Insights into the charge carrier terahertz mobility in polyfluorenes from large-scale atomistic simulations and time-resolved terahertz spectroscopy

Czech Academy of Sciences Publication Activity Database

Vukmirović, N.; Ponseca, C.S.; Němec, Hynek; Yartsev, A.; Sundström, V.

2012-01-01

Roč. 116, č. 37 (2012), s. 19665-1972 ISSN 1932-7447 Institutional research plan: CEZ:AV0Z10100520 Keywords : charge carrier mobility * time-resolved terahertz spectroscopy * multiscale atomistic calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.814, year: 2012

A coupled atomistics and discrete dislocation plasticity simulation of nanoindentation into single crystal thin films

International Nuclear Information System (INIS)

Miller, Ronald E.; Shilkrot, L.E.; Curtin, William A.

2004-01-01

The phenomenon of 2D nanoindentation of circular 'Brinell' indenter into a single crystal metal thin film bonded to a rigid substrate is investigated. The simulation method is the coupled atomistics and discrete dislocation (CADD) model recently developed by the authors. The CADD model couples a continuum region containing any number of discrete dislocations to an atomistic region, and permits accurate, automatic detection and passing of dislocations between the atomistic and continuum regions. The CADD model allows for a detailed study of nanoindentation to large penetration depths (up to 60 A here) using only a small region of atoms just underneath the indenter where dislocation nucleation, cross-slip, and annihilation occur. Indentation of a model hexagonal aluminum crystal shows: (i) the onset of homogeneous dislocation nucleation at points away from the points of maximum resolved shear stress; (ii) size-dependence of the material hardness, (iii) the role of dislocation dissociation on deformation; (iv) reverse plasticity, including nucleation of dislocations on unloading and annihilation; (v) permanent deformation, including surface uplift, after full unloading; (vi) the effects of film thickness on the load-displacement response; and (vii) the differences between displacement and force controlled loading. This application demonstrates the power of the CADD method in capturing both long-range dislocation plasticity and short-range atomistic phenomena. The use of CADD permits for a clear study of the physical and mechanical influence of both complex plastic flow and non-continuum atomistic-level processes on the macroscopic response of material under indentation loading

Atomistic computer simulations a practical guide

CERN Document Server

Brazdova, Veronika

2013-01-01

Many books explain the theory of atomistic computer simulations; this book teaches you how to run them This introductory ""how to"" title enables readers to understand, plan, run, and analyze their own independent atomistic simulations, and decide which method to use and which questions to ask in their research project. It is written in a clear and precise language, focusing on a thorough understanding of the concepts behind the equations and how these are used in the simulations. As a result, readers will learn how to design the computational model and which parameters o

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

Science.gov (United States)

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

2018-01-01

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

Key role of water in proton transfer at the Q(o)-site of the cytochrome bc(1) complex predicted by atomistic molecular dynamics simulations

DEFF Research Database (Denmark)

Postila, P. A.; Kaszuba, K.; Sarewicz, M.

2013-01-01

of the cyt bc(1) function have remained unclear especially regarding the substrate binding at the Q(o)-site. In this work we address this issue by performing extensive atomistic molecular dynamics simulations with the cyt bc(1) complex of Rhodobacter capsulatus embedded in a lipid bilayer. Based...... on the simulations we are able to show the atom-level binding modes of two substrate forms: quinol (QH(2)) and quinone (Q). The QH(2) binding at the Q(o)-site involves a coordinated water arrangement that produces an exceptionally close and stable interaction between the cyt b and iron sulfur protein subunits...

Atomistic simulations of surfactant adsorption kinetics at interfaces

Science.gov (United States)

Iskrenova, Eugeniya; Patnaik, Soumya

2014-03-01

Heat transfer control and enhancement is an important and challenging problem in a variety of industrial and technological applications including aircraft thermal management. The role of additives in nucleate boiling and phase change in general has long been recognized and studied experimentally and modeled theoretically but in-depth description and atomistic understanding of the multiscale processes involved are still needed for better prediction and control of the heat transfer efficiency. Surfactant additives have been experimentally observed to either enhance or inhibit the boiling heat transfer depending on the surfactant concentration and chemistry and, on a molecular level, their addition leads to dynamic surface tension and changes in interfacial and transfer properties, thus contributing to the complexity of the problem. We present our atomistic modeling study of the interfacial adsorption kinetics of aqueous surfactant (sodium dodecyl sulfate) systems at a range of concentrations at room and boiling temperatures. Classical molecular dynamics and Umbrella Sampling simulations were used to study the surfactant transport properties and estimate the adsorption and desorption rates at liquid-vacuum and liquid-solid interfaces. The authors gratefully acknowledge funding from AFOSR Thermal Science Program and the Air Force Research Laboratory DoD Supercomputing Resource Center for computing time and resources.

Adaptive spacetime method using Riemann jump conditions for coupled atomistic-continuum dynamics

International Nuclear Information System (INIS)

Kraczek, B.; Miller, S.T.; Haber, R.B.; Johnson, D.D.

2010-01-01

We combine the Spacetime Discontinuous Galerkin (SDG) method for elastodynamics with the mathematically consistent Atomistic Discontinuous Galerkin (ADG) method in a new scheme that concurrently couples continuum and atomistic models of dynamic response in solids. The formulation couples non-overlapping continuum and atomistic models across sharp interfaces by weakly enforcing jump conditions, for both momentum balance and kinematic compatibility, using Riemann values to preserve the characteristic structure of the underlying hyperbolic system. Momentum balances to within machine-precision accuracy over every element, on each atom, and over the coupled system, with small, controllable energy dissipation in the continuum region that ensures numerical stability. When implemented on suitable unstructured spacetime grids, the continuum SDG model offers linear computational complexity in the number of elements and powerful adaptive analysis capabilities that readily bridge between atomic and continuum scales in both space and time. A special trace operator for the atomic velocities and an associated atomistic traction field enter the jump conditions at the coupling interface. The trace operator depends on parameters that specify, at the scale of the atomic spacing, the position of the coupling interface relative to the atoms. In a key finding, we demonstrate that optimizing these parameters suppresses spurious reflections at the coupling interface without the use of non-physical damping or special boundary conditions. We formulate the implicit SDG-ADG coupling scheme in up to three spatial dimensions, and describe an efficient iterative solution scheme that outperforms common explicit schemes, such as the Velocity Verlet integrator. Numerical examples, in 1dxtime and employing both linear and nonlinear potentials, demonstrate the performance of the SDG-ADG method and show how adaptive spacetime meshing reconciles disparate time steps and resolves atomic-scale signals in

General atomistic approach for modeling metal-semiconductor interfaces using density functional theory and nonequilibrium Green's function

DEFF Research Database (Denmark)

Stradi, Daniele; Martinez, Umberto; Blom, Anders

2016-01-01

Metal-semiconductor contacts are a pillar of modern semiconductor technology. Historically, their microscopic understanding has been hampered by the inability of traditional analytical and numerical methods to fully capture the complex physics governing their operating principles. Here we introduce...... an atomistic approach based on density functional theory and nonequilibrium Green's function, which includes all the relevant ingredients required to model realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via I-Vbias curve simulations. We apply...... interfaces as it neglects electron tunneling, and that finite-size atomistic models have problems in describing these interfaces in the presence of doping due to a poor representation of space-charge effects. Conversely, the present method deals effectively with both issues, thus representing a valid...

Atomistic and holistic understanding in physics

International Nuclear Information System (INIS)

Bohm, A.

1992-01-01

Understanding means always reduction to the simpler. In the atomistic understanding the reduction is to the simpler objects. One asks the question: what does it consist of? For instance, one asks: What does the molecule consist of? and the answer is: The molecule consists of electrons and nuclei. Or: what does the nucleus consist of? And the answer is: The nucleus consists of protons and neutrons. The parts in the atomistic understanding are the constituents. In the holistic understanding, the reduction is to the simpler functions, the simpler motions. One asks the question: What does it do? What does the molecule do? What does the nucleus do? And the answer is: The molecule rotates and oscillates. The nucleus rotates and oscillates

Diffusion in energy materials: Governing dynamics from atomistic modelling

Science.gov (United States)

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.

Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design

International Nuclear Information System (INIS)

Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.

2010-01-01

This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and

Atomistic simulations in Si processing: Bridging the gap between atoms and experiments

International Nuclear Information System (INIS)

Marques, Luis A.; Pelaz, Lourdes; Lopez, Pedro; Aboy, Maria; Santos, Ivan; Barbolla, Juan

2005-01-01

With devices shrinking to nanometric scale, process simulation tools have to shift from continuum models to an atomistic description of the material. However, the limited sizes and time scales accessible for detailed atomistic techniques usually lead to the difficult task of relating the information obtained from simulations to experimental data. The solution consists of the use of a hierarchical simulation scheme: more fundamental techniques are employed to extract parameters and models that are then feed into less detailed simulators which allow direct comparison with experiments. This scheme will be illustrated with the modeling of the amorphization and recrystallization of Si, which has been defined as a key challenge in the last edition of the International Technology Roadmap for Semiconductors. The model is based on the bond defect or IV pair, which is used as the building block of the amorphous phase. The properties of this defect have been studied using ab initio methods and classical molecular dynamics techniques. It is shown that the recombination of this defect depends on the surrounding bond defects, which accounts for the cooperative nature of the amorphization and recrystallization processes. The implementation of this model in a kinetic Monte Carlo code allows extracting data directly comparable with experiments. This approach provides physical insight on the amorphization and recrystallization mechanisms and a tool for the optimization of solid-phase epitaxial-related processes

FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

KAUST Repository

Harmandaris, Vagelis

2017-10-03

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

On the atomistic mechanisms of alkane (methane-pentane) separation by distillation: a molecular dynamics study.

Science.gov (United States)

Zahn, Dirk

2007-11-01

Insights into the liquid-vapor transformation of methane-pentane mixtures were obtained from transition path sampling molecular dynamics simulations. This case study of the boiling of non-azeotropic mixtures demonstrates an unprejudiced identification of the atomistic mechanisms of phase separation in the course of vaporization which form the basis of distillation processes. From our simulations we observe spontaneous segregation events in the liquid mixture to trigger vapor nucleation. The formation of vapor domains stabilizes and further promotes the separation process by preferential evaporation of methane molecules. While this discrimination holds for all mixtures of different composition studied, a full account of the boiling process requires a more complex picture. At low methane concentration the nucleation of the vapor domains includes both methane and pentane molecules. The pentane molecules, however, tend to form small aggregates and undergo rapid re-condensation within picoseconds to nanoseconds scales. Accordingly, two aspects of selectivity accounting for methane-pentane separation in the course of liquid-vapor transformations were made accessible to molecular dynamics simulations: spontaneous segregation in the liquid phase leading to selective vapor nucleation and growth favoring methane vaporization and selective re-condensation of pentane molecules.

An object oriented Python interface for atomistic simulations

Science.gov (United States)

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.

Elastic dipoles of point defects from atomistic simulations

Science.gov (United States)

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.

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

Science.gov (United States)

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.

Chaotic, fractional, and complex dynamics new insights and perspectives

CERN Document Server

Macau, Elbert; Sanjuan, Miguel

2018-01-01

The book presents nonlinear, chaotic and fractional dynamics, complex systems and networks, together with cutting-edge research on related topics. The fifteen chapters – written by leading scientists working in the areas of nonlinear, chaotic and fractional dynamics, as well as complex systems and networks – offer an extensive overview of cutting-edge research on a range of topics, including fundamental and applied research. These include but are not limited to aspects of synchronization in complex dynamical systems, universality features in systems with specific fractional dynamics, and chaotic scattering. As such, the book provides an excellent and timely snapshot of the current state of research, blending the insights and experiences of many prominent researchers.

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

DEFF Research Database (Denmark)

Euro, Liliya; Haapanen, Outi; Róg, Tomasz

2017-01-01

of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

AACSD: An atomistic analyzer for crystal structure and defects

Science.gov (United States)

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.

Addressing uncertainty in atomistic machine learning

DEFF Research Database (Denmark)

Peterson, Andrew A.; Christensen, Rune; Khorshidi, Alireza

2017-01-01

Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility of the predi......Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility...... of the predictions. In this perspective, we address the types of errors that might arise in atomistic machine learning, the unique aspects of atomistic simulations that make machine-learning challenging, and highlight how uncertainty analysis can be used to assess the validity of machine-learning predictions. We...... suggest this will allow researchers to more fully use machine learning for the routine acceleration of large, high-accuracy, or extended-time simulations. In our demonstrations, we use a bootstrap ensemble of neural network-based calculators, and show that the width of the ensemble can provide an estimate...

Robust mode space approach for atomistic modeling of realistically large nanowire transistors

Science.gov (United States)

Huang, Jun Z.; Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard

2018-01-01

Nanoelectronic transistors have reached 3D length scales in which the number of atoms is countable. Truly atomistic device representations are needed to capture the essential functionalities of the devices. Atomistic quantum transport simulations of realistically extended devices are, however, computationally very demanding. The widely used mode space (MS) approach can significantly reduce the numerical cost, but a good MS basis is usually very hard to obtain for atomistic full-band models. In this work, a robust and parallel algorithm is developed to optimize the MS basis for atomistic nanowires. This enables engineering-level, reliable tight binding non-equilibrium Green's function simulation of nanowire metal-oxide-semiconductor field-effect transistor (MOSFET) with a realistic cross section of 10 nm × 10 nm using a small computer cluster. This approach is applied to compare the performance of InGaAs and Si nanowire n-type MOSFETs (nMOSFETs) with various channel lengths and cross sections. Simulation results with full-band accuracy indicate that InGaAs nanowire nMOSFETs have no drive current advantage over their Si counterparts for cross sections up to about 10 nm × 10 nm.

An atomistic vision of the Mass Action Law: Prediction of carbon/oxygen defects in silicon

Energy Technology Data Exchange (ETDEWEB)

Brenet, G.; Timerkaeva, D.; Caliste, D.; Pochet, P. [CEA, INAC-SP2M, Atomistic Simulation Laboratory, F-38000 Grenoble (France); Univ. Grenoble Alpes, INAC-SP2M, L-Sim, F-38000 Grenoble (France); Sgourou, E. N.; Londos, C. A. [University of Athens, Solid State Physics Section, Panepistimiopolis Zografos, Athens 157 84 (Greece)

2015-09-28

We introduce an atomistic description of the kinetic Mass Action Law to predict concentrations of defects and complexes. We demonstrate in this paper that this approach accurately predicts carbon/oxygen related defect concentrations in silicon upon annealing. The model requires binding and migration energies of the impurities and complexes, here obtained from density functional theory (DFT) calculations. Vacancy-oxygen complex kinetics are studied as a model system during both isochronal and isothermal annealing. Results are in good agreement with experimental data, confirming the success of the methodology. More importantly, it gives access to the sequence of chain reactions by which oxygen and carbon related complexes are created in silicon. Beside the case of silicon, the understanding of such intricate reactions is a key to develop point defect engineering strategies to control defects and thus semiconductors properties.

