warren–Averbach method. PMID:23396818

Graphene quantum dots with visible light absorption of the carbon core: insights from single-particle spectroscopy and first principles based theory

NASA Astrophysics Data System (ADS)

Ghosh, Siddharth; Awasthi, Manohar; Ghosh, Moumita; Seibt, Michael; Niehaus, Thomas A.

2016-12-01

Luminescent carbon nanodots (CND) are a recent addition to the family of carbon nanostructures. Interestingly, a large group of CNDs are fluorescent in the visible spectrum and possess single dipole emitters with potential applications in super-resolution microscopy, quantum information science, and optoelectronics. There is a large diversity of CND’s size as well as a strong variability of edge topology and functional groups in real samples. This hampers a direct comparison of experimental and theoretical findings that is necessary to understand the unusual photophysics of these systems. Here, we derive atomistic models of finite sized (<2.5 nm) CNDs from high resolution transmission electron microscopy (HRTEM) which are studied using approximate time-dependent density functional theory. The atomistic models are found to be primarily two-dimensional (2D) and can hence be categorised as graphene quantum dots (GQD). The GQD model structures that are presented here show excitation energies in the visible spectrum matching previous single GQD level photoluminescence studies. We also present the effect of edge hydroxyl and carboxyl functional groups on the absorption spectrum. Overall, the study reveals the atomistic origin of CNDs photoluminescence in the visible range.

Communication: Role of explicit water models in the helix folding/unfolding processes

NASA Astrophysics Data System (ADS)

Palazzesi, Ferruccio; Salvalaglio, Matteo; Barducci, Alessandro; Parrinello, Michele

2016-09-01

In the last years, it has become evident that computer simulations can assume a relevant role in modelling protein dynamical motions for their ability to provide a full atomistic image of the processes under investigation. The ability of the current protein force-fields in reproducing the correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve our understanding of many relevant biological functionalities. In this work, employing the last developments of the metadynamics framework, we compare the ability of state-of-the-art all-atom empirical functions and water models to consistently reproduce the folding and unfolding of a helix turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water models can influence the thermodynamic and the kinetics of the system under investigation, and for this reason cannot be considered trivial.

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations.

PubMed

Quevillon, Michael J; Whitmer, Jonathan K

2018-01-02

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure-constant temperature ensemble. These materials exhibit a distinct "smectic" liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications.

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

Ortoleva, Peter J.

Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

Modeling Amorphous Microporous Polymers for CO2 Capture and Separations.

PubMed

Kupgan, Grit; Abbott, Lauren J; Hart, Kyle E; Colina, Coray M

2018-06-13

This review concentrates on the advances of atomistic molecular simulations to design and evaluate amorphous microporous polymeric materials for CO 2 capture and separations. A description of atomistic molecular simulations is provided, including simulation techniques, structural generation approaches, relaxation and equilibration methodologies, and considerations needed for validation of simulated samples. The review provides general guidelines and a comprehensive update of the recent literature (since 2007) to promote the acceleration of the discovery and screening of amorphous microporous polymers for CO 2 capture and separation processes.

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

PubMed

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

A Continuum-Atomistic Analysis of Transgranular Crack Propagation in Aluminum

NASA Technical Reports Server (NTRS)

Yamakov, V.; Saether, E.; Glaessgen, E.

2009-01-01

A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain is used to study plastic processes at a crack tip in a single crystal of aluminum. The case of mode I loading is studied. A transition from deformation twinning to full dislocation emission from the crack tip is found when the crack plane is rotated around the [111] crystallographic axis. When the crack plane normal coincides with the [112] twinning direction, the crack propagates through a twinning mechanism. When the crack plane normal coincides with the [011] slip direction, the crack propagates through the emission of full dislocations. In intermediate orientations, a transition from full dislocation emission to twinning is found to occur with an increase in the stress intensity at the crack tip. This finding confirms the suggestion that the very high strain rates, inherently present in MD simulations, which produce higher stress intensities at the crack tip, over-predict the tendency for deformation twinning compared to experiments. The present study, therefore, aims to develop a more realistic and accurate predictive modeling of fracture processes.

doGlycans–Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

PubMed Central

2017-01-01

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell–cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS. PMID:28906114

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

DOE PAGES

Abbott, Lauren J.; Stevens, Mark J.

2015-12-22

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

Computer modelling of the optical behaviour of rare earth dopants in BaY2F8

NASA Astrophysics Data System (ADS)

Jackson, R. A.; Valerio, M. E. G.; Couto Dos Santos, M. A.; Amaral, J. B.

2005-01-01

BaY2F8, when doped with rare earth elements is a material of interest in the development of solid-state laser systems, especially for use in the infrared region. This paper presents the application of a new computational technique, which combines atomistic modelling and crystal field calculations in a study of rare earth doping of the material. Atomistic modelling is used to calculate the symmetry and detailed geometry of the dopant ion-host lattice system, and this information is then used to calculate the crystal field parameters, which are an important indicator in assessing the optical behaviour of the dopant-crystal system. Comparisons with the results of recent experimental work on this material are made.

An atomistic model for cross-linked HNBR elastomers used in seals

NASA Astrophysics Data System (ADS)

Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

2015-03-01

Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

Intergranular fracture in UO{sub 2}: derivation of traction-separation law from atomistic simulations

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

Zhang, Yongfeng; Millett, P.C.; Tonks, M.R.

2013-07-01

In this study, the intergranular fracture behavior of UO{sub 2} was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt Σ5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at themore » propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior. (authors)« less

Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations

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

Yongfeng Zhang; Paul C Millett; Michael R Tonks

2013-10-01

In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagatingmore » crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.« less

Atomistic simulation of defect formation and structure transitions in U-Mo alloys in swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Kolotova, L. N.; Starikov, S. V.

2017-11-01

In irradiation of swift heavy ions, the defects formation frequently takes place in crystals. High energy transfer into the electronic subsystem and relaxations processes lead to the formation of structural defects and cause specific effects, such as the track formation. There is a large interest to understanding of the mechanisms of defects/tracks formation due to the heating of the electron subsystem. In this work, the atomistic simulation of defects formation and structure transitions in U-Mo alloys in irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes in irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation in irradiation in the various conditions are calculated.

A jellium model of a catalyst particle in carbon nanotube growth

NASA Astrophysics Data System (ADS)

Artyukhov, Vasilii I.; Liu, Mingjie; Penev, Evgeni S.; Yakobson, Boris I.

2017-06-01

We show how a jellium model can represent a catalyst particle within the density-functional theory based approaches to the growth mechanism of carbon nanotubes (CNTs). The advantage of jellium is an abridged, less computationally taxing description of the multi-atom metal particle, while at the same time in avoiding the uncertainty of selecting a particular atomic geometry of either a solid or ever-changing liquid catalyst particle. A careful choice of jellium sphere size and its electron density as a descriptive parameter allows one to calculate the CNT-metal interface energies close to explicit full atomistic models. Further, we show that using jellium permits computing and comparing the formation of topological defects (sole pentagons or heptagons, the culprits of growth termination) as well as pentagon-heptagon pairs 5|7 (known as chirality-switching dislocation).

Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method.

PubMed

Ardham, Vikram Reddy; Deichmann, Gregor; van der Vegt, Nico F A; Leroy, Frédéric

2015-12-28

We address the question of how reducing the number of degrees of freedom modifies the interfacial thermodynamic properties of heterogeneous solid-liquid systems. We consider the example of n-hexane interacting with multi-layer graphene which we model both with fully atomistic and coarse-grained (CG) models. The CG models are obtained by means of the conditional reversible work (CRW) method. The interfacial thermodynamics of these models is characterized by the solid-liquid work of adhesion WSL calculated by means of the dry-surface methodology through molecular dynamics simulations. We find that the CRW potentials lead to values of WSL that are larger than the atomistic ones. Clear understanding of the relationship between the structure of n-hexane in the vicinity of the surface and WSL is elucidated through a detailed study of the energy and entropy components of WSL. We highlight the crucial role played by the solid-liquid energy fluctuations. Our approach suggests that CG potentials should be designed in such a way that they preserve the range of solid-liquid interaction energies, but also their fluctuations in order to preserve the reference atomistic value of WSL. Our study thus opens perspectives into deriving CG interaction potentials that preserve the thermodynamics of solid-liquid contacts and will find application in studies that intend to address materials driven by interfaces.

Molecular Simulation Studies of Covalently and Ionically Grafted Nanoparticles

NASA Astrophysics Data System (ADS)

Hong, Bingbing

Solvent-free covalently- or ionically-grafted nanoparticles (CGNs and IGNs) are a new class of organic-inorganic hybrid composite materials exhibiting fluid-like behaviors around room temperature. With similar structures to prior systems, e.g. nanocomposites, neutral or charged colloids, ionic liquids, etc, CGNs and IGNs inherit the functionality of inorganic nanopariticles, the facile processibility of polymers, as well as conductivity and nonvolatility from their constituent materials. In spite of the extensive prior experimental research having covered synthesis and measurements of thermal and dynamic properties, little progress in understanding of these new materials at the molecular level has been achieved, because of the lack of simulation work in this new area. Atomistic and coarse-grained molecular dynamics simulations have been performed in this thesis to investigate the thermodynamics, structure, and dynamics of these systems and to seek predictive methods predictable for their properties. Starting from poly(ethylene oxide) oligomers (PEO) melts, we established atomistic models based on united-atom representations of methylene. The Green-Kubo and Einstein-Helfand formulas were used to calculate the transport properties. The simulations generate densities, viscosities, diffusivities, in good agreement with experimental data. The chain-length dependence of the transport properties suggests that neither Rouse nor reptation models are applicable in the short-chain regime investigated. Coupled with thermodynamic integration methods, the models give good predictions of pressure-composition-density relations for CO 2 + PEO oligomers. Water effects on the Henry's constant of CO 2 in PEO have also been investigated. The dependence of the calculated Henry's constants on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. CGNs are modeled by the inclusion of solid-sphere nanoparticles into the atomistic oligomers. The calculated viscosities from Green-Kubo relationships and temperature extrapolation are of the same order of magnitude as experimental values, but show a smaller activation energy relative to real CGNs systems. Grafted systems have higher viscosities, smaller diffusion coefficients, and slower chain dynamics than the ungrafted counterparts - nanocomposites - at high temperatures. At lower temperatures, grafted systems exhibit faster dynamics for both nanoparticles and chains relative to ungrafted systems, because of lower aggregation of nanoparticles and enhanced correlations between nanoparticles and chains. This agrees with the experimental observation that the new materials have liquid-like behavior in the absence of a solvent. To lower the simulated temperatures into the experimental range, we established a coarse-grained CGNs model by matching structural distribution functions to atomistic simulation data. In contrast with linear polymer systems, for which coarse-graining always accelerate dynamics, coarse-graining of grafted nanoparticles can either accelerate or slowdown the core motions, depending on the length of the grafted chains. This can be qualitatively predicted by a simple transition-state theory. Similar atomistic models to CGNs were developed for IGNs, with ammonium counterions described by an explicit-hydrogen way; these were in turn compared with "generic" coarse-grained IGNs. The elimination of chemical details in the coarse-grained models does not bring in qualitative changes to the radial distribution functions and diffusion of atomistic IGNs, but saves considerable simulation resources and make simulations near room temperatures affordable. The chain counterions in both atomistic and coarse-grained models are mobile, moving from site to site and from nanoparticle to nanoparticle. At the same temperature and the same core volume fractions, the nanoparticle diffusivities in coarse-grained IGNs are slower by a factor ten than the cores of CGNs. The coarse-grained IGNs models are later used to investigate the system dynamics through analysis of the dependence on temperature and structural parameters of the transport properties (self-diffusion coefficients, viscosities and conductivities). Further, migration kinetics of oligomeric counterions is analyzed in a manner analogous to unimer exchange between micellar aggregates. The counterion migrations follow the "double-core" mechanism and are kinetically controlled by neighboring-core collisions. (Abstract shortened by UMI.)

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

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

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

2016-08-07

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

Simulating the flow of entangled polymers.

PubMed

Masubuchi, Yuichi

2014-01-01

To optimize automation for polymer processing, attempts have been made to simulate the flow of entangled polymers. In industry, fluid dynamics simulations with phenomenological constitutive equations have been practically established. However, to account for molecular characteristics, a method to obtain the constitutive relationship from the molecular structure is required. Molecular dynamics simulations with atomic description are not practical for this purpose; accordingly, coarse-grained models with reduced degrees of freedom have been developed. Although the modeling of entanglement is still a challenge, mesoscopic models with a priori settings to reproduce entangled polymer dynamics, such as tube models, have achieved remarkable success. To use the mesoscopic models as staging posts between atomistic and fluid dynamics simulations, studies have been undertaken to establish links from the coarse-grained model to the atomistic and macroscopic simulations. Consequently, integrated simulations from materials chemistry to predict the macroscopic flow in polymer processing are forthcoming.

Parallel multiscale simulations of a brain aneurysm

PubMed Central

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

2012-01-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work. PMID:23734066

Parallel multiscale simulations of a brain aneurysm.

PubMed

Grinberg, Leopold; Fedosov, Dmitry A; Karniadakis, George Em

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr . The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

Parallel multiscale simulations of a brain aneurysm

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

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em, E-mail: george_karniadakis@brown.edu

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm.more » The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.« less

Atomistic cluster alignment method for local order mining in liquids and glasses

NASA Astrophysics Data System (ADS)

Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.

2010-11-01

An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.

Enhanced densification under shock compression in porous silicon

NASA Astrophysics Data System (ADS)

Lane, J. Matthew D.; Thompson, Aidan P.; Vogler, Tracy J.

2014-10-01

Under shock compression, most porous materials exhibit lower densities for a given pressure than that of a full-dense sample of the same material. However, some porous materials exhibit an anomalous, or enhanced, densification under shock compression. We demonstrate a molecular mechanism that drives this behavior. We also present evidence from atomistic simulation that silicon belongs to this anomalous class of materials. Atomistic simulations indicate that local shear strain in the neighborhood of collapsing pores nucleates a local solid-solid phase transformation even when bulk pressures are below the thermodynamic phase transformation pressure. This metastable, local, and partial, solid-solid phase transformation, which accounts for the enhanced densification in silicon, is driven by the local stress state near the void, not equilibrium thermodynamics. This mechanism may also explain the phenomenon in other covalently bonded materials.

Atomistic nucleation sites of Pt nanoparticles on N-doped carbon nanotubes.

PubMed

Sun, Chia-Liang; Pao, Chih-Wen; Tsai, Huang-Ming; Chiou, Jau-Wern; Ray, Sekhar C; Wang, Houng-Wei; Hayashi, Michitoshi; Chen, Li-Chyong; Lin, Hong-Ji; Lee, Jyh-Fu; Chang, Li; Tsai, Min-Hsiung; Chen, Kuei-Hsien; Pong, Way-Faung

2013-08-07

The atomistic nucleation sites of Pt nanoparticles (Pt NPs) on N-doped carbon nanotubes (N-CNTs) were investigated using C and N K-edge and Pt L3-edge X-ray absorption near-edge structure (XANES)/extended X-ray absorption fine structure (EXAFS) spectroscopy. Transmission electron microscopy and XANES/EXAFS results revealed that the self-organized Pt NPs on N-CNTs are uniformly distributed because of the relatively high binding energies of the adsorbed Pt atoms at the imperfect sites. During the atomistic nucleation process of Pt NPs on N-CNTs, stable Pt-C and Pt-N bonds are presumably formed, and charge transfer occurs at the surface/interface of the N-CNTs. The findings in this study were consistent with density functional theory calculations performed using cluster models for the undoped, substitutional-N-doped and pyridine-like-N-doped CNTs.

Atomic-Scale Lightning Rod Effect in Plasmonic Picocavities: A Classical View to a Quantum Effect.

PubMed

Urbieta, Mattin; Barbry, Marc; Zhang, Yao; Koval, Peter; Sánchez-Portal, Daniel; Zabala, Nerea; Aizpurua, Javier

2018-01-23

Plasmonic gaps are known to produce nanoscale localization and enhancement of optical fields, providing small effective mode volumes of about a few hundred nm 3 . Atomistic quantum calculations based on time-dependent density functional theory reveal the effect of subnanometric localization of electromagnetic fields due to the presence of atomic-scale features at the interfaces of plasmonic gaps. Using a classical model, we explain this as a nonresonant lightning rod effect at the atomic scale that produces an extra enhancement over that of the plasmonic background. The near-field distribution of atomic-scale hot spots around atomic features is robust against dynamical screening and spill-out effects and follows the potential landscape determined by the electron density around the atomic sites. A detailed comparison of the field distribution around atomic hot spots from full quantum atomistic calculations and from the local classical approach considering the geometrical profile of the atoms' electronic density validates the use of a classical framework to determine the effective mode volume in these extreme subnanometric optical cavities. This finding is of practical importance for the community of surface-enhanced molecular spectroscopy and quantum nanophotonics, as it provides an adequate description of the local electromagnetic fields around atomic-scale features with use of simplified classical methods.

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations

PubMed Central

2018-01-01

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure–constant temperature ensemble. These materials exhibit a distinct “smectic” liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications. PMID:29301305

An efficient Monte Carlo algorithm for the fast equilibration and atomistic simulation of alkanethiol self-assembled monolayers on a Au(111) substrate.

PubMed

Alexiadis, Orestis; Daoulas, Kostas Ch; Mavrantzas, Vlasis G

2008-01-31

A new Monte Carlo algorithm is presented for the simulation of atomistically detailed alkanethiol self-assembled monolayers (R-SH) on a Au(111) surface. Built on a set of simpler but also more complex (sometimes nonphysical) moves, the new algorithm is capable of efficiently driving all alkanethiol molecules to the Au(111) surface, thereby leading to full surface coverage, irrespective of the initial setup of the system. This circumvents a significant limitation of previous methods in which the simulations typically started from optimally packed structures on the substrate close to thermal equilibrium. Further, by considering an extended ensemble of configurations each one of which corresponds to a different value of the sulfur-sulfur repulsive core potential, sigmass, and by allowing for configurations to swap between systems characterized by different sigmass values, the new algorithm can adequately simulate model R-SH/Au(111) systems for values of sigmass ranging from 4.25 A corresponding to the Hautman-Klein molecular model (J. Chem. Phys. 1989, 91, 4994; 1990, 93, 7483) to 4.97 A corresponding to the Siepmann-McDonald model (Langmuir 1993, 9, 2351), and practically any chain length. Detailed results are presented quantifying the efficiency and robustness of the new method. Representative simulation data for the dependence of the structural and conformational properties of the formed monolayer on the details of the employed molecular model are reported and discussed; an investigation of the variation of molecular organization and ordering on the Au(111) substrate for three CH3-(CH2)n-SH/Au(111) systems with n=9, 15, and 21 is also included.

Simulation of dense amorphous polymers by generating representative atomistic models

NASA Astrophysics Data System (ADS)

Curcó, David; Alemán, Carlos

2003-08-01

A method for generating atomistic models of dense amorphous polymers is presented. The generated models can be used as starting structures of Monte Carlo and molecular dynamics simulations, but also are suitable for the direct evaluation physical properties. The method is organized in a two-step procedure. First, structures are generated using an algorithm that minimizes the torsional strain. After this, an iterative algorithm is applied to relax the nonbonding interactions. In order to check the performance of the method we examined structure-dependent properties for three polymeric systems: polyethyelene (ρ=0.85 g/cm3), poly(L,D-lactic) acid (ρ=1.25 g/cm3), and polyglycolic acid (ρ=1.50 g/cm3). The method successfully generated representative packings for such dense systems using minimum computational resources.

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

NASA Astrophysics Data System (ADS)

Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

2014-01-01

Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.

Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

PubMed

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Revised Atomistic Models of the Crystal Structure of C-S-H with high C/S Ratio

NASA Astrophysics Data System (ADS)

Kovačević, Goran; Nicoleau, Luc; Nonat, André; Veryazov, Valera

2016-09-01

The atomic structure of calcium-silicate-hydrate (C1.67-S-Hx) has been studied. Atomistic C-S-H models suggested in our previous study have been revised in order to perform a direct comparison of energetic stability of the different structures. An extensive set of periodic structures of C-S-H with variation of water content was created, and then optimized using molecular dynamics with reactive force field ReaxFF and quantum chemical semiempirical method PM6. All models show organization of water molecules inside the structure of C-S-H. The new geometries of C-S-H, reported in this paper, show lower relative energy with respect to the geometries from the original definition of C-S-H models. Model that corresponds to calcium enriched tobermorite structure has the lowest relative energy and the density closest to the experimental values.

Alloy Design Workbench-Surface Modeling Package Developed

NASA Technical Reports Server (NTRS)

Abel, Phillip B.; Noebe, Ronald D.; Bozzolo, Guillermo H.; Good, Brian S.; Daugherty, Elaine S.

2003-01-01

NASA Glenn Research Center's Computational Materials Group has integrated a graphical user interface with in-house-developed surface modeling capabilities, with the goal of using computationally efficient atomistic simulations to aid the development of advanced aerospace materials, through the modeling of alloy surfaces, surface alloys, and segregation. The software is also ideal for modeling nanomaterials, since surface and interfacial effects can dominate material behavior and properties at this level. Through the combination of an accurate atomistic surface modeling methodology and an efficient computational engine, it is now possible to directly model these types of surface phenomenon and metallic nanostructures without a supercomputer. Fulfilling a High Operating Temperature Propulsion Components (HOTPC) project level-I milestone, a graphical user interface was created for a suite of quantum approximate atomistic materials modeling Fortran programs developed at Glenn. The resulting "Alloy Design Workbench-Surface Modeling Package" (ADW-SMP) is the combination of proven quantum approximate Bozzolo-Ferrante-Smith (BFS) algorithms (refs. 1 and 2) with a productivity-enhancing graphical front end. Written in the portable, platform independent Java programming language, the graphical user interface calls on extensively tested Fortran programs running in the background for the detailed computational tasks. Designed to run on desktop computers, the package has been deployed on PC, Mac, and SGI computer systems. The graphical user interface integrates two modes of computational materials exploration. One mode uses Monte Carlo simulations to determine lowest energy equilibrium configurations. The second approach is an interactive "what if" comparison of atomic configuration energies, designed to provide real-time insight into the underlying drivers of alloying processes.

From atomistic interfaces to dendritic patterns

NASA Astrophysics Data System (ADS)

Galenko, P. K.; Alexandrov, D. V.

2018-01-01

Transport processes around phase interfaces, together with thermodynamic properties and kinetic phenomena, control the formation of dendritic patterns. Using the thermodynamic and kinetic data of phase interfaces obtained on the atomic scale, one can analyse the formation of a single dendrite and the growth of a dendritic ensemble. This is the result of recent progress in theoretical methods and computational algorithms calculated using powerful computer clusters. Great benefits can be attained from the development of micro-, meso- and macro-levels of analysis when investigating the dynamics of interfaces, interpreting experimental data and designing the macrostructure of samples. The review and research articles in this theme issue cover the spectrum of scales (from nano- to macro-length scales) in order to exhibit recently developing trends in the theoretical analysis and computational modelling of dendrite pattern formation. Atomistic modelling, the flow effect on interface dynamics, the transition from diffusion-limited to thermally controlled growth existing at a considerable driving force, two-phase (mushy) layer formation, the growth of eutectic dendrites, the formation of a secondary dendritic network due to coalescence, computational methods, including boundary integral and phase-field methods, and experimental tests for theoretical models-all these themes are highlighted in the present issue. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

Atomistic Simulation of High-Density Uranium Fuels

DOE PAGES

Garcés, Jorge Eduardo; Bozzolo, Guillermo

2011-01-01

We apply an atomistic modeling approach to deal with interfacial phenomena in high-density uranium fuels. The effects of Si, as additive to Al or as U-Mo-particles coating, on the behavior of the Al/U-Mo interface is modeled by using the Bozzolo-Ferrante-Smith (BFS) method for alloys. The basic experimental features characterizing the real system are identified, via simulations and atom-by-atom analysis. These include (1) the trend indicating formation of interfacial compounds, (2) much reduced diffusion of Al into U-Mo solid solution due to the high Si concentration, (3) Si depletion in the Al matrix, (4) an unexpected interaction between Mo and Simore » which inhibits Si diffusion to deeper layers in the U-Mo solid solution, and (5) the minimum amount of Si needed to perform as an effective diffusion barrier. Simulation results related to alternatives to Si dispersed in the Al matrix, such as the use of C coating of U-Mo particles or Zr instead of the Al matrix, are also shown. Recent experimental results confirmed early theoretical proposals, along the lines of the results reported in this work, showing that atomistic computational modeling could become a valuable tool to aid the experimental work in the development of nuclear fuels.« less

Modeling the atomistic growth behavior of gold nanoparticles in solution

NASA Astrophysics Data System (ADS)

Turner, C. Heath; Lei, Yu; Bao, Yuping

2016-04-01

The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions.

Transferable atomistic model to describe the energetics of zirconia

NASA Astrophysics Data System (ADS)

Wilson, Mark; Schönberger, Uwe; Finnis, Michael W.

1996-10-01

We have investigated the energies of a number of phases of ZrO2 using models of an increasing degree of sophistication: the simple ionic model, the polarizable ion model, the compressible ion model, and finally a model including quadrupole polarizability of the oxygen ions. The three structures which are observed with increasing temperatures are monoclinic, tetragonal, and cubic (fluorite). Besides these we have studied some hypothetical structures which certain potentials erroneously predict or which occur in other oxides with this stoichiometry, e.g., the α-PbO2 structure and rutile. We have also performed ab initio density functional calculations with the full-potential linear combination of muffin-tin orbitals method to investigate the cubic-tetragonal distortion. A detailed comparison is made between the results using classical potentials, the experimental data, and our own and other ab initio results. The factors which stabilize the various structure are analyzed. We find the only genuinely transferable model is the one including compressible ions and anion polarizability to the quadrupole level.

On the Reduction of Molecular Degrees of Freedom in Computer Simulations

NASA Astrophysics Data System (ADS)

Lyubartsev, Alexander P.; Laaksonen, Aatto

Molecular simulations, based on atomistic force fields are a standard theoretical tool in materials, polymers and biosciences. While various methods, with quantum chemistry incorporated, have been developed for condensed phase simulations during the last decade, there is another line of development with the purpose to bridge the time and length scales based on coarse-graining. This is expected to lead to some very interesting breakthroughs in the near future. In this lecture we will first give some background to common atomistic force fields. After that, we review a few common simple techniques for reducing the number of motional degrees of freedom to speed up the simulations. Finally, we present a powerful method for reducing uninteresting degrees of freedom. This is done by solving the Inverse Problem to obtain the interaction potentials. More precisely, we make use of the radial distribution functions, and by using the method of Inverse Monte Carlo [Lyubartsev & Laaksonen, Phys. Rev. E. 52, 3730 (1995)], we can construct effective potentials which are consistent with the original RDFs. This makes it possible to simulate much larger system than would have been possible by using atomistic force fields. We present many examples: How to simulate aqueous electrolyte solutions without any water molecules but still having the hydration structure around the ions - at the speed of a primitive electrolyte model calculation. We demonstrate how a coarse-grained model can be constructed for a double-helix DNA and how it can be used. It is accurate enough to reproduce the experimental results for ion condensation around DNA for several different counterions. We also show how we can construct site-site potentials for large-scale atomistic classical simulations of arbitrary liquids from smaller scale ab initio simulations. This methodology allows us to start from a simulation with the electrons and atomic nuclei, to construct a set of atomistic effective interaction potentials, and to use them in classical simulations. As a next step we can construct a new set of potentials beyond the atomistic description and carry out mesoscopic simulations, for example by using Dissipative Particle Dynamics. In this way we can tie together three different levels of description. The Dissipative Particle Dynamics method appears as a very promising tool to use with our coarse-grained potentials.

Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2004-01-01

We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Computational Modeling of Hydroxypropyl-Methylcellulose Acetate Succinate (HPMCAS) and Phenytoin Interactions: A Systematic Coarse-Graining Approach.

PubMed

Huang, Wenjun; Mandal, Taraknath; Larson, Ronald G

2017-03-06

We present coarse-grained (CG) force fields for hydroxypropyl-methylcellulose acetate succinate (HPMCAS) polymers and the drug molecule phenytoin using a bead/stiff spring model, with each bead representing a HPMCAS monomer or monomer side group (hydroxypropyl acetyl, acetyl, or succinyl) or a single phenytoin ring. We obtain the bonded and nonbonded interaction parameters in our CG model using the RDFs from atomistic simulations of short HPMCAS model oligomers (20-mer) and atomistic simulations of phenytoin molecules. The nonbonded interactions are modeled using a LJ 12-6 potential, with separate parameters for each monomer substitution type, which allows heterogeneous polymer chains to be modeled. The cross interaction terms between the polymer and phenytoin CG beads are obtained explicitly from atomistic level polymer-phenytoin simulations, rather than from mixing rules. We study the solvation behavior of 50-mer and 100-mer polymer chains and find chain-length-dependent aggregation. We also compare the phenytoin CG force field developed in this work with that in Mandal et al. (Soft Matter, 2016, 12, 8246-8255) and conclude both are suitable for studying the interaction between polymer and drug in solvated solid dispersion formulation, in the absence of drug crystallization. Finally, we present simulations of heterogeneous HPMCAS model polymer chains and phenytoin molecules. Polymer and drug form a complex in a short period of simulation time due to strong intermolecular interactions. Moreover, the protonated polymer chains are more effective than deprotonated ones in inhibiting the drug aggregation in the polymer-drug complex.

Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method

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

Ardham, Vikram Reddy; Leroy, Frédéric, E-mail: vandervegt@csi.tu-darmstadt.de, E-mail: f.leroy@theo.chemie.tu-darmstadt.de; Deichmann, Gregor

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 thanmore » 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.« less

Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations.

PubMed

Ithuralde, Raúl Esteban; Roitberg, Adrián Enrique; Turjanski, Adrián Gustavo

2016-07-20

Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs.

Penetration scaling in atomistic simulations of hypervelocity impact

NASA Astrophysics Data System (ADS)

Ruestes, C. J.; Bringa, E. M.; Fioretti, F.; Higginbotham, A.; Taylor, E. A.; Graham, G.

2011-06-01

We present atomistic molecular dynamics simulations of the impact of copper nano particles at 5 km/s on copper films ranging in thickness from 0.5 to 4 times the projectile diameter. We access both penetration and cratering regimes with final cratering morphologies showing considerable similarity to experimental impacts on both micron and millimeter scales. Both craters and holes are formed from a molten region, with relatively low defect densities remaining after cooling and recrystallisation. Crater diameter and penetration limits are compared to analytical scaling models: in agreement with some models we find the onset of penetration occurs for 1.0 < f/d < 1.5, where f is the film thickness and d is the projectile diameter. However, our results for the hole size agree well with scaling laws based on macroscopic experiments providing enhanced strength of a nano-film that melts completely at the impact region is taken into account. Penetration in films with pre-existing nanocracks is qualitatively similar to penetration in perfect films, including the lack of back-spall. Simulations using ``peridynamics'' are also described and compared to the atomistic simulations. Work supported by PICT2007-PRH, PICT-2008 1325, and SeCTyP.

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

PubMed

Shen, Lin; Hu, Hao

2014-06-10

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

Implementation of the nudged elastic band method in a dislocation dynamics formalism: Application to dislocation nucleation

NASA Astrophysics Data System (ADS)

Geslin, Pierre-Antoine; Gatti, Riccardo; Devincre, Benoit; Rodney, David

2017-11-01

We propose a framework to study thermally-activated processes in dislocation glide. This approach is based on an implementation of the nudged elastic band method in a nodal mesoscale dislocation dynamics formalism. Special care is paid to develop a variational formulation to ensure convergence to well-defined minimum energy paths. We also propose a methodology to rigorously parametrize the model on atomistic data, including elastic, core and stacking fault contributions. To assess the validity of the model, we investigate the homogeneous nucleation of partial dislocation loops in aluminum, recovering the activation energies and loop shapes obtained with atomistic calculations and extending these calculations to lower applied stresses. The present method is also applied to heterogeneous nucleation on spherical inclusions.

Closed-system 'economic' models for psychiatric disorders: Western atomism and its culture-bound syndromes.

PubMed

Wallace, Rodrick

2015-08-01

The stabilization of human cognition via feedback from embedding social and cultural contexts is a dynamic process deeply intertwined with it, constituting, in a sense, the riverbanks directing the flow of a stream of generalized consciousness at different scales: Cultural norms and social interaction are synergistic with individual and group cognition and their disorders. A canonical failure mode in atomistic cultures is found to be a 'ground state' collapse well represented by atomistic models of economic interaction that are increasingly characterized as divorced from reality by heterodox economists. That is, high rates of psychopathic and antisocial personality disorder and obsessive compulsive disorder emerge as culture-bound syndromes particular to Western or Westernizing societies, or to those undergoing social disintegration.

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

Man, Viet Hoang; Pan, Feng; Sagui, Celeste, E-mail: sagui@ncsu.edu

We explore the use of a fast laser melting simulation approach combined with atomistic molecular dynamics simulations in order to determine the melting and healing responses of B-DNA and Z-DNA dodecamers with the same d(5′-CGCGCGCGCGCG-3′){sub 2} sequence. The frequency of the laser pulse is specifically tuned to disrupt Watson-Crick hydrogen bonds, thus inducing melting of the DNA duplexes. Subsequently, the structures relax and partially refold, depending on the field strength. In addition to the inherent interest of the nonequilibrium melting process, we propose that fast melting by an infrared laser pulse could be used as a technique for a fastmore » comparison of relative stabilities of same-sequence oligonucleotides with different secondary structures with full atomistic detail of the structures and solvent. This could be particularly useful for nonstandard secondary structures involving non-canonical base pairs, mismatches, etc.« less

Exploration of the folding dynamics of human telomeric G-quadruplex with a hybrid atomistic structure-based model

NASA Astrophysics Data System (ADS)

Bian, Yunqiang; Ren, Weitong; Song, Feng; Yu, Jiafeng; Wang, Jihua

2018-05-01

Structure-based models or Gō-like models, which are built from one or multiple particular experimental structures, have been successfully applied to the folding of proteins and RNAs. Recently, a variant termed the hybrid atomistic model advances the description of backbone and side chain interactions of traditional structure-based models, by borrowing the description of local interactions from classical force fields. In this study, we assessed the validity of this model in the folding problem of human telomeric DNA G-quadruplex, where local dihedral terms play important roles. A two-state model was developed and a set of molecular dynamics simulations was conducted to study the folding dynamics of sequence Htel24, which was experimentally validated to adopt two different (3 + 1) hybrid G-quadruplex topologies in K+ solution. Consistent with the experimental observations, the hybrid-1 conformation was found to be more stable and the hybrid-2 conformation was kinetically more favored. The simulations revealed that the hybrid-2 conformation folded in a higher cooperative manner, which may be the reason why it was kinetically more accessible. Moreover, by building a Markov state model, a two-quartet G-quadruplex state and a misfolded state were identified as competing states to complicate the folding process of Htel24. Besides, the simulations also showed that the transition between hybrid-1 and hybrid-2 conformations may proceed an ensemble of hairpin structures. The hybrid atomistic structure-based model reproduced the kinetic partitioning folding dynamics of Htel24 between two different folds, and thus can be used to study the complex folding processes of other G-quadruplex structures.

Computer modelling of BaY2F8: defect structure, rare earth doping and optical behaviour

NASA Astrophysics Data System (ADS)

Amaral, J. B.; Couto Dos Santos, M. A.; Valerio, M. E. G.; Jackson, R. A.

2005-10-01

BaY2F8, when doped with rare earth elements, is a material of interest in the development of solid-state laser systems, especially for use in the infrared region. This paper presents the application of a computational technique, which combines atomistic modelling and crystal field calculations, in a study of rare earth doping of the material. Atomistic modelling is used to calculate the intrinsic defect structure and the symmetry and detailed geometry of the dopant ion-host lattice system, and this information is then used to calculate the crystal field parameters, which are an important indicator in assessing the optical behaviour of the dopant-crystal system. Energy levels are then calculated for the Dy3+-substituted material, and comparisons with the results of recent experimental work are made.