Adhesive contact: from atomistic model to continuum model

International Nuclear Information System (INIS)

Fan Kang-Qi; Jia Jian-Yuan; Zhu Ying-Min; Zhang Xiu-Yan

2011-01-01

Two types of Lennard-Jones potential are widely used in modeling adhesive contacts. However, the relationships between the parameters of the two types of Lennard-Jones potential are not well defined. This paper employs a self-consistent method to derive the Lennard-Jones surface force law from the interatomic Lennard-Jones potential with emphasis on the relationships between the parameters. The effect of using correct parameters in the adhesion models is demonstrated in single sphere-flat contact via continuum models and an atomistic model. Furthermore, the adhesion hysteresis behaviour is investigated, and the S-shaped force-distance relation is revealed by the atomistic model. It shows that the adhesion hysteresis loop is generated by the jump-to-contact and jump-off-contact, which are illustrated by the S-shaped force-distance curve. (atomic and molecular physics)

Insight into the influence of liquid paraffin for methanol synthesis on Cu(110) surface using continuum and atomistic models

Energy Technology Data Exchange (ETDEWEB)

Jiao, Wei-Hong [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Liu, Shi-Zhong [Department of Chemistry, Stony Brook University, Stony Brook, NY 11794 (United States); Zuo, Zhi-Jun, E-mail: zuozhijun@tyut.edu.cn [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Ren, Rui-Peng; Gao, Zhi-Hua [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Huang, Wei, E-mail: huangwei@tyut.edu.cn [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China)

2016-11-30

Highlights: • The influence of liquid paraffin is studied using continuum and atomistic models. • Liquid paraffin does not alter the reaction pathways of CO hydrogenation and WGS. • Liquid paraffin alters the reaction pathways of CO{sub 2} hydrogenation. - Abstract: Methanol synthesis from CO/CO{sub 2} hydrogenation and water-gas shift (WGS) reaction on Cu(110) in liquid paraffin and vacuum have been systematically researched with density functional theory calculation (DFT). For methanol synthesis from CO hydrogenation, the reaction pathways in liquid paraffin and vacuum are CO + H → HCO → H{sub 2}CO → H{sub 3}CO → H{sub 3}COH; in the case of WGS, the reaction pathways in liquid paraffin and vacuum are CO + 2H{sub 2}O → CO + 2OH + 2H → CO + H{sub 2}O + O + H{sub 2} → CO{sub 2} + H{sub 2}O + H{sub 2}; the reaction pathways of methanol synthesis from CO{sub 2} hydrogenation in liquid paraffin and vacuum are CO{sub 2} + H → HCOO → H{sub 2}COO → H{sub 2}CO → H{sub 3}CO → H{sub 3}COH and CO{sub 2} + H → HCOO → HCOOH → H{sub 2}COOH → H{sub 3}CO → H{sub 3}COH, respectively. The result shows that liquid paraffin does not affect the reaction mechanisms of methanol synthesis from CO and WGS, but it changes the reaction mechanisms of methanol synthesis from CO{sub 2} hydrogenation. Hirshfeld charge and the d-band centers indicate that the catalytic activity of Cu(110) in liquid paraffin is smaller than that in vacuum. Our results also show that it is necessary to consider both continuum and atomistic models in the slurry bed.

Assessing the fracture strength of geological and related materials via an atomistically based J-integral

Science.gov (United States)

Jones, R. E.; Criscenti, L. J.; Rimsza, J.

2016-12-01

Predicting fracture initiation and propagation in low-permeability geomaterials is a critical yet un- solved problem crucial to assessing shale caprocks at carbon dioxide sequestration sites, and controlling fracturing for gas and oil extraction. Experiments indicate that chemical reactions at fluid-geomaterial interfaces play a major role in subcritical crack growth by weakening the material and altering crack nu- cleation and growth rates. Engineering the subsurface fracture environment, however, has been hindered by a lack of understanding of the mechanisms relating chemical environment to mechanical outcome, and a lack of capability directly linking atomistic insight to macroscale observables. We have developed a fundamental atomic-level understanding of the chemical-mechanical mecha- nisms that control subcritical cracks through coarse-graining data from reactive molecular simulations. Previous studies of fracture at the atomic level have typically been limited to producing stress-strain curves, quantifying either the system-level stress or energy at which fracture propagation occurs. As such, these curves are neither characteristic of nor insightful regarding fracture features local to the crack tip. In contrast, configurational forces, such as the J-integral, are specific to the crack in that they measure the energy available to move the crack and truly quantify fracture resistance. By development and use of field estimators consistent with the continuum conservation properties we are able to connect the data produced by atomistic simulation to the continuum-level theory of fracture mechanics and thus inform engineering decisions. In order to trust this connection we have performed theoretical consistency tests and validation with experimental data. Although we have targeted geomaterials, this capability can have direct impact on other unsolved technological problems such as predicting the corrosion and embrittlement of metals and ceramics. Sandia National

Atomistically-informed dislocation dynamics in FCC crystals

International Nuclear Information System (INIS)

Martinez, E.; Marian, J.; Arsenlis, A.; Victoria, M.; Martinez, E.; Victoria, M.; Perlado, J.M.

2008-01-01

Full text of publication follows. We will present a nodal dislocation dynamics (DD) model to simulate plastic processes in fcc crystals. The model explicitly accounts for all slip systems and Burgers vectors observed in fcc systems, including stacking faults and partial dislocations. We derive simple conservation rules that describe all partial dislocation interactions rigorously and allow us to model and quantify cross-slip processes, the structure and strength of dislocation junctions, and the formation of fcc-specific structures such as stacking fault tetrahedra. The DD framework is built upon isotropic non-singular linear elasticity, and supports itself on information transmitted from the atomistic scale. In this fashion, connection between the meso and micro scales is attained self-consistently with core parameters fitted to atomistic data. We perform a series of targeted simulations to demonstrate the capabilities of the model, including dislocation reactions and dissociations and dislocation junction strength. Additionally we map the four-dimensional stress space relevant for cross-slip and relate our fundings to the plastic behaviour of' monocrystalline fcc metals. (authors)

Spectral and theoretical study on complexation of sulfamethoxazole with β- and HPβ-cyclodextrins in binary and ternary systems

Science.gov (United States)

Varghese, Beena; Suliman, FakhrEldin O.; Al-Hajri, Aalia; Al Bishri, Nahed Surur S.; Al-Rwashda, Nathir

2018-02-01

The inclusion complexes of sulfamethoxazole (SMX) with β-cyclodextrin (βCD) and (2-hydroxypropyl) β-cyclodextrin (HPβCD) were prepared. Fluorescence spectroscopy and electrospray mass spectrometry, ESI-MS, were used to investigate and characterize the inclusion complexation of SMX with cyclodextrins in solutions. Whereas in the solid state the complexes were characterized by Fourier transform infrared spectroscopy (FTIR), powder X-ray diffraction (PXRD) and Raman techniques. Enhanced twisted intramolecular charge transfer (TICT), emission as well as local excited (LE) bands were observed upon addition of HPβCD indicate that SMX enters deeper into the cyclodextrins cavity. The stoichiometries and association constants of these complexes have been determined by monitoring the fluorescence data. The effect of presence of ternary components like arginine and cysteine on the complexation efficiency of SMX with cyclodextrins was investigated. Molecular Dynamic simulations were also performed to shed an atomistic insight into the complexation mechanism. The results obtained showed that complexes of SMX with both cyclodextrins are stabilized in aqueous media by strong hydrogen bonding interactions.

Definition and detection of contact in atomistic simulations

NARCIS (Netherlands)

Solhjoo, Soheil; Vakis, Antonis I.

In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,

Definition and detection of contact in atomistic simulations

NARCIS (Netherlands)

Solhjoo, Soheil; Vakis, Antonis I.

2015-01-01

In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,

Ionic diffusion in quartz studied by transport measurements, SIMS and atomistic simulations

International Nuclear Information System (INIS)

Sartbaeva, Asel; Wells, Stephen A; Redfern, Simon A T; Hinton, Richard W; Reed, Stephen J B

2005-01-01

Ionic diffusion in the quartz-β-eucryptite system is studied by DC transport measurements, SIMS and atomistic simulations. Transport data show a large transient increase in ionic current at the α-β phase transition of quartz (the Hedvall effect). The SIMS data indicate two diffusion processes, one involving rapid Li + motion and the other involving penetration of Al and Li atoms into quartz at the phase transition. Atomistic simulations explain why the fine microstructure of twin domain walls in quartz near the transition does not hinder Li + diffusion

Structural and functional analysis of glycoprotein butyrylcholinesterase using atomistic molecular dynamics

Science.gov (United States)

Bernardi, Austen; Faller, Roland

Atomistic molecular dynamics (MD) has proven to be a powerful tool for studying the structure and dynamics of biological systems on nanosecond to microsecond time scales and nanometer length scales. In this work we study the effects of modifying the glycan distribution on the structure and function of full length monomeric butyrylcholinesterase (BChE). BChE exists as a monomer, dimer, or tetramer, and is a therapeutic glycoprotein with nine asparagine glycosylation sites per monomer. Each monomer acts as a stoichiometric scavenger for organophosphorus (OP) nerve agents (e.g. sarin, soman). Glycan distributions are highly heterogeneous and have been shown experimentally to affect certain glycoproteins' stability and reactivity. We performed structural analysis of various biologically relevant glycoforms of BChE using classical atomistic MD. Functional analysis was performed through binding energy simulations using umbrella sampling with BChE and OP cofactors. Additionally, we assess the quality of the glycans' conformational sampling. We found that the glycan distribution has a significant effect on the structure and function of BChE on timescales available to atomistic MD. This project is funded by the DTRA Grant HDTRA1-15-1-0054.

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

Science.gov (United States)

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.

Ion beam processing of surfaces and interfaces. Modeling and atomistic simulations

International Nuclear Information System (INIS)

Liedke, Bartosz

2011-01-01

Self-organization of regular surface pattern under ion beam erosion was described in detail by Navez in 1962. Several years later in 1986 Bradley and Harper (BH) published the first self-consistent theory on this phenomenon based on the competition of surface roughening described by Sigmund's sputter theory and surface smoothing by Mullins-Herring diffusion. Many papers that followed BH theory introduced other processes responsible for the surface patterning e.g. viscous flow, redeposition, phase separation, preferential sputtering, etc. The present understanding is still not sufficient to specify the dominant driving forces responsible for self-organization. 3D atomistic simulations can improve the understanding by reproducing the pattern formation with the detailed microscopic description of the driving forces. 2D simulations published so far can contribute to this understanding only partially. A novel program package for 3D atomistic simulations called TRIDER (TRansport of Ions in matter with DEfect Relaxation), which unifies full collision cascade simulation with atomistic relaxation processes, has been developed. The collision cascades are provided by simulations based on the Binary Collision Approximation, and the relaxation processes are simulated with the 3D lattice kinetic Monte-Carlo method. This allows, without any phenomenological model, a full 3D atomistic description on experimental spatiotemporal scales. Recently discussed new mechanisms of surface patterning like ballistic mass drift or the dependence of the local morphology on sputtering yield are inherently included in our atomistic approach. The atomistic 3D simulations do not depend so much on experimental assumptions like reported 2D simulations or continuum theories. The 3D computer experiments can even be considered as 'cleanest' possible experiments for checking continuum theories. This work aims mainly at the methodology of a novel atomistic approach, showing that: (i) In general

Ion beam processing of surfaces and interfaces. Modeling and atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Liedke, Bartosz

2011-03-24

Self-organization of regular surface pattern under ion beam erosion was described in detail by Navez in 1962. Several years later in 1986 Bradley and Harper (BH) published the first self-consistent theory on this phenomenon based on the competition of surface roughening described by Sigmund's sputter theory and surface smoothing by Mullins-Herring diffusion. Many papers that followed BH theory introduced other processes responsible for the surface patterning e.g. viscous flow, redeposition, phase separation, preferential sputtering, etc. The present understanding is still not sufficient to specify the dominant driving forces responsible for self-organization. 3D atomistic simulations can improve the understanding by reproducing the pattern formation with the detailed microscopic description of the driving forces. 2D simulations published so far can contribute to this understanding only partially. A novel program package for 3D atomistic simulations called TRIDER (TRansport of Ions in matter with DEfect Relaxation), which unifies full collision cascade simulation with atomistic relaxation processes, has been developed. The collision cascades are provided by simulations based on the Binary Collision Approximation, and the relaxation processes are simulated with the 3D lattice kinetic Monte-Carlo method. This allows, without any phenomenological model, a full 3D atomistic description on experimental spatiotemporal scales. Recently discussed new mechanisms of surface patterning like ballistic mass drift or the dependence of the local morphology on sputtering yield are inherently included in our atomistic approach. The atomistic 3D simulations do not depend so much on experimental assumptions like reported 2D simulations or continuum theories. The 3D computer experiments can even be considered as 'cleanest' possible experiments for checking continuum theories. This work aims mainly at the methodology of a novel atomistic approach, showing that: (i) In

Atomistic simulations of Mg-Cu metallic glasses: Mechanical properties

DEFF Research Database (Denmark)

Bailey, Nicholas; Schiøtz, Jakob; Jacobsen, Karsten Wedel

2004-01-01

The atomistic mechanisms of plastic deformation in amorphous metals are far from being understood. We have derived potential parameters for molecular dynamics simulations of Mg-Cu amorphous alloys using the Effective Medium Theory. We have simulated the formation of alloys by cooling from the melt...

Atomistic Properties of Solids

CERN Document Server

Sirdeshmukh, Dinker B; Subhadra, K G

2011-01-01

The book deals with atomistic properties of solids which are determined by the crystal structure, interatomic forces and atomic displacements influenced by the effects of temperature, stress and electric fields. The book gives equal importance to experimental details and theory. There are full chapters dedicated to the tensor nature of physical properties, mechanical properties, lattice vibrations, crystal structure determination and ferroelectricity. The other crystalline states like nano-, poly-, liquid- and quasi crystals are discussed. Several new topics like nonlinear optics and the Rietveld method are presented in the book. The book lays emphasis on the role of symmetry in crystal properties. Comprehensiveness is the strength of the book; this allows users at different levels a choice of chapters according to their requirements.

Comparison of continuum and atomistic methods for the analysis of InAs/GaAs quantum dots

DEFF Research Database (Denmark)

Barettin, D.; Pecchia, A.; Penazzi, G.

2011-01-01

We present a comparison of continuum k · p and atomistic empirical Tight Binding methods for the analysis of the optoelectronic properties of InAs/GaAs quantum dots.......We present a comparison of continuum k · p and atomistic empirical Tight Binding methods for the analysis of the optoelectronic properties of InAs/GaAs quantum dots....

Atomistic modeling of carbon Cottrell atmospheres in bcc iron

Science.gov (United States)

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.

Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex.

Directory of Open Access Journals (Sweden)

Yunqiang Bian

2014-04-01

Full Text Available In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and K(+ 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.

Atomistic computer simulations on multi-loaded PAMAM dendrimers: a comparison of amine- and hydroxyl-terminated dendrimers

Science.gov (United States)

Badalkhani-Khamseh, Farideh; Ebrahim-Habibi, Azadeh; Hadipour, Nasser L.

2017-12-01

Poly(amidoamine) (PAMAM) dendrimers have been extensively studied as delivery vectors in biomedical applications. A limited number of molecular dynamics (MD) simulation studies have investigated the effect of surface chemistry on therapeutic molecules loading, with the aim of providing insights for biocompatibility improvement and increase in drug loading capacity of PAMAM dendrimers. In this work, fully atomistic MD simulations were employed to study the association of 5-Fluorouracil (5-FU) with amine (NH2)- and hydroxyl (OH)-terminated PAMAM dendrimers of generations 3 and 4 (G3 and G4). MD results show a 1:12, 1:1, 1:27, and 1:4 stoichiometry, respectively, for G3NH2-FU, G3OH-FU, G4NH2-FU, and G4OH-FU complexes, which is in good agreement with the isothermal titration calorimetry results. The results obtained showed that NH2-terminated dendrimers assume segmented open structures with large cavities and more drug molecules can encapsulate inside the dendritic cavities of amine terminated dendrimers. However, OH-terminated have a densely packed structure and therefore, 5-FU drug molecules are more stable to locate close to the surface of the dendrimers. Intermolecular hydrogen bonding analysis showed that 5-FU drug molecules have more tendency to form hydrogen bonds with terminal monomers of OH-terminated dendrimers, while in NH2-terminated these occur both in the inner region and the surface. Furthermore, MM-PBSA analysis revealed that van der Waals and electrostatic energies are both important to stabilize the complexes. We found that drug molecules are distributed uniformly inside the amine and hydroxyl terminated dendrimers and therefore, both dendrimers are promising candidates as drug delivery systems for 5-FU drug molecules.

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

Science.gov (United States)

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.

Atomistic simulations of bulk, surface and interfacial polymer properties

Science.gov (United States)

Natarajan, Upendra

In chapter I, quasi-static molecular mechanics based simulations are used to estimate the activation energy of phenoxy rings flips in the amorphous region of a semicrystalline polyimide. Intra and intermolecular contributions to the flip activation energy, the torsional cooperativity accompanying the flip, and the effect of the flip on the motion in the glassy bulk state, are looked at. Also, comparison of the weighted mean activation energy is made with experimental data from solid state NMR measurements; the simulated value being 17.5 kcal/mol., while the experimental value was observed to be 10.5 kcal/mol. Chapter II deals with construction of random copolymer thin films of styrene-butadiene (SB) and styrene-butadiene-acrylonitrile (SBA). The structure and properties of the free surfaces presented by these thin films are analysed by, the atom mass density profiles, backbone bond orientation function, and the spatial distribution of acrylonitrile groups and styrene rings. The surface energies of SB and SBA are calculated using an atomistic equation and are compared with experimental data in the literature. In chapter III, simulations of polymer-polymer interfaces between like and unlike polymers, specifically cis-polybutadiene (PBD) and atatic polypropylene (PP), are presented. The structure of an incompatible polymer-polymer interface, and the estimation of the thermodynamic work of adhesion and interfacial energy between different incompatible polymers, form the focus here. The work of adhesion is calculated using an atomistic equation and is further used in a macroscopic equation to estimate the interfacial energy. The interfacial energy is compared with typical values for other immiscible systems in the literature. The interfacial energy compared very well with interfacial energy values for a few other immiscible hydrocarbon pairs. In chapter IV, the study proceeds to look at the interactions between nonpolar and polar small molecules with SB and SBA thin

Beyond disease susceptibility-Leveraging genome-wide association studies for new insights into complex disease biology.

Science.gov (United States)

Lee, J C

2017-12-01

Genetic studies in complex diseases have been highly successful, but have also been largely one-dimensional: predominantly focusing on the genetic contribution to disease susceptibility. While this is undoubtedly important-indeed it is a pre-requisite for understanding the mechanisms underlying disease development-there are many other important aspects of disease biology that have received comparatively little attention. In this review, I will discuss how existing genetic data can be leveraged to provide new insights into other aspects of disease biology, why such insights could change the way we think about complex disease, and how this could provide opportunities for better therapies and/or facilitate personalised medicine. To do this, I will use the example of Crohn's disease-a chronic form of inflammatory bowel disease that has been one of the main success stories in complex disease genetics. Indeed, thanks to genetic studies, we now have a much more detailed understanding of the processes involved in Crohn's disease development, but still know relatively little about what determines the subsequent disease course (prognosis) and why this differs so considerably between individuals. I will discuss how we came to realise that genetic variation plays an important role in determining disease prognosis and how this has changed the way we think about Crohn's disease genetics. This will illustrate how phenotypic data can be used to leverage new insights from genetic data and will provide a broadly applicable framework that could yield new insights into the biology of multiple diseases. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Complexity of International Sign for inexperienced interpreters: Insights From a Deaf IS Instructor

NARCIS (Netherlands)

Oyserman, J.; Rosenstock, R.; Napier, J.

2016-01-01

In lieu of an abstract, here is a brief excerpt of the content: 192 Complexity of International Sign for Inexperienced Interpreters: Insights From a Deaf IS Instructor Joni Oyserman In this chapter, I focus on how inexperienced interpreters view, acquire, and use International Sign (IS). A profile

Atomistic simulation of CO 2 solubility in poly(ethylene oxide) oligomers

KAUST Repository

Hong, Bingbing; Panagiotopoulos, Athanassios Z.

2013-01-01

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

Prediction of Thermal Transport Properties of Materials with Microstructural Complexity

Energy Technology Data Exchange (ETDEWEB)

Chen, Youping

2017-10-10

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 as 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.

Spontaneous Formation of A Nanotube From A Square Ag Nanowire: An Atomistic View

Science.gov (United States)

Konuk Onat, Mine; Durukanoglu, Sondan

2012-02-01

We have performed molecular static calculations to investigate the recently observed phenomenon of the spontaneous formation of a nanotube from a regular, square Ag nanowire[1]. In the simulations, atoms are allowed to interact via the model potential obtained from the modified embedded atom method. Our simulations predict that this particular type of structural phase transformation is controlled by the nature of applied strain, length of the wire and initial cross-sectional shape. For such a perfect structural transformation, the axially oriented fcc nanowire needs (1) to be formed by stacking A and B layers of an fcc crystal, both possessing the geometry of two interpenetrating one-lattice-parameter-wide squares, containing four atoms each, (2) to have an optimum length of eight layers, and (3) to be exposed to a combination of low and high stress along the length direction. The results further offer insights into atomistic nature of this specific structural transformation into a nanotube with the smallest possible cross-section. [1] M.J. Lagos et al., Nature Nanotech. 4, 149 (2009).

Ethics in Publishing: Complexity Science and Human Factors Offer Insights to Develop a Just Culture.

Science.gov (United States)

Saurin, Tarcisio Abreu

2016-12-01

While ethics in publishing has been increasingly debated, there seems to be a lack of a theoretical framework for making sense of existing rules of behavior as well as for designing, managing and enforcing such rules. This letter argues that systems-oriented disciplines, such as complexity science and human factors, offer insights into new ways of dealing with ethics in publishing. Some examples of insights are presented. Also, a call is made for empirical studies that unveil the context and details of both retracted papers and the process of writing and publishing academic papers. This is expected to shed light on the complexity of the publication system as well as to support the development of a just culture, in which all participants are accountable.

Insights on activation enthalpy for non-Schmid slip in body-centered cubic metals

International Nuclear Information System (INIS)

Hale, Lucas M.; Lim, Hojun; Zimmerman, Jonathan A.; Battaile, Corbett C.; Weinberger, Christopher R.

2015-01-01

We use insights gained from atomistic simulation to develop an activation enthalpy model for dislocation slip in body-centered cubic iron. 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. Our model enlarges the applicability of the classic Kocks activation enthalpy model to materials with non-Schmid behavior

Cynefin as Reference Framework to Facilitate Insight and Decision-Making in Complex Contexts of Biomedical Research

Directory of Open Access Journals (Sweden)

Gerd Kempermann

2017-11-01

Full Text Available The Cynefin scheme is a concept of knowledge management, originally devised to support decision making in management, but more generally applicable to situations, in which complexity challenges the quality of insight, prediction, and decision. Despite the fact that life itself, and especially the brain and its diseases, are complex to the extent that complexity could be considered their cardinal feature, complex problems in biomedicine are often treated as if they were actually not more than the complicated sum of solvable sub-problems. Because of the emergent properties of complex contexts this is not correct. With a set of clear criteria Cynefin helps to set apart complex problems from “simple/obvious,” “complicated,” “chaotic,” and “disordered” contexts in order to avoid misinterpreting the relevant causality structures. The distinction comes with the insight, which specific kind of knowledge is possible in each of these categories and what are the consequences for resulting decisions and actions. From student's theses over the publication and grant writing process to research politics, misinterpretation of complexity can have problematic or even dangerous consequences, especially in clinical contexts. Conceptualization of problems within a straightforward reference language like Cynefin improves clarity and stringency within projects and facilitates communication and decision-making about them.

The Paradox of Migration and the Interests of the Atomistic Nation ...

African Journals Online (AJOL)

The Paradox of Migration and the Interests of the Atomistic Nation- States: The Southern ... Internationally as well as regionally, States are concerned with issues of ... within the nationstates in general, and in their labour markets in particular.

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

Science.gov (United States)

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.

Atomistic simulations of dislocation processes in copper

DEFF Research Database (Denmark)

Vegge, T.; Jacobsen, K.W.

2002-01-01

We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example......, the stability of screw dislocation dipoles is discussed. We show that the presence of jogs will strongly influence cross slip barriers and dipole stability. We furthermore present some new results on jogged edge dislocations and edge dislocation dipoles. The jogs are found to be extended, and simulations...

Atomistic simulation studies of iron sulphide, platinum antimonide and platinum arsenide

CSIR Research Space (South Africa)

Ngoepe, PE

2005-09-01

Full Text Available The authors present the results of atomistic simulations using derived interatomic potentials for the pyrite-structured metal chalcogenides FeS2, PtSb2 and PtAs2. Structural and elastic constants were calculated and compared with experimental...

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

International Nuclear Information System (INIS)

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

2013-01-01

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 H 2 S and H 2 O/H 2 S mixtures on GO materials and compare the results with experiment. We find that H 2 S molecules dissociate on the carbonyl functional groups, and H 2 O, CO 2 , and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H 2 O/H 2 S mixtures, H 2 O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H 2 S 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

Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations

Science.gov (United States)

Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.

2016-09-01

Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an

Fatigue mechanisms in an austenitic steel under cyclic loading: Experiments and atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Soppa, E.A., E-mail: ewa.soppa@mpa.uni-stuttgart.de; Kohler, C., E-mail: christopher.kohler@mpa.uni-stuttgart.de; Roos, E., E-mail: eberhard.roos@mpa.uni-stuttgart.de

2014-03-01

Experimental investigations on the austenitic stainless steel X6CrNiNb18-10 (AISI – 347) and concomitant atomistic simulations of a FeNi nanocrystalline model system have been performed in order to understand the basic mechanisms of fatigue damage under cyclic loading. Using electron backscatter diffraction (EBSD) the influence of deformation induced martensitic transformation and NbC size distribution on the fatigue crack formation has been demonstrated. The martensite nucleates prevalently at grain boundaries, triple points and at the specimen free surface and forms small (∼1 µm sized) differently oriented grains. The atomistic simulations show the role of regions of a high density of stacking faults for the martensitic transformation.

Coupling Strategies Investigation of Hybrid Atomistic-Continuum Method Based on State Variable Coupling

Directory of Open Access Journals (Sweden)

Qian Wang

2017-01-01

Full Text Available Different configurations of coupling strategies influence greatly the accuracy and convergence of the simulation results in the hybrid atomistic-continuum method. This study aims to quantitatively investigate this effect and offer the guidance on how to choose the proper configuration of coupling strategies in the hybrid atomistic-continuum method. We first propose a hybrid molecular dynamics- (MD- continuum solver in LAMMPS and OpenFOAM that exchanges state variables between the atomistic region and the continuum region and evaluate different configurations of coupling strategies using the sudden start Couette flow, aiming to find the preferable configuration that delivers better accuracy and efficiency. The major findings are as follows: (1 the C→A region plays the most important role in the overlap region and the “4-layer-1” combination achieves the best precision with a fixed width of the overlap region; (2 the data exchanging operation only needs a few sampling points closer to the occasions of interactions and decreasing the coupling exchange operations can reduce the computational load with acceptable errors; (3 the nonperiodic boundary force model with a smoothing parameter of 0.1 and a finer parameter of 20 can not only achieve the minimum disturbance near the MD-continuum interface but also keep the simulation precision.

A continuum-atomistic simulation of heat transfer in micro- and nano-flows

International Nuclear Information System (INIS)

Liu Jin; Chen Shiyi; Nie Xiaobo; Robbins, Mark O.

2007-01-01

We develop a hybrid atomistic-continuum scheme for simulating micro- and nano-flows with heat transfer. The approach is based on spatial 'domain decomposition' in which molecular dynamics (MD) is used in regions where atomistic details are important, while classical continuum fluid dynamics is used in the remaining regions. The two descriptions are matched in a coupling region where we ensure continuity of mass, momentum, energy and their fluxes. The scheme for including the energy equation is implemented in 1-D and 2-D, and used to study steady and unsteady heat transfer in channel flows with and without nano roughness. Good agreement between hybrid results and analytical or pure MD results is found, demonstrating the accuracy of this multiscale method and its potential applications in thermal engineering

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

Science.gov (United States)

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.

Atomistic materials modeling of complex systems: Carbynes, carbon nanotube devices and bulk metallic glasses

Science.gov (United States)

Luo, Weiqi

The key to understanding and predicting the behavior of materials is the knowledge of their structures. Many properties of materials samples are not solely determined by their average chemical compositions which one may easily control. Instead, they are profoundly influenced by structural features of different characteristic length scales. Starting in the last century, metallurgical engineering has mostly been microstructure engineering. With the further evolution of materials science, structural features of smaller length scales down to the atomic structure, have become of interest for the purpose of properties engineering and functionalizing materials and are, therefore, subjected to study. As computer modeling is becoming more powerful due to the dramatic increase of computational resources and software over the recent decades, there is an increasing demand for atomistic simulations with the goal of better understanding materials behavior on the atomic scale. Density functional theory (DFT) is a quantum mechanics based approach to calculate electron distribution, total energy and interatomic forces with high accuracy. From these, atomic structures and thermal effects can be predicted. However, DFT is mostly applied to relatively simple systems because it is computationally very demanding. In this thesis, the current limits of DFT applications are explored by studying relatively complex systems, namely, carbynes, carbon nanotube (CNT) devices and bulk metallic glasses (BMGs). Special care is taken to overcome the limitations set by small system sizes and time scales that often prohibit DFT from being applied to realistic systems under realistic external conditions. In the first study, we examine the possible existence of a third solid phase of carbon with linear bonding called carbyne, which has been suggested in the literature and whose formation has been suggested to be detrimental to high-temperature carbon materials. We have suggested potential structures for

Atomistic approach for modeling metal-semiconductor interfaces

DEFF Research Database (Denmark)

Stradi, Daniele; Martinez, Umberto; Blom, Anders

2016-01-01

realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via the I–V curve. In particular, it will be demonstrated how doping — and bias — modifies the Schottky barrier, and how finite size models (the slab approach) are unable to describe these interfaces......We present a general framework for simulating interfaces using an atomistic approach based on density functional theory and non-equilibrium Green's functions. The method includes all the relevant ingredients, such as doping and an accurate value of the semiconductor band gap, required to model...