Interwell Connectivity Evaluation Using Injection and Production Fluctuation Data

NASA Astrophysics Data System (ADS)

Shang, Barry Zhongqi

The development of multiscale methods for computational simulation of biophysical systems represents a significant challenge. Effective computational models that bridge physical insights obtained from atomistic simulations and experimental findings are lacking. An accurate passing of information between these scales would enable: (1) an improved physical understanding of structure-function relationships, and (2) enhanced rational strategies for molecular engineering and materials design. Two approaches are described in this dissertation to facilitate these multiscale goals. In Part I, we develop a lattice kinetic Monte Carlo model to simulate cellulose decomposition by cellulase enzymes and to understand the effects of spatial confinement on enzyme kinetics. An enhanced mechanistic understanding of this reaction system could enhance the design of cellulose bioconversion technologies for renewable and sustainable energy. Using our model, we simulate the reaction up to experimental conversion times of days, while simultaneously capturing the microscopic kinetic behaviors. Therefore, the influence of molecular-scale kinetics on the macroscopic conversion rate is made transparent. The inclusion of spatial constraints in the kinetic model represents a significant advance over classical mass-action models commonly used to describe this reaction system. We find that restrictions due to enzyme jamming and substrate heterogeneity at the molecular level play a dominate role in limiting cellulose conversion. We identify that the key rate limitations are the slow rates of enzyme complexation with glucan chains and the competition between enzyme processivity and jamming. We show that the kinetics of complexation, which involves extraction of a glucan chain end from the cellulose surface and threading through the enzyme active site, occurs slowly on the order of hours, while intrinsic hydrolytic bond cleavage occurs on the order of seconds. We also elucidate the subtle trade-off between processivity and jamming. Highly processive enzymes cleave a large fraction of a glucan chain during each processive run but are prone to jamming at obstacles. Less processive enzymes avoid jamming but cleave only a small fraction of a chain. Optimizing this trade-off maximizes the cellulose conversion rate. We also elucidate the molecular-scale kinetic origins for synergy among cellulases in enzyme mixtures. In contrast to the currently accepted theory, we show that the ability of an endoglucanase to increase the concentration of chain ends for exoglucanases is insufficient for synergy to occur. Rather, endoglucanases must enhance the rate of complexation between exoglucanases and the newly created chain ends. This enhancement occurs when the endoglucanase is able to partially decrystallize the cellulose surface. We show generally that the driving forces for complexation and jamming, which govern the kinetics of pure exoglucanases, also control the degree of synergy in endo-exo mixtures. In Part II, we focus our attention on a different multiscale problem. This challenge is the development of coarse-grained models from atomistic models to access larger length- and time-scales in a simulation. This problem is difficult because it requires a delicate balance between maintaining (1) physical simplicity in the coarse-grained model and (2) physical consistency with the atomistic model. To achieve these goals, we develop a scheme to coarse-grain an atomistic fluid model into a fluctuating hydrodynamics (FHD) model. The FHD model describes the solvent as a field of fluctuating mass, momentum, and energy densities. The dynamics of the fluid are governed by continuum balance equations and fluctuation-dissipation relations based on the constitutive transport laws. The incorporation of both macroscopic transport and microscopic fluctuation phenomena could provide richer physical insight into the behaviors of biophysical systems driven by hydrodynamic fluctuations, such as hydrophobic assembly and crystal nucleation. We further extend our coarse-graining method by developing an interfacial FHD model using information obtained from simulations of an atomistic liquid-vapor interface. We illustrate that a phenomenological Ginzburg-Landau free energy employed in the FHD model can effectively represent the attractive molecular interactions of the atomistic model, which give rise to phase separation. For argon and water, we show that the interfacial FHD model can reproduce the compressibility, surface tension, and capillary wave spectrum of the atomistic model. Via this approach, simulations that explore the coupling between hydrodynamic fluctuations and phase equilibria with molecular-scale consistency are now possible. In both Parts I and II, the emerging theme is that the combination of bottom-up coarse graining and top-down phenomenology is essential for enabling a multiscale approach to remain physically consistent with molecular-scale interactions while simultaneously capturing the collective macroscopic behaviors. This hybrid strategy enables the resulting computational models to be both physically insightful and practically meaningful. (Abstract shortened by UMI.).

CO adsorption on the “29” Cu xO/Cu(111) surface: An integrated DFT, STM, and TPD study

DOE PAGES

Hensley, Alyssa J. R.; Therrien, Andrew J.; Zhang, Renqin; ...

2016-10-04

The elucidation of an accurate atomistic model of surface structures is crucial for the design and understanding of effective catalysts, a process requiring a close collaboration between experimental observations and theoretical models. Any developed surface theoretical model must agree with experimental results for the surface when both clean and adsorbate covered. Here, we present a detailed study of the adsorption of CO on the “29” Cu xO/ Cu(111) surface, which is important in the understanding of ubiquitous Cubased catalysis. This study uses scanning tunneling microscopy, temperatureprogrammed desorption, and density functional theory to analyze CO adsorption on the “29” Cu xO/Cu(111)more » surface. From the experimental scanning tunneling microscopy images, CO was found to form six different ordered structures on the “29” Cu xO/Cu(111) surface depending on the surface CO coverage. By modeling the adsorption of CO on our atomistic model of the “29” Cu xO/Cu(111) surface at different coverages, we were able to match the experimentally observed CO ordered structures to specific combinations of sites on the “29” Cu xO/Cu(111) surface. Lastly, the high degree of agreement seen here between experiment and theory for the adsorption of CO on the “29” Cu xO/Cu(111) surface at various CO coverages provides further support that our atomistic model of the “29” Cu xO/Cu(111) surface is experimentally accurate.« less

Modes of Modelling Assessment--A Literature Review

ERIC Educational Resources Information Center

Frejd, Peter

2013-01-01

This paper presents a critical review of literature investigating assessment of mathematical modelling. Written tests, projects, hands-on tests, portfolio and contests are modes of modelling assessment identified in this study. The written tests found in the reviewed papers draw on an atomistic view on modelling competencies, whereas projects are…

Boundary Condition for Modeling Semiconductor Nanostructures

NASA Technical Reports Server (NTRS)

Lee, Seungwon; Oyafuso, Fabiano; von Allmen, Paul; Klimeck, Gerhard

2006-01-01

A recently proposed boundary condition for atomistic computational modeling of semiconductor nanostructures (particularly, quantum dots) is an improved alternative to two prior such boundary conditions. As explained, this boundary condition helps to reduce the amount of computation while maintaining accuracy.

The reaction mechanism with free energy barriers at constant potentials for the oxygen evolution reaction at the IrO 2 (110) surface

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

Ping, Yuan; Nielsen, Robert J.; Goddard, William A.

How to efficiently oxidize H 2O to O 2 (oxygen evolution reaction, OER) in photoelectrochemical cells (PEC) is a great challenge due to its complex charge transfer process, high overpotential, and corrosion. So far no OER mechanism has been fully explained atomistically with both thermodynamic and kinetics. IrO 2 is the only known OER catalyst with both high catalytic activity and stability in acidic conditions. This is important because PEC experiments often operate at extreme pH conditions. In this work, we performed first-principles calculations integrated with implicit solvation at constant potentials to examine the detailed atomistic reaction mechanism of OERmore » at the IrO 2 (110) surface. We determined the surface phase diagram, explored the possible reaction pathways including kinetic barriers, and computed reaction rates based on the microkinetic models. Furthermore, this allowed us to resolve several long-standing puzzles about the atomistic OER mechanism.« less

Nanoscale deicing by molecular dynamics simulation.

PubMed

Xiao, Senbo; He, Jianying; Zhang, Zhiliang

2016-08-14

Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.

The reaction mechanism with free energy barriers at constant potentials for the oxygen evolution reaction at the IrO 2 (110) surface

DOE PAGES

Ping, Yuan; Nielsen, Robert J.; Goddard, William A.

2016-12-09

How to efficiently oxidize H 2O to O 2 (oxygen evolution reaction, OER) in photoelectrochemical cells (PEC) is a great challenge due to its complex charge transfer process, high overpotential, and corrosion. So far no OER mechanism has been fully explained atomistically with both thermodynamic and kinetics. IrO 2 is the only known OER catalyst with both high catalytic activity and stability in acidic conditions. This is important because PEC experiments often operate at extreme pH conditions. In this work, we performed first-principles calculations integrated with implicit solvation at constant potentials to examine the detailed atomistic reaction mechanism of OERmore » at the IrO 2 (110) surface. We determined the surface phase diagram, explored the possible reaction pathways including kinetic barriers, and computed reaction rates based on the microkinetic models. Furthermore, this allowed us to resolve several long-standing puzzles about the atomistic OER mechanism.« less

Mono- and polynucleation, atomistic growth, and crystal phase of III-V nanowires under varying group V flow

NASA Astrophysics Data System (ADS)

Dubrovskii, V. G.

2015-05-01

We present a refined model for the vapor-liquid-solid growth and crystal structure of Au-catalyzed III-V nanowires, which revisits several assumptions used so far and is capable of describing the transition from mononuclear to polynuclear regime and ultimately to regular atomistic growth. We construct the crystal phase diagrams and calculate the wurtzite percentages, elongation rates, critical sizes, and polynucleation thresholds of Au-catalyzed GaAs nanowires depending on the As flow. We find a non-monotonic dependence of the crystal phase on the group V flow, with the zincblende structure being preferred at low and high group V flows and the wurtzite structure forming at intermediate group V flows. This correlates with most of the available experimental data. Finally, we discuss the atomistic growth picture which yields zincblende crystal structure and should be very advantageous for fabrication of ternary III-V nanowires with well-controlled composition and heterointerfaces.

Materials-by-design: computation, synthesis, and characterization from atoms to structures

NASA Astrophysics Data System (ADS)

Yeo, Jingjie; Jung, Gang Seob; Martín-Martínez, Francisco J.; Ling, Shengjie; Gu, Grace X.; Qin, Zhao; Buehler, Markus J.

2018-05-01

In the 50 years that succeeded Richard Feynman’s exposition of the idea that there is ‘plenty of room at the bottom’ for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.

Using experimental and computational energy equilibration to understand hierarchical self-assembly of Fmoc-dipeptide amphiphiles.

PubMed

Sasselli, I R; Pappas, C G; Matthews, E; Wang, T; Hunt, N T; Ulijn, R V; Tuttle, T

2016-10-12

Despite progress, a fundamental understanding of the relationships between the molecular structure and self-assembly configuration of Fmoc-dipeptides is still in its infancy. In this work, we provide a combined experimental and computational approach that makes use of free energy equilibration of a number of related Fmoc-dipeptides to arrive at an atomistic model of Fmoc-threonine-phenylalanine-amide (Fmoc-TF-NH 2 ) which forms twisted fibres. By using dynamic peptide libraries where closely related dipeptide sequences are dynamically exchanged to eventually favour the formation of the thermodynamically most stable configuration, the relative importance of C-terminus modifications (amide versus methyl ester) and contributions of aliphatic versus aromatic amino acids (phenylalanine F vs. leucine L) is determined (F > L and NH 2 > OMe). The approach enables a comparative interpretation of spectroscopic data, which can then be used to aid the construction of the atomistic model of the most stable structure (Fmoc-TF-NH 2 ). The comparison of the relative stabilities of the models using molecular dynamic simulations and the correlation with experimental data using dynamic peptide libraries and a range of spectroscopy methods (FTIR, CD, fluorescence) allow for the determination of the nanostructure with atomistic resolution. The final model obtained through this process is able to reproduce the experimentally observed formation of intertwining fibres for Fmoc-TF-NH 2 , providing information of the interactions involved in the hierarchical supramolecular self-assembly. The developed methodology and approach should be of general use for the characterization of supramolecular structures.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

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

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

2015-12-28

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

Empirical Estimation of Local Dielectric Constants: Toward Atomistic Design of Collagen Mimetic Peptides

PubMed Central

Pike, Douglas H.; Nanda, Vikas

2017-01-01

One of the key challenges in modeling protein energetics is the treatment of solvent interactions. This is particularly important in the case of peptides, where much of the molecule is highly exposed to solvent due to its small size. In this study, we develop an empirical method for estimating the local dielectric constant based on an additive model of atomic polarizabilities. Calculated values match reported apparent dielectric constants for a series of Staphylococcus aureus nuclease mutants. Calculated constants are used to determine screening effects on Coulombic interactions and to determine solvation contributions based on a modified Generalized Born model. These terms are incorporated into the protein modeling platform protCAD, and benchmarked on a data set of collagen mimetic peptides for which experimentally determined stabilities are available. Computing local dielectric constants using atomistic protein models and the assumption of additive atomic polarizabilities is a rapid and potentially useful method for improving electrostatics and solvation calculations that can be applied in the computational design of peptides. PMID:25784456

Development of a Coarse-grained Model of Polypeptoids for Studying Self-assembly in Solution

NASA Astrophysics Data System (ADS)

Du, Pu; Rick, Steven; Kumar, Revati

Polypeptoid, a class of highly tunable biomimetic analogues of peptides, are used as a prototypical model system to study self-assembly. The focus of this work is to glean insight into the effect of electrostatic and other non-covalent secondary interactions on the self-assembly of sequence-defined polypeptoids, with different charged and uncharged side groups, in solution that will complement experiments. Atomistic (AA) molecular dynamics simulation can provide a complete description of self-assembly of polypeptoid systems. However, the long simulation length and time scales needed for these processes require the development of a computationally cheaper alternative, namely coarse-grained (CG) models. A CG model for studying polypeptoid micellar interactions is being developed, parameterized on atomistic simulations, using a hybridized approach involving the OPLS-UA force filed and the Stillinger-Weber (SW) potential form. The development of the model as well as the results from the simulations on the self-assembly as function of polypeptoid chemical structure and sequences will be presented.

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

PubMed

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

2015-03-26

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

Coarse-Grained MD Simulations and Protein-Protein Interactions: The Cohesin-Dockerin System.

PubMed

Hall, Benjamin A; Sansom, Mark S P

2009-09-08

Coarse-grained molecular dynamics (CG-MD) may be applied as part of a multiscale modeling approach to protein-protein interactions. The cohesin-dockerin interaction provides a valuable test system for evaluation of the use of CG-MD, as structural (X-ray) data indicate a dual binding mode for the cohesin-dockerin pair. CG-MD simulations (of 5 μs duration) of the association of cohesin and dockerin identify two distinct binding modes, which resemble those observed in X-ray structures. For each binding mode, ca. 80% of interfacial residues are predicted correctly. Furthermore, each of the binding modes identified by CG-MD is conformationally stable when converted to an atomistic model and used as the basis of a conventional atomistic MD simulation of duration 20 ns.

Atomistic Modeling of Quaternary Alloys: Ti and Cu in NiAl

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Mosca, Hugo O.; Wilson, Allen W.; Noebe, Ronald D.; Garces, Jorge E.

2002-01-01

The change in site preference in NiAl(Ti,Cu) alloys with concentration is examined experimentally via ALCHEMI and theoretically using the Bozzolo-Ferrante-Smith (BFS) method for alloys. Results for the site occupancy of Ti and Cu additions as a function of concentration are determined experimentally for five alloys. These results are reproduced with large-scale BFS-based Monte Carlo atomistic simulations. The original set of five alloys is extended to 25 concentrations, which are modeled by means of the BFS method for alloys, showing in more detail the compositional range over which major changes in behavior occur. A simple but powerful approach based on the definition of atomic local environments also is introduced to describe energetically the interactions between the various elements and therefore to explain the observed behavior.

Amyloid β-Peptide 25–35 Self-Assembly and Its Inhibition: A Model Undecapeptide System to Gain Atomistic and Secondary Structure Details of the Alzheimer’s Disease Process and Treatment

PubMed Central

2012-01-01

Combined results of theoretical molecular dynamic simulations and in vitro spectroscopic (circular dichroism and fluorescence) studies are presented, providing the atomistic and secondary structure details of the process by which a selected small molecule may destabilize the β-sheet ordered “amyloid” oligomers formed by the model undecapeptide of amyloid β-peptide 25–35 [Aβ(25–35)]. Aβ(25–35) was chosen because it is the shortest fragment capable of forming large β-sheet fibrils and retaining the toxicity of the full length Aβ(1–40/42) peptides. The conformational transition, that leads to the formation of β-sheet fibrils from soluble unordered structures, was found to depend on the environmental conditions, whereas the presence of myricetin destabilizes the self-assembly and antagonizes this conformational shift. In parallel, we analyzed several molecular dynamics trajectories describing the evolution of five monomer fragments, without inhibitor as well as in the presence of myricetin. Other well-known inhibitors (curcumin and (−)-tetracycline), found to be stronger and weaker Aβ(1–42) aggregation inhibitors, respectively, were also studied. The combined in vitro and theoretical studies of the Aβ(25–35) self-assembly and its inhibition contribute to understanding the mechanism of action of well-known inhibitors and the peptide amino acid residues involved in the interaction leading to a rational drug design of more potent new molecules able to antagonize the self-assembly process. PMID:23173074

How to Run FAST Simulations.

PubMed

Zimmerman, M I; Bowman, G R

2016-01-01

Molecular dynamics (MD) simulations are a powerful tool for understanding enzymes' structures and functions with full atomistic detail. These physics-based simulations model the dynamics of a protein in solution and store snapshots of its atomic coordinates at discrete time intervals. Analysis of the snapshots from these trajectories provides thermodynamic and kinetic properties such as conformational free energies, binding free energies, and transition times. Unfortunately, simulating biologically relevant timescales with brute force MD simulations requires enormous computing resources. In this chapter we detail a goal-oriented sampling algorithm, called fluctuation amplification of specific traits, that quickly generates pertinent thermodynamic and kinetic information by using an iterative series of short MD simulations to explore the vast depths of conformational space. © 2016 Elsevier Inc. All rights reserved.

Diffusion in energy materials: Governing dynamics from atomistic modelling

NASA Astrophysics Data System (ADS)

Parfitt, D.; Kordatos, A.; Filippatos, P. P.; Chroneos, A.

2017-09-01

Understanding diffusion in energy materials is critical to optimising the performance of solid oxide fuel cells (SOFCs) and batteries both of which are of great technological interest as they offer high efficiency for cleaner energy conversion and storage. In the present review, we highlight the insights offered by atomistic modelling of the ionic diffusion mechanisms in SOFCs and batteries and how the growing predictive capability of high-throughput modelling, together with our new ability to control compositions and microstructures, will produce advanced materials that are designed rather than chosen for a given application. The first part of the review focuses on the oxygen diffusion mechanisms in cathode and electrolyte materials for SOFCs and in particular, doped ceria and perovskite-related phases with anisotropic structures. The second part focuses on disordered oxides and two-dimensional materials as these are very promising systems for battery applications.

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

PubMed

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-11-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.

Viabilty of atomistic potentials for thermodynamic properties of carbon dioxide at low temperatures.

PubMed

Kuznetsova, Tatyana; Kvamme, Bjørn

2001-11-30

Investigation into volumetric and energetic properties of several atomistic models mimicking carbon dioxide geometry and quadrupole momentum covered the liquid-vapor coexistence curve. Thermodynamic integration over a polynomial and an exponential-polynomial path was used to calculate free energy. Computational results showed that model using GROMOS Lennard-Jones parameters was unsuitable for bulk CO(2) simulations. On the other hand, model with potential fitted to reproduce only correct density-pressure relationship in the supercritical region proved to yield correct enthalpy of vaporization and free energy of liquid CO(2) in the low-temperature region. Except for molar volume at the upper part of the vapor-liquid equilibrium line, the bulk properties of exp-6-1 parametrization of ab initio CO(2) potential were in a close agreement with the experimental results. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1772-1781, 2001

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

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

Grest, Gary S.

2017-09-01

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

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

PubMed

Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

2015-01-01

Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

Enhanced densification under shock compression in porous silicon

DOE PAGES

Lane, J. Matthew; Thompson, Aidan Patrick; Vogler, Tracy

2014-10-27

Under shock compression, most porous materials exhibit lower densities for a given pressure than that of a full-dense sample of the same material. However, some porous materials exhibit an anomalous, or enhanced, densification under shock compression. The mechanism driving this behavior was not completely determined. We present evidence from atomistic simulation that pure silicon belongs to this anomalous class of materials and demonstrate the associated mechanisms responsible for the effect in porous silicon. Atomistic response indicates that local shear strain in the neighborhood of collapsing pores catalyzes a local solid-solid phase transformation even when bulk pressures are below the thermodynamicmore » phase transformation pressure. This metastable, local, and partial, solid-solid phase transformation, which accounts for the enhanced densification in silicon, is driven by the local stress state near the void, not equilibrium thermodynamics. This mechanism may also explain the phenomenon in other covalently bonded materials.« less

Morphology dependent near-field response in atomistic plasmonic nanocavities.

PubMed

Chen, Xing; Jensen, Lasse

2018-06-21

In this work we examine how the atomistic morphologies of plasmonic dimers control the near-field response by using an atomistic electrodynamics model. At large separations, the field enhancement in the junction follows a simple inverse power law as a function of the gap separation, which agrees with classical antenna theory. However, when the separations are smaller than 0.8 nm, the so-called quantum size regime, the field enhancement is screened and thus deviates from the simple power law. Our results show that the threshold distance for the deviation depends on the specific morphology of the junction. The near field in the junction can be localized to an area of less than 1 nm2 in the presence of an atomically sharp tip, but the separation distances leading to a large confinement of near field depend strongly on the specific atomistic configuration. More importantly, the highly confined fields lead to large field gradients particularly in a tip-to-surface junction, which indicates that such a plasmonic structure favors observing strong field gradient effects in near-field spectroscopy. We find that for atomically sharp tips the field gradient becomes significant and depends strongly on the local morphology of a tip. We expect our findings to be crucial for understanding the origin of high-resolution near-field spectroscopy and for manipulating optical cavities through atomic structures in the strongly coupled plasmonic systems.

Atomistic simulation and XAS investigation of Mn induced defects in Bi{sub 12}TiO{sub 20}

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

Rezende, Marcos V dos S.; Santos, Denise J.; Jackson, Robert A.

2016-06-15

This work reports an investigation of the valence and site occupancy of Mn dopants in Bi{sub 12}TiO{sub 20} (BTO: Mn) host using X-ray Absorption (XAS) and atomistic simulation techniques based on energy minimisation. X-ray Absorption Near Edge Structure (XANES) at the Mn K-edges gave typical results for Mn ions with mixed valences of 3+ and 4+. Extended X-ray Absorption Fine Structure (EXAFS) results indicated that Mn ions are probably substituted at Ti sites. Atomistic simulation was performed assuming the incorporation of Mn{sup 2+}, Mn{sup 3+} and Mn{sup 4+} ions at either Bi{sup 3+} or Ti{sup 4+} sites, and the resultsmore » were compared to XANES and EXAFS measurements. Electrical conductivity for pure and doped samples was used to evaluate the consistency of the proposed model. - Graphical abstract: The structure of Bi{sub 12}TiO{sub 20} (BTO). Display Omitted - Highlights: • Pure and Mn-doped Bi{sub 12}TiO{sub 20} samples were studied by experimental techniques combined with atomistic simulation. • Good agreement between experimental and simulation results was obtained. • XANES results suggest a mixture of 3+ and 4+ valences for Mn, occupying the Ti4+ site in both cases. • Charge compensation by holes is most energetically favoured, explaining the enhancement observed in AC dark conductivity.« less

Microstructure Design of Tempered Martensite by Atomistically Informed Full-Field Simulation: From Quenching to Fracture

PubMed Central

Borukhovich, Efim; Du, Guanxing; Stratmann, Matthias; Boeff, Martin; Shchyglo, Oleg; Hartmaier, Alexander; Steinbach, Ingo

2016-01-01

Martensitic steels form a material class with a versatile range of properties that can be selected by varying the processing chain. In order to study and design the desired processing with the minimal experimental effort, modeling tools are required. In this work, a full processing cycle from quenching over tempering to mechanical testing is simulated with a single modeling framework that combines the features of the phase-field method and a coupled chemo-mechanical approach. In order to perform the mechanical testing, the mechanical part is extended to the large deformations case and coupled to crystal plasticity and a linear damage model. The quenching process is governed by the austenite-martensite transformation. In the tempering step, carbon segregation to the grain boundaries and the resulting cementite formation occur. During mechanical testing, the obtained material sample undergoes a large deformation that leads to local failure. The initial formation of the damage zones is observed to happen next to the carbides, while the final damage morphology follows the martensite microstructure. This multi-scale approach can be applied to design optimal microstructures dependent on processing and materials composition. PMID:28773791

Protein-Backbone Thermodynamics across the Membrane Interface.

PubMed

Bereau, Tristan; Kremer, Kurt

2016-07-07

The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups.

Multi-million atom electronic structure calculations for quantum dots

NASA Astrophysics Data System (ADS)

Usman, Muhammad

Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined stark shift, coherent coupling of electronic states in a quantum dot molecule etc.; (3) to assess the potential use of the quantum dots in real device implementation and to provide physical insight to the experimentalists. Full three dimensional strain and electronic structure simulations of quantum dot structures containing multi-million atoms are done using NEMO 3-D. Both single and vertically stacked quantum dot structures are analyzed in detail. The results show that the strain and the piezoelectricity significantly impact the electronic structure of these devices. This work shows that the InAs quantum dots when placed in the InGaAs quantum well red shifts the emission wavelength. Such InAs/GaAs-based optical devices can be used for optical-fiber based communication systems at longer wavelengths (1.3um -- 1.5um). Our atomistic simulations of InAs/InGaAs/GaAs quantum dots quantitatively match with the experiment and give the critical insight of the physics involved in these structures. A single quantum dot molecule is studied for coherent quantum coupling of electronic states under the influence of static electric field applied in the growth direction. Such nanostructures can be used in the implementation of quantum information technologies. A close quantitative match with the experimental optical measurements allowed us to get a physical insight into the complex physics of quantum tunnel couplings of electronic states as the device operation switches between atomic and molecular regimes. Another important aspect is to design the quantum dots for a desired isotropic polarization of the optical emissions. Both single and coupled quantum dots are studied for TE/TM ratio engineering. The atomistic study provides a detailed physical analysis of these computationally expensive large nanostructures and serves as a guide for the experimentalists for the design of the polarization independent devices for the optical communication systems.

Aluminum Pitting Corrosion in Halide Media: A Quantum Model and Empirical Evidence

NASA Astrophysics Data System (ADS)

Lashgari, Mohsen; Kianpour, Effat; Mohammadi, Esmaeil

2013-12-01

The phenomenon of localized damage of aluminum oxide surface in the presence of halide anions was scrutinized at an atomistic level, through the cluster approach and density functional theory. The phenomenon was also investigated empirically through Tafel polarization plots and scanning electron microscopy. A distinct behavior witnessed in the fluoride medium was justified through the hard-soft acid-base principle. The atomistic investigations revealed the greatest potency for chloride entrance into the metal oxide lattice and rationalized to the severity of damage. The interaction of halide anions with the oxide surface causing some displacements on the position of Al atoms provides a mechanistic insight of the phenomenon.

Coarse-Grained and Atomistic Modeling of Polyimides

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Hinkley, Jeffrey A.

2004-01-01

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

Understanding dislocation mechanics at the mesoscale using phase field dislocation dynamics

PubMed Central

Hunter, A.

2016-01-01

In this paper, we discuss the formulation, recent developments and findings obtained from a mesoscale mechanics technique called phase field dislocation dynamics (PFDD). We begin by presenting recent advancements made in modelling face-centred cubic materials, such as integration with atomic-scale simulations to account for partial dislocations. We discuss calculations that help in understanding grain size effects on transitions from full to partial dislocation-mediated slip behaviour and deformation twinning. Finally, we present recent extensions of the PFDD framework to alternative crystal structures, such as body-centred cubic metals, and two-phase materials, including free surfaces, voids and bi-metallic crystals. With several examples we demonstrate that the PFDD model is a powerful and versatile method that can bridge the length and time scales between atomistic and continuum-scale methods, providing a much needed understanding of deformation mechanisms in the mesoscale regime. PMID:27002063

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

PubMed

Ardham, Vikram Reddy; Leroy, Frédéric

2017-10-21

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

Slow relaxation of cascade-induced defects in Fe

DOE PAGES

Béland, Laurent Karim; Osetsky, Yuri N.; Stoller, Roger E.; ...

2015-02-17

On-the-fly kinetic Monte Carlo (KMC) simulations are performed to investigate slow relaxation of non-equilibrium systems. Point defects induced by 25 keV cascades in α -Fe are shown to lead to a characteristic time-evolution, described by the replenish and relax mechanism. Then, we produce an atomistically-based assessment of models proposed to explain the slow structural relaxation by focusing on the aggregation of 50 vacancies and 25 self-interstital atoms (SIA) in 10-lattice-parameter α-Fe boxes, two processes that are closely related to cascade annealing and exhibit similar time signature. Four atomistic effects explain the timescales involved in the evolution: defect concentration heterogeneities, concentration-enhancedmore » mobility, cluster-size dependent bond energies and defect-induced pressure. In conclusion, these findings suggest that the two main classes of models to explain slow structural relaxation, the Eyring model and the Gibbs model, both play a role to limit the rate of relaxation of these simple point-defect systems.« less

Calculation of single chain cellulose elasticity using fully atomistic modeling

Treesearch

Xiawa Wu; Robert J. Moon; Ashlie Martini

2011-01-01

Cellulose nanocrystals, a potential base material for green nanocomposites, are ordered bundles of cellulose chains. The properties of these chains have been studied for many years using atomic-scale modeling. However, model predictions are difficult to interpret because of the significant dependence of predicted properties on model details. The goal of this study is...

Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique

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

Junghans, Christoph; Agarwal, Animesh; Delle Site, Luigi

Here, we discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within 10%–15% accuracy, is given by the Amdahl’s Law adapted to the specific quantities involved in the problem. The derivation of the predictive formula is general enough that it may be applied to the general case of molecular dynamics approaches where a reduction of degrees of freedom in a multi scale fashion occurs.

Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique

DOE PAGES

Junghans, Christoph; Agarwal, Animesh; Delle Site, Luigi

2017-06-01

Here, we discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within 10%–15% accuracy, is given by the Amdahl’s Law adapted to the specific quantities involved in the problem. The derivation of the predictive formula is general enough that it may be applied to the general case of molecular dynamics approaches where a reduction of degrees of freedom in a multi scale fashion occurs.

Multiscale atomistic simulation of metal-oxygen surface interactions: Methodological development, theoretical investigation, and correlation with experiment

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

Yang, Judith C.

The purpose of this grant is to develop the multi-scale theoretical methods to describe the nanoscale oxidation of metal thin films, as the PI (Yang) extensive previous experience in the experimental elucidation of the initial stages of Cu oxidation by primarily in situ transmission electron microscopy methods. Through the use and development of computational tools at varying length (and time) scales, from atomistic quantum mechanical calculation, force field mesoscale simulations, to large scale Kinetic Monte Carlo (KMC) modeling, the fundamental underpinings of the initial stages of Cu oxidation have been elucidated. The development of computational modeling tools allows for acceleratedmore » materials discovery. The theoretical tools developed from this program impact a wide range of technologies that depend on surface reactions, including corrosion, catalysis, and nanomaterials fabrication.« less

Mathematical and Computational Aspects of Multiscale Materials Modeling, Mathematics-Numerical analysis, Section II.A.a.3.4, Conference and symposia organization II.A.2.a

DTIC Science & Technology

2015-02-04

dislocation dynamics models ( DDD ), continuum representations). Coupling of these models is difficult. Coupling of atomistics and DDD models has been...explored to some extent, but the coupling between DDD and continuum models of the evolution of large populations of dislocations is essentially unexplored

Atomistic potentials based energy flux integral criterion for dynamic adiabatic shear banding

NASA Astrophysics Data System (ADS)

Xu, Yun; Chen, Jun

2015-02-01

The energy flux integral criterion based on atomistic potentials within the framework of hyperelasticity-plasticity is proposed for dynamic adiabatic shear banding (ASB). System Helmholtz energy decomposition reveals that the dynamic influence on the integral path dependence is originated from the volumetric strain energy and partial deviatoric strain energy, and the plastic influence only from the rest part of deviatoric strain energy. The concept of critical shear banding energy is suggested for describing the initiation of ASB, which consists of the dynamic recrystallization (DRX) threshold energy and the thermal softening energy. The criterion directly relates energy flux to the basic physical processes that induce shear instability such as dislocation nucleations and multiplications, without introducing ad-hoc parameters in empirical constitutive models. It reduces to the classical path independent J-integral for quasi-static loading and elastic solids. The atomistic-to-continuum multiscale coupling method is used to simulate the initiation of ASB. Atomic configurations indicate that DRX induced microstructural softening may be essential to the dynamic shear localization and hence the initiation of ASB.

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

Temperature-Dependent Implicit-Solvent Model of Polyethylene Glycol in Aqueous Solution.

PubMed

Chudoba, Richard; Heyda, Jan; Dzubiella, Joachim

2017-12-12

A temperature (T)-dependent coarse-grained (CG) Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution is reported to be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range. The T-dependent nonbonded CG interactions are derived from a combined "bottom-up" and "top-down" approach. The pair potentials calculated from atomistic replica-exchange molecular dynamics simulations in combination with the iterative Boltzmann inversion are postrefined by benchmarking to experimental data of the radius of gyration. For better handling and a fully continuous transferability in T-space, the pair potentials are conveniently truncated and mapped to an analytic formula with three structural parameters expressed as explicit continuous functions of T. It is then demonstrated that this model without further adjustments successfully reproduces other experimentally known key thermodynamic properties of semidilute PEG solutions such as the full equation of state (i.e., T-dependent osmotic pressure) for various chain lengths as well as their cloud point (or collapse) temperature.

Quantifying chain reptation in entangled polymer melts: Topological and dynamical mapping of atomistic simulation results onto the tube model

NASA Astrophysics Data System (ADS)

Stephanou, Pavlos S.; Baig, Chunggi; Tsolou, Georgia; Mavrantzas, Vlasis G.; Kröger, Martin

2010-03-01

The topological state of entangled polymers has been analyzed recently in terms of primitive paths which allowed obtaining reliable predictions of the static (statistical) properties of the underlying entanglement network for a number of polymer melts. Through a systematic methodology that first maps atomistic molecular dynamics (MD) trajectories onto time trajectories of primitive chains and then documents primitive chain motion in terms of a curvilinear diffusion in a tubelike region around the coarse-grained chain contour, we are extending these static approaches here even further by computing the most fundamental function of the reptation theory, namely, the probability ψ(s,t) that a segment s of the primitive chain remains inside the initial tube after time t, accounting directly for contour length fluctuations and constraint release. The effective diameter of the tube is independently evaluated by observing tube constraints either on atomistic displacements or on the displacement of primitive chain segments orthogonal to the initial primitive path. Having computed the tube diameter, the tube itself around each primitive path is constructed by visiting each entanglement strand along the primitive path one after the other and approximating it by the space of a small cylinder having the same axis as the entanglement strand itself and a diameter equal to the estimated effective tube diameter. Reptation of the primitive chain longitudinally inside the effective constraining tube as well as local transverse fluctuations of the chain driven mainly from constraint release and regeneration mechanisms are evident in the simulation results; the latter causes parts of the chains to venture outside their average tube surface for certain periods of time. The computed ψ(s,t) curves account directly for both of these phenomena, as well as for contour length fluctuations, since all of them are automatically captured in the atomistic simulations. Linear viscoelastic properties such as the zero shear rate viscosity and the spectra of storage and loss moduli obtained on the basis of the obtained ψ(s,t) curves for three different polymer melts (polyethylene, cis-1,4-polybutadiene, and trans-1,4-polybutadiene) are consistent with experimental rheological data and in qualitative agreement with the double reptation and dual constraint models. The new methodology is general and can be routinely applied to analyze primitive path dynamics and chain reptation in atomistic trajectories (accumulated through long MD simulations) of other model polymers or polymeric systems (e.g., bidisperse, branched, grafted, etc.); it is thus believed to be particularly useful in the future in evaluating proposed tube models and developing more accurate theories for entangled systems.

Extraction of effective solid-liquid interfacial free energies for full 3D solid crystallites from equilibrium MD simulations

DOE PAGES

Zepeda-Ruiz, L. A.; Sadigh, B.; Chernov, A. A.; ...

2017-11-21

Molecular dynamics simulations of an embedded atom copper system in the NPH ensemble are used to study the e ective solid-liquid interfacial free energy of quasispherical solid crystals within a liquid. This is within the larger context of MD simulations of this system undergoing solidi cation, where single individually-prepared crystallites of di erent sizes grow until they reach a thermodynamically stable nal state. The resulting equilibrium shapes possess the full structural details expected for solids with weakly anisotropic surface free energies (in these cases, ~5 % radial attening and rounded [111] octahedral faces). The simplifying assumption of sphericity and perfectmore » isotropy leads to an e ective interfacial free energy as appearing in the Gibbs-Thomson equation, which we determine to be ~179 erg/cm 2, roughly independent of crystal size for radii in the 50 - 250 A range. This quantity may be used in atomistically-informed models of solidi cation kinetics for this system.« less

Extraction of effective solid-liquid interfacial free energies for full 3D solid crystallites from equilibrium MD simulations

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

Zepeda-Ruiz, L. A.; Sadigh, B.; Chernov, A. A.

Molecular dynamics simulations of an embedded atom copper system in the NPH ensemble are used to study the e ective solid-liquid interfacial free energy of quasispherical solid crystals within a liquid. This is within the larger context of MD simulations of this system undergoing solidi cation, where single individually-prepared crystallites of di erent sizes grow until they reach a thermodynamically stable nal state. The resulting equilibrium shapes possess the full structural details expected for solids with weakly anisotropic surface free energies (in these cases, ~5 % radial attening and rounded [111] octahedral faces). The simplifying assumption of sphericity and perfectmore » isotropy leads to an e ective interfacial free energy as appearing in the Gibbs-Thomson equation, which we determine to be ~179 erg/cm 2, roughly independent of crystal size for radii in the 50 - 250 A range. This quantity may be used in atomistically-informed models of solidi cation kinetics for this system.« less

NEAMS FPL M2 Milestone Report: Development of a UO₂ Grain Size Model using Multicale Modeling and Simulation

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

Tonks, Michael R; Zhang, Yongfeng; Bai, Xianming

2014-06-01

This report summarizes development work funded by the Nuclear Energy Advanced Modeling Simulation program's Fuels Product Line (FPL) to develop a mechanistic model for the average grain size in UO₂ fuel. The model is developed using a multiscale modeling and simulation approach involving atomistic simulations, as well as mesoscale simulations using INL's MARMOT code.