Atomistic Galois insertions for flow sensitive integrity

DEFF Research Database (Denmark)

Nielson, Flemming; Nielson, Hanne Riis

2017-01-01

Several program verification techniques assist in showing that software adheres to the required security policies. Such policies may be sensitive to the flow of execution and the verification may be supported by combinations of type systems and Hoare logics. However, this requires user assistance...... and to obtain full automation we shall explore the over-approximating nature of static analysis. We demonstrate that the use of atomistic Galois insertions constitutes a stable framework in which to obtain sound and fully automatic enforcement of flow sensitive integrity. The framework is illustrated...

Self-evolving atomistic kinetic Monte Carlo: fundamentals and applications

International Nuclear Information System (INIS)

Xu Haixuan; Osetsky, Yuri N; Stoller, Roger E

2012-01-01

The fundamentals of the framework and the details of each component of the self-evolving atomistic kinetic Monte Carlo (SEAKMC) are presented. The strength of this new technique is the ability to simulate dynamic processes with atomistic fidelity that is comparable to molecular dynamics (MD) but on a much longer time scale. The observation that the dimer method preferentially finds the saddle point (SP) with the lowest energy is investigated and found to be true only for defects with high symmetry. In order to estimate the fidelity of dynamics and accuracy of the simulation time, a general criterion is proposed and applied to two representative problems. Applications of SEAKMC for investigating the diffusion of interstitials and vacancies in bcc iron are presented and compared directly with MD simulations, demonstrating that SEAKMC provides results that formerly could be obtained only through MD. The correlation factor for interstitial diffusion in the dumbbell configuration, which is extremely difficult to obtain using MD, is predicted using SEAKMC. The limitations of SEAKMC are also discussed. The paper presents a comprehensive picture of the SEAKMC method in both its unique predictive capabilities and technically important details.

Development of Sulfur and Carbon Tolerant Reforming Alloy Catalysts Aided Fundamental Atomistic Insights

Energy Technology Data Exchange (ETDEWEB)

Suljo Linic

2008-12-31

Current hydrocarbon reforming catalysts suffer from rapid carbon and sulfur poisoning. Even though there is a tremendous incentive to develop more efficient catalysts, these materials are currently formulated using inefficient trial and error experimental approaches. We have utilized a hybrid experimental/theoretical approach, combining quantum Density Functional Theory (DFT) calculations and various state-of-the-art experimental tools, to formulate carbon tolerant reforming catalysts. We have employed DFT calculations to develop molecular insights into the elementary chemical transformations that lead to carbon poisoning of Ni catalysts. Based on the obtained molecular insights, we have identified, using DFT quantum calculation, various Ni alloy catalysts as potential carbon tolerant reforming catalysts. The alloy catalysts were synthesized and tested in steam reforming and partial oxidation of methane, propane, and isooctane. We demonstrated that the alloy catalysts are much more carbon-tolerant than monometallic Ni catalysts under nearly stoichiometric steam-to-carbon ratios. Under these conditions, monometallic Ni is rapidly poisoned by sp2 carbon deposits. The research approach is distinguished by two characteristics: (a) knowledge-based, bottomup approach, compared to the traditional trial and error approach, allows for a more efficient and systematic discovery of improved catalysts. (b) the focus is on exploring alloy materials which have been largely unexplored as potential reforming catalysts.

Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

Science.gov (United States)

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.

Atomistic characterization of pseudoelasticity and shape memory in NiTi nanopillars

International Nuclear Information System (INIS)

Zhong Yuan; Gall, Ken; Zhu Ting

2012-01-01

Molecular dynamics simulations are performed to study the atomistic mechanisms governing the pseudoelasticity and shape memory in nickel–titanium (NiTi) nanostructures. For a 〈1 1 0〉 – oriented nanopillar subjected to compressive loading–unloading, we observe either a pseudoelastic or shape memory response, depending on the applied strain and temperature that control the reversibility of phase transformation and deformation twinning. We show that irreversible twinning arises owing to the dislocation pinning of twin boundaries, while hierarchically twinned microstructures facilitate the reversible twinning. The nanoscale size effects are manifested as the load serration, stress plateau and large hysteresis loop in stress–strain curves that result from the high stresses required to drive the nucleation-controlled phase transformation and deformation twinning in nanosized volumes. Our results underscore the importance of atomistically resolved modeling for understanding the phase and deformation reversibilities that dictate the pseudoelasticity and shape memory behavior in nanostructured shape memory alloys.

Atomistic studies of nucleation of He clusters and bubbles in bcc iron

International Nuclear Information System (INIS)

Yang, L.; Deng, H.Q.; Gao, F.; Heinisch, H.L.; Kurtz, R.J.; Hu, S.Y.; Li, Y.L.; Zu, X.T.

2013-01-01

Atomistic simulations of the nucleation of He clusters and bubbles in bcc iron at 800 K have been carried out using the newly developed Fe–Fe interatomic potential, along with Ackland potential for the Fe–Fe interactions. Microstructure changes were analyzed in detail. We found that a He cluster with four He atoms is able to push out an iron interstitial from the cluster, creating a Frenkel pair. Small He clusters and self-interstitial atom (SIA) can migrate in the matrix, but He-vacancy (He-V) clusters are immobile. Most SIAs form clusters, and only the dislocation loops with a Burgers vector of b = 1/2 appear in the simulations. SIA clusters (or loops) are attached to He-V clusters for He implantation up to 1372 appm, while the He-V cluster–loop complexes with more than one He-V cluster are formed at the He concentration of 2057 appm and larger

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

Science.gov (United States)

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.

Atomistic simulations of graphite etching at realistic time scales.

Science.gov (United States)

Aussems, D U B; Bal, K M; Morgan, T W; van de Sanden, M C M; Neyts, E C

2017-10-01

Hydrogen-graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe time-scale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of ∼10 20 m -2 s -1 . The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C-C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching - chemical erosion - is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.

Dislocation climb models from atomistic scheme to dislocation dynamics

OpenAIRE

Niu, Xiaohua; Luo, Tao; Lu, Jianfeng; Xiang, Yang

2016-01-01

We develop a mesoscopic dislocation dynamics model for vacancy-assisted dislocation climb by upscalings from a stochastic model on the atomistic scale. Our models incorporate microscopic mechanisms of (i) bulk diffusion of vacancies, (ii) vacancy exchange dynamics between bulk and dislocation core, (iii) vacancy pipe diffusion along the dislocation core, and (iv) vacancy attachment-detachment kinetics at jogs leading to the motion of jogs. Our mesoscopic model consists of the vacancy bulk dif...

Simulating Surface-Enhanced Hyper-Raman Scattering Using Atomistic Electrodynamics-Quantum Mechanical Models.

Science.gov (United States)

Hu, Zhongwei; Chulhai, Dhabih V; Jensen, Lasse

2016-12-13

Surface-enhanced hyper-Raman scattering (SEHRS) is the two-photon analogue of surface-enhanced Raman scattering (SERS), which has proven to be a powerful tool to study molecular structures and surface enhancements. However, few theoretical approaches to SEHRS exist and most neglect the atomistic descriptions of the metal surface and molecular resonance effects. In this work, we present two atomistic electrodynamics-quantum mechanical models to simulate SEHRS. The first is the discrete interaction model/quantum mechanical (DIM/QM) model, which combines an atomistic electrodynamics model of the nanoparticle with a time-dependent density functional theory description of the molecule. The second model is a dressed-tensors method that describes the molecule as a point-dipole and point-quadrupole object interacting with the enhanced local field and field-gradients (FG) from the nanoparticle. In both of these models, the resonance effects are treated efficiently by means of damped quadratic response theory. Using these methods, we simulate SEHRS spectra for benzene and pyridine. Our results show that the FG effects in SEHRS play an important role in determining both the surface selection rules and the enhancements. We find that FG effects are more important in SEHRS than in SERS. We also show that the spectral features of small molecules can be accurately described by accounting for the interactions between the molecule and the local field and FG of the nanoparticle. However, at short distances between the metal and molecule, we find significant differences in the SEHRS enhancements predicted using the DIM/QM and the dressed-tensors methods.

Adaptive resolution simulation of an atomistic protein in MARTINI water

International Nuclear Information System (INIS)

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

2014-01-01

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the 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

Fluorinated Phosphorene: Electrochemical Synthesis, Atomistic Fluorination, and Enhanced Stability.

Science.gov (United States)

Tang, Xian; Liang, Weiyuan; Zhao, Jinlai; Li, Zhongjun; Qiu, Meng; Fan, Taojian; Luo, Crystal Shaojuan; Zhou, Ye; Li, Yu; Guo, Zhinan; Fan, Dianyuan; Zhang, Han

2017-12-01

Phosphorene has attracted great interest due to its unique electronic and optoelectronic properties owing to its tunable direct and moderate band-gap in association with high carrier mobility. However, its intrinsic instability in air seriously hinders its practical applications, and problems of technical complexity and in-process degradation exist in currently proposed stabilization strategies. A facile pathway in obtaining and stabilizing phosphorene through a one-step, ionic liquid-assisted electrochemical exfoliation and synchronous fluorination process is reported in this study. This strategy enables fluorinated phosphorene (FP) to be discovered and large-scale, highly selective few-layer FP (3-6 atomic layers) to be obtained. The synthesized FP is found to exhibit unique morphological and optical characteristics. Possible atomistic fluorination configurations of FP are revealed by core-level binding energy shift calculations in combination with spectroscopic measurements, and the results indicate that electrolyte concentration significantly modulates the fluorination configurations. Furthermore, FP is found to exhibit enhanced air stability thanks to the antioxidation and antihydration effects of the introduced fluorine adatoms, and demonstrate excellent photothermal stability during a week of air exposure. These findings pave the way toward real applications of phosphorene-based nanophotonics. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computer simulations of plasma-biomolecule and plasma-tissue interactions for a better insight in plasma medicine

Science.gov (United States)

Neyts, Erik C.; Yusupov, Maksudbek; Verlackt, Christof C.; Bogaerts, Annemie

2014-07-01

Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficult—if not impossible—to obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasma-biomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance the field.

Time-Domain Ab Initio Analysis of Excitation Dynamics in a Quantum Dot/Polymer Hybrid: Atomistic Description Rationalizes Experiment.

Science.gov (United States)

Long, Run; Prezhdo, Oleg V

2015-07-08

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

Science.gov (United States)

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.

Amp: A modular approach to machine learning in atomistic simulations

Science.gov (United States)

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

Redox reactions with empirical potentials: Atomistic battery discharge simulations

OpenAIRE

Dapp, Wolf B.; Müser, Martin H.

2013-01-01

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 ...

Development of Sulfur and Carbon Tolerant Reforming Alloy Catalysts Aided by Fundamental Atomistics Insights

Energy Technology Data Exchange (ETDEWEB)

Suljo Linic

2006-08-31

Current hydrocarbon reforming catalysts suffer from rapid carbon and sulfur poisoning. Even though there is a tremendous incentive to develop more efficient catalysts, these materials are currently formulated using inefficient trial and error experimental approaches. We have utilized a novel hybrid experimental/theoretical approach, combining quantum Density Functional Theory (DFT) calculations and various state-of-the-art experimental tools, to formulate carbon tolerant reforming catalysts. We have employed DFT calculations to develop molecular insights into the elementary chemical transformations that lead to carbon poisoning of Ni catalysts. Based on the obtained molecular insights, we have identified, using DFT quantum calculation, Sn/Ni alloy as a potential carbon tolerant reforming catalyst. Sn/Ni alloy was synthesized and tested in steam reforming of methane, propane, and isooctane. We demonstrated that the alloy catalyst is carbon-tolerant under nearly stoichiometric steam-to-carbon ratios. Under these conditions, monometallic Ni is rapidly poisoned by sp2 carbon deposits. The research approach is distinguished by a few characteristics: (a) Knowledge-based, bottom-up approach, compared to the traditional trial and error approach, allows for a more efficient and systematic discovery of improved catalysts. (b) The focus is on exploring alloy materials which have been largely unexplored as potential reforming catalysts.

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

NARCIS (Netherlands)

Zavadlav, J.; Podgornik, R.; Melo, M.n.; Marrink, S.j.; Praprotnik, M.

2016-01-01

We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell

Mobility and stability of large vacancy and vacancy-copper clusters in iron: An atomistic kinetic Monte Carlo study

Energy Technology Data Exchange (ETDEWEB)

Castin, N., E-mail: ncastin@sckcen.be [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium); Pascuet, M.I., E-mail: pascuet@cnea.gov.ar [Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires (Argentina); Malerba, L. [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium)

2012-10-15

The formation of Cu-rich precipitates under irradiation is a major cause for changes in the mechanical response to load of reactor pressure vessel steels. In previous works, it has been shown that the mechanism under which precipitation occurs is governed by diffusion of vacancy-copper (VCu) complexes, also in the absence of irradiation. Coarse-grained computer models (such as object kinetic Monte Carlo) aimed at simulating irradiation processes in model alloys or steels should therefore explicitly include the mobility of Cu precipitates, as a consequence of vacancy hops at their surface. For this purpose, in this work we calculate diffusion coefficients and lifetimes for a large variety of VCu complexes. We use an innovative atomistic model, where vacancy migration energies are calculated with little approximations, taking into account all effects of static relaxation and long-range chemical interaction as predicted by an interatomic potential. Our results show that, contrary to what intuition might suggest, saturation in vacancies tend to slow down the transport of Cu atoms.

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

Science.gov (United States)

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.

Atomistic simulation of graphene-based polymer nanocomposites

International Nuclear Information System (INIS)

Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

2016-01-01

Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

Dynamic aspects of dislocation motion: atomistic simulations

International Nuclear Information System (INIS)

Bitzek, Erik; Gumbsch, Peter

2005-01-01

Atomistic simulations of accelerating edge and screw dislocations were carried out to study the dynamics of dislocations in a face centered cubic metal. Using two different embedded atom potentials for nickel and a simple slab geometry, the Peierls stress, the effective mass, the line tension and the drag coefficient were determined. A dislocation intersecting an array of voids is used to study dynamic effects in dislocation-obstacle interactions. A pronounced effect caused by inertial overshooting is found. A dynamic line tension model is developed which reproduces the simulation results. The model can be used to easily estimate the magnitude of inertial effects in the interaction of dislocations with localized obstacles for different obstacle strengths, -spacings and temperatures

Quantum Corrections to the 'Atomistic' MOSFET Simulations

Science.gov (United States)

Asenov, Asen; Slavcheva, G.; Kaya, S.; Balasubramaniam, R.

2000-01-01

We have introduced in a simple and efficient manner quantum mechanical corrections in our 3D 'atomistic' MOSFET simulator using the density gradient formalism. We have studied in comparison with classical simulations the effect of the quantum mechanical corrections on the simulation of random dopant induced threshold voltage fluctuations, the effect of the single charge trapping on interface states and the effect of the oxide thickness fluctuations in decanano MOSFETs with ultrathin gate oxides. The introduction of quantum corrections enhances the threshold voltage fluctuations but does not affect significantly the amplitude of the random telegraph noise associated with single carrier trapping. The importance of the quantum corrections for proper simulation of oxide thickness fluctuation effects has also been demonstrated.

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

Science.gov (United States)

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.

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

DEFF Research Database (Denmark)

Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector

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...

Solid solution hardening in face centered binary alloys: Gliding statistics of a dislocation in random solid solution by atomistic simulation

International Nuclear Information System (INIS)

Patinet, S.

2009-12-01

The glide of edge and screw dislocation in solid solution is modeled through atomistic simulations in two model alloys of Ni(Al) and Al(Mg) described within the embedded atom method. Our approach is based on the study of the elementary interaction between dislocations and solutes to derive solid solution hardening of face centered cubic binary alloys. We identify the physical origins of the intensity and range of the interaction between a dislocation and a solute atom. The thermally activated crossing of a solute atom by a dislocation is studied at the atomistic scale. We show that hardening of edge and screw segments are similar. We develop a line tension model that reproduces quantitatively the atomistic calculations of the flow stress. We identify the universality class to which the dislocation depinning transition in solid solution belongs. (author)

An atomistic interpretation of Planck's 1900 derivation of his radiation law

International Nuclear Information System (INIS)

Irons, F.E.

2000-01-01

In deriving his radiation law in 1900, Max Planck employed a simple harmonic oscillator to model the exchange of energy between radiation and matter. Traditionally the harmonic oscillator has been viewed as modelling an entity which is itself oscillating, although a suitable oscillating entity has not been forthcoming. (Opinion is divided between a material oscillator, an imaginary oscillator and a need to revise Planck's derivation to apply to cavity modes of oscillation). We offer a novel, atomistic interpretation of Planck's derivation wherein the harmonic oscillator models a transition between the internal quantum states of an atom|not a normal electronic atom characterised by possible energies 0 and hν, but an atom populated by subatomic bosons (such as pions) and characterised by multiple occupancy of quantum states and possible energies nhν (n = 0;1;2; ...). We show how Planck's derivation can be varied to accommodate electronic atoms. A corollary to the atomistic interpretation is that Planck's derivation can no longer be construed as support for the postulate that material oscillating entities can have only those energies that are multiples of hν. Copyright (2000) CSIRO Australia

Optimal kernel shape and bandwidth for atomistic support of continuum stress

International Nuclear Information System (INIS)

Ulz, Manfred H; Moran, Sean J

2013-01-01

The treatment of atomistic scale interactions via molecular dynamics simulations has recently found favour for multiscale modelling within engineering. The estimation of stress at a continuum point on the atomistic scale requires a pre-defined kernel function. This kernel function derives the stress at a continuum point by averaging the contribution from atoms within a region surrounding the continuum point. This averaging volume, and therefore the associated stress at a continuum point, is highly dependent on the bandwidth and shape of the kernel. In this paper we propose an effective and entirely data-driven strategy for simultaneously computing the optimal shape and bandwidth for the kernel. We thoroughly evaluate our proposed approach on copper using three classical elasticity problems. Our evaluation yields three key findings: firstly, our technique can provide a physically meaningful estimation of kernel bandwidth; secondly, we show that a uniform kernel is preferred, thereby justifying the default selection of this kernel shape in future work; and thirdly, we can reliably estimate both of these attributes in a data-driven manner, obtaining values that lead to an accurate estimation of the stress at a continuum point. (paper)

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

Science.gov (United States)

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.

3d visualization of atomistic simulations on every desktop

Science.gov (United States)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-08-01

Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

3d visualization of atomistic simulations on every desktop

International Nuclear Information System (INIS)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-01-01

Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given

Atomistic-level non-equilibrium model for chemically reactive systems based on steepest-entropy-ascent quantum thermodynamics

International Nuclear Information System (INIS)

Li, Guanchen; Al-Abbasi, Omar; Von Spakovsky, Michael R

2014-01-01

This paper outlines an atomistic-level framework for modeling the non-equilibrium behavior of chemically reactive systems. The framework called steepest- entropy-ascent quantum thermodynamics (SEA-QT) is based on the paradigm of intrinsic quantum thermodynamic (IQT), which is a theory that unifies quantum mechanics and thermodynamics into a single discipline with wide applications to the study of non-equilibrium phenomena at the atomistic level. SEA-QT is a novel approach for describing the state of chemically reactive systems as well as the kinetic and dynamic features of the reaction process without any assumptions of near-equilibrium states or weak-interactions with a reservoir or bath. Entropy generation is the basis of the dissipation which takes place internal to the system and is, thus, the driving force of the chemical reaction(s). The SEA-QT non-equilibrium model is able to provide detailed information during the reaction process, providing a picture of the changes occurring in key thermodynamic properties (e.g., the instantaneous species concentrations, entropy and entropy generation, reaction coordinate, chemical affinities, reaction rate, etc). As an illustration, the SEA-QT framework is applied to an atomistic-level chemically reactive system governed by the reaction mechanism F + H 2 ↔ FH + H

Hierarchical Statistical 3D ' Atomistic' Simulation of Decanano MOSFETs: Drift-Diffusion, Hydrodynamic and Quantum Mechanical Approaches

Science.gov (United States)

Asenov, Asen; Brown, A. R.; Slavcheva, G.; Davies, J. H.

2000-01-01

When MOSFETs are scaled to deep submicron dimensions the discreteness and randomness of the dopant charges in the channel region introduces significant fluctuations in the device characteristics. This effect, predicted 20 year ago, has been confirmed experimentally and in simulation studies. The impact of the fluctuations on the functionality, yield, and reliability of the corresponding systems shifts the paradigm of the numerical device simulation. It becomes insufficient to simulate only one device representing one macroscopical design in a continuous charge approximation. An ensemble of macroscopically identical but microscopically different devices has to be characterized by simulation of statistically significant samples. The aims of the numerical simulations shift from predicting the characteristics of a single device with continuous doping towards estimating the mean values and the standard deviations of basic design parameters such as threshold voltage, subthreshold slope, transconductance, drive current, etc. for the whole ensemble of 'atomistically' different devices in the system. It has to be pointed out that even the mean values obtained from 'atomistic' simulations are not identical to the values obtained from continuous doping simulations. In this paper we present a hierarchical approach to the 'atomistic' simulation of aggressively scaled decanano MOSFETs. A full scale 3D drift-diffusion'atomostic' simulation approach is first described and used for verification of the more economical, but also more restricted, options. To reduce the processor time and memory requirements at high drain voltage we have developed a self-consistent option based on a thin slab solution of the current continuity equation only in the channel region. This is coupled to the Poisson's equation solution in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison with the full self-consistent solution. At low drain

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-12-28

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

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

International Nuclear Information System (INIS)

Vögele, Martin; Holm, Christian; Smiatek, Jens

2015-01-01

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

Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

Science.gov (United States)

Tiwary, Pratyush

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Paavilainen, S.; Rog, T.; Vattulainen, I.

2011-01-01

We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile......, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril....

SCT: a suite of programs for comparing atomistic models with small-angle scattering data.

Science.gov (United States)

Wright, David W; Perkins, Stephen J

2015-06-01

Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, the SCT suite of tools was developed. SCT also includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The original SCT software, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions of SCT have been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct.

Relaxation of a steep density gradient in a simple fluid: Comparison between atomistic and continuum modeling

International Nuclear Information System (INIS)

Pourali, Meisam; Maghari, Ali; Meloni, Simone; Magaletti, Francesco; Casciola, Carlo Massimo; Ciccotti, Giovanni

2014-01-01

We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (∼10 times the molecular size). In presence of molecular scale features some of the continuum fields (e.g., density and momentum) are in good agreement with atomistic counterparts, but are smoother. On the contrary, other fields, such as the temperature field, present very large difference with respect to reference (atomistic) ones. This is due to the limited accuracy of some of the empirical relations used in continuum models, the equation of state of the fluid in the present example

Understanding and revisiting the most complex perovskite system via atomistic simulations

Science.gov (United States)

Yang, Yali; Xu, Bin; Xu, Changsong; Ren, Wei; Bellaiche, Laurent

2018-05-01

A first-principles-based effective Hamiltonian is developed and used, along with direct ab initio techniques, to investigate finite-temperature properties of the system commonly coined the most complex perovskite, that is NaNbO3. Such simulations successfully reproduce the existence of seven different phases in its phase diagram. The decomposition of the total energy of this effective Hamiltonian into different terms, altogether with the values of the parameters associated with these terms, also allow us to shed some light into puzzling features of such a compound. Examples include revealing the microscopic reasons of why R 3 c is its ground state and why it solely adopts in-phase tiltings at high temperatures versus complex nanotwins for intermediate temperatures. The results of the computations also call for a revisiting of the so-called P ,R , and S states, in the sense that an unexpected and previously overlooked inhomogeneous electrical polarization is numerically found in the P state while complex tiltings associated with the simultaneous condensation of several k points are predicted for the controversial R and S phases.

Tunable thermodynamic stability of Au-CuPt core-shell trimetallic nanoparticles by controlling the alloy composition: insights from atomistic simulations.

Science.gov (United States)

Huang, Rao; Shao, Gui-Fang; Wen, Yu-Hua; Sun, Shi-Gang

2014-11-07

A microscopic understanding of the thermal stability of metallic core-shell nanoparticles is of importance for their synthesis and ultimately application in catalysis. In this article, molecular dynamics simulations have been employed to investigate the thermodynamic evolution of Au-CuPt core-shell trimetallic nanoparticles with various Cu/Pt ratios during heating processes. Our results show that the thermodynamic stability of these nanoparticles is remarkably enhanced upon rising Pt compositions in the CuPt shell. The melting of all the nanoparticles initiates at surface and gradually spreads into the core. Due to the lattice mismatch among Au, Cu and Pt, stacking faults have been observed in the shell and their numbers are associated with the Cu/Pt ratios. With the increasing temperature, they have reduced continuously for the Cu-dominated shell while more stacking faults have been produced for the Pt-dominated shell because of the significantly different thermal expansion coefficients of the three metals. Beyond the overall melting, all nanoparticles transform into a trimetallic mixing alloy coated by an Au-dominated surface. This work provides a fundamental perspective on the thermodynamic behaviors of trimetallic, even multimetallic, nanoparticles at the atomistic level, indicating that controlling the alloy composition is an effective strategy to realize tunable thermal stability of metallic nanocatalysts.

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

Directory of Open Access Journals (Sweden)

Radhakrishna Bettadapura

2015-10-01

Full Text Available 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.

Atomistic simulation and continuum modeling of graphene nanoribbons under uniaxial tension

International Nuclear Information System (INIS)

Lu, Qiang; Gao, Wei; Huang, Rui

2011-01-01

Atomistic simulations are performed to study the nonlinear mechanical behavior of graphene nanoribbons under quasistatic uniaxial tension, emphasizing the effects of edge structures (armchair and zigzag, without and with hydrogen passivation) on elastic modulus and fracture strength. The numerical results are analyzed within a theoretical model of thermodynamics, which enables determination of the bulk strain energy density, the edge energy density and the hydrogen adsorption energy density as nonlinear functions of the applied strain based on static molecular mechanics simulations. These functions can be used to describe mechanical behavior of graphene nanoribbons from the initial linear elasticity to fracture. It is found that the initial Young's modulus of a graphene nanoribbon depends on the ribbon width and the edge chirality. Furthermore, it is found that the nominal strain to fracture is considerably lower for graphene nanoribbons with armchair edges than for ribbons with zigzag edges. Molecular dynamics simulations reveal two distinct fracture nucleation mechanisms: homogeneous nucleation for the zigzag-edged graphene nanoribbons and edge-controlled heterogeneous nucleation for the armchair-edged ribbons. The modeling and simulations in this study highlight the atomistic mechanisms for the nonlinear mechanical behavior of graphene nanoribbons with the edge effects, which is potentially important for developing integrated graphene-based devices

An atomistic fingerprint algorithm for learning ab initio molecular force fields

Science.gov (United States)

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.

Inter-ribbon tunneling in graphene: An atomistic Bardeen approach

Energy Technology Data Exchange (ETDEWEB)

Van de Put, Maarten L., E-mail: maarten.vandeput@uantwerpen.be; Magnus, Wim [Department of Physics, Universiteit Antwerpen, B-2020 Antwerpen (Belgium); imec, B-3001 Heverlee (Belgium); Vandenberghe, William G.; Fischetti, Massimo V. [Department of Material Science, University of Texas at Dallas, Texas 75080 (United States); Sorée, Bart [Department of Physics, Universiteit Antwerpen, B-2020 Antwerpen (Belgium); imec, B-3001 Heverlee (Belgium); Department of Electrical Engineering, KU Leuven, B-3001 Leuven (Belgium)

2016-06-07

A weakly coupled system of two crossed graphene nanoribbons exhibits direct tunneling due to the overlap of the wavefunctions of both ribbons. We apply the Bardeen transfer Hamiltonian formalism, using atomistic band structure calculations to account for the effect of the atomic structure on the tunneling process. The strong quantum-size confinement of the nanoribbons is mirrored by the one-dimensional character of the electronic structure, resulting in properties that differ significantly from the case of inter-layer tunneling, where tunneling occurs between bulk two-dimensional graphene sheets. The current-voltage characteristics of the inter-ribbon tunneling structures exhibit resonance, as well as stepwise increases in current. Both features are caused by the energetic alignment of one-dimensional peaks in the density-of-states of the ribbons. Resonant tunneling occurs if the sign of the curvature of the coupled energy bands is equal, whereas a step-like increase in the current occurs if the signs are opposite. Changing the doping modulates the onset-voltage of the effects as well as their magnitude. Doping through electrostatic gating makes these structures promising for application towards steep slope switching devices. Using the atomistic empirical pseudopotentials based Bardeen transfer Hamiltonian method, inter-ribbon tunneling can be studied for the whole range of two-dimensional materials, such as transition metal dichalcogenides. The effects of resonance and of step-like increases in the current we observe in graphene ribbons are also expected in ribbons made from these alternative two-dimensional materials, because these effects are manifestations of the one-dimensional character of the density-of-states.

Impact of amphiphilic molecules on the structure and stability of homogeneous sphingomyelin bilayer: Insights from atomistic simulations

Science.gov (United States)

Kumari, Pratibha; Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K.

2018-04-01

Modulation of lipid membrane properties due to the permeation of amphiphiles is an important biological process pertaining to many applications in the field of pharmaceutics, toxicology, and biotechnology. Sphingolipids are both structural and functional lipids that constitute an important component of mechanically stable and chemically resistant outer leaflets of plasma membranes. Here, we present an atomistic molecular dynamics simulation study to appreciate the concentration-dependent effects of small amphiphilic molecules, such as ethanol, acetone, and dimethyl sulfoxide (DMSO), on the structure and stability of a fully hydrated homogeneous N-palmitoyl-sphingomyelin (PSM) bilayer. The study reveals an increase in the lateral expansion of the bilayer along with disordering of the hydrophobic lipid tails on increasing the concentration of ethanol. At higher concentrations of ethanol, rupturing of the bilayer is quite evident through the analysis of partial electron density profiles and lipid tail order parameters. For ethanol containing systems, permeation of water molecules in the hydrophobic part of the bilayer is allowed through local defects made due to the entry of ethanol molecules via ethanol-ethanol and ethanol-PSM hydrogen bonds. Moreover, the extent of PSM-PSM hydrogen bonding decreases with increasing ethanol concentration. On the other hand, acetone and DMSO exhibit minimal effects on the stability of the PSM bilayer at their lower concentrations, but at higher concentrations they tend to enhance the stability of the bilayer. The simulated potential of mean force (PMF) profiles for the translocation of the three solutes studied reveal that the free-energy of transfer of an ethanol molecule across the PSM lipid head region is lower than that for acetone and DMSO molecules. However, highest free-energy rise in the core hydrophobic part of the bilayer is observed for the DMSO molecule, whereas the ethanol and acetone PMF profiles show a lower barrier in

Crystal plasticity model for BCC iron atomistically informed by kinetics of correlated kinkpair nucleation on screw dislocation

Science.gov (United States)

Narayanan, Sankar; McDowell, David L.; Zhu, Ting

2014-04-01

The mobility of dislocation in body-centered cubic (BCC) metals is controlled by the thermally activated nucleation of kinks along the dislocation core. By employing a recent interatomic potential and the Nudged Elastic Band method, we predict the atomistic saddle-point state of 1/2 screw dislocation motion in BCC iron that involves the nucleation of correlated kinkpairs and the resulting double superkinks. This unique process leads to a single-humped minimum energy path that governs the one-step activation of a screw dislocation to move into the adjacent {110} Peierls valley, which contrasts with the double-humped energy path and the two-step transition predicted by other interatomic potentials. Based on transition state theory, we use the atomistically computed, stress-dependent kinkpair activation parameters to inform a coarse-grained crystal plasticity flow rule. Our atomistically-informed crystal plasticity model quantitatively predicts the orientation dependent stress-strain behavior of BCC iron single crystals in a manner that is consistent with experimental results. The predicted temperature and strain-rate dependencies of the yield stress agree with experimental results in the 200-350 K temperature regime, and are rationalized by the small activation volumes associated with the kinkpair-mediated motion of screw dislocations.