Atomistic modeling of interphases in spider silk fibers

NASA Astrophysics Data System (ADS)

Fossey, Stephen Andrew

The objective of this work is to create an atomistic model to account for the unusual physical properties of silk fibers. Silk fibers have exceptional mechanical toughness, which makes them of interest as high performance fibers. In order to explain the toughness, a model for the molecular structure based on simple geometric reasoning was formulated. The model consists of very small crystallites, on the order of 5 nm, connected by a noncrystalline interphase. The interphase is a region between the crystalline phase and the amorphous phase, which is defined by the geometry of the system. The interphase is modeled as a very thin (<5 nm) film of noncrystalline polymer constructed using a Monte Carlo, rotational isomeric states approach followed by simulated annealing in order to achieve equilibrium chain configurations and density. No additional assumptions are made about density, orientation, or packing. The mechanical properties of the interphase are calculated using the method of Theodoreau and Suter. Finally, observable properties such as wide angle X-ray scattering and methyl rotation rates are calculated and compared with experimental data available in the literature.

Protein displacements under external forces: An atomistic Langevin dynamics approach.

PubMed

Gnandt, David; Utz, Nadine; Blumen, Alexander; Koslowski, Thorsten

2009-02-28

We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

PubMed Central

2017-01-01

The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments. PMID:28666087

Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

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

McCarty, Keven F.; Zhou, Xiaowang; Ward, Donald K.

2015-09-01

In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expandmore » the number of potential types of graphene electronic devices.« less

Reaction pathways in atomistic models of thin film growth

NASA Astrophysics Data System (ADS)

Lloyd, Adam L.; Zhou, Ying; Yu, Miao; Scott, Chris; Smith, Roger; Kenny, Steven D.

2017-10-01

The atomistic processes that form the basis of thin film growth often involve complex multi-atom movements of atoms or groups of atoms on or close to the surface of a substrate. These transitions and their pathways are often difficult to predict in advance. By using an adaptive kinetic Monte Carlo (AKMC) approach, many complex mechanisms can be identified so that the growth processes can be understood and ultimately controlled. Here the AKMC technique is briefly described along with some special adaptions that can speed up the simulations when, for example, the transition barriers are small. Examples are given of such complex processes that occur in different material systems especially for the growth of metals and metallic oxides.

Atomic scale simulations for improved CRUD and fuel performance modeling

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

Andersson, Anders David Ragnar; Cooper, Michael William Donald

2017-01-06

A more mechanistic description of fuel performance codes can be achieved by deriving models and parameters from atomistic scale simulations rather than fitting models empirically to experimental data. The same argument applies to modeling deposition of corrosion products on fuel rods (CRUD). Here are some results from publications in 2016 carried out using the CASL allocation at LANL.

A Unified Approach to Optimization

DTIC Science & Technology

2014-10-02

employee scheduling, ad placement, latin squares, disjunctions of linear systems, temporal modeling with interval variables, and traveling salesman problems ...integrating technologies. A key to integrated modeling is to formulate a problem with high-levelmetaconstraints, which are inspired by the “global... problem substructure to the solver. This contrasts with the atomistic modeling style of mixed integer programming (MIP) and satisfiability (SAT) solvers

Mechanical response of collagen molecule under hydrostatic compression.

PubMed

Saini, Karanvir; Kumar, Navin

2015-04-01

Proteins like collagen are the basic building blocks of various body tissues (soft and hard). Collagen molecules find their presence in the skeletal system of the body where they bear mechanical loads from different directions, either individually or along with hydroxy-apatite crystals. Therefore, it is very important to understand the mechanical behavior of the collagen molecule which is subjected to multi-axial state of loading. The estimation of strains of collagen molecule along different directions resulting from the changes in hydrostatic pressure magnitude, can provide us new insights into its mechanical behavior. In the present work, full atomistic simulations have been used to study global (volumetric) as well as local (along different directions) mechanical properties of the hydrated collagen molecule which is subjected to different hydrostatic pressure magnitudes. To estimate the local mechanical properties, the strains of collagen molecule along its longitudinal and transverse directions have been acquired at different hydrostatic pressure magnitudes. In spite of non-homogeneous distribution of atoms within the collagen molecule, the calculated values of local mechanical properties have been found to carry the same order of magnitude along the longitudinal and transverse directions. It has been demonstrated that the values of global mechanical properties like compressibility, bulk modulus, etc. as well as local mechanical properties like linear compressibility, linear elastic modulus, etc. are functions of magnitudes of applied hydrostatic pressures. The mechanical characteristics of collagen molecule based on the atomistic model have also been compared with that of the continuum model in the present work. The comparison showed up orthotropic material behavior for the collagen molecule. The information on collagen molecule provided in the present study can be very helpful in designing the future bio-materials. Copyright © 2015 Elsevier B.V. All rights reserved.

Multiscale investigation of chemical interference in proteins

NASA Astrophysics Data System (ADS)

Samiotakis, Antonios; Homouz, Dirar; Cheung, Margaret S.

2010-05-01

We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in better exploring the energy landscape of a small protein under chemical interference such as chemical denaturation. An excessive amount of water molecules in all-atomistic molecular dynamics simulations often negatively impacts the sampling efficiency of some advanced sampling techniques such as the replica exchange method and it makes the investigation of chemical interferences on protein dynamics difficult. Thus, there is a need to develop an effective strategy that focuses on sampling structural changes in protein conformations rather than solvent molecule fluctuations. In this work, we address this issue by devising a multiscale simulation scheme (MultiSCAAL) that bridges the gap between all-atomistic molecular dynamics simulation and coarse-grained molecular simulation. The two key features of this scheme are the Boltzmann inversion and a protein atomistic reconstruction method we previously developed (SCAAL). Using MultiSCAAL, we were able to enhance the sampling efficiency of proteins solvated by explicit water molecules. Our method has been tested on the folding energy landscape of a small protein Trp-cage with explicit solvent under 8M urea using both the all-atomistic replica exchange molecular dynamics and MultiSCAAL. We compared computational analyses on ensemble conformations of Trp-cage with its available experimental NOE distances. The analysis demonstrated that conformations explored by MultiSCAAL better agree with the ones probed in the experiments because it can effectively capture the changes in side-chain orientations that can flip out of the hydrophobic pocket in the presence of urea and water molecules. In this regard, MultiSCAAL is a promising and effective sampling scheme for investigating chemical interference which presents a great challenge when modeling protein interactions in vivo.

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

PubMed

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

Parallel algorithm for multiscale atomistic/continuum simulations using LAMMPS

NASA Astrophysics Data System (ADS)

Pavia, F.; Curtin, W. A.

2015-07-01

Deformation and fracture processes in engineering materials often require simultaneous descriptions over a range of length and time scales, with each scale using a different computational technique. Here we present a high-performance parallel 3D computing framework for executing large multiscale studies that couple an atomic domain, modeled using molecular dynamics and a continuum domain, modeled using explicit finite elements. We use the robust Coupled Atomistic/Discrete-Dislocation (CADD) displacement-coupling method, but without the transfer of dislocations between atoms and continuum. The main purpose of the work is to provide a multiscale implementation within an existing large-scale parallel molecular dynamics code (LAMMPS) that enables use of all the tools associated with this popular open-source code, while extending CADD-type coupling to 3D. Validation of the implementation includes the demonstration of (i) stability in finite-temperature dynamics using Langevin dynamics, (ii) elimination of wave reflections due to large dynamic events occurring in the MD region and (iii) the absence of spurious forces acting on dislocations due to the MD/FE coupling, for dislocations further than 10 Å from the coupling boundary. A first non-trivial example application of dislocation glide and bowing around obstacles is shown, for dislocation lengths of ∼50 nm using fewer than 1 000 000 atoms but reproducing results of extremely large atomistic simulations at much lower computational cost.

Adhesion of single- and multi-walled carbon nanotubes to silicon substrate: atomistic simulations and continuum analysis

NASA Astrophysics Data System (ADS)

Yuan, Xuebo; Wang, Youshan

2017-10-01

The radial deformation of carbon nanotubes (CNTs) adhering to a substrate may prominently affect their mechanical and physical properties. In this study, both classical atomistic simulations and continuum analysis are carried out, to investigate the lateral adhesion of single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs) to a silicon substrate. A linear elastic model for analyzing the adhesion of 2D shells to a rigid semi-infinite substrate is constructed in the framework of continuum mechanics. Good agreement is achieved between the cross-section profiles of adhesive CNTs obtained by the continuum model and by the atomistic simulation approach. It is found that the adhesion of a CNT to the silicon substrate is significantly influenced by its initial diameter and the number of walls. CNTs with radius larger than a certain critical radius are deformed radially on the silicon substrate with flat contact regions. With increasing number of walls, the extent of radial deformation of a MWCNT on the substrate decreases dramatically, and the flat contact area reduces—and eventually vanishes—due to increasing equivalent bending stiffness. It is analytically predicted that large-diameter MWCNTs with a large number of walls are likely to ‘stand’ on the silicon substrate. The present work can be useful for understanding the radial deformation of CNTs adhering to a solid planar substrate.

Strain-dependent activation energy of shear transformation in metallic glasses

NASA Astrophysics Data System (ADS)

Xu, Bin; Falk, Michael; Li, Jinfu; Kong, Lingti

2017-04-01

Shear transformation (ST) plays a decisive role in determining the mechanical behavior of metallic glasses, which is believed to be a stress-assisted thermally activated process. Understanding the dependence in its activation energy on the stress imposed on the material is of central importance to model the deformation process of metallic glasses and other amorphous solids. Here a theoretical model is proposed to predict the variation of the minimum energy path (MEP) associated with a particular ST event upon further deformation. Verification based on atomistic simulations and calculations are also conducted. The proposed model reproduces the MEP and activation energy of an ST event under different imposed macroscopic strains based on a known MEP at a reference strain. Moreover, an analytical approach is proposed based on the atomistic calculations, which works well when the stress varies linearity along the MEP. These findings provide necessary background for understanding the activation processes and, in turn, the mechanical behavior of metallic glasses.

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

El-Atwani, O.; Norris, S. A.; Ludwig, K.

In this study, several proposed mechanisms and theoretical models exist concerning nanostructure evolution on III-V semiconductors (particularly GaSb) via ion beam irradiation. However, making quantitative contact between experiment on the one hand and model-parameter dependent predictions from different theories on the other is usually difficult. In this study, we take a different approach and provide an experimental investigation with a range of targets (GaSb, GaAs, GaP) and ion species (Ne, Ar, Kr, Xe) to determine new parametric trends regarding nanostructure evolution. Concurrently, atomistic simulations using binary collision approximation over the same ion/target combinations were performed to determine parametric trends onmore » several quantities related to existing model. A comparison of experimental and numerical trends reveals that the two are broadly consistent under the assumption that instabilities are driven by chemical instability based on phase separation. Furthermore, the atomistic simulations and a survey of material thermodynamic properties suggest that a plausible microscopic mechanism for this process is an ion-enhanced mobility associated with energy deposition by collision cascades.« less

Atomistic modeling and simulation of the role of Be and Bi in Al diffusion in U-Mo fuel

NASA Astrophysics Data System (ADS)

Hofman, G. L.; Bozzolo, G.; Mosca, H. O.; Yacout, A. M.

2011-07-01

Within the RERTR program, previous experimental and modeling studies identified Si as the alloying addition to the Al cladding responsible for inhibiting Al interdiffusion in the UMo fuel. However, difficulties with reprocessing have rendered this choice inappropriate, leading to the need to study alternative elements. In this work, we discuss the results of an atomistic modeling effort which allows for the systematic study of several possible alloying additions. Based on the behavior observed in the phase diagrams, beryllium or bismuth additions suggest themselves as possible options to replace Si. The results of temperature-dependent simulations using the Bozzolo-Ferrante-Smith (BFS) method for the energetics for varying concentrations of either element are shown, indicating that Be could have a substantial effect in stopping Al interdiffusion, while Bi does not. Details of the calculations and the dependence of the role of each alloying addition as a function of temperature and concentration (of beryllium or bismuth in Al) are shown.

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

PubMed Central

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-01-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

A generalized Poisson solver for first-principles device simulations

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

Bani-Hashemian, Mohammad Hossein; VandeVondele, Joost, E-mail: joost.vandevondele@mat.ethz.ch; Brück, Sascha

2016-01-28

Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices. Dirichlet conditions are enforced as constraints in a variational framework giving rise to a saddle point problem. The resulting system of equations is then solved using a stationary iterative methodmore » in which the generalized Poisson operator is preconditioned with the standard Laplace operator. The solver can make use of any sufficiently smooth function modelling the dielectric constant, including density dependent dielectric continuum models. For all the boundary conditions, consistent derivatives are available and molecular dynamics simulations can be performed. The convergence behaviour of the scheme is investigated and its capabilities are demonstrated.« less

Molecular and Subcellular-Scale Modeling of Nucleotide Diffusion in the Cardiac Myofilament Lattice

PubMed Central

Kekenes-Huskey, Peter M.; Liao, Tao; Gillette, Andrew K.; Hake, Johan E.; Zhang, Yongjie; Michailova, Anushka P.; McCulloch, Andrew D.; McCammon, J. Andrew

2013-01-01

Contractile function of cardiac cells is driven by the sliding displacement of myofilaments powered by the cycling myosin crossbridges. Critical to this process is the availability of ATP, which myosin hydrolyzes during the cross-bridge cycle. The diffusion of adenine nucleotides through the myofilament lattice has been shown to be anisotropic, with slower radial diffusion perpendicular to the filament axis relative to parallel, and is attributed to the periodic hexagonal arrangement of the thin (actin) and thick (myosin) filaments. We investigated whether atomistic-resolution details of myofilament proteins can refine coarse-grain estimates of diffusional anisotropy for adenine nucleotides in the cardiac myofibril, using homogenization theory and atomistic thin filament models from the Protein Data Bank. Our results demonstrate considerable anisotropy in ATP and ADP diffusion constants that is consistent with experimental measurements and dependent on lattice spacing and myofilament overlap. A reaction-diffusion model of the half-sarcomere further suggests that diffusional anisotropy may lead to modest adenine nucleotide gradients in the myoplasm under physiological conditions. PMID:24209858

A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulations.

PubMed

Ghaemi, Zhaleh; Minozzi, Manuela; Carloni, Paolo; Laio, Alessandro

2012-07-26

Predicting the permeability coefficient (P) of drugs permeating through the cell membrane is of paramount importance in drug discovery. We here propose an approach for calculating P based on bias-exchange metadynamics. The approach allows constructing from atomistic simulations a model of permeation taking explicitly into account not only the "trivial" reaction coordinate, the position of the drug along the direction normal to the lipid membrane plane, but also other degrees of freedom, for example, the torsional angles of the permeating molecule, or variables describing its solvation/desolvation. This allows deriving an accurate picture of the permeation process, and constructing a detailed molecular model of the transition state, making a rational control of permeation properties possible. We benchmarked this approach on the permeation of ethanol molecules through a POPC membrane, showing that the value of P calculated with our model agrees with the one calculated by a long unbiased molecular dynamics of the same system.

A transformation theory of stochastic evolution in Red Moon methodology to time evolution of chemical reaction process in the full atomistic system.

PubMed

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H 2 + I 2  ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H 2 and I 2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H 2 ] eq and equilibrium constants K eq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H 2 ] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

Atomistic modeling of La 3+ doping segregation effect on nanocrystalline yttria-stabilized zirconia

DOE PAGES

Zhang, Shenli; Sha, Haoyan; Castro, Ricardo H. R.; ...

2018-01-01

The effect of La 3+ doping on the structure and ionic conductivity change in nanocrystalline yttria-stabilized zirconia (YSZ) was studied using a combination of Monte Carlo and molecular dynamics simulations.

Stabilization of Model Membrane Systems by Disaccharides. Quasielastic Neutron Scattering Experiments and Atomistic Simulations

NASA Astrophysics Data System (ADS)

Doxastakis, Emmanouil; Garcia Sakai, Victoria; Ohtake, Satoshi; Maranas, Janna K.; de Pablo, Juan J.

2006-03-01

Trehalose, a disaccharide of glucose, is often used for the stabilization of cell membranes in the absence of water. This work studies the effects of trehalose on model membrane systems as they undergo a melting transition using a combination of experimental methods and atomistic molecular simulations. Quasielastic neutron scattering experiments on selectively deuterated samples provide the incoherent dynamic structure over a wide time range. Elastic scans probing the lipid tail dynamics display clear evidence of a main melting transition that is significantly lowered in the presence of trehalose. Lipid headgroup mobility is considerably restricted at high temperatures and directly associated with the dynamics of the sugar in the mixture. Molecular simulations provide a detailed overview of the dynamics and their spatial and time dependence. The combined simulation and experimental methodology offers a unique, molecular view of the physics of systems commonly employed in cryopreservation and lyophilization processes.

Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

DOE PAGES

Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; ...

2017-01-26

When using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. Furthermore, by calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. A comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnonsmore » leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.« less

Adaptive resolution simulation of oligonucleotides

NASA Astrophysics Data System (ADS)

Netz, Paulo A.; Potestio, Raffaello; Kremer, Kurt

2016-12-01

Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods.

Solute-defect interactions in Al-Mg alloys from diffusive variational Gaussian calculations

NASA Astrophysics Data System (ADS)

Dontsova, E.; Rottler, J.; Sinclair, C. W.

2014-11-01

Resolving atomic-scale defect topologies and energetics with accurate atomistic interaction models provides access to the nonlinear phenomena inherent at atomic length and time scales. Coarse graining the dynamics of such simulations to look at the migration of, e.g., solute atoms, while retaining the rich atomic-scale detail required to properly describe defects, is a particular challenge. In this paper, we present an adaptation of the recently developed "diffusive molecular dynamics" model to describe the energetics and kinetics of binary alloys on diffusive time scales. The potential of the technique is illustrated by applying it to the classic problems of solute segregation to a planar boundary (stacking fault) and edge dislocation in the Al-Mg system. Our approach provides fully dynamical solutions in situations with an evolving energy landscape in a computationally efficient way, where atomistic kinetic Monte Carlo simulations are difficult or impractical to perform.

Molecular design and MD simulations of epitaxial superlattice of self-assembling ternary lipid bilayers

NASA Astrophysics Data System (ADS)

Chou, George; Vaughn, Mark; Cheng, K.

2011-10-01

Multicomponent lipid bilayers represent an important model system for studying cell membranes. At present, an ordered multicomponent phospholipid/cholesterol bilayer system involving charged lipid is still not available. Using a lipid superlattice (SL) model, a 13 x 15 x 15 nm^3 ternary phosphatidylcholine/phosphatidylserine/cholesterol bilayer system in water with simultaneous headgroup SL and acyl chain SL at different depths, or epitaxial SL, of the bilayer has been designed with atomistic detail. The arrangements of this epitaxial SL system were optimized by only two molecular parameters, lattice space and rotational angle of the lipids. Using atomistic MD simulations, we demonstrated the stability of the ordered structures for more than 100 ns. A positional restrained system was also used as a control. This system will provide new insights into understanding the nanodomain structures of cell membranes at the molecular level.

Multiscale study of metal nanoparticles

NASA Astrophysics Data System (ADS)

Lee, Byeongchan

Extremely small structures with reduced dimensionality have emerged as a scientific motif for their interesting properties. In particular, metal nanoparticles have been identified as a fundamental material in many catalytic activities; as a consequence, a better understanding of structure-function relationship of nanoparticles has become crucial. The functional analysis of nanoparticles, reactivity for example, requires an accurate method at the electronic structure level, whereas the structural analysis to find energetically stable local minima is beyond the scope of quantum mechanical methods as the computational cost becomes prohibitingly high. The challenge is that the inherent length scale and accuracy associated with any single method hardly covers the broad scale range spanned by both structural and functional analyses. In order to address this, and effectively explore the energetics and reactivity of metal nanoparticles, a hierarchical multiscale modeling is developed, where methodologies of different length scales, i.e. first principles density functional theory, atomistic calculations, and continuum modeling, are utilized in a sequential fashion. This work has focused on identifying the essential information that bridges two different methods so that a successive use of different methods is seamless. The bond characteristics of low coordination systems have been obtained with first principles calculations, and incorporated into the atomistic simulation. This also rectifies the deficiency of conventional interatomic potentials fitted to bulk properties, and improves the accuracy of atomistic calculations for nanoparticles. For the systematic shape selection of nanoparticles, we have improved the Wulff-type construction using a semi-continuum approach, in which atomistic surface energetics and crystallinity of materials are added on to the continuum framework. The developed multiscale modeling scheme is applied to the rational design of platinum nanoparticles in the range of 2.4 nm to 3.1 nm: energetically favorable structures have been determined in terms of semi-continuum binding energy, and the reactivity of the selected nanoparticle has been investigated based on local density of states from first principles calculations. The calculation suggests that the reactivity landscape of particles is more complex than the simple reactivity of clean surfaces, and the reactivity towards a particular reactant can be predicted for a given structure.

Surface Adsorption in Nonpolarizable Atomic Models.

PubMed

Whitmer, Jonathan K; Joshi, Abhijeet A; Carlton, Rebecca J; Abbott, Nicholas L; de Pablo, Juan J

2014-12-09

Many ionic solutions exhibit species-dependent properties, including surface tension and the salting-out of proteins. These effects may be loosely quantified in terms of the Hofmeister series, first identified in the context of protein solubility. Here, our interest is to develop atomistic models capable of capturing Hofmeister effects rigorously. Importantly, we aim to capture this dependence in computationally cheap "hard" ionic models, which do not exhibit dynamic polarization. To do this, we have performed an investigation detailing the effects of the water model on these properties. Though incredibly important, the role of water models in simulation of ionic solutions and biological systems is essentially unexplored. We quantify this via the ion-dependent surface attraction of the halide series (Cl, Br, I) and, in so doing, determine the relative importance of various hypothesized contributions to ionic surface free energies. Importantly, we demonstrate surface adsorption can result in hard ionic models combined with a thermodynamically accurate representation of the water molecule (TIP4Q). The effect observed in simulations of iodide is commensurate with previous calculations of the surface potential of mean force in rigid molecular dynamics and polarizable density-functional models. Our calculations are direct simulation evidence of the subtle but sensitive role of water thermodynamics in atomistic simulations.

Experimentally driven atomistic model of 1,2 polybutadiene

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

Gkourmpis, Thomas, E-mail: thomas.gkourmpis@borealisgroup.com; Mitchell, Geoffrey R.; Centre for Rapid and Sustainable Product Development, Institute Polytechnic Leiria, Marinha Grande

2014-02-07

We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for themore » models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120–400 K. Analysis of the experimental data yields bond lengths for Cî—¸C and C î—» C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.« less

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

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

Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M.

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-bodymore » 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 numerical errors in mapping out the dissipative forces. The framework presented herein can be used to develop computational models of real liquids which are capable of bridging the atomistic and mesoscopic scales.« less

Summation rules for a fully nonlocal energy-based quasicontinuum method

NASA Astrophysics Data System (ADS)

Amelang, J. S.; Venturini, G. N.; Kochmann, D. M.

2015-09-01

The quasicontinuum (QC) method coarse-grains crystalline atomic ensembles in order to bridge the scales from individual atoms to the micro- and mesoscales. A crucial cornerstone of all QC techniques, summation or quadrature rules efficiently approximate the thermodynamic quantities of interest. Here, we investigate summation rules for a fully nonlocal, energy-based QC method to approximate the total Hamiltonian of a crystalline atomic ensemble by a weighted sum over a small subset of all atoms in the crystal lattice. Our formulation does not conceptually differentiate between atomistic and coarse-grained regions and thus allows for seamless bridging without domain-coupling interfaces. We review traditional summation rules and discuss their strengths and weaknesses with a focus on energy approximation errors and spurious force artifacts. Moreover, we introduce summation rules which produce no residual or spurious force artifacts in centrosymmetric crystals in the large-element limit under arbitrary affine deformations in two dimensions (and marginal force artifacts in three dimensions), while allowing us to seamlessly bridge to full atomistics. Through a comprehensive suite of examples with spatially non-uniform QC discretizations in two and three dimensions, we compare the accuracy of the new scheme to various previous ones. Our results confirm that the new summation rules exhibit significantly smaller force artifacts and energy approximation errors. Our numerical benchmark examples include the calculation of elastic constants from completely random QC meshes and the inhomogeneous deformation of aggressively coarse-grained crystals containing nano-voids. In the elastic regime, we directly compare QC results to those of full atomistics to assess global and local errors in complex QC simulations. Going beyond elasticity, we illustrate the performance of the energy-based QC method with the new second-order summation rule by the help of nanoindentation examples with automatic mesh adaptation. Overall, our findings provide guidelines for the selection of summation rules for the fully nonlocal energy-based QC method.

Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses.

PubMed

Huber, Roland G; Marzinek, Jan K; Holdbrook, Daniel A; Bond, Peter J

2017-09-01

Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals. In recent years, advances in computing architecture and algorithms have begun to allow us to use simulations to study the structure and dynamics of viral ultrastructures at various stages of their life cycle in atomistic or near-atomistic detail. In this review, we outline specific challenges and solutions that have emerged to allow for structurally detailed modelling of viruses in silico. We focus on the history and state of the art of atomistic and coarse-grained approaches to simulate the dynamics of the large, macromolecular structures associated with viral infection, and on their usefulness in explaining and expanding upon experimental data. We discuss the types of interactions that need to be modeled to describe major components of the virus particle and advances in modelling techniques that allow for the treatment of these systems, highlighting recent key simulation studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water

NASA Astrophysics Data System (ADS)

Limmer, David T.; Chandler, David

2011-10-01

We use numerical simulation to examine the possibility of a reversible liquid-liquid transition in supercooled water and related systems. In particular, for two atomistic models of water, we have computed free energies as functions of multiple order parameters, where one is density and another distinguishes crystal from liquid. For a range of temperatures and pressures, separate free energy basins for liquid and crystal are found, conditions of phase coexistence between these phases are demonstrated, and time scales for equilibration are determined. We find that at no range of temperatures and pressures is there more than a single liquid basin, even at conditions where amorphous behavior is unstable with respect to the crystal. We find a similar result for a related model of silicon. This result excludes the possibility of the proposed liquid-liquid critical point for the models we have studied. Further, we argue that behaviors others have attributed to a liquid-liquid transition in water and related systems are in fact reflections of transitions between liquid and crystal.

Object kinetic Monte Carlo model for neutron and ion irradiation in tungsten: Impact of transmutation and carbon impurities

NASA Astrophysics Data System (ADS)

Castin, N.; Bonny, G.; Bakaev, A.; Ortiz, C. J.; Sand, A. E.; Terentyev, D.

2018-03-01

We upgrade our object kinetic Monte Carlo (OKMC) model, aimed at describing the microstructural evolution in tungsten (W) under neutron and ion irradiation. Two main improvements are proposed based on recently published atomistic data: (a) interstitial carbon impurities, and their interaction with radiation-induced defects (point defect clusters and loops), are more accurately parameterized thanks to ab initio findings; (b) W transmutation to rhenium (Re) upon neutron irradiation, impacting the diffusivity of radiation defects, is included, also relying on recent atomistic data. These essential amendments highly improve the portability of our OKMC model, providing a description for the formation of SIA-type loops under different irradiation conditions. The model is applied to simulate neutron and ion irradiation in pure W samples, in a wide range of fluxes and temperatures. We demonstrate that it performs a realistic prediction of the population of TEM-visible voids and loops, as compared to experimental evidence. The impact of the transmutation of W to Re, and of carbon trapping, is assessed.

Continuum and atomistic description of excess electrons in TiO2

NASA Astrophysics Data System (ADS)

Maggio, Emanuele; Martsinovich, Natalia; Troisi, Alessandro

2016-02-01

The modelling of an excess electron in a semiconductor in a prototypical dye sensitised solar cell is carried out using two complementary approaches: atomistic simulation of the TiO2 nanoparticle surface is complemented by a dielectric continuum model of the solvent-semiconductor interface. The two methods are employed to characterise the bound (excitonic) states formed by the interaction of the electron in the semiconductor with a positive charge opposite the interface. Density-functional theory (DFT) calculations show that the excess electron in TiO2 in the presence of a counterion is not fully localised but extends laterally over a large region, larger than system sizes accessible to DFT calculations. The numerical description of the excess electron at the semiconductor-electrolyte interface based on the continuum model shows that the exciton is also delocalised over a large area: the exciton radius can have values from tens to hundreds of Ångströms, depending on the nature of the semiconductor (characterised by the dielectric constant and the electron effective mass in our model).

Consistent Temperature Coupling with Thermal Fluctuations of Smooth Particle Hydrodynamics and Molecular Dynamics

PubMed Central

Ganzenmüller, Georg C.; Hiermaier, Stefan; Steinhauser, Martin O.

2012-01-01

We propose a thermodynamically consistent and energy-conserving temperature coupling scheme between the atomistic and the continuum domain. The coupling scheme links the two domains using the DPDE (Dissipative Particle Dynamics at constant Energy) thermostat and is designed to handle strong temperature gradients across the atomistic/continuum domain interface. The fundamentally different definitions of temperature in the continuum and atomistic domain – internal energy and heat capacity versus particle velocity – are accounted for in a straightforward and conceptually intuitive way by the DPDE thermostat. We verify the here-proposed scheme using a fluid, which is simultaneously represented as a continuum using Smooth Particle Hydrodynamics, and as an atomistically resolved liquid using Molecular Dynamics. In the case of equilibrium contact between both domains, we show that the correct microscopic equilibrium properties of the atomistic fluid are obtained. As an example of a strong non-equilibrium situation, we consider the propagation of a steady shock-wave from the continuum domain into the atomistic domain, and show that the coupling scheme conserves both energy and shock-wave dynamics. To demonstrate the applicability of our scheme to real systems, we consider shock loading of a phospholipid bilayer immersed in water in a multi-scale simulation, an interesting topic of biological relevance. PMID:23300586

Psycholinguistic Theory of Learning to Read Compared to the Traditional Theory Model.

ERIC Educational Resources Information Center

Murphy, Robert F.

A comparison of two models of the reading process--the psycholinguistic model, in which learning to read is seen as a top-down, holistic procedure, and the traditional theory model, in which learning to read is seen as a bottom-up, atomistic procedure--is provided in this paper. The first part of the paper provides brief overviews of the following…

Theoretical modeling of zircon's crystal morphology according to data of atomistic calculations

NASA Astrophysics Data System (ADS)

Gromalova, Natalia; Nikishaeva, Nadezhda; Eremin, Nikolay

2017-04-01

Zircon is an essential mineral that is used in the U-Pb dating. Moreover, zircon is highly resistant to radioactive exposure. It is of great interest in solving both fundamental and applied problems associated with the isolation of high-level radioactive waste. There is significant progress in forecasting of the most energetically favorable crystal structures at the present time. Unfortunately, the theoretical forecast of crystal morphology at high technological level is under-explored nowadays, though the estimation of crystal equilibrium habit is extremely important in studying the physical and chemical properties of new materials. For the first time, the thesis about relation of the equilibrium shape of a crystal with its crystal structure was put forward in the works by O.Brave. According to it, the idealized habit is determined in the simplest case by a correspondence with the reticular densities Rhkl of individual faces. This approach, along with all subsequent corrections, does not take into account the nature of atoms and the specific features of the chemical bond in crystals. The atomistic calculations of crystal surfaces are commonly performed using the energetic characteristics of faces, namely, the surface energy (Esurf), which is a measure of the thermodynamic stability of the crystal face. The stable crystal faces are characterized by small positive values of Esurf. As we know from our previous research (Gromalova et al.,2015) one of the constitutive factors affecting the value of the surface energy in calculations is a choice of potentials model. In this regard, we studied several sets of parameters of atomistic interatomic potentials optimized previously. As the first test model («Zircon 1») were used sets of interatomic potentials of interaction Zr-O, Si-O and O-O in the form of Buckingham potentials. To improve playback properties of zircon additionally used Morse potential for a couple of Zr-Si, as well as the three-particle angular harmonic potential. The other sets of interatomic potentials («Zircon 2, Zircon 3») differed from the first in that parameters was found with the help of quantum-chemical calculations of the structure «ab initio».The surface energies for different faces of zircon were calculated using Metadise code (Watson et al., 1996) at P4-3000 personal computer with Windows XP operating system. The computation time for one simple form was from 30 minutes to 12 hours. Calculations have shown that depending on the chosen model the surface energy of zircons faces several changes. For example, Esurf of face (331) obtained using models of potentials «Zircon 2», «Zircon 3» sufficiently similar (2.82 and 3.01 J/mol2 respectively). Meaning of Esurf of this face, calculated on the basis of set «Zircon 1» significantly lower (1,54 J/mol2). With regard to the face (100), it has low surface energies when selecting all three models, with a minimum value (1,14 J/mol2) in the model «Zircon 1». References: Gromalova N.A., Eremin N.N., Urusov V.S. Atomistic computer modeling of the crystal-morpology of corundum group minerals // Zapiski RMO. V. 144. №4. 2015. p. 84-92. Watson G.W., Kelsey E.T., de Leeuw N.H., Harris D.J, Parker S.C. Atomistic simulation of dislocations, surfaces and interfaces in MgO. Journal of the Chemical Society Faraday Transactions. 1996. V.92 P. 433-438.

Simulating the Physical World

NASA Astrophysics Data System (ADS)

Berendsen, Herman J. C.

2004-06-01

The simulation of physical systems requires a simplified, hierarchical approach which models each level from the atomistic to the macroscopic scale. From quantum mechanics to fluid dynamics, this book systematically treats the broad scope of computer modeling and simulations, describing the fundamental theory behind each level of approximation. Berendsen evaluates each stage in relation to its applications giving the reader insight into the possibilities and limitations of the models. Practical guidance for applications and sample programs in Python are provided. With a strong emphasis on molecular models in chemistry and biochemistry, this book will be suitable for advanced undergraduate and graduate courses on molecular modeling and simulation within physics, biophysics, physical chemistry and materials science. It will also be a useful reference to all those working in the field. Additional resources for this title including solutions for instructors and programs are available online at www.cambridge.org/9780521835275. The first book to cover the wide range of modeling and simulations, from atomistic to the macroscopic scale, in a systematic fashion Providing a wealth of background material, it does not assume advanced knowledge and is eminently suitable for course use Contains practical examples and sample programs in Python

Accessible, almost ab initio multi-scale modeling of entangled polymers via slip-links

NASA Astrophysics Data System (ADS)

Andreev, Marat

It is widely accepted that dynamics of entangled polymers can be described by the tube model. Here we advocate for an alternative approach to entanglement modeling known as slip-links. Recently, slip-links were shown to possess important advantages over tube models, namely they have strong connections to atomistic, multichain levels of description, agree with non-equilibrium thermodynamics, are applicable to any chain architecture and can be used in linear or non-linear rheology. We present a hierarchy of slip-link models that are connected to each other through successive coarse graining. Models in the hierarchy are consistent in their overlapping domains of applicability in order to allow a straightforward mapping of parameters. In particular, the most--detailed level of description has four parameters, three of which can be determined directly from atomistic simulations. On the other hand, the least--detailed member of the hierarchy is numerically accessible, and allows for non-equilibrium flow predictions of complex chain architectures. Using GPU implementation these predictions can be obtained in minutes of computational time on a single desktop equipped with a mainstream gaming GPU. The GPU code is available online for free download.

The indispensable role of the transversal spin fluctuations mechanism in laser-induced demagnetization of Co/Pt multilayers with nanoscale magnetic domains.

PubMed

Zhang, Wei; He, Wei; Peng, Li-Cong; Zhang, Ying; Cai, Jian-Wang; Evans, Richard F L; Zhang, Xiang-Qun; Cheng, Zhao-Hua

2018-07-06

The switching of magnetic domains induced by an ultrashort laser pulse has been demonstrated in nanostructured ferromagnetic films. This leads to the dawn of a new era in breaking the ultimate physical limit for the speed of magnetic switching and manipulation, which is relevant to current and future information storage. However, our understanding of the interactions between light and spins in magnetic heterostructures with nanoscale domain structures is still lacking. Here, both time-resolved magneto-optical Kerr effect experiments and atomistic simulations are carried out to investigate the dominant mechanism of laser-induced ultrafast demagnetization in [Co/Pt] 20 multilayers with nanoscale magnetic domains. It is found that the ultrafast demagnetization time remains constant with various magnetic configurations, indicating that the domain structures play a minor role in laser-induced ultrafast demagnetization. In addition, both in experiment and atomistic simulations, we find a dependence of ultrafast demagnetization time τ M on the laser fluence, which is in contrast to the observations of spin transport within magnetic domains. The remarkable agreement between experiment and atomistic simulations indicates that the local dissipation of spin angular momentum is the dominant demagnetization mechanism in this system. More interestingly, we made a comparison between the atomistic spin dynamic simulation and the longitudinal spin flip model, highlighting that the transversal spin fluctuations mechanism is responsible for the ultrafast demagnetization in the case of inhomogeneous magnetic structures. This is a significant advance in clarifying the microscopic mechanism underlying the process of ultrafast demagnetization in inhomogeneous magnetic structures.

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

Thermochemistry of organic reactions in microporous oxides by atomistic simulations: benchmarking against periodic B3LYP.