Multiscale modelling of precipitation in concentrated alloys: from atomistic Monte Carlo simulations to cluster dynamics I thermodynamics

Science.gov (United States)

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.

Experimentally driven atomistic model of 1,2 polybutadiene

Energy Technology Data Exchange (ETDEWEB)

Gkourmpis, Thomas, E-mail: thomas.gkourmpis@borealisgroup.com [Polymer Science Centre, J. J. Thomson Physical Laboratory, Department of Physics, University of Reading, Reading RG6 6AF (United Kingdom); Mitchell, Geoffrey R. [Polymer Science Centre, J. J. Thomson Physical Laboratory, Department of Physics, University of Reading, Reading RG6 6AF (United Kingdom); Centre for Rapid and Sustainable Product Development, Institute Polytechnic Leiria, Marinha Grande (Portugal)

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 the 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.

Ab-initio and atomistic study of the ferroelectric properties of Cu doped potassium niobate

Energy Technology Data Exchange (ETDEWEB)

Koerbel, Sabine; Elsaesser, Christian [Fraunhofer-Institut fuer Werkstoffmechanik IWM, Woehlerstrasse 11, 79108 Freiburg (Germany)

2011-07-01

KNbO{sub 3} is one end member of the solid solution (K,Na)NbO{sub 3} (KNN), which has promising ferroelectric properties to become a future lead-free substitute for lead zirconate titanate Pb(Zr,Ti)O{sub 3} (PZT) in piezoelectric actors and sensors. Both KNN and PZT exhibit a phase transition with composition and a morphotropic phase boundary, at which enhanced piezoelectric coefficients are obtained. The material properties of PZT and KNN are commonly optimized by doping. E.g., CuO can be added when fabricating KNN as a sintering aid. Ab initio density functional theory and atomistic simulation using a classical shell model potential have been combined to investigate low Cu concentrations in the KNbO{sub 3}-CuNbO{sub 3} system. The atomistic model predicts a morphotropic phase boundary at a few percent Cu, analogous to the one found in the LiNbO{sub 3}-KNbO{sub 3} system.

Atomistic nature in band-to-band tunneling in two-dimensional silicon pn tunnel diodes

International Nuclear Information System (INIS)

Tabe, Michiharu; Tan, Hoang Nhat; Mizuno, Takeshi; Muruganathan, Manoharan; Anh, Le The; Mizuta, Hiroshi; Nuryadi, Ratno; Moraru, Daniel

2016-01-01

We study low-temperature transport properties of two-dimensional (2D) Si tunnel diodes, or Si Esaki diodes, with a lateral layout. In ordinary Si Esaki diodes, interband tunneling current is severely limited because of the law of momentum conservation, while nanoscale Esaki diodes may behave differently due to the dopants in the narrow depletion region, by atomistic effects which release such current limitation. In thin-Si lateral highly doped pn diodes, we find clear signatures of interband tunneling between 2D-subbands involving phonon assistance. More importantly, the tunneling current is sharply enhanced in a narrow voltage range by resonance via a pair of a donor- and an acceptor-atom in the pn junction region. Such atomistic behavior is recognized as a general feature showing up only in nanoscale tunnel diodes. In particular, a donor-acceptor pair with deeper ground-state energies is likely to be responsible for such a sharply enhanced current peak, tunable by external biases.

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

Energy Technology Data Exchange (ETDEWEB)

Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

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 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.

A novel multi-tiered experimental approach unfolding the mechanisms behind cyclodextrin-vitamin inclusion complexes for enhanced vitamin solubility and stability.

Science.gov (United States)

Braithwaite, Miles C; Kumar, Pradeep; Choonara, Yahya E; du Toit, Lisa C; Tomar, Lomas K; Tyagi, Charu; Pillay, Viness

2017-10-30

This study was conducted to provide a mechanistic account for understanding the synthesis, characterization and solubility phenomena of vitamin complexes with cyclodextrins (CD) for enhanced solubility and stability employing experimental and in silico molecular modeling strategies. New geometric, molecular and energetic analyses were pursued to explicate experimentally derived cholecalciferol complexes. Various CD molecules (α-, β-, γ-, and hydroxypropyl β-) were complexed with three vitamins: cholecalciferol, ascorbic acid and α-tocopherol. The Inclusion Efficiency (IE%) was computed for each CD-vitamin complex. The highest IE% achieved for a cholecalciferol complex was for 'βCDD 3 -8', after utilizing a unique CD:cholecalciferol molar synthesis ratio of 2.5:1, never before reported as successful. 2HPβCD-cholecalciferol, γCD-cholecalciferol and α-tocopherol inclusion complexes (IC's) reached maximal IE% with a CD:vitamin molar ratio of 5:1. The results demonstrate that IE%, thermal stability, concentration, carrier solubility, molecular mechanics and intended release profile are key factors to consider when synthesizing vitamin-CD complexes. Phase-solubility data provided insights into the design of formulations with IC's that may provide analogous oral vitamin release profiles even when hydrophobic and hydrophilic vitamins are co-incorporated. Static lattice atomistic simulations were able to validate experimentally derived cholecalciferol IE phenomena and are invaluable parameters when approaching formulation strategies using CD's for improved solubility and efficacy of vitamins. Copyright © 2017 Elsevier B.V. All rights reserved.

An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

Energy Technology Data Exchange (ETDEWEB)

Wang, Zhi [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Jiang, Xiang-Wei; Li, Shu-Shen [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Wang, Lin-Wang, E-mail: lwwang@lbl.gov [Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

2014-03-24

We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10{sup 5} atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose.

An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

International Nuclear Information System (INIS)

Wang, Zhi; Jiang, Xiang-Wei; Li, Shu-Shen; Wang, Lin-Wang

2014-01-01

We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10 5 atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose

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

Science.gov (United States)

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...

Finite element analysis of an atomistically derived cohesive model for brittle fracture

International Nuclear Information System (INIS)

Lloyd, J T; McDowell, D L; Zimmerman, J A; Jones, R E; Zhou, X W

2011-01-01

In order to apply information from molecular dynamics (MD) simulations in problems governed by engineering length and time scales, a coarse graining methodology must be used. In previous work by Zhou et al (2009 Acta Mater. 57 4671–86), a traction-separation cohesive model was developed using results from MD simulations with atomistic-to-continuum measures of stress and displacement. Here, we implement this cohesive model within a combined finite element/cohesive surface element framework (referred to as a finite element approach or FEA), and examine the ability for the atomistically informed FEA to directly reproduce results from MD. We find that FEA shows close agreement of both stress and crack opening displacement profiles at the cohesive interface, although some differences do exist that can be attributed to the stochastic nature of finite temperature MD. The FEA methodology is then used to study slower loading rates that are computationally expensive for MD. We find that the crack growth process initially exhibits a rate-independent relationship between crack length and boundary displacement, followed by a rate-dependent regime where, at a given amount of boundary displacement, a lower applied strain rate produces a longer crack length. Our method is also extended to larger length scales by simulating a compact tension fracture-mechanics specimen with sub-micrometer dimensions. Such a simulation shows a computational speedup of approximately four orders of magnitude over conventional atomistic simulation, while exhibiting the expected fracture-mechanics response. Finally, differences between FEA and MD are explored with respect to ensemble and temperature effects in MD, and their impact on the cohesive model and crack growth behavior. These results enable us to make several recommendations to improve the methodology used to derive cohesive laws from MD simulations. In light of this work, which has critical implications for efforts to derive continuum laws

The complex jujube genome provides insights into fruit tree biology.

Science.gov (United States)

Liu, Meng-Jun; Zhao, Jin; Cai, Qing-Le; Liu, Guo-Cheng; Wang, Jiu-Rui; Zhao, Zhi-Hui; Liu, Ping; Dai, Li; Yan, Guijun; Wang, Wen-Jiang; Li, Xian-Song; Chen, Yan; Sun, Yu-Dong; Liu, Zhi-Guo; Lin, Min-Juan; Xiao, Jing; Chen, Ying-Ying; Li, Xiao-Feng; Wu, Bin; Ma, Yong; Jian, Jian-Bo; Yang, Wei; Yuan, Zan; Sun, Xue-Chao; Wei, Yan-Li; Yu, Li-Li; Zhang, Chi; Liao, Sheng-Guang; He, Rong-Jun; Guang, Xuan-Min; Wang, Zhuo; Zhang, Yue-Yang; Luo, Long-Hai

2014-10-28

The jujube (Ziziphus jujuba Mill.), a member of family Rhamnaceae, is a major dry fruit and a traditional herbal medicine for more than one billion people. Here we present a high-quality sequence for the complex jujube genome, the first genome sequence of Rhamnaceae, using an integrated strategy. The final assembly spans 437.65 Mb (98.6% of the estimated) with 321.45 Mb anchored to the 12 pseudo-chromosomes and contains 32,808 genes. The jujube genome has undergone frequent inter-chromosome fusions and segmental duplications, but no recent whole-genome duplication. Further analyses of the jujube-specific genes and transcriptome data from 15 tissues reveal the molecular mechanisms underlying some specific properties of the jujube. Its high vitamin C content can be attributed to a unique high level expression of genes involved in both biosynthesis and regeneration. Our study provides insights into jujube-specific biology and valuable genomic resources for the improvement of Rhamnaceae plants and other fruit trees.

Scalable Atomistic Simulation Algorithms for Materials Research

Directory of Open Access Journals (Sweden)

Aiichiro Nakano

2002-01-01

Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

Atomistic simulations of dislocation-precipitate interactions emphasize importance of cross-slip

International Nuclear Information System (INIS)

Singh, C.V.; Mateos, A.J.; Warner, D.H.

2011-01-01

This work examines the interaction of screw dislocations with Guinier-Preston (GP) zones using atomistic simulations. Both Orowan looping and cross-slip mechanisms are found to control the interactions. Cross-slip, occurring both at zero and finite temperatures, is found to either significantly reduce or enhance precipitate strengthening, depending upon the orientation of the dislocation-GP zone interaction. The orientation dependence, and its dependence on temperature, provides a micromechanical explanation for the experiments of Muraishi et al. (Philos. Mag. A 82 (2002) 2755).

NanoPSE: Nanoscience Problem Solving Environment for atomistic electronic structure of semiconductor nanostructures

International Nuclear Information System (INIS)

Jones, Wesley B; Bester, Gabriel; Canning, Andrew; Franceschetti, Alberto; Graf, Peter A; Kim, Kwiseon; Langou, Julien; Wang Linwang; Dongarra, Jack; Zunger, Alex

2005-01-01

Researchers at the National Renewable Energy Laboratory and their collaborators have developed over the past ∼10 years a set of algorithms for an atomistic description of the electronic structure of nanostructures, based on plane-wave pseudopotentials and configurationinteraction. The present contribution describes the first step in assembling these various codes into a single, portable, integrated set of software packages. This package is part of an ongoing research project in the development stage. Components of NanoPSE include codes for atomistic nanostructure generation and passivation, valence force field model for atomic relaxation, code for potential field generation, empirical pseudopotential method solver, strained linear combination of bulk bands method solver, configuration interaction solver for excited states, selection of linear algebra methods, and several inverse band structure solvers. Although not available for general distribution at this time as it is being developed and tested, the design goal of the NanoPSE software is to provide a software context for collaboration. The software package is enabled by fcdev, an integrated collection of best practice GNU software for open source development and distribution augmented to better support FORTRAN

Multi-scale modelling of ions in solution: from atomistic descriptions to chemical engineering

International Nuclear Information System (INIS)

Molina, J.J.

2011-01-01

Ions in solution play a fundamental role in many physical, chemical, and biological processes. The PUREX process used in the nuclear industry to the treatment of spent nuclear fuels is considered as an example. For industrial applications these systems are usually described using simple analytical models which are fitted to reproduce the available experimental data. In this work, we propose a multi-scale coarse graining procedure to derive such models from atomistic descriptions. First, parameters for classical force-fields of ions in solution are extracted from ab-initio calculations. Effective (McMillan-Mayer) ion-ion potentials are then derived from radial distribution functions measured in classical molecular dynamics simulations, allowing us to define an implicit solvent model of electrolytes. Finally, perturbation calculations are performed to define the best possible representation for these systems, in terms of charged hard-sphere models. Our final model is analytical and contains no free 'fitting' parameters. It shows good agreement with the exact results obtained from Monte-Carlo simulations for the thermodynamic and structural properties. Development of a similar model for the electrolyte viscosity, from information derived from atomistic descriptions, is also introduced. (author)

Multiscale methods coupling atomistic and continuum mechanics: analysis of a simple case

OpenAIRE

Blanc , Xavier; Le Bris , Claude; Legoll , Frédéric

2007-01-01

International audience; The description and computation of fine scale localized phenomena arising in a material (during nanoindentation, for instance) is a challenging problem that has given birth to many multiscale methods. In this work, we propose an analysis of a simple one-dimensional method that couples two scales, the atomistic one and the continuum mechanics one. The method includes an adaptive criterion in order to split the computational domain into two subdomains, that are described...

New insights into roles of acidocalcisomes and contractile vacuole complex in osmoregulation in protists.

Science.gov (United States)

Docampo, Roberto; Jimenez, Veronica; Lander, Noelia; Li, Zhu-Hong; Niyogi, Sayantanee

2013-01-01

While free-living protists are usually subjected to hyposmotic environments, parasitic protists are also in contact with hyperosmotic habitats. Recent work in one of these parasites, Trypanosoma cruzi, has revealed that its contractile vacuole complex, which usually collects and expels excess water as a mechanism of regulatory volume decrease after hyposmotic stress, has also a role in cell shrinking when the cells are submitted to hyperosmotic stress. Trypanosomes also have an acidic calcium store rich in polyphosphate (polyP), named the acidocalcisome, which is involved in their response to osmotic stress. Here, we review newly emerging insights on the role of acidocalcisomes and the contractile vacuole complex in the cellular response to hyposmotic and hyperosmotic stresses. We also review the current state of knowledge on the composition of these organelles and their other roles in calcium homeostasis and protein trafficking. © 2013, Elsevier Inc. All Rights Reserved.

Atomistic simulation of the premelting of iron and aluminum : Implications for high-pressure melting-curve measurements

NARCIS (Netherlands)

Starikov, Sergey V.; Stegailov, Vladimir V.

2009-01-01

Using atomistic simulations we show the importance of the surface premelting phenomenon for the melting-curve measurements at high pressures. The model under consideration mimics the experimental conditions deployed for melting studies with diamond-anvil cells. The iron is considered in this work

Near-ideal strength in metal nanotubes revealed by atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Sun, Mingfei; Xiao, Fei [Department of Materials Science, Fudan University, 220 Handan Road, Shanghai 200433 (China); Deng, Chuang, E-mail: dengc@ad.umanitoba.ca [Department of Mechanical and Manufacturing Engineering, The University of Manitoba, 15Gillson Street, Winnipeg, Manitoba R3T 5V6 (Canada)

2013-12-02

Here we report extraordinary mechanical properties revealed by atomistic simulations in metal nanotubes with hollow interior that have been long overlooked. Particularly, the yield strength in [1 1 1] Au nanotubes is found to be up to 60% higher than the corresponding solid Au nanowire, which approaches the theoretical ideal strength in Au. Furthermore, a remarkable transition from sharp to smooth yielding is observed in Au nanotubes with decreasing wall thickness. The ultrahigh tensile strength in [1 1 1] Au nanotube might originate from the repulsive image force exerted by the interior surface against dislocation nucleation from the outer surface.

New Insight into Carbon Nanotube Electronic Structure Selectivity

Energy Technology Data Exchange (ETDEWEB)

Sumpter, Bobby G [ORNL; Meunier, Vincent [ORNL; Jiang, Deen [ORNL

2009-01-01

The fundamental role of aryl diazonium salts for post synthesis selectivity of carbon nanotubes is investigated using extensive electronic structure calculations. The resulting understanding for diazonium salt based selective separation of conducting and semiconducting carbon nanotubes shows how the primary contributions come from the interplay between the intrinsic electronic structure of the carbon nanotubes and that of the anion of the salt. We demonstrate how the electronic transport properties change upon the formation of charge transfer complexes and upon their conversion into covalently attached functional groups. Our results are found to correlate well with experiments and provide for the first time an atomistic description for diazonium salt based chemical separation of carbon nanotubes

Quantum-based Atomistic Simulation of Transition Metals

International Nuclear Information System (INIS)

Moriarty, J A; Benedict, L X; Glosli, J N; Hood, R Q; Orlikowski, D A; Patel, M V; Soderlind, P; Streitz, F H; Tang, M; Yang, L H

2005-01-01

First-principles generalized pseudopotential theory (GPT) provides a fundamental basis for transferable multi-ion interatomic potentials in d-electron transition metals within density-functional quantum mechanics. In mid-period bcc metals, where multi-ion angular forces are important to structural properties, simplified model GPT or MGPT potentials have been developed based on canonical d bands to allow analytic forms and large-scale atomistic simulations. Robust, advanced-generation MGPT potentials have now been obtained for Ta and Mo and successfully applied to a wide range of structural, thermodynamic, defect and mechanical properties at both ambient and extreme conditions of pressure and temperature. Recent algorithm improvements have also led to a more general matrix representation of MGPT beyond canonical bands allowing increased accuracy and extension to f-electron actinide metals, an order of magnitude increase in computational speed, and the current development of temperature-dependent potentials

From HADES to PARADISE-atomistic simulation of defects in minerals

Energy Technology Data Exchange (ETDEWEB)

Parker, Stephen C; Cooke, David J; Kerisit, Sebastien; Marmier, Arnaud S; Taylor, Sarah L; Taylor, Stuart N [Department of Chemistry, University of Bath, Bath BA2 7AY (United Kingdom)

2004-07-14

The development of the HADES code by Michael Norgett in the 1970s enabled, for the first time, the routine simulation of point defects in inorganic solids at the atomic scale. Using examples from current research we illustrate how the scope and applications of atomistic simulations have widened with time and yet still follow an approach readily identifiable with this early work. Firstly we discuss the use of the Mott-Littleton methodology to study the segregation of various isovalent cations to the (00.1) and (01.2) surfaces of haematite ({alpha}-Fe{sub 2}O{sub 3}). The results show that the size of the impurities has a considerable effect on the magnitude of the segregation energy. We then extend these simulations to investigate the effect of the concentration of the impurities at the surface on the segregation process using a supercell approach. We consider next the effect of segregation to stepped surfaces illustrating this with recent work on segregation of La{sup 3+} to CaF{sub 2} surfaces, which show enhanced segregation to step edges. We discuss next the application of lattice dynamics to modelling point defects in complex oxide materials by applying this to the study of hydrogen incorporation into {beta}-Mg{sub 2}SiO{sub 4}. Finally our attention is turned to a method for considering the surface energy of physically defective surfaces and we illustrate its approach by considering the low index surfaces of {alpha}-Al{sub 2}O{sub 3}.

Drug design: Insights from atomistic simulations

International Nuclear Information System (INIS)

Collu, F.; Spiga, E.; Kumar, A.; Hajjar, E.; Vargiu, A.V.; Ceccarelli, M.; Ruggerone, P.

2009-01-01

Computer simulations have become a widely used and powerful tool to study the behaviour of many-particle and many-interaction systems and processes such as nucleic acid dynamics, drug-DNA interactions, enzymatic processes, membrane, antibiotics. The increased reliability of computational techniques has made possible to plane a bottom-up approach in drug design, i.e. designing molecules with improved properties starting from the knowledge of the molecular mechanisms. However, the in silico techniques have to face the fact that the number of degrees of freedom involved in biological systems is very large while the time scale of several biological processes is not accessible to standard simulations. Algorithms and methods have been developed and are still under construction to bridge these gaps. Here we review the activities of our group focussed on the time-scale bottleneck and, in particular, on the use of the meta dynamics scheme that allows the investigation of rare events in reasonable computer time without reducing the accuracy of the calculation. In particular, we have devoted particular attention to the characterization at microscopic level of translocation of antibiotics through membrane pores, aiming at the identification of structural and dynamical features helpful for a rational drug design.

Physically representative atomistic modeling of atomic-scale friction

Science.gov (United States)

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

Control of density fluctuations in atomistic-continuum simulations of dense liquids

DEFF Research Database (Denmark)

Kotsalis, E.M.; Walther, Jens Honore; Koumoutsakos, P.

2007-01-01

with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force...... is usually employed to remedy this situation.We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity...

Using a scalar parameter to trace dislocation evolution in atomistic modeling

Energy Technology Data Exchange (ETDEWEB)

Yang, Jinbo [ORNL; Zhang, Z F [Shenyang National Laboratory for Materials Science; Osetskiy, Yury N [ORNL; Stoller, Roger E [ORNL

2015-01-01

A scalar gamma-parameter is proposed from the Nye tensor. Its maximum value occurs along a dislocation line, either straight or curved, when the coordinate system is purposely chosen. This parameter can be easily obtained from the Nye tensor calculated at each atom in atomistic modeling. Using the gamma-parameter, a fully automated approach is developed to determine core atoms and the Burgers vectors of dislocations simultaneously. The approach is validated by revealing the smallest dislocation loop and by tracing the whole formation process of complicated dislocation networks on the fly.

On the use of atomistic simulations to aid bulk metallic glasses structural elucidation with solid-state NMR.

Science.gov (United States)

Ferreira, Ary R; Rino, José P

2017-08-24

Solid-state nuclear magnetic resonance (ssNMR) experimental 27 Al metallic shifts reported in the literature for bulk metallic glasses (BMGs) were revisited in the light of state-of-the-art atomistic simulations. In a consistent way, the Gauge-Including Projector Augmented-Wave (GIPAW) method was applied in conjunction with classical molecular dynamics (CMD). A series of Zr-Cu-Al alloys with low Al concentrations were selected as case study systems, for which realistic CMD derived structural models were used for a short- and medium-range order mining. That initial procedure allowed the detection of trends describing changes on the microstructure of the material upon Al alloying, which in turn were used to guide GIPAW calculations with a set of abstract systems in the context of ssNMR. With essential precision and accuracy, the ab initio simulations also yielded valuable trends from the electronic structure point of view, which enabled an overview of the bonding nature of Al-centered clusters as well as its influence on the experimental ssNMR outcomes. The approach described in this work might promote the use of ssNMR spectroscopy in research on glassy metals. Moreover, the results presented demonstrate the possibility to expand the applications of this technique, with deeper insight into nuclear interactions and less speculative assignments.

Dynamic characteristics of nanoindentation using atomistic simulation

International Nuclear Information System (INIS)

Fang, Te-Hua; Chang, Wen-Yang; Huang, Jian-Jin

2009-01-01

Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0 o , is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

Dynamic characteristics of nanoindentation using atomistic simulation

Energy Technology Data Exchange (ETDEWEB)

Fang, Te-Hua, E-mail: fang.tehua@msa.hinet.net [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China); Chang, Wen-Yang [Microsystems Technology Center, Industrial Technology Research Institute, Tainan 709, Taiwan (China); Huang, Jian-Jin [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China)

2009-06-15

Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0{sup o}, is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

Long-time atomistic simulations with the Parallel Replica Dynamics method

Science.gov (United States)

Perez, Danny

Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

Comparison of atomistic and elasticity approaches for carbon diffusion near line defects in {alpha}-iron

Energy Technology Data Exchange (ETDEWEB)

Veiga, R.G.A., E-mail: rgaveiga@gmail.com [Universite de Lyon, INSA Lyon, Laboratoire MATEIS, UMR CNRS 5510, 25 Avenue Jean Capelle, F69621, Villeurbanne (France); Perez, M. [Universite de Lyon, INSA Lyon, Laboratoire MATEIS, UMR CNRS 5510, 25 Avenue Jean Capelle, F69621, Villeurbanne (France); Becquart, C.S. [Unite Materiaux et Transformations (UMET), Ecole Nationale Superieure de Chimie de Lille, UMR CNRS 8207, Bat. C6, F59655 Villeneuve d' Ascq Cedex (France); Laboratoire commun EDF-CNRS Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France); Clouet, E. [Service de Recherches de Metallurgie Physique, CEA/Saclay, 91191 Gif-sur-Yvette (France); Domain, C. [EDF, Recherche et Developpement, Materiaux et Mecanique des Composants, Les Renardieres, F77250 Moret sur Loing (France); Laboratoire commun EDF-CNRS Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France)

2011-10-15

Energy barriers for carbon migration in the neighborhood of line defects in body-centered cubic iron have been obtained by atomistic simulations. For this purpose, molecular statics with an Fe-C interatomic potential, based on the embedded atom method, has been employed. Results of these simulations have been compared to the predictions of anisotropic elasticity theory. The agreement is better for a carbon atom sitting on an octahedral site (energy minimum) than one on a tetrahedral site (saddle point). Absolute differences in the energy barriers obtained by the two methods are usually below 5 meV at distances larger than 1.5 nm from a screw dislocation and 2 nm (up to 4 nm in the glide plane) from the edge dislocation. Atomistic kinetic Monte Carlo simulations performed at T = 300 K and additional analysis based on the activation energies obtained by both methods show that they are in good qualitative agreement, despite some important quantitative discrepancies due to the large absolute errors found near the dislocation cores.

Atomistic Simulation of the Rate-Dependent Ductile-to-Brittle Failure Transition in Bicrystalline Metal Nanowires.

Science.gov (United States)

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 (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.

An Atomistic Carbide-Derived Carbon Model Generated Using ReaxFF-Based Quenched Molecular Dynamics

Directory of Open Access Journals (Sweden)

Matthew W. Thompson

2017-10-01

Full Text Available We report a novel atomistic model of carbide-derived carbons (CDCs, which are nanoporous carbons with high specific surface areas, synthesis-dependent degrees of graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, and catalytic supports. These materials are heterogenous, non-ideal structures and include several important parameters that govern their performance. Therefore, a realistic model of the CDC structure is needed in order to study these systems and their nanoscale and macroscale properties with molecular simulation. We report the use of the ReaxFF reactive force field in a quenched molecular dynamics routine to generate atomistic CDC models. The pair distribution function, pore size distribution, and adsorptive properties of this model are reported and corroborated with experimental data. Simulations demonstrate that compressing the system after quenching changes the pore size distribution to better match the experimental target. Ring size distributions of this model demonstrate the prevalence of non-hexagonal carbon rings in CDCs. These effects may contrast the properties of CDCs against those of activated carbons with similar pore size distributions and explain higher energy densities of CDC-based supercapacitors.

Modelling radiation-induced phase changes in binary FeCu and ternary FeCuNi alloys using an artificial intelligence-based atomistic kinetic Monte Carlo approach

Science.gov (United States)

Castin, N.; Malerba, L.; Bonny, G.; Pascuet, M. I.; Hou, M.

2009-09-01

We apply a novel atomistic kinetic Monte Carlo model, which includes local chemistry and relaxation effects when assessing the migration energy barriers of point defects, to the study of the microchemical evolution driven by vacancy diffusion in FeCu and FeCuNi alloys. These alloys are of importance for nuclear applications because Cu precipitation, enhanced by the presence of Ni, is one of the main causes of hardening and embrittlement in reactor pressure vessel steels used in existing nuclear power plants. Local chemistry and relaxation effects are introduced using artificial intelligence techniques, namely a conveniently trained artificial neural network, to calculate the migration energy barriers of vacancies as functions of the local atomic configuration. We prove, through a number of results, that the use of the neural network is fully equivalent to calculating the migration energy barriers on-the-fly, using computationally expensive methods such as nudged elastic bands with an interatomic potential. The use of the neural network makes the computational cost affordable, so that simulations of the same type as those hitherto carried out using heuristic formulas for the assessment of the energy barriers can now be performed, at the same computational cost, using more rigorously calculated barriers. This method opens the way to properly treating more complex problems, such as the case of self-interstitial cluster formation, in an atomistic kinetic Monte Carlo framework.

Modelling radiation-induced phase changes in binary FeCu and ternary FeCuNi alloys using an artificial intelligence-based atomistic kinetic Monte Carlo approach

International Nuclear Information System (INIS)

Castin, N.; Malerba, L.; Bonny, G.; Pascuet, M.I.; Hou, M.

2009-01-01

We apply a novel atomistic kinetic Monte Carlo model, which includes local chemistry and relaxation effects when assessing the migration energy barriers of point defects, to the study of the microchemical evolution driven by vacancy diffusion in FeCu and FeCuNi alloys. These alloys are of importance for nuclear applications because Cu precipitation, enhanced by the presence of Ni, is one of the main causes of hardening and embrittlement in reactor pressure vessel steels used in existing nuclear power plants. Local chemistry and relaxation effects are introduced using artificial intelligence techniques, namely a conveniently trained artificial neural network, to calculate the migration energy barriers of vacancies as functions of the local atomic configuration. We prove, through a number of results, that the use of the neural network is fully equivalent to calculating the migration energy barriers on-the-fly, using computationally expensive methods such as nudged elastic bands with an interatomic potential. The use of the neural network makes the computational cost affordable, so that simulations of the same type as those hitherto carried out using heuristic formulas for the assessment of the energy barriers can now be performed, at the same computational cost, using more rigorously calculated barriers. This method opens the way to properly treating more complex problems, such as the case of self-interstitial cluster formation, in an atomistic kinetic Monte Carlo framework.