PubMed

Bleken, Francesca; Svelle, Stian; Lillerud, Karl Petter; Olsbye, Unni; Arstad, Bjørnar; Swang, Ole

2010-07-15

The methylation of ethene by methyl chloride and methanol in the microporous materials SAPO-34 and SSZ-13 has been studied using different periodic atomistic modeling approaches based on density functional theory. The RPBE functional, which earlier has been used successfully in studies of surface reactions on metals, fails to yield a qualitatively correct description of the transition states under study. Employing B3LYP as functional gives results in line with experimental data: (1) Methanol is adsorbed more strongly than methyl chloride to the acid site. (2) The activation energies for the methylation of ethene are slightly lower for SSZ-13. Furthermore, the B3LYP activation energies are lower for methyl chloride than for methanol.

Emergence of linear elasticity from the atomistic description of matter

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

Cakir, Abdullah, E-mail: acakir@ntu.edu.sg; Pica Ciamarra, Massimo; Dipartimento di Scienze Fisiche, CNR–SPIN, Università di Napoli Federico II, I-80126 Napoli

2016-08-07

We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of themore » fluctuations of the local elastic constants close to the jamming transition.« less

An atomistic fingerprint algorithm for learning ab initio molecular force fields

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

Time scale bridging in atomistic simulation of slow dynamics: viscous relaxation and defect activation

NASA Astrophysics Data System (ADS)

Kushima, A.; Eapen, J.; Li, Ju; Yip, S.; Zhu, T.

2011-08-01

Atomistic simulation methods are known for timescale limitations in resolving slow dynamical processes. Two well-known scenarios of slow dynamics are viscous relaxation in supercooled liquids and creep deformation in stressed solids. In both phenomena the challenge to theory and simulation is to sample the transition state pathways efficiently and follow the dynamical processes on long timescales. We present a perspective based on the biased molecular simulation methods such as metadynamics, autonomous basin climbing (ABC), strain-boost and adaptive boost simulations. Such algorithms can enable an atomic-level explanation of the temperature variation of the shear viscosity of glassy liquids, and the relaxation behavior in solids undergoing creep deformation. By discussing the dynamics of slow relaxation in two quite different areas of condensed matter science, we hope to draw attention to other complex problems where anthropological or geological-scale time behavior can be simulated at atomic resolution and understood in terms of micro-scale processes of molecular rearrangements and collective interactions. As examples of a class of phenomena that can be broadly classified as materials ageing, we point to stress corrosion cracking and cement setting as opportunities for atomistic modeling and simulations.

Quasi-Continuum Reduction of Field Theories: A Route to Seamlessly Bridge Quantum and Atomistic Length-Scales with Continuum

DTIC Science & Technology

2016-04-01

AFRL-AFOSR-VA-TR-2016-0145 Quasi-continuum reduction of field theories: A route to seamlessly bridge quantum and atomistic length-scales with...field theories: A route to seamlessly bridge quantum and atomistic length-scales with continuum Principal Investigator: Vikram Gavini Department of...calculations on tens of thousands of atoms, and enable continuing efforts towards a seamless bridging of the quantum and continuum length-scales

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

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

A general adaptive modeling algorithm for selection and validation of coarse-grained models of atomistic systems is presented. A Bayesian framework is developed to address uncertainties in parameters, data, and model selection. Algorithms for computing output sensitivities to parameter variances, model evidence and posterior model plausibilities for given data, and for computing what are referred to as Occam Categories in reference to a rough measure of model simplicity, make up components of the overall approach. Computational results are provided for representative applications.

Open-Source Software for Modeling of Nanoelectronic Devices

NASA Technical Reports Server (NTRS)

Oyafuso, Fabiano; Hua, Hook; Tisdale, Edwin; Hart, Don

2004-01-01

The Nanoelectronic Modeling 3-D (NEMO 3-D) computer program has been upgraded to open-source status through elimination of license-restricted components. The present version functions equivalently to the version reported in "Software for Numerical Modeling of Nanoelectronic Devices" (NPO-30520), NASA Tech Briefs, Vol. 27, No. 11 (November 2003), page 37. To recapitulate: NEMO 3-D performs numerical modeling of the electronic transport and structural properties of a semiconductor device that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantum-mechanical behavior of the device resolved to the atomistic level of granularity. NEMO 3-D solves the applicable quantum matrix equation on a Beowulf-class cluster computer by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. A prior upgrade of NEMO 3-D incorporated a capability for a strain treatment, parameterized for bulk material properties of GaAs and InAs, for two tight-binding submodels. NEMO 3-D has been demonstrated in atomistic analyses of effects of disorder in alloys and, in particular, in bulk In(x)Ga(1-x)As and in In(0.6)Ga(0.4)As quantum dots.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport.

PubMed

Komarov, Pavel V; Khalatur, Pavel G; Khokhlov, Alexei R

2013-01-01

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25-50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics

PubMed Central

Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott

2015-01-01

We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling. PMID:25637963

A Statistical Approach for the Concurrent Coupling of Molecular Dynamics and Finite Element Methods

NASA Technical Reports Server (NTRS)

Saether, E.; Yamakov, V.; Glaessgen, E.

2007-01-01

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, increasing the size of the MD domain quickly presents intractable computational demands. A robust approach to surmount this computational limitation has been to unite continuum modeling procedures such as the finite element method (FEM) with MD analyses thereby reducing the region of atomic scale refinement. The challenging problem is to seamlessly connect the two inherently different simulation techniques at their interface. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the typical boundary value problem used to define a coupled domain. The method uses statistical averaging of the atomistic MD domain to provide displacement interface boundary conditions to the surrounding continuum FEM region, which, in return, generates interface reaction forces applied as piecewise constant traction boundary conditions to the MD domain. The two systems are computationally disconnected and communicate only through a continuous update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM) as opposed to a direct coupling method where interface atoms and FEM nodes are individually related. The methodology is inherently applicable to three-dimensional domains, avoids discretization of the continuum model down to atomic scales, and permits arbitrary temperatures to be applied.

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2018-04-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2017-12-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer.

PubMed

Daily, Michael D; Baer, Marcel D; Mundy, Christopher J

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described.

Transition in coupled replicas may not imply a finite-temperature ideal glass transition in glass-forming systems.

PubMed

Garrahan, Juan P

2014-03-01

A key open question in the glass transition field is whether a finite temperature thermodynamic transition to the glass state exists or not. Recent simulations of coupled replicas in atomistic models have found signatures of a static transition as a function of replica coupling. This can be viewed as evidence of an associated thermodynamic glass transition in the uncoupled system. We demonstrate here that a different interpretation is possible. We consider the triangular plaquette model, an interacting spin system which displays (East model-like) glassy dynamics in the absence of any static transition. We show that when two replicas are coupled, there is a curve of equilibrium phase transitions, between phases of small and large overlap, in the temperature-coupling plane (located on the self-dual line of an exact temperature-coupling duality of the system) which ends at a critical point. Crucially, in the limit of vanishing coupling the finite temperature transition disappears, and the uncoupled system is in the disordered phase at all temperatures. We discuss an interpretation of atomistic simulations in light of this result.

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

PubMed

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

2016-10-04

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

Deformation behaviors of three-dimensional graphene honeycombs under out-of-plane compression: Atomistic simulations and predictive modeling

NASA Astrophysics Data System (ADS)

Meng, Fanchao; Chen, Cheng; Hu, Dianyin; Song, Jun

2017-12-01

Combining atomistic simulations and continuum modeling, a comprehensive study of the out-of-plane compressive deformation behaviors of equilateral three-dimensional (3D) graphene honeycombs was performed. It was demonstrated that under out-of-plane compression, the honeycomb exhibits two critical deformation events, i.e., elastic mechanical instability (including elastic buckling and structural transformation) and inelastic structural collapse. The above events were shown to be strongly dependent on the honeycomb cell size and affected by the local atomic bonding at the cell junction. By treating the 3D graphene honeycomb as a continuum cellular solid, and accounting for the structural heterogeneity and constraint at the junction, a set of analytical models were developed to accurately predict the threshold stresses corresponding to the onset of those deformation events. The present study elucidates key structure-property relationships of 3D graphene honeycombs under out-of-plane compression, and provides a comprehensive theoretical framework to predictively analyze their deformation responses, and more generally, offers critical new knowledge for the rational bottom-up design of 3D networks of two-dimensional nanomaterials.

Mechanism of Kinetically Controlled Capillary Condensation in Nanopores: A Combined Experimental and Monte Carlo Approach.

PubMed

Hiratsuka, Tatsumasa; Tanaka, Hideki; Miyahara, Minoru T

2017-01-24

We find the rule of capillary condensation from the metastable state in nanoscale pores based on the transition state theory. The conventional thermodynamic theories cannot achieve it because the metastable capillary condensation inherently includes an activated process. We thus compute argon adsorption isotherms on cylindrical pore models and atomistic silica pore models mimicking the MCM-41 materials by the grand canonical Monte Carlo and the gauge cell Monte Carlo methods and evaluate the rate constant for the capillary condensation by the transition state theory. The results reveal that the rate drastically increases with a small increase in the chemical potential of the system, and the metastable capillary condensation occurs for any mesopores when the rate constant reaches a universal critical value. Furthermore, a careful comparison between experimental adsorption isotherms and the simulated ones on the atomistic silica pore models reveals that the rate constant of the real system also has a universal value. With this finding, we can successfully estimate the experimental capillary condensation pressure over a wide range of temperatures and pore sizes by simply applying the critical rate constant.

Atomistic minimal model for estimating profile of electrodeposited nanopatterns

NASA Astrophysics Data System (ADS)

Asgharpour Hassankiadeh, Somayeh; Sadeghi, Ali

2018-06-01

We develop a computationally efficient and methodologically simple approach to realize molecular dynamics simulations of electrodeposition. Our minimal model takes into account the nontrivial electric field due a sharp electrode tip to perform simulations of the controllable coating of a thin layer on a surface with an atomic precision. On the atomic scale a highly site-selective electrodeposition of ions and charged particles by means of the sharp tip of a scanning probe microscope is possible. A better understanding of the microscopic process, obtained mainly from atomistic simulations, helps us to enhance the quality of this nanopatterning technique and to make it applicable in fabrication of nanowires and nanocontacts. In the limit of screened inter-particle interactions, it is feasible to run very fast simulations of the electrodeposition process within the framework of the proposed model and thus to investigate how the shape of the overlayer depends on the tip-sample geometry and dielectric properties, electrolyte viscosity, etc. Our calculation results reveal that the sharpness of the profile of a nano-scale deposited overlayer is dictated by the normal-to-sample surface component of the electric field underneath the tip.

Ion beam nanopatterning of III-V semiconductors: Consistency of experimental and simulation trends within a chemistry-driven theory

DOE PAGES

El-Atwani, O.; Norris, S. A.; Ludwig, K.; ...

2015-12-16

In this study, several proposed mechanisms and theoretical models exist concerning nanostructure evolution on III-V semiconductors (particularly GaSb) via ion beam irradiation. However, making quantitative contact between experiment on the one hand and model-parameter dependent predictions from different theories on the other is usually difficult. In this study, we take a different approach and provide an experimental investigation with a range of targets (GaSb, GaAs, GaP) and ion species (Ne, Ar, Kr, Xe) to determine new parametric trends regarding nanostructure evolution. Concurrently, atomistic simulations using binary collision approximation over the same ion/target combinations were performed to determine parametric trends onmore » several quantities related to existing model. A comparison of experimental and numerical trends reveals that the two are broadly consistent under the assumption that instabilities are driven by chemical instability based on phase separation. Furthermore, the atomistic simulations and a survey of material thermodynamic properties suggest that a plausible microscopic mechanism for this process is an ion-enhanced mobility associated with energy deposition by collision cascades.« less

Wetting behavior of nonpolar nanotubes in simple dipolar liquids for varying nanotube diameter and solute-solvent interactions

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

Rana, Malay Kumar; Chandra, Amalendu, E-mail: amalen@iitk.ac.in

2015-01-21

Atomistic simulations of model nonpolar nanotubes in a Stockmayer liquid are carried out for varying nanotube diameter and nanotube-solvent interactions to investigate solvophobic interactions in generic dipolar solvents. We have considered model armchair type single-walled nonpolar nanotubes with increasing radii from (5,5) to (12,12). The interactions between solute and solvent molecules are modeled by the well-known Lennard-Jones and repulsive Weeks-Chandler-Andersen potentials. We have investigated the density profiles and microscopic arrangement of Stockmayer molecules, orientational profiles of their dipole vectors, time dependence of their occupation, and also the translational and rotational motion of solvent molecules in confined environments of the cylindricalmore » nanopores and also in their external peripheral regions. The present results of structural and dynamical properties of Stockmayer molecules inside and near atomistically rough nonpolar surfaces including their wetting and dewetting behavior for varying interactions provide a more generic picture of solvophobic effects experienced by simple dipolar liquids without any specific interactions such as hydrogen bonds.« less

Multiscale modeling and simulation for nano/micro materials

NASA Astrophysics Data System (ADS)

Wang, Xianqiao

Continuum description and atomic description used to be two distinct methods in the community of modeling and simulations. Science and technology have become so advanced that our understanding of many physical phenomena involves the concepts of both. So our goal now is to build a bridge to make atoms and continua communicate with each other. Micromorphic theory (MMT) envisions a material body as a continuous collection of deformable particles; each possesses finite size and inner structure. It is considered as the most successful top-down formulation of a two-level continuum model to bridge the gap between the micro level and macro level. Therefore MMT can be expected to unveil many new classes of physical phenomena that fall beyond classical field theories. In this work, the constitutive equations for generalized Micromorphic thermoviscoelastic solid and generalized Micromorphic fluid have been formulated. To enlarge the domain of applicability of MMT, from nano, micro to macro, we take a bottom-up approach to re-derive the generalized atomistic field theory (AFT) comprehensively and completely and establish the relationship between AFT and MMT. Finite element (FE) method is then implemented to pursue the numerical solutions of the governing equations derived in AFT. When the finest mesh is used, i.e., the size of FE mesh is equal to the lattice constant of the material, the computational model becomes identical to molecular dynamics simulation. When a coarse mesh is used, the resulting model is a coarse-grained model, the majority of the degrees of freedom are eliminated and the computational cost is largely reduced. When the coarse mesh and finest mesh exist concurrently, i.e., the finest mesh is used in the critical regions and the coarser mesh is used in the far field, it leads naturally to a concurrent atomistic/continuum model. Atomic scale, coarse-grained scale and concurrent atomistic/continuum simulations have demonstrated the potential capability of AFT to simulate most grand challenging problems in nano/micro physics, and shown that AFT has the advantages of both atomic model and MMT. Therefore, AFT has accomplished the mission to bridge the gap between continuum mechanics and atomic physics.

Electrocaloric effects in the lead-free Ba (Zr ,Ti )O3 relaxor ferroelectric from atomistic simulations

NASA Astrophysics Data System (ADS)

Jiang, Zhijun; Prokhorenko, Sergei; Prosandeev, Sergey; Nahas, Y.; Wang, D.; Íñiguez, Jorge; Defay, E.; Bellaiche, L.

2017-07-01

Atomistic effective Hamiltonian simulations are used to investigate electrocaloric (EC) effects in the lead-free Ba (Zr0.5Ti0.5)O3 (BZT) relaxor ferroelectric. We find that the EC coefficient varies nonmonotonically with the field at any temperature, presenting a maximum that can be traced back to the behavior of BZT's polar nanoregions. We also introduce a simple Landau-based model that reproduces the EC behavior of BZT as a function of field and temperature, and which is directly applicable to other compounds. Finally, we confirm that, for low temperatures (i.e., in nonergodic conditions), the usual indirect approach to measure the EC response provides an estimate that differs quantitatively from a direct evaluation of the field-induced temperature change.

Redox reactions with empirical potentials: atomistic battery discharge simulations.

PubMed

Dapp, Wolf B; Müser, Martin H

2013-08-14

Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

Atomistic models of vacancy-mediated diffusion in silicon

NASA Astrophysics Data System (ADS)

Dunham, Scott T.; Wu, Can Dong

1995-08-01

Vacancy-mediated diffusion of dopants in silicon is investigated using Monte Carlo simulations of hopping diffusion, as well as analytic approximations based on atomistic considerations. Dopant/vacancy interaction potentials are assumed to extend out to third-nearest neighbor distances, as required for pair diffusion theories. Analysis focusing on the third-nearest neighbor sites as bridging configurations for uncorrelated hops leads to an improved analytic model for vacancy-mediated dopant diffusion. The Monte Carlo simulations of vacancy motion on a doped silicon lattice verify the analytic results for moderate doping levels. For very high doping (≳2×1020 cm-3) the simulations show a very rapid increase in pair diffusivity due to interactions of vacancies with more than one dopant atom. This behavior has previously been observed experimentally for group IV and V atoms in silicon [Nylandsted Larsen et al., J. Appl. Phys. 73, 691 (1993)], and the simulations predict both the point of onset and doping dependence of the experimentally observed diffusivity enhancement.

Molecular Dynamics Studies of Self-Assembling Biomolecules and DNA-functionalized Gold Nanoparticles

NASA Astrophysics Data System (ADS)

Cho, Vince Y.

This thesis is organized as following. In Chapter 2, we use fully atomistic MD simulations to study the conformation of DNA molecules that link gold nanoparticles to form nanoparticle superlattice crystals. In Chapter 3, we study the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber by using CGMD simulations. Compared to fully atomistic MD simulations, CGMD simulations prove to be computationally cost-efficient and reasonably accurate for exploring self-assembly, and are used in all subsequent chapters. In Chapter 4, we apply CGMD methods to study the self-assembly of small molecule-DNA hybrid (SMDH) building blocks into well-defined cage-like dimers, and reveal the role of kinetics and thermodynamics in this process. In Chapter 5, we extend the CGMD model for this system and find that the assembly of SMDHs can be fine-tuned by changing parameters. In Chapter 6, we explore superlattice crystal structures of DNA-functionalized gold nanoparticles (DNA-AuNP) with the CGMD model and compare the hybridization.

Simulations of noble gases adsorbed on graphene

NASA Astrophysics Data System (ADS)

Maiga, Sidi; Gatica, Silvina

2014-03-01

We present results of Grand Canonical Monte Carlo simulations of adsorption of Kr, Ar and Xe on a suspended graphene sheet. We compute the adsorbate-adsorbate interaction by a Lennard-Jones potential. We adopt a hybrid model for the graphene-adsorbate force; in the hybrid model, the potential interaction with the nearest carbon atoms (within a distance rnn) is computed with an atomistic pair potential Ua; for the atoms at r>rnn, we compute the interaction energy as a continuous integration over a carbon uniform sheet with the density of graphene. For the atomistic potential Ua, we assume the anisotropic LJ potential adapted from the graphite-He interaction proposed by Cole et.al. This interaction includes the anisotropy of the C atoms on graphene, which originates in the anisotropic π-bonds. The adsorption isotherms, energy and structure of the layer are obtained and compared with experimental results. We also compare with the adsorption on graphite and carbon nanotubes. This research was supported by NSF/PRDM (Howard University) and NSF (DMR 1006010).

Atomistic modeling of L10 FePt: path to HAMR 5Tb/in2

NASA Astrophysics Data System (ADS)

Chen, Tianran; Benakli, Mourad; Rea, Chris

2015-03-01

Heat assisted magnetic recording (HAMR) is a promising approach for increasing the storage density of hard disk drives. To increase data density, information must be written in small grains, which requires materials with high anisotropy energy such as L10 FePt. On the other hand, high anisotropy implies high coercivity, making it difficult to write the data with existing recording heads. This issue can be overcome by the technique of HAMR, where a laser is used to heat the recording medium to reduce its coercivity while retaining good thermal stability at room temperature due to the large anisotropy energy. One of the keys to the success of HAMR is the precise control of writing process. In this talk, I will propose a Monte Carlo simulation, based on an atomistic model, that would allow us to study the magnetic properties of L10 FePt and dynamics of spin reversal for the writing process in HAMR.

Multi-Million Atom Molecular Dynamics Simulations of Shocked Materials

DTIC Science & Technology

2006-11-01

chose this system for two reasons: First, accurate and widely tested atomistic models are available (van Beest et. al., 1990; Yuan and Cormack...Surface (PES) We have identified a model of silica (van Beest et. al., 1990) that has been extensively tested and that predicts several polymorphic...states (Saika-Voivod et. al., 2004). This model, hereafter denoted as the BKS model after its authors (van Beest et. al., 1990), assumes that the

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

NASA Astrophysics Data System (ADS)

Sayar, Mehmet; Avşaroǧlu, Barış; Kabakçıoǧlu, Alkan

2010-04-01

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

Moisture effect on interfacial integrity of epoxy-bonded system: a hierarchical approach

NASA Astrophysics Data System (ADS)

Tam, Lik-ho; Lun Chow, Cheuk; Lau, Denvid

2018-01-01

The epoxy-bonded system has been widely used in various applications across different scale lengths. Prior investigations have indicated that the moisture-affected interfacial debonding is the major failure mode of such a system, but the fundamental mechanism remains unknown, such as the basis for the invasion of water molecules in the cross-linked epoxy and the epoxy-bonded interface. This prevents us from predicting the long-term performance of the epoxy-related applications under the effect of the moisture. Here, we use full atomistic models to investigate the response of the epoxy-bonded system towards the adhesion test, and provide a detailed analysis of the interfacial integrity under the moisture effect and the associated debonding mechanism. Molecular dynamics simulations show that water molecules affect the hierarchical structure of the epoxy-bonded system at the nanoscale by disrupting the film-substrate interaction and the molecular interaction within the epoxy, which leads to the detachment of the epoxy thin film, and the final interfacial debonding. The simulation results show good agreement with the experimental results of the epoxy-bonded system. Through identifying the relationship between the epoxy structure and the debonding mechanism at multiple scales, it is shown that the hierarchical structure of the epoxy-bonded system is crucial for the interfacial integrity. In particular, the available space of the epoxy-bonded system, which consists of various sizes ranging from the atomistic scale to the macroscale and is close to the interface facilitates the moisture accumulation, leading to a distinct interfacial debonding when compared to the dry scenario.

Self-folding and aggregation of amyloid nanofibrils

NASA Astrophysics Data System (ADS)

Paparcone, Raffaella; Cranford, Steven W.; Buehler, Markus J.

2011-04-01

Amyloids are highly organized protein filaments, rich in β-sheet secondary structures that self-assemble to form dense plaques in brain tissues affected by severe neurodegenerative disorders (e.g. Alzheimer's Disease). Identified as natural functional materials in bacteria, in addition to their remarkable mechanical properties, amyloids have also been proposed as a platform for novel biomaterials in nanotechnology applications including nanowires, liquid crystals, scaffolds and thin films. Despite recent progress in understanding amyloid structure and behavior, the latent self-assembly mechanism and the underlying adhesion forces that drive the aggregation process remain poorly understood. On the basis of previous full atomistic simulations, here we report a simple coarse-grain model to analyze the competition between adhesive forces and elastic deformation of amyloid fibrils. We use simple model system to investigate self-assembly mechanisms of fibrils, focused on the formation of self-folded nanorackets and nanorings, and thereby address a critical issue in linking the biochemical (Angstrom) to micrometre scales relevant for larger-scale states of functional amyloid materials. We investigate the effect of varying the interfibril adhesion energy on the structure and stability of self-folded nanorackets and nanorings and demonstrate that these aggregated amyloid fibrils are stable in such states even when the fibril-fibril interaction is relatively weak, given that the constituting amyloid fibril length exceeds a critical fibril length-scale of several hundred nanometres. We further present a simple approach to directly determine the interfibril adhesion strength from geometric measures. In addition to providing insight into the physics of aggregation of amyloid fibrils our model enables the analysis of large-scale amyloid plaques and presents a new method for the estimation and engineering of the adhesive forces responsible of the self-assembly process of amyloidnanostructures, filling a gap that previously existed between full atomistic simulations of primarily ultra-short fibrils and much larger micrometre-scale amyloid aggregates. Via direct simulation of large-scale amyloid aggregates consisting of hundreds of fibrils we demonstrate that the fibril length has a profound impact on their structure and mechanical properties, where the critical fibril length-scale derived from our analysis of self-folded nanorackets and nanorings defines the structure of amyloid aggregates. A multi-scale modeling approach as used here, bridging the scales from Angstroms to micrometres, opens a wide range of possible nanotechnology applications by presenting a holistic framework that balances mechanical properties of individual fibrils, hierarchical self-assembly, and the adhesive forces determining their stability to facilitate the design of de novoamyloid materials.

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Study of Structure and Deformation Pathways in Ti-7Al Using Atomistic Simulations, Experiments, and Characterization

NASA Astrophysics Data System (ADS)

Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.

2017-05-01

Ti-7Al is a good model material for mimicking the α phase response of near- α and α+ β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.

Structure, Kinetics, and Thermodynamics of the Aqueous Uranyl(VI) Cation

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

Kerisit, Sebastien N.; Liu, Chongxuan

2013-08-20

Molecular simulation techniques are employed to gain insights into the structural, kinetic, and thermodynamic properties of the uranyl(VI) cation (UO22+) in aqueous solution. The simulations make use of an atomistic potential model (force field) derived in this work and based on the model of Guilbaud and Wipff (Guilbaud, P.; Wipff, G. J. Mol. Struct. (THEOCHEM) 1996, 366, 55-63). Reactive flux and thermodynamic integration calculations show that the derived potential model yields predictions for the water exchange rate and free energy of hydration, respectively, that are in agreement with experimental data. The water binding energies, hydration shell structure, and self-diffusion coefficientmore » are also calculated and discussed. Finally, a combination of metadynamics and transition path sampling simulations is employed to probe the mechanisms of water exchange reactions in the first hydration shell of the uranyl ion. These atomistic simulations indicate, based on two-dimensional free energy surfaces, that water exchanges follow an associative interchange mechanism. The nature and structure of the water exchange transition states are also determined. The improved potential model is expected to lead to more accurate predictions of uranyl adsorption energies at mineral surfaces using potential-based molecular dynamics simulations.« less

Polarizabilities and van der Waals C{sub 6} coefficients of fullerenes from an atomistic electrodynamics model: Anomalous scaling with number of carbon atoms

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

Saidi, Wissam A., E-mail: alsaidi@pitt.edu; Norman, Patrick

2016-07-14

The van der Waals C{sub 6} coefficients of fullerenes are shown to exhibit an anomalous dependence on the number of carbon atoms N such that C{sub 6} ∝ N{sup 2.2} as predicted using state-of-the-art quantum mechanical calculations based on fullerenes with small sizes, and N{sup 2.75} as predicted using a classical-metallic spherical-shell approximation of the fullerenes. We use an atomistic electrodynamics model where each carbon atom is described by a polarizable object to extend the quantum mechanical calculations to larger fullerenes. The parameters of this model are optimized to describe accurately the static and complex polarizabilities of the fullerenes bymore » fitting against accurate ab initio calculations. This model shows that C{sub 6} ∝ N{sup 2.8}, which is supportive of the classical-metallic spherical-shell approximation. Additionally, we show that the anomalous dependence of the polarizability on N is attributed to the electric charge term, while the dipole–dipole term scales almost linearly with the number of carbon atoms.« less

Numerical Modeling of Nanoelectronic Devices

NASA Technical Reports Server (NTRS)

Klimeck, Gerhard; Oyafuso, Fabiano; Bowen, R. Chris; Boykin, Timothy

2003-01-01

Nanoelectronic Modeling 3-D (NEMO 3-D) is a computer program for numerical modeling of the electronic structure properties of a semiconductor device that is embodied in a crystal containing as many as 16 million atoms in an arbitrary configuration and that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantummechanical behavior of the device resolved to the atomistic level of granularity. The system of electrons in the device is represented by a sparse Hamiltonian matrix that contains hundreds of millions of terms. NEMO 3-D solves the matrix equation on a Beowulf-class cluster computer, by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. In a recent update of NEMO 3-D, a new strain treatment, parameterized for bulk material properties of GaAs and InAs, was developed for two tight-binding submodels. The utility of the NEMO 3-D was demonstrated in an atomistic analysis of the effects of disorder in alloys and, in particular, in bulk In(x)Ga(l-x)As and in In0.6Ga0.4As quantum dots.

Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin.

PubMed

Tiwary, Pratyush

2017-12-07

Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its exceptionally high kinetic stability, being one of the strongest known noncovalent interactions in nature, and it is heavily used across the biotechnological industry. In this work, we gain understanding of the molecular determinants and bottlenecks in the dissociation of the dimeric biotin-streptavidin system in wild type and with a point mutation. Using recently proposed enhanced sampling methods with full atomistic resolution, we reproduce the experimentally reported effect of the mutation on the dissociation rate. We also answer a longstanding question regarding cause/effect in the coupled events of bond stretching and bond hydration during dissociation and establish that in this system, it is the bond stretching and not hydration which forms the bottleneck in the early parts of the dissociation process. We believe these calculations represent a step forward in the use of atomistic simulations to study pharmacokinetics. An improved understanding of biotin-streptavidin dissociation dynamics should also have direct benefits in biotechnological and nanobiotechnological applications.

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

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

Neilson, James R.; McQueen, Tyrel M.

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE PAGES

Neilson, James R.; McQueen, Tyrel M.

2015-09-20

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Physics and performances of III-V nanowire broken-gap heterojunction TFETs using an efficient tight-binding mode-space NEGF model enabling million-atom nanowire simulations.

PubMed

Afzalian, A; Vasen, T; Ramvall, P; Shen, T-M; Wu, J; Passlack, M

2018-06-27

We report the capability to simulate in a quantum-mechanical atomistic fashion record-large nanowire devices, featuring several hundred to millions of atoms and a diameter up to 18.2 nm. We have employed a tight-binding mode-space NEGF technique demonstrating by far the fastest (up to 10 000  ×  faster) but accurate (error  <  1%) atomistic simulations to date. Such technique and capability opens new avenues to explore and understand the physics of nanoscale and mesoscopic devices dominated by quantum effects. In particular, our method addresses in an unprecedented way the technologically-relevant case of band-to-band tunneling (BTBT) in III-V nanowire broken-gap heterojunction tunnel-FETs (HTFETs). We demonstrate an accurate match of simulated BTBT currents to experimental measurements in a 12 nm diameter InAs NW and in an InAs/GaSb Esaki tunneling diode. We apply our TB MS simulations and report the first in-depth atomistic study of the scaling potential of III-V GAA nanowire HTFETs including the effect of electron-phonon scattering and discrete dopant impurity band tails, quantifying the benefits of this technology for low-power low-voltage CMOS applications.

On coarse projective integration for atomic deposition in amorphous systems

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

Chuang, Claire Y., E-mail: yungc@seas.upenn.edu, E-mail: meister@unm.edu, E-mail: zepedaruiz1@llnl.gov; Sinno, Talid, E-mail: talid@seas.upenn.edu; Han, Sang M., E-mail: yungc@seas.upenn.edu, E-mail: meister@unm.edu, E-mail: zepedaruiz1@llnl.gov

2015-10-07

Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the “equation-free” framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to themore » application of this technique in realistic settings is the “lifting” operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO{sub 2} substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO{sub 2} using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.« less

Physics and performances of III–V nanowire broken-gap heterojunction TFETs using an efficient tight-binding mode-space NEGF model enabling million-atom nanowire simulations

NASA Astrophysics Data System (ADS)

Afzalian, A.; Vasen, T.; Ramvall, P.; Shen, T.-M.; Wu, J.; Passlack, M.

2018-06-01

We report the capability to simulate in a quantum-mechanical atomistic fashion record-large nanowire devices, featuring several hundred to millions of atoms and a diameter up to 18.2 nm. We have employed a tight-binding mode-space NEGF technique demonstrating by far the fastest (up to 10 000  ×  faster) but accurate (error  <  1%) atomistic simulations to date. Such technique and capability opens new avenues to explore and understand the physics of nanoscale and mesoscopic devices dominated by quantum effects. In particular, our method addresses in an unprecedented way the technologically-relevant case of band-to-band tunneling (BTBT) in III–V nanowire broken-gap heterojunction tunnel-FETs (HTFETs). We demonstrate an accurate match of simulated BTBT currents to experimental measurements in a 12 nm diameter InAs NW and in an InAs/GaSb Esaki tunneling diode. We apply our TB MS simulations and report the first in-depth atomistic study of the scaling potential of III–V GAA nanowire HTFETs including the effect of electron–phonon scattering and discrete dopant impurity band tails, quantifying the benefits of this technology for low-power low-voltage CMOS applications.

On Coarse Projective Integration for Atomic Deposition in Amorphous Systems

DOE PAGES

Chuang, Claire Y.; Han, Sang M.; Zepeda-Ruiz, Luis A.; ...

2015-10-02

Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of timescales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity and computational efficiency. Coarse projective integration, an example application of the ‘equation-free’ framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute gradients of slowly-evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of thismore » technique in realistic settings is the ‘lifting’ operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO 2 substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO 2 using only a few measures of the island size distribution. In conclusion, the approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.« less

Multiscale simulations of defect dipole-enhanced electromechanical coupling at dilute defect concentrations

NASA Astrophysics Data System (ADS)

Liu, Shi; Cohen, R. E.

2017-08-01

The role of defects in solids of mixed ionic-covalent bonds such as ferroelectric oxides is complex. Current understanding of defects on ferroelectric properties at the single-defect level remains mostly at the empirical level, and the detailed atomistic mechanisms for many defect-mediated polarization-switching processes have not been convincingly revealed quantum mechanically. We simulate the polarization-electric field (P-E) and strain-electric field (ɛ-E) hysteresis loops for BaTiO3 in the presence of generic defect dipoles with large-scale molecular dynamics and provide a detailed atomistic picture of the defect dipole-enhanced electromechanical coupling. We develop a general first-principles-based atomistic model, enabling a quantitative understanding of the relationship between macroscopic ferroelectric properties and dipolar impurities of different orientations, concentrations, and dipole moments. We find that the collective orientation of dipolar defects relative to the external field is the key microscopic structure feature that strongly affects materials hardening/softening and electromechanical coupling. We show that a small concentration (≈0.1 at. %) of defect dipoles dramatically improves electromechanical responses. This offers the opportunity to improve the performance of inexpensive polycrystalline ferroelectric ceramics through defect dipole engineering for a range of applications including piezoelectric sensors, actuators, and transducers.

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

NASA Astrophysics Data System (ADS)

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

2012-10-01

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

Real-Time Examination of Atomistic Mechanisms during Shock-Induced Structural Transformation in Silicon

DOE PAGES

Turneaure, Stefan J.; Sinclair, N.; Gupta, Y. M.

2016-07-20

Experimental determination of atomistic mechanisms linking crystal structures during a compression driven solid-solid phase transformation is a long standing and challenging scientific objective. Also, when using new capabilities at the Dynamic Compression Sector at the Advanced Photon Source, the structure of shocked Si at 19 GPa was identified as simple hexagonal and the lattice orientations between ambient cubic diamond and simple hexagonal structures were related. Furthermore, this approach is general and provides a powerful new method for examining atomistic mechanisms during stress-induced structural changes.

An object oriented Python interface for atomistic simulations

NASA Astrophysics Data System (ADS)

Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.

2016-01-01

Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.

Atomistic study of two-level systems in amorphous silica

NASA Astrophysics Data System (ADS)

Damart, T.; Rodney, D.

2018-01-01

Internal friction is analyzed in an atomic-scale model of amorphous silica. The potential energy landscape of more than 100 glasses is explored to identify a sample of about 700 two-level systems (TLSs). We discuss the properties of TLSs, particularly their energy asymmetry and barrier as well as their deformation potential, computed as longitudinal and transverse averages of the full deformation potential tensors. The discrete sampling is used to predict dissipation in the classical regime. Comparison with experimental data shows a better agreement with poorly relaxed thin films than well relaxed vitreous silica, as expected from the large quench rates used to produce numerical glasses. The TLSs are categorized in three types that are shown to affect dissipation in different temperature ranges. The sampling is also used to discuss critically the usual approximations employed in the literature to represent the statistical properties of TLSs.

Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A.

PubMed

Yoo, Jejoong; Cui, Qiang

2013-01-08

Using both atomistic and coarse-grained (CG) models, we compute the three-dimensional stress field around a gramicidin A (gA) dimer in lipid bilayers that feature different degrees of negative hydrophobic mismatch. The general trends in the computed stress field are similar at the atomistic and CG levels, supporting the use of the CG model for analyzing the mechanical features of protein/lipid/water interfaces. The calculations reveal that the stress field near the protein-lipid interface exhibits a layered structure with both significant repulsive and attractive regions, with the magnitude of the stress reaching 1000 bar in certain regions. Analysis of density profiles and stress field distributions helps highlight the Trp residues at the protein/membrane/water interface as mechanical anchors, suggesting that similar analysis is useful for identifying tension sensors in other membrane proteins, especially membrane proteins involved in mechanosensation. This work fosters a connection between microscopic and continuum mechanics models for proteins in complex environments and makes it possible to test the validity of assumptions commonly made in continuum mechanics models for membrane mediated processes. For example, using the calculated stress field, we estimate the free energy of membrane deformation induced by the hydrophobic mismatch, and the results for regions beyond the annular lipids are in general consistent with relevant experimental data and previous theoretical estimates using elasticity theory. On the other hand, the assumptions of homogeneous material properties for the membrane and a bilayer thickness at the protein/lipid interface being independent of lipid type (e.g., tail length) appear to be oversimplified, highlighting the importance of annular lipids of membrane proteins. Finally, the stress field analysis makes it clear that the effect of even rather severe hydrophobic mismatch propagates to only about two to three lipid layers, thus putting a limit on the range of cooperativity between membrane proteins in crowded cellular membranes. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

PubMed Central

2015-01-01

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

Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding.

PubMed

Tamura, Koichi; Hayashi, Shigehiko

2015-07-14

Molecular functions of proteins are often fulfilled by global conformational changes that couple with local events such as the binding of ligand molecules. High molecular complexity of proteins has, however, been an obstacle to obtain an atomistic view of the global conformational transitions, imposing a limitation on the mechanistic understanding of the functional processes. In this study, we developed a new method of molecular dynamics (MD) simulation called the linear response path following (LRPF) to simulate a protein's global conformational changes upon ligand binding. The method introduces a biasing force based on a linear response theory, which determines a local reaction coordinate in the configuration space that represents linear coupling between local events of ligand binding and global conformational changes and thus provides one with fully atomistic models undergoing large conformational changes without knowledge of a target structure. The overall transition process involving nonlinear conformational changes is simulated through iterative cycles consisting of a biased MD simulation with an updated linear response force and a following unbiased MD simulation for relaxation. We applied the method to the simulation of global conformational changes of the yeast calmodulin N-terminal domain and successfully searched out the end conformation. The atomistically detailed trajectories revealed a sequence of molecular events that properly lead to the global conformational changes and identified key steps of local-global coupling that induce the conformational transitions. The LRPF method provides one with a powerful means to model conformational changes of proteins such as motors and transporters where local-global coupling plays a pivotal role in their functional processes.

Effective Particle Size From Molecular Dynamics Simulations in Fluids

DOE PAGES

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov; ...

2017-12-08

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

PubMed Central

Komarov, Pavel V; Khokhlov, Alexei R

2013-01-01

Summary Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity. PMID:24205452

Effective Particle Size From Molecular Dynamics Simulations in Fluids

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

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Development and assessment of atomistic models for predicting static friction coefficients

NASA Astrophysics Data System (ADS)

Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.

2016-08-01

The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.

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

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

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

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

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

DOE PAGES

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

2016-10-10

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

A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity.

PubMed

Anwar-Mohamed, Anwar; Barakat, Khaled H; Bhat, Rakesh; Noskov, Sergei Y; Tyrrell, D Lorne; Tuszynski, Jack A; Houghton, Michael

2014-11-04

Acquired cardiac long QT syndrome (LQTS) is a frequent drug-induced toxic event that is often caused through blocking of the human ether-á-go-go-related (hERG) K(+) ion channel. This has led to the removal of several major drugs post-approval and is a frequent cause of termination of clinical trials. We report here a computational atomistic model derived using long molecular dynamics that allows sensitive prediction of hERG blockage. It identified drug-mediated hERG blocking activity of a test panel of 18 compounds with high sensitivity and specificity and was experimentally validated using hERG binding assays and patch clamp electrophysiological assays. The model discriminates between potent, weak, and non-hERG blockers and is superior to previous computational methods. This computational model serves as a powerful new tool to predict hERG blocking thus rendering drug development safer and more efficient. As an example, we show that a drug that was halted recently in clinical development because of severe cardiotoxicity is a potent inhibitor of hERG in two different biological assays which could have been predicted using our new computational model. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

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

Holm, Christian; Gompper, Gerhard; Dill, Ken A.

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.

Private Forests: Management and Policy in a Market Economy

Treesearch

Frederick W. Cubbage; Anthony G. Snider; Karen Lee Abt; Robert L. Moulton

2003-01-01

This chapter discusses privately owned forests and timber management in a market economy, including private property rights and tenure, landowner objectives and characteristics, markets, and government policies. Private forest land ownership and management-whether it be industrial or nonindustrial-is often assumed to represent the classic model of atomistic competition...

An atomistic-continuum hybrid simulation of fluid flows over superhydrophobic surfaces

PubMed Central

Li, Qiang; He, Guo-Wei

2009-01-01

Recent experiments have found that slip length could be as large as on the order of 1 μm for fluid flows over superhydrophobic surfaces. Superhydrophobic surfaces can be achieved by patterning roughness on hydrophobic surfaces. In the present paper, an atomistic-continuum hybrid approach is developed to simulate the Couette flows over superhydrophobic surfaces, in which a molecular dynamics simulation is used in a small region near the superhydrophobic surface where the continuum assumption is not valid and the Navier-Stokes equations are used in a large region for bulk flows where the continuum assumption does hold. These two descriptions are coupled using the dynamic coupling model in the overlap region to ensure momentum continuity. The hybrid simulation predicts a superhydrophobic state with large slip lengths, which cannot be obtained by molecular dynamics simulation alone. PMID:19693344

A Review of Molecular-Level Mechanism of Membrane Degradation in the Polymer Electrolyte Fuel Cell

PubMed Central

Ishimoto, Takayoshi; Koyama, Michihisa

2012-01-01

Chemical degradation of perfluorosulfonic acid (PFSA) membrane is one of the most serious problems for stable and long-term operations of the polymer electrolyte fuel cell (PEFC). The chemical degradation is caused by the chemical reaction between the PFSA membrane and chemical species such as free radicals. Although chemical degradation of the PFSA membrane has been studied by various experimental techniques, the mechanism of chemical degradation relies much on speculations from ex-situ observations. Recent activities applying theoretical methods such as density functional theory, in situ experimental observation, and mechanistic study by using simplified model compound systems have led to gradual clarification of the atomistic details of the chemical degradation mechanism. In this review paper, we summarize recent reports on the chemical degradation mechanism of the PFSA membrane from an atomistic point of view. PMID:24958288

Dynamics of biomolecular processes

NASA Astrophysics Data System (ADS)

Behringer, Hans; Eichhorn, Ralf; Wallin, Stefan

2013-05-01

The last few years have seen enormous progress in the availability of computational resources, so that the size and complexity of physical systems that can be investigated numerically has increased substantially. The physical mechanisms behind the processes creating life, such as those in a living cell, are of foremost interest in biophysical research. A main challenge here is that complexity not only emerges from interactions of many macro-molecular compounds, but is already evident at the level of a single molecule. An exciting recent development in this context is, therefore, that detailed atomistic level characterization of large-scale dynamics of individual bio-macromolecules, such as proteins and DNA, is starting to become feasible in some cases. This has contributed to a better understanding of the molecular mechanisms of, e.g. protein folding and aggregation, as well as DNA dynamics. Nevertheless, simulations of the dynamical behaviour of complex multicomponent cellular processes at an all-atom level will remain beyond reach for the foreseeable future, and may not even be desirable. Ultimate understanding of many biological processes will require the development of methods targeting different time and length scales and, importantly, ways to bridge these in multiscale approaches. At the scientific programme Dynamics of biomolecular processes: from atomistic representations to coarse-grained models held between 27 February and 23 March 2012, and hosted by the Nordic Institute for Theoretical Physics, new modelling approaches and results for particular biological systems were presented and discussed. The programme was attended by around 30 scientists from the Nordic countries and elsewhere. It also included a PhD and postdoc 'winter school', where basic theoretical concepts and techniques of biomolecular modelling and simulations were presented. One to two decades ago, the biomolecular modelling field was dominated by two widely different and largely independent approaches. On the one hand, computationally convenient and highly simplified lattice models were being used to elucidate the fundamental aspects of biomolecular conformational transitions, such as protein folding. On the other hand, these generic coarse-grained approaches were complemented by atomistic representations of the biomolecules. Physico-chemical all-atom models, often with an explicit representation of the surrounding solvent, were applied to specific protein structures to investigate their detailed dynamical behaviour. Today the situation is strikingly different, as was evident during the programme, where several new efforts were presented that try to combine the atomistic and the generic modelling approaches. The aim is to develop coarse-grained models at an intermediate-level resolution that are detailed enough to study specific biomolecular systems, and yet remain computationally efficient. These attempts are accompanied by the emergence of systematic coarse-graining techniques which bridge the physics of different lengths and timescales in a single simulation dynamically by applying appropriate representations of the associated degrees of freedom. Such adaptive resolution schemes represent promising candidates to tackle systems with an intrinsic multiscale nature, such as hierarchical chains and networks of biochemical reactions on a cellular level, calling for a very detailed description on an atomistic particle (or even quantum) level but simultaneously allowing the investigation of large-scale structuring and transport phenomena. The presentations and discussions during the programme also showed that the numerical evidence from (multiscale) simulations needs to be complemented by analytical and theoretical investigations to provide, eventually, a combined and deepened insight into the properties of biomolecular processes. The contributions from this scientific programme published in this issue of Physica Scripta highlight some of these new developments while also addressing related issues, such as the challenge of achieving efficient conformational sampling for chain molecules, and the interaction of nano-particles with biomolecules. The latter topic is especially timely as nano-particles are currently being considered for use as drug delivery devices, and present concerns about the general safety of their use might be resolved (or substantiated) by studies of this kind. This scientific programme and the contributions presented here were made possible by the financial and administrative support of the Nordic Institute for Theoretical Physics.

Atomistic models of Cu diffusion in CuInSe2 under variations in composition

NASA Astrophysics Data System (ADS)

Sommer, David E.; Dunham, Scott T.

2018-03-01

We construct an analytic model for the composition dependence of the vacancy-mediated Cu diffusion coefficient in undoped CuInSe2 using parameters from density functional theory. The applicability of this model is supported numerically with kinetic lattice Monte Carlo and Onsager transport tensors. We discuss how this model relates to experimental measurements of Cu diffusion, arguing that our results can account for significant contributions to the bulk diffusion of Cu tracers in non-stoichiometric CuInSe2.

Multiscale Molecular Dynamics Simulations of Model Hydrophobically Modified Ethylene Oxide Urethane Micelles.

PubMed

Yuan, Fang; Larson, Ronald G

2015-09-24

The flower-like micelles of various aggregation numbers of a model hydrophobically modified ethylene oxide urethane (HEUR) molecule, C16E45C16, and their corresponding starlike micelles, containing the surfactants C16E22 and C16E23, were studied by atomistic and coarse-grained molecular dynamic (MD) simulations. We used free energies from umbrella sampling to calculate the size distribution of micelle sizes and the average time for escape of a hydrophobic group from the micelle. Using the coarse-grained MARTINI force field, the most probable size of the model HEUR molecule was thereby determined to be about 80 hydrophobes per micelle and the average hydrophobe escape time to be about 0.1 s, both of which are consistent with previous experimental studies. Atomistic simulations reveal that hydrogen bond formation and the mean lifetime of hydration waters of the poly(ethylene oxide) (or PEO) groups are location-dependent in the HEUR micelle, with PEO groups immediately adjacent to the C16 groups forming the fewest hydrogen bonds with water and having hydration waters with longer lifetimes than those of the PEO groups located further away from the C16 groups.

Atomistic Molecular Dynamics Simulations of Carbon Dioxide Diffusivity in n-Hexane, n-Decane, n-Hexadecane, Cyclohexane, and Squalane.

PubMed

Moultos, Othonas A; Tsimpanogiannis, Ioannis N; Panagiotopoulos, Athanassios Z; Trusler, J P Martin; Economou, Ioannis G

2016-12-22

Atomistic molecular dynamics simulations were carried out to obtain the diffusion coefficients of CO 2 in n-hexane, n-decane, n-hexadecane, cyclohexane, and squalane at temperatures up to 423.15 K and pressures up to 65 MPa. Three popular models were used for the representation of hydrocarbons: the united atom TraPPE (TraPPE-UA), the all-atom OPLS, and an optimized version of OPLS, namely, L-OPLS. All models qualitatively reproduce the pressure dependence of the diffusion coefficient of CO 2 in hydrocarbons measured recently, and L-OPLS was found to be the most accurate. Specifically for n-alkanes, L-OPLS also reproduced the measured viscosities and densities much more accurately than the original OPLS and TraPPE-UA models, indicating that the optimization of the torsional potential is crucial for the accurate description of transport properties of long chain molecules. The three force fields predict different microscopic properties such as the mean square radius of gyration for the n-alkane molecules and pair correlation functions for the CO 2 -n-alkane interactions. CO 2 diffusion coefficients in all hydrocarbons studied are shown to deviate significantly from the Stokes-Einstein behavior.

Nucleation of ripplocations through atomistic modeling of surface nanoindentation in graphite

NASA Astrophysics Data System (ADS)

Freiberg, D.; Barsoum, M. W.; Tucker, G. J.

2018-05-01

In this work, we study the nucleation and subsequent evolution behavior of ripplocations - a newly proposed strain accommodating defect in layered materials where one, or more, layers buckle orthogonally to the layers - using atomistic modeling of graphite. To that effect, we model the response to cylindrical indenters with radii R of 50, 100, and 250 nm, loaded edge-on into graphite layers and the strain gradient effects beneath the indenter are quantified. We show that the response is initially elastic followed by ripplocation nucleation, and growth of multiple fully reversible ripplocation boundaries below the indenter. In the elastic region, the stress is found to be a function of indentation volume; beyond the elastic regime, the interlayer strain gradient emerges as paramount in the onset of ripplocation nucleation and subsequent in-plane stress relaxation. Furthermore, ripplocation boundaries that nucleate from the alignment of ripplocations on adjacent layers are exceedingly nonlocal and propagate, wavelike, away from the indented surface. This work not only provides a critical understanding of the mechanistic underpinnings of the deformation of layered solids and formation of kink boundaries, but also provides a more complete description of the nucleation mechanics of ripplocations and their strain field dependence.

Atomistic modeling of phonon transport in turbostratic graphitic structures

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

Mao, Rui; Chen, Yifeng; Kim, Ki Wook, E-mail: kwk@ncsu.edu

2016-05-28

Thermal transport in turbostratic graphitic systems is investigated by using an atomistic analytical model based on the 4th-nearest-neighbor force constant approximation and a registry-dependent interlayer potential. The developed model is shown to produce an excellent agreement with the experimental data and ab initio results in the calculation of bulk properties. Subsequent analysis of phonon transport in combination with the Green's function method illustrates the significant dependence of key characteristics on the misorientation angle, clearly indicating the importance of this degree of freedom in multi-stacked structures. Selecting three angles with the smallest commensurate unit cells, the thermal resistance is evaluated atmore » the twisted interface between two AB stacked graphite. The resulting values in the range of 35 × 10{sup −10} K m{sup 2}/W to 116 × 10{sup −10} K m{sup 2}/W are as large as those between two dissimilar material systems such as a metal and graphene. The strong rotational effect on the cross-plane thermal transport may offer an effective means of phonon engineering for applications such as thermoelectric materials.« less

A Site Density Functional Theory for Water: Application to Solvation of Amino Acid Side Chains.

PubMed

Liu, Yu; Zhao, Shuangliang; Wu, Jianzhong

2013-04-09

We report a site density functional theory (SDFT) based on the conventional atomistic models of water and the universality ansatz of the bridge functional. The excess Helmholtz energy functional is formulated in terms of a quadratic expansion with respect to the local density deviation from that of a uniform system and a universal functional for all higher-order terms approximated by that of a reference hard-sphere system. With the atomistic pair direct correlation functions of the uniform system calculated from MD simulation and an analytical expression for the bridge functional from the modified fundamental measure theory, the SDFT can be used to predict the structure and thermodynamic properties of water under inhomogeneous conditions with a computational cost negligible in comparison to that of brute-force simulations. The numerical performance of the SDFT has been demonstrated with the predictions of the solvation free energies of 15 molecular analogs of amino acid side chains in water represented by SPC/E, SPC, and TIP3P models. For theTIP3P model, a comparison of the theoretical predictions with MD simulation and experimental data shows agreement within 0.64 and 1.09 kcal/mol on average, respectively.

Multi-Scale Simulation of High Energy Density Ionic Liquids

DTIC Science & Technology

2007-06-19

and simulation of ionic liquids (ILs). A polarizable model was developed to simulate ILs more accurately at the atomistic level. A multiscale coarse...propellant, 1- hydroxyethyl-4-amino-1, 2, 4-triazolium nitrate (HEATN), were studied with the all-atom polarizable model. The mechanism suggested for HEATN...with this AFOSR-supported project, a polarizable forcefield for the ionic liquids such as 1-ethyl-3-methylimidazolium nitrate (EMIM*/NO3-) was

Representation and Structure in Connectionist Models

DTIC Science & Technology

1989-08-01

among those who are actively exploring the to wonder how these models might differ topic (cf. Dolan & Dyer, 1987; Dolan & from traditional theories , and...because one of the critical ways in which cognitive theories may differ is in the Elman Representation & Structure some of the specific questions raised...that whereas Classi- atomistic or can they possess internal struc- cal theories (e.g., the Language of Thought, ture? Can that structure be used to

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

PubMed

Haxton, Thomas K

2015-03-10

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

Molecular Simulation of the Free Energy for the Accurate Determination of Phase Transition Properties of Molecular Solids

NASA Astrophysics Data System (ADS)

Sellers, Michael; Lisal, Martin; Brennan, John

2015-06-01

Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.

The Development of Models to Optimize Selection of Nuclear Fuels through Atomic-Level Simulation

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

Prof. Simon Phillpot; Prof. Susan B. Sinnott; Prof. Hans Seifert

2009-01-26

Demonstrated that FRAPCON can be modified to accept data generated from first principles studies, and that the result obtained from the modified FRAPCON make sense in terms of the inputs. Determined the temperature dependence of the thermal conductivity of single crystal UO2 from atomistic simulation.

Lattice Thermal Conductivity of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2 from Atomistic Simulations

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, T.

1986-01-01

During this reporting period three investigations were carried out. The first area of research concerned the analysis of the structure-energy relationship in small clusters. This study is very closely related to the improvement of the potential energy functions which are suitable and simple enough to be used in atomistic simulation studies. Parameters obtained from ab initio calculations for dimers and trimers of Al were used to estimate energetics and global minimum energy structures of clusters continuing up to 15 Al atoms. The second research topic addressed modeling of the collision process for atoms impinging on surfaces. In this simulation study qualitative aspects of the O atom collision with a graphite surface were analyzed. Four different O/graphite systems were considered and the aftermath of the impact was analyzed. The final area of investigation was related to the simulation of thin amorphous Si films on crystalline Si substrates. Parameters obtained in an earlier study were used to model an exposed amorphous Si surface and an a-Si/c-Si interface. Structural details for various film thicknesses were investigated at an atomistic level.

Anharmonic phonon-phonon scattering modeling of three-dimensional atomistic transport: An efficient quantum treatment

NASA Astrophysics Data System (ADS)

Lee, Y.; Bescond, M.; Logoteta, D.; Cavassilas, N.; Lannoo, M.; Luisier, M.

2018-05-01

We propose an efficient method to quantum mechanically treat anharmonic interactions in the atomistic nonequilibrium Green's function simulation of phonon transport. We demonstrate that the so-called lowest-order approximation, implemented through a rescaling technique and analytically continued by means of the Padé approximants, can be used to accurately model third-order anharmonic effects. Although the paper focuses on a specific self-energy, the method is applicable to a very wide class of physical interactions. We apply this approach to the simulation of anharmonic phonon transport in realistic Si and Ge nanowires with uniform or discontinuous cross sections. The effect of increasing the temperature above 300 K is also investigated. In all the considered cases, we are able to obtain a good agreement with the routinely adopted self-consistent Born approximation, at a remarkably lower computational cost. In the more complicated case of high temperatures (≫300 K), we find that the first-order Richardson extrapolation applied to the sequence of the Padé approximants N -1 /N results in a significant acceleration of the convergence.

Accurate atomistic potentials and training sets for boron-nitride nanostructures

NASA Astrophysics Data System (ADS)

Tamblyn, Isaac

Boron nitride nanotubes exhibit exceptional structural, mechanical, and thermal properties. They are optically transparent and have high thermal stability, suggesting a wide range of opportunities for structural reinforcement of materials. Modeling can play an important role in determining the optimal approach to integrating nanotubes into a supporting matrix. Developing accurate, atomistic scale models of such nanoscale interfaces embedded within composites is challenging, however, due to the mismatch of length scales involved. Typical nanotube diameters range from 5-50 nm, with a length as large as a micron (i.e. a relevant length-scale for structural reinforcement). Unlike their carbon-based counterparts, well tested and transferable interatomic force fields are not common for BNNT. In light of this, we have developed an extensive training database of BN rich materials, under conditions relevant for BNNT synthesis and composites based on extensive first principles molecular dynamics simulations. Using this data, we have produced an artificial neural network potential capable of reproducing the accuracy of first principles data at significantly reduced computational cost, allowing for accurate simulation at the much larger length scales needed for composite design.

Nonlocal Gilbert damping tensor within the torque-torque correlation model

NASA Astrophysics Data System (ADS)

Thonig, Danny; Kvashnin, Yaroslav; Eriksson, Olle; Pereiro, Manuel

2018-01-01

An essential property of magnetic devices is the relaxation rate in magnetic switching, which depends strongly on the damping in the magnetization dynamics. It was recently measured that damping depends on the magnetic texture and, consequently, is a nonlocal quantity. The damping enters the Landau-Lifshitz-Gilbert equation as the phenomenological Gilbert damping parameter α , which does not, in a straightforward formulation, account for nonlocality. Efforts were spent recently to obtain Gilbert damping from first principles for magnons of wave vector q . However, to the best of our knowledge, there is no report about real-space nonlocal Gilbert damping αi j. Here, a torque-torque correlation model based on a tight-binding approach is applied to the bulk elemental itinerant magnets and it predicts significant off-site Gilbert damping contributions, which could be also negative. Supported by atomistic magnetization dynamics simulations, we reveal the importance of the nonlocal Gilbert damping in atomistic magnetization dynamics. This study gives a deeper understanding of the dynamics of the magnetic moments and dissipation processes in real magnetic materials. Ways of manipulating nonlocal damping are explored, either by temperature, materials doping, or strain.

Landau-Lifshitz-Bloch equation for exchange-coupled grains

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

NASA Astrophysics Data System (ADS)

Zhang, Zhiwei; Chen, Pei; Qin, Fei; An, Tong; Yu, Huiping

2018-05-01

Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD) layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young's modulus, ultimate tensile strength (UTS), and strain at fracture is observed.

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

PubMed

Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

2015-10-08

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs

PubMed Central

Krepl, Miroslav; Cléry, Antoine; Blatter, Markus; Allain, Frederic H.T.; Sponer, Jiri

2016-01-01

RNA recognition motif (RRM) proteins represent an abundant class of proteins playing key roles in RNA biology. We present a joint atomistic molecular dynamics (MD) and experimental study of two RRM-containing proteins bound with their single-stranded target RNAs, namely the Fox-1 and SRSF1 complexes. The simulations are used in conjunction with NMR spectroscopy to interpret and expand the available structural data. We accumulate more than 50 μs of simulations and show that the MD method is robust enough to reliably describe the structural dynamics of the RRM–RNA complexes. The simulations predict unanticipated specific participation of Arg142 at the protein–RNA interface of the SRFS1 complex, which is subsequently confirmed by NMR and ITC measurements. Several segments of the protein–RNA interface may involve competition between dynamical local substates rather than firmly formed interactions, which is indirectly consistent with the primary NMR data. We demonstrate that the simulations can be used to interpret the NMR atomistic models and can provide qualified predictions. Finally, we propose a protocol for ‘MD-adapted structure ensemble’ as a way to integrate the simulation predictions and expand upon the deposited NMR structures. Unbiased μs-scale atomistic MD could become a technique routinely complementing the NMR measurements of protein–RNA complexes. PMID:27193998

A universal strategy for the creation of machine learning-based atomistic force fields

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

2017-09-01

Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.

Calculation of surface potentials at the silica–water interface using molecular dynamics: Challenges and opportunities

NASA Astrophysics Data System (ADS)

Lowe, Benjamin M.; Skylaris, Chris-Kriton; Green, Nicolas G.; Shibuta, Yasushi; Sakata, Toshiya

2018-04-01

Continuum-based methods are important in calculating electrostatic properties of interfacial systems such as the electric field and surface potential but are incapable of providing sufficient insight into a range of fundamentally and technologically important phenomena which occur at atomistic length-scales. In this work a molecular dynamics methodology is presented for interfacial electric field and potential calculations. The silica–water interface was chosen as an example system, which is highly relevant for understanding the response of field-effect transistors sensors (FET sensors). Detailed validation work is presented, followed by the simulated surface charge/surface potential relationship. This showed good agreement with experiment at low surface charge density but at high surface charge density the results highlighted challenges presented by an atomistic definition of the surface potential. This methodology will be used to investigate the effect of surface morphology and biomolecule addition; both factors which are challenging using conventional continuum models.

Advances in first-principles calculations of thermodynamic properties of planetary materials (Invited)

NASA Astrophysics Data System (ADS)

Wilson, H. F.

2013-12-01

First-principles atomistic simulation is a vital tool for understanding the properties of materials at the high-pressure high-temperature conditions prevalent in giant planet interiors, but properties such as solubility and phase boundaries are dependent on entropy, a quantity not directly accessible in simulation. Determining entropic properties from atomistic simulations is a difficult problem typically requiring a time-consuming integration over molecular dynamics trajectories. Here I will describe recent advances in first-principles thermodynamic calculations which substantially increase the simplicity and efficiency of thermodynamic integration and make entropic properties more readily accessible. I will also describe the use of first-principles thermodynamic calculations for understanding problems including core solubility in gas giants and superionic phase changes in ice giants, as well as future prospects for combining first-principles thermodynamics with planetary-scale models to help us understand the origin and consequences of compositional inhomogeneity in giant planet interiors.

Atomistic basis for the plastic yield criterion of metallic glass.

PubMed

Schuh, Christopher A; Lund, Alan C

2003-07-01

Because of their disordered atomic structure, amorphous metals (termed metallic glasses) have fundamentally different deformation mechanisms compared with polycrystalline metals. These different mechanisms give metallic glasses high strength, but the extent to which they affect other macroscopic deformation properties is uncertain. For example, the nature of the plastic-yield criterion is a point of contention, with some studies reporting yield behaviour roughly in line with that of polycrystalline metals, and others indicating strong fundamental differences. In particular, it is unclear whether pressure- or normal stress-dependence needs to be included in the plastic-yield criterion of metallic glasses, and how such a dependence could arise from their disordered structure. In this work we provide an atomic-level explanation for pressure-dependent yield in amorphous metals, based on an elementary unit of deformation. This simple model compares favourably with new atomistic simulations of metallic glasses, as well as existing experimental data.

Multiscale modelling of precipitation in concentrated alloys: from atomistic Monte Carlo simulations to cluster dynamics I thermodynamics

NASA Astrophysics Data System (ADS)

Lépinoux, J.; Sigli, C.

2018-01-01

In a recent paper, the authors showed how the clusters free energies are constrained by the coagulation probability, and explained various anomalies observed during the precipitation kinetics in concentrated alloys. This coagulation probability appeared to be a too complex function to be accurately predicted knowing only the cluster distribution in Cluster Dynamics (CD). Using atomistic Monte Carlo (MC) simulations, it is shown that during a transformation at constant temperature, after a short transient regime, the transformation occurs at quasi-equilibrium. It is proposed to use MC simulations until the system quasi-equilibrates then to switch to CD which is mean field but not limited by a box size like MC. In this paper, we explain how to take into account the information available before the quasi-equilibrium state to establish guidelines to safely predict the cluster free energies.

Realistic finite temperature simulations of magnetic systems using quantum statistics

NASA Astrophysics Data System (ADS)

Bergqvist, Lars; Bergman, Anders

2018-01-01

We have performed realistic atomistic simulations at finite temperatures using Monte Carlo and atomistic spin dynamics simulations incorporating quantum (Bose-Einstein) statistics. The description is much improved at low temperatures compared to classical (Boltzmann) statistics normally used in these kind of simulations, while at higher temperatures the classical statistics are recovered. This corrected low-temperature description is reflected in both magnetization and the magnetic specific heat, the latter allowing for improved modeling of the magnetic contribution to free energies. A central property in the method is the magnon density of states at finite temperatures, and we have compared several different implementations for obtaining it. The method has no restrictions regarding chemical and magnetic order of the considered materials. This is demonstrated by applying the method to elemental ferromagnetic systems, including Fe and Ni, as well as Fe-Co random alloys and the ferrimagnetic system GdFe3.

Docking 90Sr radionuclide in cement: An atomistic modeling study

NASA Astrophysics Data System (ADS)

Youssef, Mostafa; Pellenq, Roland J.-M.; Yildiz, Bilge

Cementitious materials are considered to be a waste form for the ultimate disposal of radioactive materials in geological repositories. We investigated by means of atomistic simulations the encapsulation of strontium-90, an important radionuclide, in calcium-silicate-hydrate (C-S-H) and its crystalline analog, the 9 Å-tobermorite. C-S-H is the major binding phase of cement. Strontium was shown to energetically favor substituting calcium in the interlayer sites in C-S-H and 9 Å-tobermorite with the trend more pronounced in the latter. The integrity of the silicate chains in both cementitious waste forms were not affected by strontium substitution within the time span of molecular dynamics simulation. Finally, we observed a limited degradation of the mechanical properties in the strontium-containing cementitious waste form with the increasing strontium concentration. These results suggest the cement hydrate as a good candidate for immobilizing radioactive strontium.

Cellulose microfibril formation within a coarse grained molecular dynamics

NASA Astrophysics Data System (ADS)

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.

229Thorium-doped calcium fluoride for nuclear laser spectroscopy.

PubMed

Dessovic, P; Mohn, P; Jackson, R A; Winkler, G; Schreitl, M; Kazakov, G; Schumm, T

2014-03-12

The (229)thorium isotope presents an extremely low-energy isomer state of the nucleus which is expected around 7.8 eV, in the vacuum ultraviolet (VUV) regime. This unique system may bridge between atomic and nuclear physics, enabling coherent manipulation and precision spectroscopy of nuclear quantum states using laser light. It has been proposed to implant (229)thorium into VUV transparent crystal matrices to facilitate laser spectroscopy and possibly realize a solid-state nuclear clock. In this work, we validate the feasibility of this approach by computer modelling of thorium doping into calcium fluoride single crystals. Using atomistic modelling and full electronic structure calculations, we find a persistent large band gap and no additional electronic levels emerging in the middle of the gap due to the presence of the dopant, which should allow direct optical interrogation of the nuclear transition.Based on the electronic structure, we estimate the thorium nuclear quantum levels within the solid-state environment. Precision laser spectroscopy of these levels will allow the study of a broad range of crystal field effects, transferring Mössbauer spectroscopy into the optical regime.

Detonation initiation in a model of explosive: Comparative atomistic and hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Murzov, S. A.; Sergeev, O. V.; Dyachkov, S. A.; Egorova, M. S.; Parshikov, A. N.; Zhakhovsky, V. V.

2016-11-01

Here we extend consistent simulations to reactive materials by the example of AB model explosive. The kinetic model of chemical reactions observed in a molecular dynamics (MD) simulation of self-sustained detonation wave can be used in hydrodynamic simulation of detonation initiation. Kinetic coefficients are obtained by minimization of difference between profiles of species calculated from the kinetic model and observed in MD simulations of isochoric thermal decomposition with a help of downhill simplex method combined with random walk in multidimensional space of fitting kinetic model parameters.

Physically representative atomistic modeling of atomic-scale friction

NASA Astrophysics Data System (ADS)

Dong, Yalin

Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the interesting physical process is buried between the two contact interfaces, thus makes a direct measurement more difficult. Atomistic simulation is able to simulate the process with the dynamic information of each single atom, and therefore provides valuable interpretations for experiments. In this, we will systematically to apply Molecular Dynamics (MD) simulation to optimally model the Atomic Force Microscopy (AFM) measurement of atomic friction. Furthermore, we also employed molecular dynamics simulation to correlate the atomic dynamics with the friction behavior observed in experiments. For instance, ParRep dynamics (an accelerated molecular dynamic technique) is introduced to investigate velocity dependence of atomic friction; we also employ MD simulation to "see" how the reconstruction of gold surface modulates the friction, and the friction enhancement mechanism at a graphite step edge. Atomic stick-slip friction can be treated as a rate process. Instead of running a direction simulation of the process, we can apply transition state theory to predict its property. We will have a rigorous derivation of velocity and temperature dependence of friction based on the Prandtl-Tomlinson model as well as transition theory. A more accurate relation to prediction velocity and temperature dependence is obtained. Furthermore, we have included instrumental noise inherent in AFM measurement to interpret two discoveries in experiments, suppression of friction at low temperature and the attempt frequency discrepancy between AFM measurement and theoretical prediction. We also discuss the possibility to treat wear as a rate process.

Amp: A modular approach to machine learning in atomistic simulations

NASA Astrophysics Data System (ADS)

Khorshidi, Alireza; Peterson, Andrew A.

2016-10-01

Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which makes it compatible with a wide variety of commercial and open-source electronic structure codes. We finally demonstrate that the neural network model inside Amp can accurately interpolate electronic structure energies as well as forces of thousands of multi-species atomic systems.

Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues

NASA Astrophysics Data System (ADS)

Fiorentini, Raffaele; Kremer, Kurt; Potestio, Raffaello; Fogarty, Aoife C.

2017-06-01

The calculation of free energy differences is a crucial step in the characterization and understanding of the physical properties of biological molecules. In the development of efficient methods to compute these quantities, a promising strategy is that of employing a dual-resolution representation of the solvent, specifically using an accurate model in the proximity of a molecule of interest and a simplified description elsewhere. One such concurrent multi-resolution simulation method is the Adaptive Resolution Scheme (AdResS), in which particles smoothly change their resolution on-the-fly as they move between different subregions. Before using this approach in the context of free energy calculations, however, it is necessary to make sure that the dual-resolution treatment of the solvent does not cause undesired effects on the computed quantities. Here, we show how AdResS can be used to calculate solvation free energies of small polar solutes using Thermodynamic Integration (TI). We discuss how the potential-energy-based TI approach combines with the force-based AdResS methodology, in which no global Hamiltonian is defined. The AdResS free energy values agree with those calculated from fully atomistic simulations to within a fraction of kBT. This is true even for small atomistic regions whose size is on the order of the correlation length, or when the properties of the coarse-grained region are extremely different from those of the atomistic region. These accurate free energy calculations are possible because AdResS allows the sampling of solvation shell configurations which are equivalent to those of fully atomistic simulations. The results of the present work thus demonstrate the viability of the use of adaptive resolution simulation methods to perform free energy calculations and pave the way for large-scale applications where a substantial computational gain can be attained.

LL13-MatModelRadDetect-PD2Jf Final Report: Materials Modeling for High-Performance Radiation Detectors

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

Lordi, Vincenzo

The aims of this project are to enable rational materials design for select high-payoff challenges in radiation detection materials by using state-of-the-art predictive atomistic modeling techniques. Three specific high-impact challenges are addressed: (i) design and optimization of electrical contact stacks for TlBr detectors to stabilize temporal response at room-temperature; (ii) identification of chemical design principles of host glass materials for large-volume, low-cost, highperformance glass scintillators; and (iii) determination of the electrical impacts of dislocation networks in Cd 1-xZn xTe (CZT) that limit its performance and usable single-crystal volume. The specific goals are to establish design and process strategies to achievemore » improved materials for high performance detectors. Each of the major tasks is discussed below in three sections, which include the goals for the task and a summary of the major results, followed by a listing of publications that contain the full details, including details of the methodologies used. The appendix lists 12 conference presentations given for this project, including 1 invited talk and 1 invited poster.« less

The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.

PubMed

Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele

2017-09-14

In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.

Prediction of TF target sites based on atomistic models of protein-DNA complexes

PubMed Central

Angarica, Vladimir Espinosa; Pérez, Abel González; Vasconcelos, Ana T; Collado-Vides, Julio; Contreras-Moreira, Bruno

2008-01-01

Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition. PMID:18922190

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

PubMed

Reshetnikov, Roman V; Sponer, Jiri; Rassokhina, Olga I; Kopylov, Alexei M; Tsvetkov, Philipp O; Makarov, Alexander A; Golovin, Andrey V

2011-12-01

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. © The Author(s) 2011. Published by Oxford University Press.

Atomistic analysis of valley-orbit hybrid states and inter-dot tunnel rates in a Si double quantum dot

NASA Astrophysics Data System (ADS)

Ferdous, Rifat; Rahman, Rajib; Klimeck, Gerhard

2014-03-01

Silicon quantum dots are promising candidates for solid-state quantum computing due to the long spin coherence times in silicon, arising from small spin-orbit interaction and a nearly spin free host lattice. However, the conduction band valley degeneracy adds an additional degree of freedom to the electronic structure, complicating the encoding and operation of qubits. Although the valley and the orbital indices can be uniquely identified in an ideal silicon quantum dot, atomic-scale disorder mixes valley and orbital states in realistic dots. Such valley-orbit hybridization, strongly influences the inter-dot tunnel rates.Using a full-band atomistic tight-binding method, we analyze the effect of atomic-scale interface disorder in a silicon double quantum dot. Fourier transform of the tight-binding wavefunctions helps to analyze the effect of disorder on valley-orbit hybridization. We also calculate and compare inter-dot inter-valley and intra-valley tunneling, in the presence of realistic disorder, such as interface tilt, surface roughness, alloy disorder, and interface charges. The method provides a useful way to compute electronic states in realistically disordered systems without any posteriori fitting parameters.

Perspectives on the simulation of protein–surface interactions using empirical force field methods

PubMed Central

Latour, Robert A.

2014-01-01

Protein–surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein–surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation. PMID:25028242

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

PubMed Central

Reshetnikov, Roman V.; Sponer, Jiri; Rassokhina, Olga I.; Kopylov, Alexei M.; Tsvetkov, Philipp O.; Makarov, Alexander A.; Golovin, Andrey V.

2011-01-01

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. PMID:21893589

In situ observations of the atomistic mechanisms of Ni catalyzed low temperature graphene growth.

PubMed

Patera, Laerte L; Africh, Cristina; Weatherup, Robert S; Blume, Raoul; Bhardwaj, Sunil; Castellarin-Cudia, Carla; Knop-Gericke, Axel; Schloegl, Robert; Comelli, Giovanni; Hofmann, Stephan; Cepek, Cinzia

2013-09-24

The key atomistic mechanisms of graphene formation on Ni for technologically relevant hydrocarbon exposures below 600 °C are directly revealed via complementary in situ scanning tunneling microscopy and X-ray photoelectron spectroscopy. For clean Ni(111) below 500 °C, two different surface carbide (Ni2C) conversion mechanisms are dominant which both yield epitaxial graphene, whereas above 500 °C, graphene predominantly grows directly on Ni(111) via replacement mechanisms leading to embedded epitaxial and/or rotated graphene domains. Upon cooling, additional carbon structures form exclusively underneath rotated graphene domains. The dominant graphene growth mechanism also critically depends on the near-surface carbon concentration and hence is intimately linked to the full history of the catalyst and all possible sources of contamination. The detailed XPS fingerprinting of these processes allows a direct link to high pressure XPS measurements of a wide range of growth conditions, including polycrystalline Ni catalysts and recipes commonly used in industrial reactors for graphene and carbon nanotube CVD. This enables an unambiguous and consistent interpretation of prior literature and an assessment of how the quality/structure of as-grown carbon nanostructures relates to the growth modes.

Simulation of the optical coating deposition

NASA Astrophysics Data System (ADS)

Grigoriev, Fedor; Sulimov, Vladimir; Tikhonravov, Alexander

2018-04-01

A brief review of the mathematical methods of thin-film growth simulation and results of their applications is presented. Both full-atomistic and multi-scale approaches that were used in the studies of thin-film deposition are considered. The results of the structural parameter simulation including density profiles, roughness, porosity, point defect concentration, and others are discussed. The application of the quantum level methods to the simulation of the thin-film electronic and optical properties is considered. Special attention is paid to the simulation of the silicon dioxide thin films.

Time-Domain Ab Initio Analysis of Excitation Dynamics in a Quantum Dot/Polymer Hybrid: Atomistic Description Rationalizes Experiment.

PubMed

Long, Run; Prezhdo, Oleg V

2015-07-08

Hybrid organic/inorganic polymer/quantum dot (QD) solar cells are an attractive alternative to the traditional cells. The original, simple models postulate that one-dimensional polymers have continuous energy levels, while zero-dimensional QDs exhibit atom-like electronic structure. A realistic, atomistic viewpoint provides an alternative description. Electronic states in polymers are molecule-like: finite in size and discrete in energy. QDs are composed of many atoms and have high, bulk-like densities of states. We employ ab initio time-domain simulation to model the experimentally observed ultrafast photoinduced dynamics in a QD/polymer hybrid and show that an atomistic description is essential for understanding the time-resolved experimental data. Both electron and hole transfers across the interface exhibit subpicosecond time scales. The interfacial processes are fast due to strong electronic donor-acceptor, as evidenced by the densities of the photoexcited states which are delocalized between the donor and the acceptor. The nonadiabatic charge-phonon coupling is also strong, especially in the polymer, resulting in rapid energy losses. The electron transfer from the polymer is notably faster than the hole transfer from the QD, due to a significantly higher density of acceptor states. The stronger molecule-like electronic and charge-phonon coupling in the polymer rationalizes why the electron-hole recombination inside the polymer is several orders of magnitude faster than in the QD. As a result, experiments exhibit multiple transfer times for the long-lived hole inside the QD, ranging from subpicoseconds to nanoseconds. In contrast, transfer of the short-lived electron inside the polymer does not occur beyond the first picosecond. The energy lost by the hole on its transit into the polymer is accommodated by polymer's high-frequency vibrations. The energy lost by the electron injected into the QD is accommodated primarily by much lower-frequency collective and QD modes. The electron dynamics is exponential, whereas evolution of the injected hole through the low density manifold of states of the polymer is highly nonexponential. The time scale of the electron-hole recombination at the interface is intermediate between those in pristine polymer and QD and is closer to that in the polymer. The detailed atomistic insights into the photoinduced charge and energy dynamics at the polymer/QD interface provide valuable guidelines for optimization of solar light harvesting and photovoltaic efficiency in modern nanoscale materials.

Multiscale Modeling and Simulation of Material Processing

DTIC Science & Technology

2006-07-01

As a re- GIMP simulations . Fig. 2 illustrates the contact algo- suit, MPM using a single mesh tends to induce early con- rithm for the contact pair ...21-07-2006 Final Performance Report 05-01-2003 - 04-30-2006 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Multiscale Modeling and Simulation of Material...development of scaling laws for multiscale simulations from atomistic to continuum using material testing techniques, such as tension and indentation

Peierls-Nabarro modeling of dislocations in UO2

NASA Astrophysics Data System (ADS)

Skelton, Richard; Walker, Andrew M.

2017-11-01

Under conditions of high stress or low temperature, glide of dislocations plays an important role in the deformation of UO2. In this paper, the Peierls-Nabarro model is used to calculate the core widths and Peierls stresses of ½<110> edge and screw dislocations gliding on {100}, {110}, and {111}. The energy of the inelastic displacement field in the dislocation core is parameterized using generalized stacking fault energies, which are calculated atomistically using interatomic potentials. We use seven different interatomic potential models, representing the variety of different models available for UO2. The different models broadly agree on the relative order of the strengths of the different slip systems, with the 1/2<110>{100} edge dislocation predicted to be the weakest slip system and 1/2<110>{110} the strongest. However, the calculated Peierls stresses depend strongly on the interatomic potential used, with values ranging between 2.7 and 12.9 GPa for glide of 1/2<110>{100} edge dislocations, 16.4-32.3 GPa for 1/2<110>{110} edge dislocations, and 6.8-13.6 GPa for 1/2<110>{111} edge dislocations. The glide of 1/2<110> screw dislocations in UO2 is also found to depend on the interatomic potential used, with some models predicting similar Peierls stresses for glide on {100} and {111}, while others predict a unique easy glide direction. Comparison with previous fully atomistic calculations show that the Peierls-Nabarro model can accurately predict dislocation properties in UO2.

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

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

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

2014-04-07

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

Prediction of Environmental Impact of High-Energy Materials with Atomistic Computer Simulations

DTIC Science & Technology

2010-11-01

from a training set of compounds. Other methods include Quantitative Struc- ture-Activity Relationship ( QSAR ) and Quantitative Structure-Property...26 28 the development of QSPR/ QSAR models, in contrast to boiling points and critical parameters derived from empirical correlations, to improve...Quadratic Configuration Interaction Singles Doubles QSAR Quantitative Structure-Activity Relationship QSPR Quantitative Structure-Property

Atomistic origin of superior performance of ionic liquid electrolytes for Al-ion batteries.

PubMed

Kamath, Ganesh; Narayanan, Badri; Sankaranarayanan, Subramanian K R S

2014-10-14

Encouraged by recent experimental findings, here we report on an in silico investigation to probe the atomistic origin behind the superior performance of ionic liquids (ILs) over traditional carbonate electrolytes for Al-ion batteries. Fundamental insights from computationally derived thermodynamic and kinetic considerations coupled with an atomistic-level description of the solvation dynamics is used to elucidate the performance improvements. The formation of low-stability ion-solvent complexes in ILs facilitates rapid Al-ion solvation-desolvation and translates into favorable transport properties (viscosity and ionic conductivity). Our results offer encouraging prospects for this approach in the a priori prediction of optimal IL formulations for Al-ion batteries.

Insights on activation enthalpy for non-Schmid slip in body-centered cubic metals

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

Hale, Lucas M.; Lim, Hojun; Zimmerman, Jonathan A.

2014-12-18

We use insights gained from atomistic simulation to develop an activation enthalpy model for dislocation slip in body-centered cubic iron. Furthermore, using a classical potential that predicts dislocation core stabilities consistent with ab initio predictions, we quantify the non-Schmid stress-dependent effects of slip. The kink-pair activation enthalpy is evaluated and a model is identified as a function of the general stress state. Thus, our model enlarges the applicability of the classic Kocks activation enthalpy model to materials with non-Schmid behavior.

Fibronectin module FN(III)9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics.

PubMed

Kubiak-Ossowska, Karina; Mulheran, Paul A; Nowak, Wieslaw

2014-08-21

The mechanism of human fibronectin adhesion synergy region (known as integrin binding region) in repeat 9 (FN(III)9) domain adsorption at pH 7 onto various and contrasting model surfaces has been studied using atomistic molecular dynamics simulations. We use an ionic model to mimic mica surface charge density but without a long-range electric field above the surface, a silica model with a long-range electric field similar to that found experimentally, and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our model silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Because it is negatively charged (-1e), FN(III)9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FN(III)9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these model surfaces does not require wholesale FN(III)9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved.

On the continuum mechanics approach for the analysis of single walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Chaudhry, M. S.; Czekanski, A.

2016-04-01

Today carbon nanotubes have found various applications in structural, thermal and almost every field of engineering. Carbon nanotubes provide great strength, stiffness resilience properties. Evaluating the structural behavior of nanoscale materials is an important task. In order to understand the materialistic behavior of nanotubes, atomistic models provide a basis for continuum mechanics modelling. Although the properties of bulk materials are consistent with the size and depends mainly on the material but the properties when we are in Nano-range, continuously change with the size. Such models start from the modelling of interatomic interaction. Modelling and simulation has advantage of cost saving when compared with the experiments. So in this project our aim is to use a continuum mechanics model of carbon nanotubes from atomistic perspective and analyses some structural behaviors of nanotubes. It is generally recognized that mechanical properties of nanotubes are dependent upon their structural details. The properties of nanotubes vary with the varying with the interatomic distance, angular orientation, radius of the tube and many such parameters. Based on such models one can analyses the variation of young's modulus, strength, deformation behavior, vibration behavior and thermal behavior. In this study some of the structural behaviors of the nanotubes are analyzed with the help of continuum mechanics models. Using the properties derived from the molecular mechanics model a Finite Element Analysis of carbon nanotubes is performed and results are verified. This study provides the insight on continuum mechanics modelling of nanotubes and hence the scope to study the effect of various parameters on some structural behavior of nanotubes.

Atomistic study on the FCC/BCC interface structure with {112}KS orientation

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

Kang, Keonwook; Beyerlein, Irene; Han, Weizhong

2011-09-23

In this study, atomistic simulation is used to explore the atomic interface structure, the intrinsic defect network, and mechanism of twin formation from the {112}KS Cu-Nb interface. The interface structure of different material systems AI-Fe and AI-Nb are also compared with Cu-Nb interface.

An atomistically informed mesoscale model for growth and coarsening during discharge in lithium-oxygen batteries

DOE PAGES

Welland, Michael J.; Lau, Kah Chun; Redfern, Paul C.; ...

2015-12-10

An atomistically informed mesoscale model is developed for the deposition of a discharge product in a Li-O 2 battery. This mescocale model includes particle growth and coarsening as well as a simplified nucleation model. The model involves LiO 2 formation through reaction of O 2 - and Li + in the electrolyte, which deposits on the cathode surface when the LiO 2 concentration reaches supersaturation in the electrolyte. A reaction-diffusion (rate-equation) model is used to describe the processes occurring in the electrolyte and a phase-field model is used to capture microstructural evolution. This model predicts that coarsening, in which largemore » particles grow and small ones disappear, has a substantial effect on the size distribution of the LiO 2 particles during the discharge process. The size evolution during discharge is the result of the interplay between this coarsening process and particle growth. The growth through continued deposition of LiO 2 has the effect of causing large particles to grow ever faster while delaying the dissolution of small particles. The predicted size evolution is consistent with experimental results for a previously reported cathode material based on activated carbon during discharge and when it is at rest, although kinetic factors need to be included. Finally, the approach described in this paper synergistically combines models on different length scales with experimental observations and should have applications in studying other related discharge processes, such as Li 2O 2 deposition, in Li-O 2 batteries and nucleation and growth in Li-S batteries.« less

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

DOE PAGES

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; ...

2017-03-08

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structuremore » of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.« less

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

NASA Astrophysics Data System (ADS)

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; Kathuria, Sagar V.; Bilsel, Osman; Matthews, C. Robert; Lane, T. J.; Pande, Vijay S.

2017-03-01

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. This prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

Free energy perturbation method for measuring elastic constants of liquid crystals

NASA Astrophysics Data System (ADS)

Joshi, Abhijeet

There is considerable interest in designing liquid crystals capable of yielding specific morphological responses in confined environments, including capillaries and droplets. The morphology of a liquid crystal is largely dictated by the elastic constants, which are difficult to measure and are only available for a handful of substances. In this work, a first-principles based method is proposed to calculate the Frank elastic constants of nematic liquid crystals directly from atomistic models. These include the standard splay, twist and bend deformations, and the often-ignored but important saddle-splay constant. The proposed method is validated using a well-studied Gay-Berne(3,5,2,1) model; we examine the effects of temperature and system size on the elastic constants in the nematic and smectic phases. We find that our measurements of splay, twist, and bend elastic constants are consistent with previous estimates for the nematic phase. We further outline the implementation of our approach for the saddle-splay elastic constant, and find it to have a value at the limits of the Ericksen inequalities. We then proceed to report results for the elastic constants commonly known liquid crystals namely 4-pentyl-4'-cynobiphenyl (5CB) using atomistic model, and show that the values predicted by our approach are consistent with a subset of the available but limited experimental literature.

Atomistic model for excitons: Capturing Strongly Bound Excitons in Monolayer Transition-Metal Dichalcogenides

NASA Astrophysics Data System (ADS)

Tseng, Frank; Simsek, Ergun; Gunlycke, Daniel

2015-03-01

Monolayer transition-metal dichalcogenides form a direct bandgap predicted in the visible regime making them attractive host materials for various electronic and optoelectronic applications. Due to a weak dielectric screening in these materials, strongly bound electron-hole pairs or excitons have binding energies up to at least several hundred meV's. While the conventional wisdom is to think of excitons as hydrogen-like quasi-particles, we show that the hydrogen model breaks down for these experimentally observed strongly bound, room-temperature excitons. To capture these non-hydrogen-like photo-excitations, we introduce an atomistic model for excitons that predicts both bright excitons and dark excitons, and their broken degeneracy in these two-dimensional materials. For strongly bound exciton states, the lattice potential significantly distorts the envelope wave functions, which affects predicted exciton peak energies. The combination of large binding energies and non-degeneracy of exciton states in monolayer transition metal dichalogendies may furthermore be exploited in room temperature applications where prolonged exciton lifetimes are necessary. This work has been funded by the Office of Naval Research (ONR), directly and through the Naval Research Laboratory (NRL). F.T and E.S acknowledge support from NRL through the NRC Research Associateship Program and ONR Summer Faculty Program, respectively.

Striped, honeycomb, and twisted moiré patterns in surface adsorption systems with highly degenerate commensurate ground states

NASA Astrophysics Data System (ADS)

Elder, K. R.; Achim, C. V.; Granato, E.; Ying, S. C.; Ala-Nissila, T.

2017-11-01

Atomistically thin adsorbate layers on surfaces with a lattice mismatch display complex spatial patterns and ordering due to strain-driven self-organization. In this work, a general formalism to model such ultrathin adsorption layers that properly takes into account the competition between strain and adhesion energy of the layers is presented. The model is based on the amplitude expansion of the two-dimensional phase field crystal (PFC) model, which retains atomistic length scales but allows relaxation of the layers at diffusive time scales. The specific systems considered here include cases where both the film and the adsorption potential can have either honeycomb (H) or triangular (T) symmetry. These systems include the so-called (1 ×1 ) , (√{3 }×√{3 }) R 30∘ , (2 ×2 ) , (√{7 }×√{7 }) R 19 .1∘ , and other higher order states that can contain a multitude of degenerate commensurate ground states. The relevant phase diagrams for many combinations of the H and T systems are mapped out as a function of adhesion strength and misfit strain. The coarsening patterns in some of these systems is also examined. The predictions are in good agreement with existing experimental data for selected strained ultrathin adsorption layers.

Components for Atomistic-to-Continuum Multiscale Modeling of Flow in Micro- and Nanofluidic Systems

DOE PAGES

Adalsteinsson, Helgi; Debusschere, Bert J.; Long, Kevin R.; ...

2008-01-01

Micro- and nanofluidics pose a series of significant challenges for science-based modeling. Key among those are the wide separation of length- and timescales between interface phenomena and bulk flow and the spatially heterogeneous solution properties near solid-liquid interfaces. It is not uncommon for characteristic scales in these systems to span nine orders of magnitude from the atomic motions in particle dynamics up to evolution of mass transport at the macroscale level, making explicit particle models intractable for all but the simplest systems. Recently, atomistic-to-continuum (A2C) multiscale simulations have gained a lot of interest as an approach to rigorously handle particle-levelmore » dynamics while also tracking evolution of large-scale macroscale behavior. While these methods are clearly not applicable to all classes of simulations, they are finding traction in systems in which tight-binding, and physically important, dynamics at system interfaces have complex effects on the slower-evolving large-scale evolution of the surrounding medium. These conditions allow decomposition of the simulation into discrete domains, either spatially or temporally. In this paper, we describe how features of domain decomposed simulation systems can be harnessed to yield flexible and efficient software for multiscale simulations of electric field-driven micro- and nanofluidics.« less

Multiscale Analysis of Delamination of Carbon Fiber-Epoxy Laminates with Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Riddick, Jaret C.; Frankland, SJV; Gates, TS

2006-01-01

A multi-scale analysis is presented to parametrically describe the Mode I delamination of a carbon fiber/epoxy laminate. In the midplane of the laminate, carbon nanotubes are included for the purposes of selectively enhancing the fracture toughness of the laminate. To analyze carbon fiber epoxy carbon nanotube laminate, the multi-scale methodology presented here links a series of parameterizations taken at various length scales ranging from the atomistic through the micromechanical to the structural level. At the atomistic scale molecular dynamics simulations are performed in conjunction with an equivalent continuum approach to develop constitutive properties for representative volume elements of the molecular structure of components of the laminate. The molecular-level constitutive results are then used in the Mori-Tanaka micromechanics to develop bulk properties for the epoxy-carbon nanotube matrix system. In order to demonstrate a possible application of this multi-scale methodology, a double cantilever beam specimen is modeled. An existing analysis is employed which uses discrete springs to model the fiber bridging affect during delamination propagation. In the absence of empirical data or a damage mechanics model describing the effect of CNTs on fracture toughness, several tractions laws are postulated, linking CNT volume fraction to fiber bridging in a DCB specimen. Results from this demonstration are presented in terms of DCB specimen load-displacement responses.

Structural and Mechanical Properties of Intermediate Filaments under Extreme Conditions and Disease

NASA Astrophysics Data System (ADS)

Qin, Zhao

Intermediate filaments are one of the three major components of the cytoskeleton in eukaryotic cells. It was discovered during the recent decades that intermediate filament proteins play key roles to reinforce cells subjected to large-deformation as well as participate in signal transduction. However, it is still poorly understood how the nanoscopic structure, as well as the biochemical properties of these protein molecules contribute to their biomechanical functions. In this research we investigate the material function of intermediate filaments under various extreme mechanical conditions as well as disease states. We use a full atomistic model and study its response to mechanical stresses. Learning from the mechanical response obtained from atomistic simulations, we build mesoscopic models following the finer-trains-coarser principles. By using this multiple-scale model, we present a detailed analysis of the mechanical properties and associated deformation mechanisms of intermediate filament network. We reveal the mechanism of a transition from alpha-helices to beta-sheets with subsequent intermolecular sliding under mechanical force, which has been inferred previously from experimental results. This nanoscale mechanism results in a characteristic nonlinear force-extension curve, which leads to a delocalization of mechanical energy and prevents catastrophic fracture. This explains how intermediate filament can withstand extreme mechanical deformation of > 1 00% strain despite the presence of structural defects. We combine computational and experimental techniques to investigate the molecular mechanism of Hutchinson-Gilford progeria syndrome, a premature aging disease. We find that the mutated lamin tail .domain is more compact and stable than the normal one. This altered structure and stability may enhance the association of intermediate filaments with the nuclear membrane, providing a molecular mechanism of the disease. We study the nuclear membrane association with intermediate filaments by focusing on the effect of calcium on the maturation process of lamin A. Our result shows that calcium plays a regulatory role in the post-translational processing of lam in A by tuning its molecular conformation and mechanics. Based on these findings we demonstrate that multiple-scale computational modeling provides a useful tool in understanding the biomechanical property and disease mechanism of intermediate filaments. We provide a perspective on research opportunities to improve the foundation for engineering the mechanical and biochemical functions of biomaterials. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs@mit.edu)

Atomistic Simulation of the Rate-Dependent Ductile-to-Brittle Failure Transition in Bicrystalline Metal Nanowires.

PubMed

Tao, Weiwei; Cao, Penghui; Park, Harold S

2018-02-14

The mechanical properties and plastic deformation mechanisms of metal nanowires have been studied intensely for many years. One of the important yet unresolved challenges in this field is to bridge the gap in properties and deformation mechanisms reported for slow strain rate experiments (∼10 -2 s -1 ), and high strain rate molecular dynamics (MD) simulations (∼10 8 s -1 ) such that a complete understanding of strain rate effects on mechanical deformation and plasticity can be obtained. In this work, we use long time scale atomistic modeling based on potential energy surface exploration to elucidate the atomistic mechanisms governing a strain-rate-dependent incipient plasticity and yielding transition for face centered cubic (FCC) copper and silver nanowires. The transition occurs for both metals with both pristine and rough surfaces for all computationally accessible diameters (<10 nm). We find that the yield transition is induced by a transition in the incipient plastic event from Shockley partials nucleated on primary slip systems at MD strain rates to the nucleation of planar defects on non-Schmid slip planes at experimental strain rates, where multiple twin boundaries and planar stacking faults appear in copper and silver, respectively. Finally, we demonstrate that, at experimental strain rates, a ductile-to-brittle transition in failure mode similar to previous experimental studies on bicrystalline silver nanowires is observed, which is driven by differences in dislocation activity and grain boundary mobility as compared to the high strain rate case.

STM experiment and atomistic modelling hand in hand: individual molecules on semiconductor surfaces

NASA Astrophysics Data System (ADS)

Briggs, G. A. D.; Fisher, A. J.

When the scanning tunnelling microscope was invented, the world was amazed at the atomic resolution images of surfaces which could be obtained. It soon became apparent that it was one thing to obtain an image, and quite another to understand the structure that was seen. Happily the developments in real space experimental techniques for studying surfaces have been accompanied by developments in real space theoretical techniques for modelling electronic structure and bonding at surfaces. The aim of this review is to describe how and why STM experiments and atomistic modelling should be combined and what they can then be expected to tell us. A summary is given of the experimental methods for theorists and vice versa, and their relationship is illustrated using a number of case studies where they have been used together. To give the review a coherent focus the examples are confined to studies of adsorbed molecules on semiconductor surfaces, in particular Si(001) and GaAs(001). Questions thus addressed include: How are experimental images and structural modelling linked by tunnelling theory? What can they tell us together that we could not learn from experiment or theory alone? What can we learn about atomic positions and bonding at semiconductor surfaces with and without adsorbed molecules? How many different ways are there to relate images to calculations?

Adaptive selection and validation of models of complex systems in the presence of uncertainty

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

Farrell-Maupin, Kathryn; Oden, J. T.

This study describes versions of OPAL, the Occam-Plausibility Algorithm in which the use of Bayesian model plausibilities is replaced with information theoretic methods, such as the Akaike Information Criterion and the Bayes Information Criterion. Applications to complex systems of coarse-grained molecular models approximating atomistic models of polyethylene materials are described. All of these model selection methods take into account uncertainties in the model, the observational data, the model parameters, and the predicted quantities of interest. A comparison of the models chosen by Bayesian model selection criteria and those chosen by the information-theoretic criteria is given.

Adaptive selection and validation of models of complex systems in the presence of uncertainty

DOE PAGES

Farrell-Maupin, Kathryn; Oden, J. T.

2017-08-01

This study describes versions of OPAL, the Occam-Plausibility Algorithm in which the use of Bayesian model plausibilities is replaced with information theoretic methods, such as the Akaike Information Criterion and the Bayes Information Criterion. Applications to complex systems of coarse-grained molecular models approximating atomistic models of polyethylene materials are described. All of these model selection methods take into account uncertainties in the model, the observational data, the model parameters, and the predicted quantities of interest. A comparison of the models chosen by Bayesian model selection criteria and those chosen by the information-theoretic criteria is given.

Atomistic simulation of damage accumulation and amorphization in Ge

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

Gomez-Selles, Jose L., E-mail: joseluis.gomezselles@imdea.org; Martin-Bragado, Ignacio; Claverie, Alain

2015-02-07

Damage accumulation and amorphization mechanisms by means of ion implantation in Ge are studied using Kinetic Monte Carlo and Binary Collision Approximation techniques. Such mechanisms are investigated through different stages of damage accumulation taking place in the implantation process: from point defect generation and cluster formation up to full amorphization of Ge layers. We propose a damage concentration amorphization threshold for Ge of ∼1.3 × 10{sup 22} cm{sup −3} which is independent on the implantation conditions. Recombination energy barriers depending on amorphous pocket sizes are provided. This leads to an explanation of the reported distinct behavior of the damage generated by different ions.more » We have also observed that the dissolution of clusters plays an important role for relatively high temperatures and fluences. The model is able to explain and predict different damage generation regimes, amount of generated damage, and extension of amorphous layers in Ge for different ions and implantation conditions.« less

Ab initio calculation of the deprotonation constants of an atomistically defined nanometer-sized, aluminium hydroxide oligomer

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

Wander, Matthew C. F.; Shuford, Kevin L.; Rustad, James R.

Aluminium possesses significant and diverse chemistry. Numerous compounds have been defined, and the elucidation of their chemistry is of significant geochemical interest. In this paper, a brucite-like, eight-aluminium aqueous cluster is modelled with density functional theory to identify its primary site of deprotonation and the associated pK(a) constant using both explicit (a full first solvent shell) and implicit solvent. Two methods for calculating the pK(a) are compared. We found that a bond density approach is better than a direct energy calculation for ions with large charge and high symmetry. The terminal aluminium atoms have equatorial ligated waters that in solventmore » have one long O-H bond. This site is more reactive than any of the other protons on the particle. Insights into the experimental crystal structure and Bader's Atoms in Molecules density analysis are presented as routes to reduce the computational time required for the identification of protonation sites.« less

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

Du, Jincheng; Rimsza, Jessica

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Microscopic origin of the optical processes in blue sapphire.

PubMed

Bristow, Jessica K; Parker, Stephen C; Catlow, C Richard A; Woodley, Scott M; Walsh, Aron

2013-06-11

Al2O3 changes from transparent to a range of intense colours depending on the chemical impurities present. In blue sapphire, Fe and Ti are incorporated; however, the chemical process that gives rise to the colour has long been debated. Atomistic modelling identifies charge transfer from Ti(III) to Fe(III) as being responsible for the characteristic blue appearance.

Structure–activity relationships for biodistribution, pharmacokinetics, and excretion of atomically precise nanoclusters in a murine model†

PubMed Central

Wong, O. Andrea; Hansen, Ryan J.; Ni, Thomas W.; Heinecke, Christine L.; Compel, W. Scott; Gustafson, Daniel L.

2013-01-01

The absorption, distribution, metabolism and excretion (ADME) and pharmacokinetic (PK) properties of inorganic nanoparticles with hydrodynamic diameters between 2 and 20 nm are presently unpredictable. It is unclear whether unpredictable in vivo properties and effects arise from a subset of molecules in a nanomaterials preparation, or if the ADME/PK properties are ensemble properties of an entire preparation. Here we characterize the ADME/PK properties of atomically precise preparations of ligand protected gold nanoclusters in a murine model system. We constructed atomistic models and tested in vivo properties for five well defined compounds, based on crystallographically resolved Au25(SR)18 and Au102(SR)44 nanoclusters with different (SR) ligand shells. To rationalize unexpected distribution and excretion properties observed for several clusters in this study and others, we defined a set of atomistic structure–activity relationships (SAR) for nanoparticles, which includes previously investigated parameters such as particle hydrodynamic diameter and net charge, and new parameters such as hydrophobic surface area and surface charge density. Overall we find that small changes in particle formulation can provoke dramatic yet potentially predictable changes in ADME/PK. PMID:24057086

Multipolar electrostatics.

PubMed

Cardamone, Salvatore; Hughes, Timothy J; Popelier, Paul L A

2014-06-14

Atomistic simulation of chemical systems is currently limited by the elementary description of electrostatics that atomic point-charges offer. Unfortunately, a model of one point-charge for each atom fails to capture the anisotropic nature of electronic features such as lone pairs or π-systems. Higher order electrostatic terms, such as those offered by a multipole moment expansion, naturally recover these important electronic features. The question remains as to why such a description has not yet been widely adopted by popular molecular mechanics force fields. There are two widely-held misconceptions about the more rigorous formalism of multipolar electrostatics: (1) Accuracy: the implementation of multipole moments, compared to point-charges, offers little to no advantage in terms of an accurate representation of a system's energetics, structure and dynamics. (2) Efficiency: atomistic simulation using multipole moments is computationally prohibitive compared to simulation using point-charges. Whilst the second of these may have found some basis when computational power was a limiting factor, the first has no theoretical grounding. In the current work, we disprove the two statements above and systematically demonstrate that multipole moments are not discredited by either. We hope that this perspective will help in catalysing the transition to more realistic electrostatic modelling, to be adopted by popular molecular simulation software.

Free vibration analysis of single-walled boron nitride nanotubes based on a computational mechanics framework

NASA Astrophysics Data System (ADS)

Yan, J. W.; Tong, L. H.; Xiang, Ping

2017-12-01

Free vibration behaviors of single-walled boron nitride nanotubes are investigated using a computational mechanics approach. Tersoff-Brenner potential is used to reflect atomic interaction between boron and nitrogen atoms. The higher-order Cauchy-Born rule is employed to establish the constitutive relationship for single-walled boron nitride nanotubes on the basis of higher-order gradient continuum theory. It bridges the gaps between the nanoscale lattice structures with a continuum body. A mesh-free modeling framework is constructed, using the moving Kriging interpolation which automatically satisfies the higher-order continuity, to implement numerical simulation in order to match the higher-order constitutive model. In comparison with conventional atomistic simulation methods, the established atomistic-continuum multi-scale approach possesses advantages in tackling atomic structures with high-accuracy and high-efficiency. Free vibration characteristics of single-walled boron nitride nanotubes with different boundary conditions, tube chiralities, lengths and radii are examined in case studies. In this research, it is pointed out that a critical radius exists for the evaluation of fundamental vibration frequencies of boron nitride nanotubes; opposite trends can be observed prior to and beyond the critical radius. Simulation results are presented and discussed.

Thermally activated vapor bubble nucleation: The Landau-Lifshitz-Van der Waals approach

NASA Astrophysics Data System (ADS)

Gallo, Mirko; Magaletti, Francesco; Casciola, Carlo Massimo

2018-05-01

Vapor bubbles are formed in liquids by two mechanisms: evaporation (temperature above the boiling threshold) and cavitation (pressure below the vapor pressure). The liquid resists in these metastable (overheating and tensile, respectively) states for a long time since bubble nucleation is an activated process that needs to surmount the free energy barrier separating the liquid and the vapor states. The bubble nucleation rate is difficult to assess and, typically, only for extremely small systems treated at an atomistic level of detail. In this work a powerful approach, based on a continuum diffuse interface modeling of the two-phase fluid embedded with thermal fluctuations (fluctuating hydrodynamics), is exploited to study the nucleation process in homogeneous conditions, evaluating the bubble nucleation rates and following the long-term dynamics of the metastable system, up to the bubble coalescence and expansion stages. In comparison with more classical approaches, this methodology allows us on the one hand to deal with much larger systems observed for a much longer time than possible with even the most advanced atomistic models. On the other, it extends continuum formulations to thermally activated processes, impossible to deal with in a purely determinist setting.

Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ′ Microstructures

PubMed Central

Prakash, Aruna; Bitzek, Erik

2017-01-01

Single-crystal Ni-base superalloys, consisting of a two-phase γ/γ′ microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ′ phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ/γ′ microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ′ particles with planar γ/γ′ interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples—the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions. PMID:28772453

Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ' Microstructures.

PubMed

Prakash, Aruna; Bitzek, Erik

2017-01-23

Single-crystal Ni-base superalloys, consisting of a two-phase γ / γ ' microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ ' phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ / γ ' microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ ' particles with planar γ / γ ' interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples-the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions.

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

NASA Astrophysics Data System (ADS)

Lyu, Dandan; Li, Shaofan

2017-10-01

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

Revealing spatially heterogeneous relaxation in a model nanocomposite.

PubMed

Cheng, Shiwang; Mirigian, Stephen; Carrillo, Jan-Michael Y; Bocharova, Vera; Sumpter, Bobby G; Schweizer, Kenneth S; Sokolov, Alexei P

2015-11-21

The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility gradient shows no "glassy" layer, but the α-relaxation time near the nanoparticle grows with cooling faster than the α-relaxation time in the bulk and is ∼20 times longer at low temperatures. The interfacial layer thickness increases from ∼1.8 nm at higher temperatures to ∼3.5 nm upon cooling to near bulk Tg. A real space microscopic description of the mobility gradient is constructed by synergistically combining high temperature atomistic simulation with theory. Our analysis suggests that the interfacial slowing down arises mainly due to an increase of the local cage scale barrier for activated hopping induced by enhanced packing and densification near the nanoparticle surface. The theory is employed to predict how local surface densification can be manipulated to control layer dynamics and shear rigidity over a wide temperature range.

Atomistic calculations of dislocation core energy in aluminium

DOE PAGES

Zhou, X. W.; Sills, R. B.; Ward, D. K.; ...

2017-02-16

A robust molecular dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: it does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield highly converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and Burgers vector. These calculations show that, for the face-centred-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elasticmore » energy: Ec = A·sin 2β + B·cos 2β, and this dependence is independent of temperature between 100 and 300 K. By further analysing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and radius of a perfect versus extended dislocation. With our methodology, the dislocation core energy can be accurately accounted for in models of plastic deformation.« less

Atomistic calculations of dislocation core energy in aluminium

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

Zhou, X. W.; Sills, R. B.; Ward, D. K.

A robust molecular dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: it does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield highly converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and Burgers vector. These calculations show that, for the face-centred-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elasticmore » energy: Ec = A·sin 2β + B·cos 2β, and this dependence is independent of temperature between 100 and 300 K. By further analysing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and radius of a perfect versus extended dislocation. With our methodology, the dislocation core energy can be accurately accounted for in models of plastic deformation.« less

Understanding and Controlling the Aggregative Growth of Platinum Nanoparticles in Atomic Layer Deposition: An Avenue to Size Selection

PubMed Central

2017-01-01

We present an atomistic understanding of the evolution of the size distribution with temperature and number of cycles in atomic layer deposition (ALD) of Pt nanoparticles (NPs). Atomistic modeling of our experiments teaches us that the NPs grow mostly via NP diffusion and coalescence rather than through single-atom processes such as precursor chemisorption, atom attachment, and Ostwald ripening. In particular, our analysis shows that the NP aggregation takes place during the oxygen half-reaction and that the NP mobility exhibits a size- and temperature-dependent scaling. Finally, we show that contrary to what has been widely reported, in general, one cannot simply control the NP size by the number of cycles alone. Instead, while the amount of Pt deposited can be precisely controlled over a wide range of temperatures, ALD-like precision over the NP size requires low deposition temperatures (e.g., T < 100 °C) when growth is dominated by atom attachment. PMID:28178779

Atomistic simulation of CO2 solubility in poly(ethylene oxide) oligomers

NASA Astrophysics Data System (ADS)

Hong, Bingbing; Panagiotopoulos, Athanassios Z.

2014-06-01

We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henry's constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henry's constant. Dependence of the calculated Henry's constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length.

X-ray Spectroscopy and Imaging as Multiscale Probes of Intercalation Phenomena in Cathode Materials

NASA Astrophysics Data System (ADS)

Horrocks, Gregory A.; De Jesus, Luis R.; Andrews, Justin L.; Banerjee, Sarbajit

2017-09-01

Intercalation phenomena are at the heart of modern electrochemical energy storage. Nevertheless, as out-of-equilibrium processes involving concomitant mass and charge transport, such phenomena can be difficult to engineer in a predictive manner. The rational design of electrode architectures requires mechanistic understanding of physical phenomena spanning multiple length scales, from atomistic distortions and electron localization at individual transition metal centers to phase inhomogeneities and intercalation gradients in individual particles and concentration variances across ensembles of particles. In this review article, we discuss the importance of the electronic structure in mediating electrochemical storage and mesoscale heterogeneity. In particular, we discuss x-ray spectroscopy and imaging probes of electronic and atomistic structure as well as statistical regression methods that allow for monitoring of the evolution of the electronic structure as a function of intercalation. The layered α-phase of V2O5 is used as a model system to develop fundamental ideas on the origins of mesoscale heterogeneity.

Atomistic modeling of Mg/Nb interfaces: shear strength and interaction with lattice glide dislocations

DOE PAGES

Yadav, Satyesh Kumar; Shao, S.; Chen, Youxing; ...

2017-10-17

Here, using a newly developed embedded-atom-method potential for Mg–Nb, the semi-coherent Mg/Nb interface with the Kurdjumov–Sachs orientation relationship is studied. Atomistic simulations have been carried out to understand the shear strength of the interface, as well as the interaction between lattice glide dislocations and the interface. The interface shear mechanisms are dependent on the shear loading directions, through either interface sliding between Mg and Nb atomic layers or nucleation and gliding of Shockley partial dislocations in between the first two atomic planes in Mg at the interface. The shear strength for the Mg/Nb interface is found to be generally high,more » in the range of 0.9–1.3 GPa depending on the shear direction. As a consequence, the extents of dislocation core spread into the interface are considerably small, especially when compared to the case of other “weak” interfaces such as the Cu/Nb interface.« less

Revealing spatially heterogeneous relaxation in a model nanocomposite

DOE PAGES

Cheng, Shiwang; Mirigian, Stephen; Carrillo, Jan-Michael Y.; ...

2015-11-18

The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility gradient shows no glassy layer, but the -relaxation time near the nanoparticle grows with cooling faster than the -relaxation time in the bulk and is ~20 times longer at low temperatures. The interfacial layer thickness increases from ~1.8 nm at higher temperatures to ~3.5 nm upon cooling to near bulk T g. A real space microscopic description of the mobility gradient is constructed by synergistically combining high temperature atomistic simulation with theory.more » Our analysis suggests that the interfacial slowing down arises mainly due to an increase of the local cage scale barrier for activated hopping induced by enhanced packing and densification near the nanoparticle surface. As a result, the theory is employed to predict how local surface densification can be manipulated to control layer dynamics and shear rigidity over a wide temperature range.« less

Improved Atomistic Monte Carlo Simulations Demonstrate that Poly-L-Proline Adopts Heterogeneous Ensembles of Conformations of Semi-Rigid Segments Interrupted by Kinks

PubMed Central

Radhakrishnan, Aditya; Vitalis, Andreas; Mao, Albert H.; Steffen, Adam T.; Pappu, Rohit V.

2012-01-01

Poly-L-proline (PLP) polymers are useful mimics of biologically relevant proline-rich sequences. Biophysical and computational studies of PLP polymers in aqueous solutions are challenging because of the diversity of length scales and the slow time scales for conformational conversions. We describe an atomistic simulation approach that combines an improved ABSINTH implicit solvation model, with conformational sampling based on standard and novel Metropolis Monte Carlo moves. Refinements to forcefield parameters were guided by published experimental data for proline-rich systems. We assessed the validity of our simulation results through quantitative comparisons to experimental data that were not used in refining the forcefield parameters. Our analysis shows that PLP polymers form heterogeneous ensembles of conformations characterized by semi-rigid, rod-like segments interrupted by kinks, which result from a combination of internal cis peptide bonds, flexible backbone ψ-angles, and the coupling between ring puckering and backbone degrees of freedom. PMID:22329658

Solute effects on edge dislocation pinning in complex alpha-Fe alloys

NASA Astrophysics Data System (ADS)

Pascuet, M. I.; Martínez, E.; Monnet, G.; Malerba, L.

2017-10-01

Reactor pressure vessel steels are well-known to harden and embrittle under neutron irradiation, mainly because of the formation of obstacles to the motion of dislocations, in particular, precipitates and clusters composed of Cu, Ni, Mn, Si and P. In this paper, we employ two complementary atomistic modelling techniques to study the heterogeneous precipitation and segregation of these elements and their effects on the edge dislocations in BCC iron. We use a special and highly computationally efficient Monte Carlo algorithm in a constrained semi-grand canonical ensemble to compute the equilibrium configurations for solute clusters around the dislocation core. Next, we use standard molecular dynamics to predict and analyze the effect of this segregation on the dislocation mobility. Consistently with expectations our results confirm that the required stress for dislocation unpinning from the precipitates formed on top of it is quite large. The identification of the precipitate resistance allows a quantitative treatment of atomistic results, enabling scale transition towards larger scale simulations, such as dislocation dynamics or phase field.

Enhanced calculation of eigen-stress field and elastic energy in atomistic interdiffusion of alloys

NASA Astrophysics Data System (ADS)

Cecilia, José M.; Hernández-Díaz, A. M.; Castrillo, Pedro; Jiménez-Alonso, J. F.

2017-02-01

The structural evolution of alloys is affected by the elastic energy associated to eigen-stress fields. However, efficient calculations of the elastic energy in evolving geometries are actually a great challenge in promising atomistic simulation techniques such as Kinetic Monte Carlo (KMC) methods. In this paper, we report two complementary algorithms to calculate the eigen-stress field by linear superposition (a.k.a. LSA, Lineal Superposition Algorithm) and the elastic energy modification in atomistic interdiffusion of alloys (the Atom Exchange Elastic Energy Evaluation (AE4) Algorithm). LSA is shown to be appropriated for fast incremental stress calculation in highly nanostructured materials, whereas AE4 provides the required input for KMC and, additionally, it can be used to evaluate the accuracy of the eigen-stress field calculated by LSA. Consequently, they are suitable to be used on-the-fly with KMC. Both algorithms are massively parallel by their definition and thus well-suited for their parallelization on modern Graphics Processing Units (GPUs). Our computational studies confirm that we can obtain significant improvements compared to conventional Finite Element Methods, and the utilization of GPUs opens up new possibilities for the development of these methods in atomistic simulation of materials.

AACSD: An atomistic analyzer for crystal structure and defects

NASA Astrophysics Data System (ADS)

Liu, Z. R.; Zhang, R. F.

2018-01-01

We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

Understanding the physical metallurgy of the CoCrFeMnNi high-entropy alloy: an atomistic simulation study

NASA Astrophysics Data System (ADS)

Choi, Won-Mi; Jo, Yong Hee; Sohn, Seok Su; Lee, Sunghak; Lee, Byeong-Joo

2018-01-01

Although high-entropy alloys (HEAs) are attracting interest, the physical metallurgical mechanisms related to their properties have mostly not been clarified, and this limits wider industrial applications, in addition to the high alloy costs. We clarify the physical metallurgical reasons for the materials phenomena (sluggish diffusion and micro-twining at cryogenic temperatures) and investigate the effect of individual elements on solid solution hardening for the equiatomic CoCrFeMnNi HEA based on atomistic simulations (Monte Carlo, molecular dynamics and molecular statics). A significant number of stable vacant lattice sites with high migration energy barriers exists and is thought to cause the sluggish diffusion. We predict that the hexagonal close-packed (hcp) structure is more stable than the face-centered cubic (fcc) structure at 0 K, which we propose as the fundamental reason for the micro-twinning at cryogenic temperatures. The alloying effect on the critical resolved shear stress (CRSS) is well predicted by the atomistic simulation, used for a design of non-equiatomic fcc HEAs with improved strength, and is experimentally verified. This study demonstrates the applicability of the proposed atomistic approach combined with a thermodynamic calculation technique to a computational design of advanced HEAs.

Prediction of Thermal Transport Properties of Materials with Microstructural Complexity

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

Chen, Youping

This project aims at overcoming the major obstacle standing in the way of progress in dynamic multiscale simulation, which is the lack of a concurrent atomistic-continuum method that allows phonons, heat and defects to pass through the atomistic-continuum interface. The research has led to the development of a concurrent atomistic-continuum (CAC) methodology for multiscale simulations of materials microstructural, mechanical and thermal transport behavior. Its efficacy has been tested and demonstrated through simulations of dislocation dynamics and phonon transport coupled with microstructural evolution in a variety of materials and through providing visual evidences of the nature of phonon transport, such asmore » showing the propagation of heat pulses in single and polycrystalline solids is partially ballistic and partially diffusive. In addition to providing understanding on phonon scattering with phase interface and with grain boundaries, the research has contributed a multiscale simulation tool for understanding of the behavior of complex materials and has demonstrated the capability of the tool in simulating the dynamic, in situ experimental studies of nonequilibrium transient transport processes in material samples that are at length scales typically inaccessible by atomistically resolved methods.« less

Understanding the Irradiation Behavior of Zirconium Carbide

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

Motta, Arthur; Sridharan, Kumar; Morgan, Dane

2013-10-11

Zirconium carbide (ZrC) is being considered for utilization in high-temperature gas-cooled reactor fuels in deep-burn TRISO fuel. Zirconium carbide possesses a cubic B1-type crystal structure with a high melting point, exceptional hardness, and good thermal and electrical conductivities. The use of ZrC as part of the TRISO fuel requires a thorough understanding of its irradiation response. However, the radiation effects on ZrC are still poorly understood. The majority of the existing research is focused on the radiation damage phenomena at higher temperatures (>450{degree}C) where many fundamental aspects of defect production and kinetics cannot be easily distinguished. Little is known aboutmore » basic defect formation, clustering, and evolution of ZrC under irradiation, although some atomistic simulation and phenomenological studies have been performed. Such detailed information is needed to construct a model describing the microstructural evolution in fast-neutron irradiated materials that will be of great technological importance for the development of ZrC-based fuel. The goal of the proposed project is to gain fundamental understanding of the radiation-induced defect formation in zirconium carbide and irradiation response by using a combination of state-of-the-art experimental methods and atomistic modeling. This project will combine (1) in situ ion irradiation at a specialized facility at a national laboratory, (2) controlled temperature proton irradiation on bulk samples, and (3) atomistic modeling to gain a fundamental understanding of defect formation in ZrC. The proposed project will cover the irradiation temperatures from cryogenic temperature to as high as 800{degree}C, and dose ranges from 0.1 to 100 dpa. The examination of this wide range of temperatures and doses allows us to obtain an experimental data set that can be effectively used to exercise and benchmark the computer calculations of defect properties. Combining the examination of radiation-induced microstructures mapped spatially and temporally, microstructural evolution during post-irradiation annealing, and atomistic modeling of defect formation and transport energetics will provide new, critical understanding about property changes in ZrC. The behavior of materials under irradiation is determined by the balance between damage production, defect clustering, and lattice response. In order to predict those effects at high temperatures so targeted testing can be expanded and extrapolated beyond the known database, it is necessary to determine the defect energetics and mobilities as these control damage accumulation and annealing. In particular, low-temperature irradiations are invaluable for determining the regions of defect mobility. Computer simulation techniques are particularly useful for identifying basic defect properties, especially if closely coupled with a well-constructed and complete experimental database. The close coupling of calculation and experiment in this project will provide mutual benchmarking and allow us to glean a deeper understanding of the irradiation response of ZrC, which can then be applied to the prediction of its behavior in reactor conditions.« less

Simulating Self-Assembly with Simple Models

NASA Astrophysics Data System (ADS)

Rapaport, D. C.

Results from recent molecular dynamics simulations of virus capsid self-assembly are described. The model is based on rigid trapezoidal particles designed to form polyhedral shells of size 60, together with an atomistic solvent. The underlying bonding process is fully reversible. More extensive computations are required than in previous work on icosahedral shells built from triangular particles, but the outcome is a high yield of closed shells. Intermediate clusters have a variety of forms, and bond counts provide a useful classification scheme

The Discontinuous Galerkin Method for the Multiscale Modeling of Dynamics of Crystalline Solids

DTIC Science & Technology

2007-08-26

number. 1. REPORT DATE 26 AUG 2007 2 . REPORT TYPE 3. DATES COVERED 00-00-2007 to 00-00-2007 4. TITLE AND SUBTITLE The Discontinuous Galerkin...Dynamics method (MAAD) [ 2 ], the bridging scale method [47], the bridging domain methods [48], the heterogeneous multiscale method (HMM) [23, 36, 24], and...method consists of three components, 1. a macro solver for the continuum model, 2 . a micro solver to equilibrate the atomistic system locally to the appro

Understanding luminescence properties of grain boundaries in GaN thin films and their atomistic origin

NASA Astrophysics Data System (ADS)

Yoo, Hyobin; Yoon, Sangmoon; Chung, Kunook; Kang, Seoung-Hun; Kwon, Young-Kyun; Yi, Gyu-Chul; Kim, Miyoung

2018-03-01

We report our findings on the optical properties of grain boundaries in GaN films grown on graphene layers and discuss their atomistic origin. We combine electron backscatter diffraction with cathodoluminescence to directly correlate the structural defects with their optical properties, enabling the high-precision local luminescence measurement of the grain boundaries in GaN films. To further understand the atomistic origin of the luminescence properties, we carefully probed atomic core structures of the grain boundaries by exploiting aberration-corrected scanning transmission electron microscopy. The atomic core structures of grain boundaries show different ordering behaviors compared with those observed previously in threading dislocations. Energetics of the grain boundary core structures and their correlation with electronic structures were studied by first principles calculation.

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

PubMed

Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane

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

Nickels, Jonathan D.; Chatterjee, Sneha; Mostofian, Barmak

Lipid extracts are an excellent choice of model biomembrane; however at present, there are no commercially available lipid extracts or computational models that mimic microbial membranes containing the branched-chain fatty acids found in many pathogenic and industrially relevant bacteria. Here, we advance the extract of Bacillus subtilis as a standard model for these diverse systems, providing a detailed experimental description and equilibrated atomistic bilayer model included as Supporting Information to this Letter and at (http://cmb.ornl.gov/members/cheng). The development and validation of this model represents an advance that enables more realistic simulations and experiments on bacterial membranes and reconstituted bacterial membrane proteins.

An explicitly solvated full atomistic model of the cardiac thin filament and application on the calcium binding affinity effects from familial hypertrophic cardiomyopathy linked mutations

NASA Astrophysics Data System (ADS)

Williams, Michael; Schwartz, Steven

2015-03-01

The previous version of our cardiac thin filament (CTF) model consisted of the troponin complex (cTn), two coiled-coil dimers of tropomyosin (Tm), and 29 actin units. We now present the newest revision of the model to include explicit solvation. The model was developed to continue our study of genetic mutations in the CTF proteins which are linked to familial hypertrophic cardiomyopathies. Binding of calcium to the cTnC subunit causes subtle conformational changes to propagate through the cTnC to the cTnI subunit which then detaches from actin. Conformational changes propagate through to the cTnT subunit, which allows Tm to move into the open position along actin, leading to muscle contraction. Calcium disassociation allows for the reverse to occur, which results in muscle relaxation. The inclusion of explicit TIP3 water solvation allows for the model to get better individual local solvent to protein interactions; which are important when observing the N-lobe calcium binding pocket of the cTnC. We are able to compare in silica and in vitro experimental results to better understand the physiological effects from mutants, such as the R92L/W and F110V/I of the cTnT, on the calcium binding affinity compared to the wild type.

Strain field determination in III-V heteroepitaxy coupling finite elements with experimental and theoretical techniques at the nanoscale

NASA Astrophysics Data System (ADS)

Florini, Nikoletta; Dimitrakopulos, George P.; Kioseoglou, Joseph; Pelekanos, Nikos T.; Kehagias, Thomas

2017-04-01

We are briefly reviewing the current status of elastic strain field determination in III-V heteroepitaxial nanostructures, linking finite elements (FE) calculations with quantitative nanoscale imaging and atomistic calculation techniques. III-V semiconductor nanostructure systems of various dimensions are evaluated in terms of their importance in photonic and microelectronic devices. As elastic strain distribution inside nano-heterostructures has a significant impact on the alloy composition, and thus their electronic properties, it is important to accurately map its components both at the interface plane and along the growth direction. Therefore, we focus on the determination of the stress-strain fields in III-V heteroepitaxial nanostructures by experimental and theoretical methods with emphasis on the numerical FE method by means of anisotropic continuum elasticity (CE) approximation. Subsequently, we present our contribution to the field by coupling FE simulations on InAs quantum dots (QDs) grown on (211)B GaAs substrate, either uncapped or buried, and GaAs/AlGaAs core-shell nanowires (NWs) grown on (111) Si, with quantitative high-resolution transmission electron microscopy (HRTEM) methods and atomistic molecular dynamics (MD) calculations. Full determination of the elastic strain distribution can be exploited for band gap tailoring of the heterostructures by controlling the content of the active elements, and thus influence the emitted radiation.

Cracking and adhesion at small scales: atomistic and continuum studies of flaw tolerant nanostructures

NASA Astrophysics Data System (ADS)

Buehler, Markus J.; Yao, Haimin; Gao, Huajian; Ji, Baohua

2006-07-01

Once the characteristic size of materials reaches nanoscale, the mechanical properties may change drastically and classical mechanisms of materials failure may cease to hold. In this paper, we focus on joint atomistic-continuum studies of failure and deformation of nanoscale materials. In the first part of the paper, we discuss the size dependence of brittle fracture. We illustrate that if the characteristic dimension of a material is below a critical length scale that can be on the order of several nanometres, the classical Griffith theory of fracture no longer holds. An important consequence of this finding is that materials with nano-substructures may become flaw-tolerant, as the stress concentration at crack tips disappears and failure always occurs at the theoretical strength of materials, regardless of defects. Our atomistic simulations complement recent continuum analysis (Gao et al 2003 Proc. Natl Acad. Sci. USA 100 5597-600) and reveal a smooth transition between Griffith modes of failure via crack propagation to uniform bond rupture at theoretical strength below a nanometre critical length. Our results may have consequences for understanding failure of many small-scale materials. In the second part of this paper, we focus on the size dependence of adhesion systems. We demonstrate that optimal adhesion can be achieved by either length scale reduction, or by optimization of the shape of the surface of the adhesion element. We find that whereas change in shape can lead to optimal adhesion strength, those systems are not robust against small deviations from the optimal shape. In contrast, reducing the dimensions of the adhesion system results in robust adhesion devices that fail at their theoretical strength, regardless of the presence of flaws. An important consequence of this finding is that even under the presence of surface roughness, optimal adhesion is possible provided the size of contact elements is sufficiently small. Our atomistic results corroborate earlier theoretical modelling at the continuum scale (Gao and Yao 2004 Proc. Natl Acad. Sci. USA 101 7851-6). We discuss the relevance of our studies with respect to nature's design of bone nanostructures and nanoscale adhesion elements in geckos.

Modeling defects and plasticity in MgSiO3 post-perovskite: Part 2-screw and edge [100] dislocations.

PubMed

Goryaeva, Alexandra M; Carrez, Philippe; Cordier, Patrick

In this study, we propose a full atomistic study of [100] dislocations in MgSiO 3 post-perovskite based on the pairwise potential parameterized by Oganov et al. (Phys Earth Planet Inter 122:277-288, 2000) for MgSiO 3 perovskite. We model screw dislocations to identify planes where they glide easier. We show that despite a small tendency to core spreading in {011}, [100] screw dislocations glide very easily (Peierls stress of 1 GPa) in (010) where only Mg-O bonds are to be sheared. Crossing the Si-layers results in a higher lattice friction as shown by the Peierls stress of [100](001): 17.5 GPa. Glide of [100] screw dislocations in {011} appears also to be highly unfavorable. Whatever the planes, (010), (001) or {011}, edge dislocations are characterized by a wider core (of the order of 2 b ). Contrary to screw character, they bear negligible lattice friction (0.1 GPa) for each slip system. The layered structure of post-perovskite results in a drastic reduction in lattice friction opposed to the easiest slip systems compared to perovskite.

Modeling direct band-to-band tunneling: From bulk to quantum-confined semiconductor devices

NASA Astrophysics Data System (ADS)

Carrillo-Nuñez, H.; Ziegler, A.; Luisier, M.; Schenk, A.

2015-06-01

A rigorous framework to study direct band-to-band tunneling (BTBT) in homo- and hetero-junction semiconductor nanodevices is introduced. An interaction Hamiltonian coupling conduction and valence bands (CVBs) is derived using a multiband envelope method. A general form of the BTBT probability is then obtained from the linear response to the "CVBs interaction" that drives the system out of equilibrium. Simple expressions in terms of the one-electron spectral function are developed to compute the BTBT current in two- and three-dimensional semiconductor structures. Additionally, a two-band envelope equation based on the Flietner model of imaginary dispersion is proposed for the same purpose. In order to characterize their accuracy and differences, both approaches are compared with full-band, atomistic quantum transport simulations of Ge, InAs, and InAs-Si Esaki diodes. As another numerical application, the BTBT current in InAs-Si nanowire tunnel field-effect transistors is computed. It is found that both approaches agree with high accuracy. The first one is considerably easier to conceive and could be implemented straightforwardly in existing quantum transport tools based on the effective mass approximation to account for BTBT in nanodevices.

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

Nedelkoski, Zlatko; Kepaptsoglou, Demie; Lari, Leonardo

We compare the structural, chemical, and magnetic properties of magnetite nanoparticles. Aberration corrected scanning transmission electron microscopy reveals the prevalence of antiphase boundaries in nanoparticles that have significantly reduced magnetization, relative to the bulk. We show that atomistic magnetic modelling of nanoparticles with and without these defects reveal the origin of the reduced moment. Strong antiferromagnetic interactions across antiphase boundaries support multiple magnetic domains even in particles as small as 12–14 nm.

Thinking of Feeling: Hasan, Vygotsky, and Some Ruminations on the Development of Narrative Sensibility in Children

ERIC Educational Resources Information Center

Kellogg, David

2017-01-01

The late Ruqaiya Hasan was an enthusiastic but exacting reader of Vygotsky: she reproached him for lacking a theory of language use, for using an asocial model of education without class variation in semantic code, and above all for using an atomistic unit of analysis, namely lexical word meaning. In this paper, I take up these criticisms and…

Microscopic theory for coupled atomistic magnetization and lattice dynamics

NASA Astrophysics Data System (ADS)

Fransson, J.; Thonig, D.; Bessarab, P. F.; Bhattacharjee, S.; Hellsvik, J.; Nordström, L.

2017-12-01

A coupled atomistic spin and lattice dynamics approach is developed which merges the dynamics of these two degrees of freedom into a single set of coupled equations of motion. The underlying microscopic model comprises local exchange interactions between the electron spin and magnetic moment and the local couplings between the electronic charge and lattice displacements. An effective action for the spin and lattice variables is constructed in which the interactions among the spin and lattice components are determined by the underlying electronic structure. In this way, expressions are obtained for the electronically mediated couplings between the spin and lattice degrees of freedom, besides the well known interatomic force constants and spin-spin interactions. These former susceptibilities provide an atomistic ab initio description for the coupled spin and lattice dynamics. It is important to notice that this theory is strictly bilinear in the spin and lattice variables and provides a minimal model for the coupled dynamics of these subsystems and that the two subsystems are treated on the same footing. Questions concerning time-reversal and inversion symmetry are rigorously addressed and it is shown how these aspects are absorbed in the tensor structure of the interaction fields. By means of these results regarding the spin-lattice coupling, simple explanations of ionic dimerization in double-antiferromagnetic materials, as well as charge density waves induced by a nonuniform spin structure, are given. In the final parts, coupled equations of motion for the combined spin and lattice dynamics are constructed, which subsequently can be reduced to a form which is analogous to the Landau-Lifshitz-Gilbert equations for spin dynamics and a damped driven mechanical oscillator for the ionic motion. It is important to notice, however, that these equations comprise contributions that couple these descriptions into one unified formulation. Finally, Kubo-like expressions for the discussed exchanges in terms of integrals over the electronic structure and, moreover, analogous expressions for the damping within and between the subsystems are provided. The proposed formalism and types of couplings enable a step forward in the microscopic first principles modeling of coupled spin and lattice quantities in a consistent format.

Probing the limits of metal plasticity with molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zepeda-Ruiz, Luis A.; Stukowski, Alexander; Oppelstrup, Tomas; Bulatov, Vasily V.

2017-10-01

Ordinarily, the strength and plasticity properties of a metal are defined by dislocations--line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocation dynamics models are usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive to perform routinely. However, atomistic simulations accurately capture every possible mechanism of material response, resolving every ``jiggle and wiggle'' of atomic motion, whereas dislocation dynamics models do not. Here we present fully dynamic atomistic simulations of bulk single-crystal plasticity in the body-centred-cubic metal tantalum. Our goal is to quantify the conditions under which the limits of dislocation-mediated plasticity are reached and to understand what happens to the metal beyond any such limit. In our simulations, the metal is compressed at ultrahigh strain rates along its [001] crystal axis under conditions of constant pressure, temperature and strain rate. To address the complexity of crystal plasticity processes on the length scales (85-340 nm) and timescales (1 ns-1μs) that we examine, we use recently developed methods of in situ computational microscopy to recast the enormous amount of transient trajectory data generated in our simulations into a form that can be analysed by a human. Our simulations predict that, on reaching certain limiting conditions of strain, dislocations alone can no longer relieve mechanical loads; instead, another mechanism, known as deformation twinning (the sudden re-orientation of the crystal lattice), takes over as the dominant mode of dynamic response. Below this limit, the metal assumes a strain-path-independent steady state of plastic flow in which the flow stress and the dislocation density remain constant as long as the conditions of straining thereafter remain unchanged. In this distinct state, tantalum flows like a viscous fluid while retaining its crystal lattice and remaining a strong and stiff metal.

Molecular Simulations of Adsorption and Diffusion in Silicalite.

NASA Astrophysics Data System (ADS)

Snurr, Randall Quentin

The adsorption and diffusion of hydrocarbons in the zeolite silicalite have been studied using molecular simulations. The simulations use an atomistic description of zeolite/sorbate interactions and are based on principles of statistical mechanics. Emphasis was placed on developing new simulation techniques to allow complex systems relevant to industrial applications in catalysis and separations processes to be studied. Adsorption isotherms and heats of sorption for methane in silicalite were calculated from grand canonical Monte Carlo (GCMC) simulations and also from molecular dynamics (MD) simulations accompanied by Widom test particle insertions. Good agreement with experimental data from the literature was found. The adsorption thermodynamics of aromatic species in silicalite at low loading was predicted by direct evaluation of the configurational integrals. Good agreement with experiment was obtained for the Henry's constants and the heats of adsorption. Molecules were predicted to be localized in the channel intersections at low loading. At higher loading, conventional GCMC simulations were found to be infeasible. Several variations of the GCMC technique were developed incorporating biased insertion moves. These new techniques are much more efficient than conventional GCMC and allow for the prediction of adsorption isotherms of tightly-fitting aromatic molecules in silicalite. Our simulations when combined with experimental evidence of a phase change in the zeolite structure at intermediate loading provide an explanation of the characteristic steps seen in the experimental isotherms. A hierarchical atomistic/lattice model for studying these systems was also developed. The hierarchical model is more than an order of magnitude more efficient computationally than direct atomistic simulation. Diffusion of benzene in silicalite was studied using transition-state theory (TST). Such an approach overcomes the time-scale limitations of using MD simulations for studying sorbate dynamics. Predicted diffusion coefficients were found to be too low compared to experiment. This was attributed to the assumption of a rigid zeolite structure in the calculations and the use of a harmonic approximation for calculating the TST rate constants. Details of sorbate motion were also investigated.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

Atomistic observation and simulation analysis of spatio-temporal fluctuations during radiation-induced amorphization.

PubMed

Watanabe, Seiichi; Hoshino, Misaki; Koike, Takuto; Suda, Takanori; Ohnuki, Soumei; Takahashi, Heishichirou; Lam, Nighi Q

2003-01-01

We performed a dynamical-atomistic study of radiation-induced amorphization in the NiTi intermetallic compound using in situ high-resolution high-voltage electron microscopy and molecular dynamics simulations in connection with image simulation. Spatio-temporal fluctuations as non-equilibrium fluctuations in an energy-dissipative system, due to transient atom-cluster formation during amorphization, were revealed by the present spatial autocorrelation analysis.

adwTools Developed: New Bulk Alloy and Surface Analysis Software for the Alloy Design Workbench

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Morse, Jeffrey A.; Noebe, Ronald D.; Abel, Phillip B.

2004-01-01

A suite of atomistic modeling software, called the Alloy Design Workbench, has been developed by the Computational Materials Group at the NASA Glenn Research Center and the Ohio Aerospace Institute (OAI). The main goal of this software is to guide and augment experimental materials research and development efforts by creating powerful, yet intuitive, software that combines a graphical user interface with an operating code suitable for real-time atomistic simulations of multicomponent alloy systems. Targeted for experimentalists, the interface is straightforward and requires minimum knowledge of the underlying theory, allowing researchers to focus on the scientific aspects of the work. The centerpiece of the Alloy Design Workbench suite is the adwTools module, which concentrates on the atomistic analysis of surfaces and bulk alloys containing an arbitrary number of elements. An additional module, adwParams, handles ab initio input for the parameterization used in adwTools. Future modules planned for the suite include adwSeg, which will provide numerical predictions for segregation profiles to alloy surfaces and interfaces, and adwReport, which will serve as a window into the database, providing public access to the parameterization data and a repository where users can submit their own findings from the rest of the suite. The entire suite is designed to run on desktop-scale computers. The adwTools module incorporates a custom OAI/Glenn-developed Fortran code based on the BFS (Bozzolo- Ferrante-Smith) method for alloys, ref. 1). The heart of the suite, this code is used to calculate the energetics of different compositions and configurations of atoms.

Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex

PubMed Central

Bian, Yunqiang; Tan, Cheng; Wang, Jun; Sheng, Yuebiao; Zhang, Jian; Wang, Wei

2014-01-01

In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and ions explicitly modeled. Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations, the free energy landscape of this G-DNA was obtained for the first time and four folding intermediates were identified, including a triplex and a basically formed quadruplex. The simulations also provided atomistic pictures for the structures and cation binding patterns of the intermediates. The results showed that the structure formation and cation binding are cooperative and mutually supporting each other. The syn/anti reorientation dynamics of the intermediates was also investigated. It was found that the nucleotides usually take correct syn/anti configurations when they form native and stable hydrogen bonds with the others, while fluctuating between two configurations when they do not. Misfolded intermediates with wrong syn/anti configurations were observed in the early intermediates but not in the later ones. Based on the simulations, we also discussed the roles of the non-native interactions. Besides, the formation process of the parallel conformation in the first two G-repeats and the associated reversal loop were studied. Based on the above results, we proposed a folding pathway for the hybrid-1 type G-quadruplex with atomistic details, which is new and more complete compared with previous ones. The knowledge gained for this type of G-DNA may provide a general insight for the folding of the other G-quadruplexes. PMID:24722458

Small-angle neutron scattering study of a monoclonal antibody using free-energy constraints.

PubMed

Clark, Nicholas J; Zhang, Hailiang; Krueger, Susan; Lee, Hyo Jin; Ketchem, Randal R; Kerwin, Bruce; Kanapuram, Sekhar R; Treuheit, Michael J; McAuley, Arnold; Curtis, Joseph E

2013-11-14

Monoclonal antibodies (mAbs) contain hinge-like regions that enable structural flexibility of globular domains that have a direct effect on biological function. A subclass of mAbs, IgG2, have several interchain disulfide bonds in the hinge region that could potentially limit structural flexibility of the globular domains and affect the overall configuration space available to the mAb. We have characterized human IgG2 mAb in solution via small-angle neutron scattering (SANS) and interpreted the scattering data using atomistic models. Molecular Monte Carlo combined with molecular dynamics simulations of a model mAb indicate that a wide range of structural configurations are plausible, spanning radius of gyration values from ∼39 to ∼55 Å. Structural ensembles and representative single structure solutions were derived by comparison of theoretical SANS profiles of mAb models to experimental SANS data. Additionally, molecular mechanical and solvation free-energy calculations were carried out on the ensemble of best-fitting mAb structures. The results of this study indicate that low-resolution techniques like small-angle scattering combined with atomistic molecular simulations with free-energy analysis may be helpful to determine the types of intramolecular interactions that influence function and could lead to deleterious changes to mAb structure. This methodology will be useful to analyze small-angle scattering data of many macromolecular systems.

Implications for plastic flow in the deep mantle from modelling dislocations in MgSiO3 minerals.

PubMed

Carrez, Philippe; Ferré, Denise; Cordier, Patrick

2007-03-01

The dynamics of the Earth's interior is largely controlled by mantle convection, which transports radiogenic and primordial heat towards the surface. Slow stirring of the deep mantle is achieved in the solid state through high-temperature creep of rocks, which are dominated by the mineral MgSiO3 perovskite. Transformation of MgSiO3 to a 'post-perovskite' phase may explain the peculiarities of the lowermost mantle, such as the observed seismic anisotropy, but the mechanical properties of these mineralogical phases are largely unknown. Plastic flow of solids involves the motion of a large number of crystal defects, named dislocations. A quantitative description of flow in the Earth's mantle requires information about dislocations in high-pressure minerals and their behaviour under stress. This property is currently out of reach of direct atomistic simulations using either empirical interatomic potentials or ab initio calculations. Here we report an alternative to direct atomistic simulations based on the framework of the Peierls-Nabarro model. Dislocation core models are proposed for MgSiO3 perovskite (at 100 GPa) and post-perovskite (at 120 GPa). We show that in perovskite, plastic deformation is strongly influenced by the orthorhombic distortions of the unit cell. In silicate post-perovskite, large dislocations are relaxed through core dissociation, with implications for the mechanical properties and seismic anisotropy of the lowermost mantle.

Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales

NASA Astrophysics Data System (ADS)

Mukherjee, Biswaroop; Peter, Christine; Kremer, Kurt

2017-09-01

Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.

Quantum Drude oscillator model of atoms and molecules: Many-body polarization and dispersion interactions for atomistic simulation

NASA Astrophysics Data System (ADS)

Jones, Andrew P.; Crain, Jason; Sokhan, Vlad P.; Whitfield, Troy W.; Martyna, Glenn J.

2013-04-01

Treating both many-body polarization and dispersion interactions is now recognized as a key element in achieving the level of atomistic modeling required to reveal novel physics in complex systems. The quantum Drude oscillator (QDO), a Gaussian-based, coarse grained electronic structure model, captures both many-body polarization and dispersion and has linear scale computational complexity with system size, hence it is a leading candidate next-generation simulation method. Here, we investigate the extent to which the QDO treatment reproduces the desired long-range atomic and molecular properties. We present closed form expressions for leading order polarizabilities and dispersion coefficients and derive invariant (parameter-free) scaling relationships among multipole polarizability and many-body dispersion coefficients that arise due to the Gaussian nature of the model. We show that these “combining rules” hold to within a few percent for noble gas atoms, alkali metals, and simple (first-row hydride) molecules such as water; this is consistent with the surprising success that models with underlying Gaussian statistics often exhibit in physics. We present a diagrammatic Jastrow-type perturbation theory tailored to the QDO model that serves to illustrate the rich types of responses that the QDO approach engenders. QDO models for neon, argon, krypton, and xenon, designed to reproduce gas phase properties, are constructed and their condensed phase properties explored via linear scale diffusion Monte Carlo (DMC) and path integral molecular dynamics (PIMD) simulations. Good agreement with experimental data for structure, cohesive energy, and bulk modulus is found, demonstrating a degree of transferability that cannot be achieved using current empirical models or fully ab initio descriptions.

Evaluating variability with atomistic simulations: the effect of potential and calculation methodology on the modeling of lattice and elastic constants

NASA Astrophysics Data System (ADS)

Hale, Lucas M.; Trautt, Zachary T.; Becker, Chandler A.

2018-07-01

Atomistic simulations using classical interatomic potentials are powerful investigative tools linking atomic structures to dynamic properties and behaviors. It is well known that different interatomic potentials produce different results, thus making it necessary to characterize potentials based on how they predict basic properties. Doing so makes it possible to compare existing interatomic models in order to select those best suited for specific use cases, and to identify any limitations of the models that may lead to unrealistic responses. While the methods for obtaining many of these properties are often thought of as simple calculations, there are many underlying aspects that can lead to variability in the reported property values. For instance, multiple methods may exist for computing the same property and values may be sensitive to certain simulation parameters. Here, we introduce a new high-throughput computational framework that encodes various simulation methodologies as Python calculation scripts. Three distinct methods for evaluating the lattice and elastic constants of bulk crystal structures are implemented and used to evaluate the properties across 120 interatomic potentials, 18 crystal prototypes, and all possible combinations of unique lattice site and elemental model pairings. Analysis of the results reveals which potentials and crystal prototypes are sensitive to the calculation methods and parameters, and it assists with the verification of potentials, methods, and molecular dynamics software. The results, calculation scripts, and computational infrastructure are self-contained and openly available to support researchers in performing meaningful simulations.

Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations

NASA Astrophysics Data System (ADS)

Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.

2016-07-01

Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.

Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

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

Hoover, W. G.; Hoover, C. G.

1993-08-01

Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

Atomistic and Ab Initio Calculations or Ternary II-IV-V2 Semiconductors

DTIC Science & Technology

1999-12-07

consisting of two- and three-body terms is developed reproducing crystal lattice constants, elastic and dielectric constants very well. The calculated...the lattice . This difference may well be due to defect-induced lattice distortion which plays a key role in stabilizing the hole states in the... lattice . 15. SUBJECT TERMS Chalcopyrites, Defects, Atomistic and AB Initio Calculations 16. SECURITY CLASSIFICATION OF: a. REPORT u b. ABSTRACT U

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

PubMed

Yang, Shengfeng; Chen, Youping

2015-03-08

In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

The Chemistry of Shocked High-energy Materials: Connecting Atomistic Simulations to Experiments

NASA Astrophysics Data System (ADS)

Islam, Md Mahbubul; Strachan, Alejandro

2017-06-01

A comprehensive atomistic-level understanding of the physics and chemistry of shocked high energy (HE) materials is crucial for designing safe and efficient explosives. Advances in the ultrafast spectroscopy and laser shocks enabled the study of shock-induced chemistry at extreme conditions occurring at picosecond timescales. Despite this progress experiments are not without limitations and do not enable a direct characterization of chemical reactions. At the same time, large-scale reactive molecular dynamics (MD) simulations are capable of providing description of the shocked-induced chemistry but the uncertainties resulting from the use of approximate descriptions of atomistic interactions remain poorly quantified. We use ReaxFF MD simulations to investigate the shock and temperature induced chemical decomposition mechanisms of polyvinyl nitrate, RDX, and nitromethane. The effect of various shock pressures on reaction initiation mechanisms is investigated for all three materials. We performed spectral analysis from atomistic velocities at different shock pressures to enable direct comparison with experiments. The simulations predict volume-increasing reactions at the shock-to-detonation transitions and the shock vs. particle velocity data are in good agreement with available experimental data. The ReaxFF MD simulations validated against experiments enabled prediction of reaction kinetics of shocked materials, and interpretation of experimental spectroscopy data via assignment of the spectral peaks to dictate various reaction pathways at extreme conditions.

Atomistic modeling of shock-induced void collapse in copper

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

Davila, L P; Erhart, P; Bringa, E M

2005-03-09

Nonequilibrium molecular dynamics (MD) simulations show that shock-induced void collapse in copper occurs by emission of shear loops. These loops carry away the vacancies which comprise the void. The growth of the loops continues even after they collide and form sessile junctions, creating a hardened region around the collapsing void. The scenario seen in our simulations differs from current models that assume that prismatic loop emission is responsible for void collapse. We propose a new dislocation-based model that gives excellent agreement with the stress threshold found in the MD simulations for void collapse as a function of void radius.

Molecular-dynamics Simulation-based Cohesive Zone Representation of Intergranular Fracture Processes in Aluminum

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.; Saether, Erik; Phillips, Dawn R.; Glaessgen, Edward H.

2006-01-01

A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation

Degenerate Ising model for atomistic simulation of crystal-melt interfaces

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

Schebarchov, D., E-mail: Dmitri.Schebarchov@gmail.com; Schulze, T. P., E-mail: schulze@math.utk.edu; Hendy, S. C.

2014-02-21

One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quantifies the difference in communal entropy between the two phases. We simulate the (stochastic) evolution of this minimal model by applying rejection-free canonical and microcanonical Monte Carlo algorithms, and we obtain caloric curves and heat capacity plots for square (2D) and face-centred cubic (3D) latticesmore » with periodic boundary conditions. Since the model admits precise adjustment of bulk latent heat and communal entropy, neither of which affect the interface properties, we are able to tune the crystal nucleation barriers at a fixed degree of undercooling and verify a dimension-dependent scaling expected from classical nucleation theory. We also analyse the equilibrium crystal-melt coexistence in the microcanonical ensemble, where we detect negative heat capacities and find that this phenomenon is more pronounced when the interface is the dominant contributor to the total entropy. The negative branch of the heat capacity appears smooth only when the equilibrium interface-area-to-volume ratio is not constant but varies smoothly with the excitation energy. Finally, we simulate microcanonical crystal nucleation and subsequent relaxation to an equilibrium Wulff shape, demonstrating the model's utility in tracking crystal-melt interfaces at the atomistic level.« less

Organic Crystal Engineering of Thermosetting Cyanate Ester Monomers: Influence of Structure on Melting Point

DTIC Science & Technology

2016-05-27

often discussed in the field of thermosetting materials, crystal engineering1-4 plays a key role in facilitating the successful utilization of these...not to alter the desirable properties of the polymerized networks. Fortunately, the field of crystal engineering provides examples where even very...Chickos and Acree.26 For molecular modeling, methods ranging from atomistic simulations with semi-empirical force fields to density functional

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

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

A relationship between three-dimensional surface hydration structures and force distribution measured by atomic force microscopy.

PubMed

Miyazawa, Keisuke; Kobayashi, Naritaka; Watkins, Matthew; Shluger, Alexander L; Amano, Ken-ichi; Fukuma, Takeshi

2016-04-07

Hydration plays important roles in various solid-liquid interfacial phenomena. Very recently, three-dimensional scanning force microscopy (3D-SFM) has been proposed as a tool to visualise solvated surfaces and their hydration structures with lateral and vertical (sub) molecular resolution. However, the relationship between the 3D force map obtained and the equilibrium water density, ρ(r), distribution above the surface remains an open question. Here, we investigate this relationship at an interface of an inorganic mineral, fluorite, and water. The force maps measured in pure water are directly compared to force maps generated using the solvent tip approximation (STA) model and from explicit molecular dynamics simulations. The results show that the simulated STA force map describes the major features of the experimentally obtained force image. The agreement between the STA data and the experiment establishes the correspondence between the water density used as an input to the STA model and the experimental hydration structure and thus provides a tool to bridge the experimental force data and atomistic solvation structures. Further applications of this method should improve the accuracy and reliability of both interpretation of 3D-SFM force maps and atomistic simulations in a wide range of solid-liquid interfacial phenomena.

Parallel implementation of approximate atomistic models of the AMOEBA polarizable model

NASA Astrophysics Data System (ADS)

Demerdash, Omar; Head-Gordon, Teresa

2016-11-01

In this work we present a replicated data hybrid OpenMP/MPI implementation of a hierarchical progression of approximate classical polarizable models that yields speedups of up to ∼10 compared to the standard OpenMP implementation of the exact parent AMOEBA polarizable model. In addition, our parallel implementation exhibits reasonable weak and strong scaling. The resulting parallel software will prove useful for those who are interested in how molecular properties converge in the condensed phase with respect to the MBE, it provides a fruitful test bed for exploring different electrostatic embedding schemes, and offers an interesting possibility for future exascale computing paradigms.

A perspective on modeling the multiscale response of energetic materials

NASA Astrophysics Data System (ADS)

Rice, Betsy M.

2017-01-01

The response of an energetic material to insult is perhaps one of the most difficult processes to model due to concurrent chemical and physical phenomena occurring over scales ranging from atomistic to continuum. Unraveling the interdependencies of these complex processes across the scales through modeling can only be done within a multiscale framework. In this paper, I will describe progress in the development of a predictive, experimentally validated multiscale reactive modeling capability for energetic materials at the Army Research Laboratory. I will also describe new challenges and research opportunities that have arisen in the course of our development which should be pursued in the future.

Recasting a model atomistic glassformer as a system of icosahedra

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

Pinney, Rhiannon; Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TS; Liverpool, Tanniemola B.

2015-12-28

We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of icosahedral structures. Upon cooling, these icosahedra organize into mesoclusters. We recast this glassformer as an effective system of icosahedra which we describe with a population dynamics model. This model we parameterize with data from the temperature regime accessible to molecular dynamics simulations. We then use the model to determine the population of icosahedra in mesoclusters at arbitrary temperature. Using simulation data to incorporate dynamics into the model, we predict relaxation behavior at temperatures inaccessible to conventional approaches. Our model predicts super-Arrhenius dynamics whose relaxation timemore » remains finite for non-zero temperature.« less

Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation.

PubMed

Finnerty, Justin John; Peyser, Alexander; Carloni, Paolo

2015-01-01

Cation selective channels constitute the gate for ion currents through the cell membrane. Here we present an improved statistical mechanical model based on atomistic structural information, cation hydration state and without tuned parameters that reproduces the selectivity of biological Na+ and Ca2+ ion channels. The importance of the inclusion of step-wise cation hydration in these results confirms the essential role partial dehydration plays in the bacterial Na+ channels. The model, proven reliable against experimental data, could be straightforwardly used for designing Na+ and Ca2+ selective nanopores.

First-Principles Approach to Model Electrochemical Reactions: Understanding the Fundamental Mechanisms behind Mg Corrosion

NASA Astrophysics Data System (ADS)

Surendralal, Sudarsan; Todorova, Mira; Finnis, Michael W.; Neugebauer, Jörg

2018-06-01

Combining concepts of semiconductor physics and corrosion science, we develop a novel approach that allows us to perform ab initio calculations under controlled potentiostat conditions for electrochemical systems. The proposed approach can be straightforwardly applied in standard density functional theory codes. To demonstrate the performance and the opportunities opened by this approach, we study the chemical reactions that take place during initial corrosion at the water-Mg interface under anodic polarization. Based on this insight, we derive an atomistic model that explains the origin of the anodic hydrogen evolution.

Single-chain behavior of poly(3-hexylthiophene)

NASA Astrophysics Data System (ADS)

Ivanov, Momchil; Gross, Jonathan; Janke, Wolfhard

2017-03-01

Poly(3-hexylthiophene) (P3HT) has been in the focus of recent studies due to its promising future use in organic photovoltaics, electronics and photonics. Recent publications investigate the melt behavior of P3HT, its interaction with other molecules, mainly various fullerene derivates, and isolated chains interacting with substrates. In this work we lay the focus on the single-chain properties of P3HT in vacuum. We compare structural properties obtained from simulations using two coarse-grained models and an atomistic model of the polymer for various chain lengths and temperatures.

Accurate atomistic first-principles calculations of electronic stopping

DOE PAGES

Schleife, André; Kanai, Yosuke; Correa, Alfredo A.

2015-01-20

In this paper, we show that atomistic first-principles calculations based on real-time propagation within time-dependent density functional theory are capable of accurately describing electronic stopping of light projectile atoms in metal hosts over a wide range of projectile velocities. In particular, we employ a plane-wave pseudopotential scheme to solve time-dependent Kohn-Sham equations for representative systems of H and He projectiles in crystalline aluminum. This approach to simulate nonadiabatic electron-ion interaction provides an accurate framework that allows for quantitative comparison with experiment without introducing ad hoc parameters such as effective charges, or assumptions about the dielectric function. Finally, our work clearlymore » shows that this atomistic first-principles description of electronic stopping is able to disentangle contributions due to tightly bound semicore electrons and geometric aspects of the stopping geometry (channeling versus off-channeling) in a wide range of projectile velocities.« less

Materials integrity in microsystems: a framework for a petascale predictive-science-based multiscale modeling and simulation system

NASA Astrophysics Data System (ADS)

To, Albert C.; Liu, Wing Kam; Olson, Gregory B.; Belytschko, Ted; Chen, Wei; Shephard, Mark S.; Chung, Yip-Wah; Ghanem, Roger; Voorhees, Peter W.; Seidman, David N.; Wolverton, Chris; Chen, J. S.; Moran, Brian; Freeman, Arthur J.; Tian, Rong; Luo, Xiaojuan; Lautenschlager, Eric; Challoner, A. Dorian

2008-09-01

Microsystems have become an integral part of our lives and can be found in homeland security, medical science, aerospace applications and beyond. Many critical microsystem applications are in harsh environments, in which long-term reliability needs to be guaranteed and repair is not feasible. For example, gyroscope microsystems on satellites need to function for over 20 years under severe radiation, thermal cycling, and shock loading. Hence a predictive-science-based, verified and validated computational models and algorithms to predict the performance and materials integrity of microsystems in these situations is needed. Confidence in these predictions is improved by quantifying uncertainties and approximation errors. With no full system testing and limited sub-system testings, petascale computing is certainly necessary to span both time and space scales and to reduce the uncertainty in the prediction of long-term reliability. This paper presents the necessary steps to develop predictive-science-based multiscale modeling and simulation system. The development of this system will be focused on the prediction of the long-term performance of a gyroscope microsystem. The environmental effects to be considered include radiation, thermo-mechanical cycling and shock. Since there will be many material performance issues, attention is restricted to creep resulting from thermal aging and radiation-enhanced mass diffusion, material instability due to radiation and thermo-mechanical cycling and damage and fracture due to shock. To meet these challenges, we aim to develop an integrated multiscale software analysis system that spans the length scales from the atomistic scale to the scale of the device. The proposed software system will include molecular mechanics, phase field evolution, micromechanics and continuum mechanics software, and the state-of-the-art model identification strategies where atomistic properties are calibrated by quantum calculations. We aim to predict the long-term (in excess of 20 years) integrity of the resonator, electrode base, multilayer metallic bonding pads, and vacuum seals in a prescribed mission. Although multiscale simulations are efficient in the sense that they focus the most computationally intensive models and methods on only the portions of the space time domain needed, the execution of the multiscale simulations associated with evaluating materials and device integrity for aerospace microsystems will require the application of petascale computing. A component-based software strategy will be used in the development of our massively parallel multiscale simulation system. This approach will allow us to take full advantage of existing single scale modeling components. An extensive, pervasive thrust in the software system development is verification, validation, and uncertainty quantification (UQ). Each component and the integrated software system need to be carefully verified. An UQ methodology that determines the quality of predictive information available from experimental measurements and packages the information in a form suitable for UQ at various scales needs to be developed. Experiments to validate the model at the nanoscale, microscale, and macroscale are proposed. The development of a petascale predictive-science-based multiscale modeling and simulation system will advance the field of predictive multiscale science so that it can be used to reliably analyze problems of unprecedented complexity, where limited testing resources can be adequately replaced by petascale computational power, advanced verification, validation, and UQ methodologies.

Critical Issues on Materials for Gen-IV Reactors

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

Caro, M; Marian, J; Martinez, E

2009-02-27

Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that seeks to relate in a near-term effort dislocation dynamics to polycrystal plasticity. The requirements originated in the reactor systems under consideration today for future sources of nuclear energy. These requirements are beyond the present day performance of nuclear materials andmore » calls for the development of new, high temperature, radiation resistant materials. Fe-Cr alloys with 9-12% Cr content are the base matrix of advanced ferritic/martensitic (FM) steels envisaged as fuel cladding and structural components of Gen-IV reactors. Predictive tools are needed to calculate structural and mechanical properties of these steels. This project represents a contribution in that direction. The synergy between the continuous progress of parallel computing and the spectacular advances in the theoretical framework that describes materials have lead to a significant advance in our comprehension of materials properties and their mechanical behavior. We took this progress to our advantage and within this LDRD were able to provide a detailed physical understanding of iron-chromium alloys microstructural behavior. By combining ab-initio simulations, many-body interatomic potential development, and mesoscale dislocation dynamics we were able to describe their microstructure evolution. For the first time in the case of Fe-Cr alloys, atomistic and mesoscale were merged and the first steps taken towards incorporating ordering and precipitation effects into dislocation dynamics (DD) simulations. Molecular dynamics (MD) studies of the transport of self-interstitial, vacancy and point defect clusters in concentrated Fe-Cr alloys were performed for future diffusion data calculations. A recently developed parallel MC code with displacement allowed us to predict the evolution of the defect microstructures, local chemistry changes, grain boundary segregation and precipitation resulting from radiation enhanced diffusion. We showed that grain boundaries, dislocations and free surfaces are not preferential for alpha-prime precipitation, and explained experimental observations of short-range order (SRO) in Fe-rich FeCr alloys. Our atomistic studies of dislocation hardening allowed us to obtain dislocation mobility functions for BCC pure iron and Fe-Cr and determine for FCC metals the dislocation interaction with precipitates with a description to be used in Dislocation Dynamic (DD) codes. A Synchronous parallel Kinetic Monte Carlo code was developed and tested which promises to expand the range of applicability of kMC simulations. This LDRD furthered the limits of the available science on the thermodynamic and mechanic behavior of metallic alloys and extended the application of physically-based multiscale materials modeling to cases of severe temperature and neutron fluence conditions in advanced future nuclear reactors. The report is organized as follows: after a brief introduction, we present the research activities, and results obtained. We give recommendations on future LLNL activities that may contribute to the progress in this area, together with examples of possible research lines to be supported.« less

Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

2017-02-01

The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

Corrosion mechanisms for metal alloy waste forms: experiment and theory Level 4 Milestone M4FT-14LA0804024 Fuel Cycle Research & Development

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

Liu, Xiang-Yang; Taylor, Christopher D.; Kim, Eunja

2014-07-31

This document meets Level 4 Milestone: Corrosion mechanisms for metal alloy waste forms - experiment and theory. A multiphysics model is introduces that will provide the framework for the quantitative prediction of corrosion rates of metallic waste forms incorporating the fission product Tc. The model requires a knowledge of the properties of not only the metallic waste form, but also the passive oxide films that will be generated on the waste form, and the chemistry of the metal/oxide and oxide/environment interfaces. in collaboration with experimental work, the focus of this work is on obtaining these properties from fundamental atomistic models.more » herein we describe the overall multiphysics model, which is based on MacDonald's point-defect model for passivity. We then present the results of detailed electronic-structure calculations for the determination of the compatibility and properties of Tc when incorporated into intermetallic oxide phases. This work is relevant to the formation of multi-component oxides on metal surfaces that will incorporate Tc, and provide a kinetic barrier to corrosion (i.e. the release of Tc to the environment). Atomistic models that build upon the electronic structure calculations are then described using the modified embedded atom method to simulate metallic dissolution, and Buckingham potentials to perform classical molecular dynamics and statics simulations of the technetium (and, later, iron-technetium) oxide phases. Electrochemical methods were then applied to provide some benchmark information of the corrosion and electrochemical properties of Technetium metal. The results indicate that published information on Tc passivity is not complete and that further investigation is warranted.« less

Vibrational properties of nanocrystals from the Debye Scattering Equation

DOE PAGES

Scardi, P.; Gelisio, L.

2016-02-26

One hundred years after the original formulation by Petrus J.W. Debije (aka Peter Debye), the Debye Scattering Equation (DSE) is still the most accurate expression to model the diffraction pattern from nanoparticle systems. A major limitation in the original form of the DSE is that it refers to a static domain, so that including thermal disorder usually requires rescaling the equation by a Debye-Waller thermal factor. The last is taken from the traditional diffraction theory developed in Reciprocal Space (RS), which is opposed to the atomistic paradigm of the DSE, usually referred to as Direct Space (DS) approach. Besides beingmore » a hybrid of DS and RS expressions, rescaling the DSE by the Debye-Waller factor is an approximation which completely misses the contribution of Temperature Diffuse Scattering (TDS). The present work proposes a solution to include thermal effects coherently with the atomistic approach of the DSE. Here, a deeper insight into the vibrational dynamics of nanostructured materials can be obtained with few changes with respect to the standard formulation of the DSE, providing information on the correlated displacement of vibrating atoms.« less

Pressure effects on enzyme-catalyzed quantum tunneling events arise from protein-specific structural and dynamic changes.

PubMed

Hay, Sam; Johannissen, Linus O; Hothi, Parvinder; Sutcliffe, Michael J; Scrutton, Nigel S

2012-06-13

The rate and kinetic isotope effect (KIE) on proton transfer during the aromatic amine dehydrogenase-catalyzed reaction with phenylethylamine shows complex pressure and temperature dependences. We are able to rationalize these effects within an environmentally coupled tunneling model based on constant pressure molecular dynamics (MD) simulations. As pressure appears to act anisotropically on the enzyme, perturbation of the reaction coordinate (donor-acceptor compression) is, in this case, marginal. Therefore, while we have previously demonstrated that pressure and temperature dependences can be used to infer H-tunneling and the involvement of promoting vibrations, these effects should not be used in the absence of atomistic insight, as they can vary greatly for different enzymes. We show that a pressure-dependent KIE is not a definitive hallmark of quantum mechanical H-tunneling during an enzyme-catalyzed reaction and that pressure-independent KIEs cannot be used to exclude tunneling contributions or a role for promoting vibrations in the enzyme-catalyzed reaction. We conclude that coupling of MD calculations with experimental rate and KIE studies is required to provide atomistic understanding of pressure effects in enzyme-catalyzed reactions.

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments

NASA Astrophysics Data System (ADS)

Brodeck, M.; Alvarez, F.; Arbe, A.; Juranyi, F.; Unruh, T.; Holderer, O.; Colmenero, J.; Richter, D.

2009-03-01

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below ≈0.6 Å-1. We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments.

PubMed

Brodeck, M; Alvarez, F; Arbe, A; Juranyi, F; Unruh, T; Holderer, O; Colmenero, J; Richter, D

2009-03-07

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below approximately 0.6 A(-1). We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Failure of cement hydrates: freeze-thaw and fracture

NASA Astrophysics Data System (ADS)

Ioannidou, Katerina; Del Gado, Emanuela; Ulm, Franz-Josef; Pellenq, Roland

Mechanical and viscoelastic behavior of concrete crucially depends on cement hydrates, the ``glue'' of cement. Even more than the atomistic structure, the mesoscale amorphous texture of cement hydrates over hundreds of nanometers plays a crucial role for material properties. We use simulations that combine information of the nano-scale building units of cement hydrates and on their effective interactions, obtained from atomistic simulations and experiments, into a statistical physics framework for aggregating nanoparticles.Our mesoscale model was able to reconcile different experimental results ranging from small-angle neutron scattering, SEM, adsorption/desorption of N2, and water to nanoindentation and gain the new fundamental insights into the microscopic origin of the properties measured. Our results suggest that heterogeneities developed during the early stages of hydration persist in the structure of C-S-H, impacting the rheological and mechanical performance of the hardened cement paste. In this talk I discuss recent investigation on failure mechanism at the mesoscale of hardened cement paste such as freeze-thaw and fracture. Using correlations between local volume fractions and local stress we provide a link between structural and mechanical heterogeneities during the failure mechanisms.

The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations

PubMed Central

Covino, Roberto; Škrbić, Tatjana; Beccara, Silvio a; Faccioli, Pietro; Micheletti, Cristian

2014-01-01

For several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins motivated researchers to look into the physico-chemical mechanisms governing the concerted sequence of folding steps leading to the consistent formation of the same knot type in the same protein location. Besides experiments, computational studies are providing considerable insight into these mechanisms. Here, we revisit a number of such recent investigations within a common conceptual and methodological framework. By considering studies employing protein models with different structural resolution (coarse-grained or atomistic) and various force fields (from pure native-centric to realistic atomistic ones), we focus on the role of native and non-native interactions. For various unrelated instances of knotted proteins, non-native interactions are shown to be very important for favoring the emergence of conformations primed for successful self-knotting events. PMID:24970203

Crystalline Structure and Surface Reactivity: Atomistic models are unique tools for dealing with the chemical and physical properties of surfaces.

PubMed

Gatos, H C

1962-08-03

The role of crystalline structure in the surface reactivity of predominantly covalent materials has been examined in terms of chemical bonding concepts. In this context a solid surface can be viewed as a giant lattice defect characterized by dangling bonds. Although it is difficult, at the present stage of development of the quantum mechanical approach to surfaces, to define precisely the perturbations resulting from the abrupt termination of the lattice at the surface, a host of experimental observations can be understood by assuming displacements of surface atoms and distortions of bonding configurations in accordance with simple chemical bonding principles. A purely atomistic approach has been shown to account not only for the chemical behavior but also for certain structural and electrical characteristics of the surfaces considered. A number of phenomena, such as crystal growth and the behavior of certain lattice defects (for example, dislocations), are intimately related to the presence of dangling bonds and the associated distortions of the lattice at the surface (32).

Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states.

PubMed

Can, Mehmet Tarik; Kurkcuoglu, Zeynep; Ezeroglu, Gokce; Uyar, Arzu; Kurkcuoglu, Ozge; Doruker, Pemra

2017-01-01

The chaperone trigger factor (TF) binds to the ribosome exit tunnel and helps cotranslational folding of nascent chains (NC) in bacterial cells and chloroplasts. In this study, we aim to investigate the functional dynamics of fully-atomistic apo TF and its complex with 50S. As TF accomodates a high percentage of charged residues on its surface, the effect of ionic strength on TF dynamics is assessed here by performing five independent molecular dynamics (MD) simulations (total of 1.3 micro-second duration) at 29 mM and 150 mM ionic strengths. At both concentrations, TF exhibits high inter- and intra-domain flexibility related to its binding (BD), core (CD), and head (HD) domains. Even though large oscillations in gyration radius exist during each run, we do not detect the so-called 'fully collapsed' state with both HD and BD collapsed upon the core. In fact, the extended conformers with relatively open HD and BD are highly populated at the physiological concentration of 150 mM. More importantly, extended TF snapshots stand out in terms of favorable docking onto the 50S subunit. Elastic network modeling (ENM) indicates significant changes in TF's functional dynamics and domain decomposition depending on its conformation and positioning on the 50S. The most dominant slow motions are the lateral sweeping and vertical opening/closing of HD relative to 50S. Finally, our ENM-based efficient technique -ClustENM- is used to sample atomistic conformers starting with an extended TF-50S complex. Specifically, BD and CD motions are restricted near the tunnel exit, while HD is highly mobile. The atomistic conformers generated without an NC are in agreement with the cryo-EM maps available for TF-ribosome-NC complex.

Envelope molecular-orbital theory of extended systems. I. Electronic states of organic quasilinear nanoheterostructures

NASA Astrophysics Data System (ADS)

Arce, J. C.; Perdomo-Ortiz, A.; Zambrano, M. L.; Mujica-Martínez, C.

2011-03-01

A conceptually appealing and computationally economical course-grained molecular-orbital (MO) theory for extended quasilinear molecular heterostructures is presented. The formalism, which is based on a straightforward adaptation, by including explicitly the vacuum, of the envelope-function approximation widely employed in solid-state physics leads to a mapping of the three-dimensional single-particle eigenvalue equations into simple one-dimensional hole and electron Schrödinger-like equations with piecewise-constant effective potentials and masses. The eigenfunctions of these equations are envelope MO's in which the short-wavelength oscillations present in the full MO's, associated with the atomistic details of the molecular potential, are smoothed out automatically. The approach is illustrated by calculating the envelope MO's of high-lying occupied and low-lying virtual π states in prototypical nanometric heterostructures constituted by oligomers of polyacetylene and polydiacetylene. Comparison with atomistic electronic-structure calculations reveals that the envelope-MO energies agree very well with the energies of the π MO's and that the envelope MO's describe precisely the long-wavelength variations of the π MO's. This envelope MO theory, which is generalizable to extended systems of any dimensionality, is seen to provide a useful tool for the qualitative interpretation and quantitative prediction of the single-particle quantum states in mesoscopic molecular structures and the design of nanometric molecular devices with tailored energy levels and wavefunctions.

Lattice Thermal Conductivity of Ultra High Temperature Ceramics ZrB2 and HfB2 from Atomistic Simulations

NASA Technical Reports Server (NTRS)

Lawson, John W.; Murray, Daw S.; Bauschlicher, Charles W., Jr.

2011-01-01

Atomistic Green-Kubo simulations are performed to evaluate the lattice thermal conductivity for single crystals of the ultra high temperature ceramics ZrB2 and HfB2 for a range of temperatures. Recently developed interatomic potentials are used for these simulations. Heat current correlation functions show rapid oscillations which can be identified with mixed metal-Boron optical phonon modes. Agreement with available experimental data is good.

Atomistic mechanisms of rapid energy transport in light-harvesting molecules

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Koga, Shiro; Akai, Ichiro; Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2011-03-01

Synthetic supermolecules such as π-conjugated light-harvesting dendrimers efficiently harvest energy from sunlight, which is of significant importance for the global energy problem. Key to their success is rapid transport of electronic excitation energy from peripheral antennas to photochemical reaction cores, the atomistic mechanisms of which remains elusive. Here, quantum-mechanical molecular dynamics simulation incorporating nonadiabatic electronic transitions reveals the key molecular motion that significantly accelerates the energy transport based on the Dexter mechanism.

Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

DOE PAGES

Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; ...

2015-01-29

The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies ismore » illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.« less

Exploring Beta-Amyloid Protein Transmembrane Insertion Behavior and Residue-Specific Lipid Interactions in Lipid Bilayers Using Multiscale MD Simulations

NASA Astrophysics Data System (ADS)

Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

2013-03-01

Beta-amyloid (Abeta) interactions with neurons are linked to Alzheimer's. Using a multiscale MD simulation strategy that combines the high efficiency of phase space sampling of coarse-grained MD (CGD) and the high spatial resolution of Atomistic MD (AMD) simulations, we studied the Abeta insertion dynamics in cholesterol-enriched and -depleted lipid bilayers that mimic the neuronal membranes domains. Forward (AMD-CGD) and reverse (CGD-AMD) mappings were used. At the atomistic level, cholesterol promoted insertion of Abeta with high (folded) or low (unfolded) helical contents of the lipid insertion domain (Lys28-Ala42), and the insertions were stabilized by the Lys28 snorkeling and Ala42-anchoring to the polar lipid groups of the bilayer up to 200ns. After the forward mapping, the folded inserted state switched to a new extended inserted state with the Lys28 descended to the middle of the bilayer while the unfolded inserted state migrated to the membrane surface up to 4000ns. The two new states remained stable for 200ns at the atomistic scale after the reverse mapping. Our results suggested that different Abeta membrane-orientation states separated by free energy barriers can be explored by the multiscale MD more effectively than by Atomistic MD simulations alone. NIH RC1-GM090897-02

Homopolyrotaxanes and Homopolyrotaxane Networks of PEO

NASA Technical Reports Server (NTRS)

Pugh, Coleen; Mattice, Wayne

2005-01-01

In order to identify the optimum size of macrocrown ether for threading, we first investigated the size and shape of simple crown ethers in the melt at 373 K, and their extent of threading with PEO in the melt using coarse-grained Monte Carlo simulations on the 2nnd (second nearest neighbor diamond) lattice, which is a high coordination lattice whose coarse-grained chains can be reverse mapped into fully atomistic models in continuous space.

Virtual Design and Testing of Materials: A Multiscale Approach

DTIC Science & Technology

2006-06-30

Impurities in Aluminum and Their Effect on Mechanical Properties ", Phys. Rev. B 65, 064102 (2002). 21. G. Lu, V. Bulatov, and N. Kioussis, "Dislocation...materials: atomistic and continuum models with application to titanium - aluminides ", Phil. Mag. A 82, 2397-2417 (2002). 31. V.S. Deshpande, A. Needleman and...be used to test, and suggest design strategies for, new advanced structured materials. IS. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: Unclassified

Atomistic-Dislocation Dynamics Modelling of Fatigue Microstructure and Crack Initiation

DTIC Science & Technology

2013-01-01

experimental) Brown 󈧊 (Upper Limit’) DD Results Mughrabi & Pschenitzka 󈧉 (Lower Limit) y = 50 nm d, = 1.2 |lm M I 4 Simulations of... Mughrabi . Introduction to the viewpoint set on: Surface effects in cyclic deformation and fatigue. Scr. Metall. Mater., 26(10): 1499-1504, 1992. [3] E...associated with dislocation cores. Acta Materialia, 53:13131321, 2005. [13] H. Mughrabi . The long-range internal stress field in the dislocation wall

Modeling Materials: Design for Planetary Entry, Electric Aircraft, and Beyond

NASA Technical Reports Server (NTRS)

Thompson, Alexander; Lawson, John W.

2014-01-01

NASA missions push the limits of what is possible. The development of high-performance materials must keep pace with the agency's demanding, cutting-edge applications. Researchers at NASA's Ames Research Center are performing multiscale computational modeling to accelerate development times and further the design of next-generation aerospace materials. Multiscale modeling combines several computationally intensive techniques ranging from the atomic level to the macroscale, passing output from one level as input to the next level. These methods are applicable to a wide variety of materials systems. For example: (a) Ultra-high-temperature ceramics for hypersonic aircraft-we utilized the full range of multiscale modeling to characterize thermal protection materials for faster, safer air- and spacecraft, (b) Planetary entry heat shields for space vehicles-we computed thermal and mechanical properties of ablative composites by combining several methods, from atomistic simulations to macroscale computations, (c) Advanced batteries for electric aircraft-we performed large-scale molecular dynamics simulations of advanced electrolytes for ultra-high-energy capacity batteries to enable long-distance electric aircraft service; and (d) Shape-memory alloys for high-efficiency aircraft-we used high-fidelity electronic structure calculations to determine phase diagrams in shape-memory transformations. Advances in high-performance computing have been critical to the development of multiscale materials modeling. We used nearly one million processor hours on NASA's Pleiades supercomputer to characterize electrolytes with a fidelity that would be otherwise impossible. For this and other projects, Pleiades enables us to push the physics and accuracy of our calculations to new levels.

MMM: A toolbox for integrative structure modeling.

PubMed

Jeschke, Gunnar

2018-01-01

Structural characterization of proteins and their complexes may require integration of restraints from various experimental techniques. MMM (Multiscale Modeling of Macromolecules) is a Matlab-based open-source modeling toolbox for this purpose with a particular emphasis on distance distribution restraints obtained from electron paramagnetic resonance experiments on spin-labelled proteins and nucleic acids and their combination with atomistic structures of domains or whole protomers, small-angle scattering data, secondary structure information, homology information, and elastic network models. MMM does not only integrate various types of restraints, but also various existing modeling tools by providing a common graphical user interface to them. The types of restraints that can support such modeling and the available model types are illustrated by recent application examples. © 2017 The Protein Society.

The Structural Basis of IKs Ion-Channel Activation: Mechanistic Insights from Molecular Simulations.

PubMed

Ramasubramanian, Smiruthi; Rudy, Yoram

2018-06-05

Relating ion channel (iCh) structural dynamics to physiological function remains a challenge. Current experimental and computational techniques have limited ability to explore this relationship in atomistic detail over physiological timescales. A framework associating iCh structure to function is necessary for elucidating normal and disease mechanisms. We formulated a modeling schema that overcomes the limitations of current methods through applications of artificial intelligence machine learning. Using this approach, we studied molecular processes that underlie human IKs voltage-mediated gating. IKs malfunction underlies many debilitating and life-threatening diseases. Molecular components of IKs that underlie its electrophysiological function include KCNQ1 (a pore-forming tetramer) and KCNE1 (an auxiliary subunit). Simulations, using the IKs structure-function model, reproduced experimentally recorded saturation of gating-charge displacement at positive membrane voltages, two-step voltage sensor (VS) movement shown by fluorescence, iCh gating statistics, and current-voltage relationship. Mechanistic insights include the following: 1) pore energy profile determines iCh subconductance; 2) the entire protein structure, not limited to the pore, contributes to pore energy and channel subconductance; 3) interactions with KCNE1 result in two distinct VS movements, causing gating-charge saturation at positive membrane voltages and current activation delay; and 4) flexible coupling between VS and pore permits pore opening at lower VS positions, resulting in sequential gating. The new modeling approach is applicable to atomistic scale studies of other proteins on timescales of physiological function. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The More, the Better? Curvilinear Effects of Job Autonomy on Well-Being From Vitamin Model and PE-Fit Theory Perspectives.

PubMed

Stiglbauer, Barbara; Kovacs, Carrie

2017-12-28

In organizational psychology research, autonomy is generally seen as a job resource with a monotone positive relationship with desired occupational outcomes such as well-being. However, both Warr's vitamin model and person-environment (PE) fit theory suggest that negative outcomes may result from excesses of some job resources, including autonomy. Thus, the current studies used survey methodology to explore cross-sectional relationships between environmental autonomy, person-environment autonomy (mis)fit, and well-being. We found that autonomy and autonomy (mis)fit explained between 6% and 22% of variance in well-being, depending on type of autonomy (scheduling, method, or decision-making) and type of (mis)fit operationalization (atomistic operationalization through the separate assessment of actual and ideal autonomy levels vs. molecular operationalization through the direct assessment of perceived autonomy (mis)fit). Autonomy (mis)fit (PE-fit perspective) explained more unique variance in well-being than environmental autonomy itself (vitamin model perspective). Detrimental effects of autonomy excess on well-being were most evident for method autonomy and least consistent for decision-making autonomy. We argue that too-much-of-a-good-thing effects of job autonomy on well-being exist, but suggest that these may be dependent upon sample characteristics (range of autonomy levels), type of operationalization (molecular vs. atomistic fit), autonomy facet (method, scheduling, or decision-making), as well as individual and organizational moderators. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A Coarse-grained Model of Stratum Corneum Lipids: Free Fatty Acids and Ceramide NS

PubMed Central

Moore, Timothy C.; Iacovella, Christopher R.; Hartkamp, Remco; Bunge, Annette L.; McCabe, Clare

2017-01-01

Ceramide (CER)-based biological membranes are used both experimentally and in simulations as simplified model systems of the skin barrier. Molecular dynamics studies have generally focused on simulating preassembled structures using atomistically detailed models of CERs, which limit the system sizes and timescales that can practically be probed, rendering them ineffective for studying particular phenomena, including self-assembly into bilayer and lamellar superstructures. Here, we report on the development of a coarse-grained (CG) model for CER NS, the most abundant CER in human stratum corneum. Multistate iterative Boltzmann inversion is used to derive the intermolecular pair potentials, resulting in a force field that is applicable over a range of state points and suitable for studying ceramide self-assembly. The chosen CG mapping, which includes explicit interaction sites for hydroxyl groups, captures the directional nature of hydrogen bonding and allows for accurate predictions of several key structural properties of CER NS bilayers. Simulated wetting experiments allow the hydrophobicity of CG beads to be accurately tuned to match atomistic wetting behavior, which affects the whole system since inaccurate hydrophobic character is found to unphysically alter the lipid packing in hydrated lamellar states. We find that CER NS can self-assemble into multilamellar structures, enabling the study of lipid systems more representative of the multilamellar lipid structures present in the skin barrier. The coarse-grained force field derived herein represents an important step in using molecular dynamics to study the human skin barrier, which gives a resolution not available through experiment alone. PMID:27564869