Modelling radiation-induced phase changes in binary FeCu and ternary FeCuNi alloys using an artificial intelligence-based atomistic kinetic Monte Carlo approach

Energy Technology Data Exchange (ETDEWEB)

Castin, N. [Structural Materials Group, Nuclear Materials Science Institute, Kernenergie Centre d' Etude de l' Energie Nucleaire (SCK CEN), Studiecentrum voor, Boeretang 200, 2400 Mol (Belgium); Physique des Solides Irradies et des Nanostructures (PSIN), Universite Libre de Bruxelles (ULB), Boulevard du Triomphe CP234, 1050 Brussels (Belgium); Malerba, L. [Structural Materials Group, Nuclear Materials Science Institute, Kernenergie Centre d' Etude de l' Energie Nucleaire (SCK CEN), Studiecentrum voor, Boeretang 200, 2400 Mol (Belgium)], E-mail: lmalerba@sckcen.be; Bonny, G. [Structural Materials Group, Nuclear Materials Science Institute, Kernenergie Centre d' Etude de l' Energie Nucleaire (SCK CEN), Studiecentrum voor, Boeretang 200, 2400 Mol (Belgium); Laboratory of Theoretical Physics, Universiteit Gent, Proeftuinstraat 86, B-9000 Gent (Belgium); Pascuet, M.I. [Structural Materials Group, Nuclear Materials Science Institute, Kernenergie Centre d' Etude de l' Energie Nucleaire (SCK CEN), Studiecentrum voor, Boeretang 200, 2400 Mol (Belgium); CAC-CNEA, Departamento de Materiales, Avda. Gral. Paz 1499, 1650 San Martin, Pcia. Buenos Aires (Argentina); CONICET, Avda. Rivadavia 1917, 1033 Buenos Aires (Argentina); Hou, M. [Physique des Solides Irradies et des Nanostructures (PSIN), Universite Libre de Bruxelles (ULB), Boulevard du Triomphe CP234, 1050 Brussels (Belgium)

2009-09-15

We apply a novel atomistic kinetic Monte Carlo model, which includes local chemistry and relaxation effects when assessing the migration energy barriers of point defects, to the study of the microchemical evolution driven by vacancy diffusion in FeCu and FeCuNi alloys. These alloys are of importance for nuclear applications because Cu precipitation, enhanced by the presence of Ni, is one of the main causes of hardening and embrittlement in reactor pressure vessel steels used in existing nuclear power plants. Local chemistry and relaxation effects are introduced using artificial intelligence techniques, namely a conveniently trained artificial neural network, to calculate the migration energy barriers of vacancies as functions of the local atomic configuration. We prove, through a number of results, that the use of the neural network is fully equivalent to calculating the migration energy barriers on-the-fly, using computationally expensive methods such as nudged elastic bands with an interatomic potential. The use of the neural network makes the computational cost affordable, so that simulations of the same type as those hitherto carried out using heuristic formulas for the assessment of the energy barriers can now be performed, at the same computational cost, using more rigorously calculated barriers. This method opens the way to properly treating more complex problems, such as the case of self-interstitial cluster formation, in an atomistic kinetic Monte Carlo framework.

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

Science.gov (United States)

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.

An atomistic methodology of energy release rate for graphene at nanoscale

International Nuclear Information System (INIS)

Zhang, Zhen; Lee, James D.; Wang, Xianqiao

2014-01-01

Graphene is a single layer of carbon atoms packed into a honeycomb architecture, serving as a fundamental building block for electric devices. Understanding the fracture mechanism of graphene under various conditions is crucial for tailoring the electrical and mechanical properties of graphene-based devices at atomic scale. Although most of the fracture mechanics concepts, such as stress intensity factors, are not applicable in molecular dynamics simulation, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at nanoscale. This work introduces an atomistic simulation methodology, based on the energy release rate, as a tool to unveil the fracture mechanism of graphene at nanoscale. This methodology can be easily extended to any atomistic material system. We have investigated both opening mode and mixed mode at different temperatures. Simulation results show that the critical energy release rate of graphene is independent of initial crack length at low temperature. Graphene with inclined pre-crack possesses higher fracture strength and fracture deformation but smaller critical energy release rate compared with the graphene with vertical pre-crack. Owing to its anisotropy, graphene with armchair chirality always has greater critical energy release rate than graphene with zigzag chirality. The increase of temperature leads to the reduction of fracture strength, fracture deformation, and the critical energy release rate of graphene. Also, higher temperature brings higher randomness of energy release rate of graphene under a variety of predefined crack lengths. The energy release rate is independent of the strain rate as long as the strain rate is small enough

Atomistic Modeling of Ion Conduction through the Voltage-Sensing Domain of the Shaker K+ Ion Channel.

Science.gov (United States)

Wood, Mona L; Freites, J Alfredo; Tombola, Francesco; Tobias, Douglas J

2017-04-20

Voltage-sensing domains (VSDs) sense changes in the membrane electrostatic potential and, through conformational changes, regulate a specific function. The VSDs of wild-type voltage-dependent K + , Na + , and Ca 2+ channels do not conduct ions, but they can become ion-permeable through pathological mutations in the VSD. Relatively little is known about the underlying mechanisms of conduction through VSDs. The most detailed studies have been performed on Shaker K + channel variants in which ion conduction through the VSD is manifested in electrophysiology experiments as a voltage-dependent inward current, the so-called omega current, which appears when the VSDs are in their resting state conformation. Only monovalent cations appear to permeate the Shaker VSD via a pathway that is believed to be, at least in part, the same as that followed by the S4 basic side chains during voltage-dependent activation. We performed μs-time scale atomistic molecular dynamics simulations of a cation-conducting variant of the Shaker VSD under applied electric fields in an experimentally validated resting-state conformation, embedded in a lipid bilayer surrounded by solutions containing guanidinium chloride or potassium chloride. Our simulations provide insights into the Shaker VSD permeation pathway, the protein-ion interactions that control permeation kinetics, and the mechanism of voltage-dependent activation of voltage-gated ion channels.

Ab Initio Analysis of Auger-Assisted Electron Transfer.

Science.gov (United States)

Hyeon-Deuk, Kim; Kim, Joonghan; Prezhdo, Oleg V

2015-01-15

Quantum confinement in nanoscale materials allows Auger-type electron-hole energy exchange. We show by direct time-domain atomistic simulation and analytic theory that Auger processes give rise to a new mechanism of charge transfer (CT) on the nanoscale. Auger-assisted CT eliminates the renown Marcus inverted regime, rationalizing recent experiments on CT from quantum dots to molecular adsorbates. The ab initio simulation reveals a complex interplay of the electron-hole and charge-phonon channels of energy exchange, demonstrating a variety of CT scenarios. The developed Marcus rate theory for Auger-assisted CT describes, without adjustable parameters, the experimental plateau of the CT rate in the region of large donor-acceptor energy gap. The analytic theory and atomistic insights apply broadly to charge and energy transfer in nanoscale systems.

Emergence of linear elasticity from the atomistic description of matter

Energy Technology Data Exchange (ETDEWEB)

Cakir, Abdullah, E-mail: acakir@ntu.edu.sg [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore); Pica Ciamarra, Massimo [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore); Dipartimento di Scienze Fisiche, CNR–SPIN, Università di Napoli Federico II, I-80126 Napoli (Italy)

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 the fluctuations of the local elastic constants close to the jamming transition.

Emergence of linear elasticity from the atomistic description of matter

International Nuclear Information System (INIS)

Cakir, Abdullah; Pica Ciamarra, Massimo

2016-01-01

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 the fluctuations of the local elastic constants close to the jamming transition.

Redox reactions with empirical potentials: atomistic battery discharge simulations.

Science.gov (United States)

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.

New Insights into the Roles of Acidocalcisomes and the Contractile Vacuole Complex in Osmoregulation in Protists

Science.gov (United States)

Docampo, Roberto; Jimenez, Veronica; Lander, Noelia; Li, Zhu-Hong; Niyogi, Sayantanee

2013-01-01

While free-living protists are usually subjected to hyposmotic environments, parasitic protists are also in contact with hyperosmotic habitats. Recent work in one of these parasites, Trypanosoma cruzi, has revealed that its contractile vacuole complex, which usually collects and expels excess water as a mechanism of regulatory volume decrease after hyposmotic stress, has also a role in cell shrinking when the cells are submitted to hyperosmotic stress. Trypanosomes also have an acidic calcium store rich in polyphosphate (polyP), named the acidocalcisome, which is involved in their response to osmotic stress. Here, we review newly emerging insights on the role of acidocalcisomes and the contractile vacuole complex in the cellular response to hyposmotic and hyperosmotic stresses. We also review the current state of knowledge on the composition of these organelles and their other roles in calcium homeostasis and protein trafficking. PMID:23890380

Atomistic approach to predict the glass-forming ability in Zr–Cu–Al ternary metallic glasses

Energy Technology Data Exchange (ETDEWEB)

Yu, C.Y. [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, X.J. [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Zheng, G.P. [Department of Mechanical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong (China); Niu, X.R. [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, C.T., E-mail: chainliu@cityu.edu.hk [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China)

2015-04-05

Highlights: • An atomistic approach has been developed to predict the glass forming ability (GFA) in Zr–Cu–Al ternary alloy system. • Both of the thermodynamic and structure-dependent kinetic effects to glass formation have been taken into account. • The first-principles calculation and molecular dynamics simulation have been performed. • The approach predicts the best glass former in the model Zr–Cu–Al alloy system. • The predicted GFA is consistent with various experimental results. - Abstract: Prediction of composition-dependent glass-forming ability (GFA) remains to be a key scientific challenge in the metallic-glass community, especially in multi-component alloy systems. In the present study, we apply an atomistic approach to predict the trend of GFA effectively in the Zr–Cu–Al ternary alloy system from alloy compositions alone. This approach is derived from the first-principles calculations based on the density-functional theory and molecular dynamic (MD) simulations. By considering of both the thermodynamic and atomic-structure induced kinetic effects, the predicted GFA trend from this approach shows an excellent agreement with experimental data available in this alloy system, manifesting its capability of seeking metallic glasses with superior GFA in ternary alloy systems.

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

Science.gov (United States)

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

Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

International Nuclear Information System (INIS)

Stukowski, Alexander

2010-01-01

The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations functions are integrated into its easy-to-use graphical user interface. The software is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface. It is distributed as open-source software and can be downloaded from the website http://ovito.sourceforge.net/

Atomistic calculation of size effects on elastic coefficients in nanometre-sized tungsten layers and wires

International Nuclear Information System (INIS)

Villain, P.; Beauchamp, P.; Badawi, K.F.; Goudeau, P.; Renault, P.-O.

2004-01-01

Equilibrium state and elastic coefficients of nanometre-sized single crystal tungsten layers and wires are investigated by atomistic simulations. The variations of the equilibrium distances as a function of the layer thickness or wire cross-section are mainly due to elastic effects of surface tension forces. A strong decrease of the Young's modulus is observed when the transverse dimensions are reduced below 2-3 nm

Insight and analysis problem solving in microbes to machines.

Science.gov (United States)

Clark, Kevin B

2015-11-01

A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices. Copyright

Atomistic simulation of dislocation nucleation barriers from cracktips in α-Fe

International Nuclear Information System (INIS)

Gordon, Peter A; Neeraj, T; Luton, Michael J

2008-01-01

In this work, we demonstrate that activation pathways for dislocation loop nucleation from cracktips can be explored with full atomistic detail using an efficient form of the nudged elastic band method. The approach is demonstrated in detail with an example of edge emission from an Fe crack under mode II loading, wherein activation energy barriers are obtained as a function of sub-critical stress intensity and the energy barriers for loop formation are compared with 2D calculations. Activation energy barriers are also computed for an intrinsically ductile cracktip orientation under mode I loading, from which we can infer the frequency of nucleation from the cracktip

Components for Atomistic-to-Continuum Multiscale Modeling of Flow in Micro- and Nanofluidic Systems

Directory of Open Access Journals (Sweden)

Helgi Adalsteinsson

2008-01-01

Full Text Available 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-level 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.

Study of the embedded atom method of atomistic calculations for metals and alloys. Final report, March 1, 1986--February 29, 1992

International Nuclear Information System (INIS)

Johnson, R.A.

1992-04-01

Solids have been studied by atomistic modeling since the earliest availability of computers for scientific research. By the mid sixties, it was understood that models for metals based on reasonably short ranged two-body forces coupled with a global volume dependent contribution to the crystal energy yielded surprisingly good results for bulk calculations, but were unsatisfactory at surfaces. Little progress was made until the early eighties, when Daw and Baskes developed the Embedded-Atom Method (EAM) based on density functional theory and intended primarily for tight-packed transitional metals, and Finnis and Sinclair developed a model based on tight binding theory and intended primarily for bcc transition metals. The underlying mathematical format of both approaches is the same, and provides an extension of the earlier models through a function which in practice provides a measure of local volume dependence. The primary purpose of this research project was to investigate the implications of this mathematical format and to use the resulting insight to correlate the known physical input data with computed results of properties that are difficult to access experimentally. Embedded-Atom Method terminology is used, but this research is applicable as well to the Finnis-Sinclair model

Structural insights into transcription complexes

NARCIS (Netherlands)

Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

2011-01-01

Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

Atomistic switch of giant magnetoresistance and spin thermopower in graphene-like nanoribbons

Science.gov (United States)

Zhai, Ming-Xing; Wang, Xue-Feng

2016-01-01

We demonstrate that the giant magnetoresistance can be switched off (on) in even- (odd-) width zigzag graphene-like nanoribbons by an atomistic gate potential or edge disorder inside the domain wall in the antiparallel (ap) magnetic configuration. A strong magneto-thermopower effect is also predicted that the spin thermopower can be greatly enhanced in the ap configuration while the charge thermopower remains low. The results extracted from the tight-binding model agree well with those obtained by first-principles simulations for edge doped graphene nanoribbons. Analytical expressions in the simplest case are obtained to facilitate qualitative analyses in general contexts. PMID:27857156

Pentacoordinated organoaluminum complexes: A computational insight

KAUST Repository

Milione, Stefano

2012-12-24

The geometry and the electronic structure of a series of organometallic pentacoordinated aluminum complexes bearing tri- or tetradentate N,O-based ligands have been investigated with theoretical methods. The BP86, B3LYP, and M06 functionals reproduce with low accuracy the geometry of the selected complexes. The worst result was obtained for the complex bearing a Schiff base ligand with a pendant donor arm, aeimpAlMe2 (aeimp = N-2-(dimethylamino)ethyl-(3,5-di-tert-butyl)salicylaldimine). In particular, the Al-Namine bond distance was unacceptably overestimated. This failure suggests a reasonably flat potential energy surface with respect to Al-N elongation, indicating a weak interaction with probably a strong component of dispersion forces. MP2 and M06-2X methods led to an acceptable value for the same Al-N distance. Better results were obtained with the addition of the dispersion correction to the hybrid B3LYP functional (B3LYP-D). Natural bond orbital analysis revealed that the contribution of the d orbital to the bonding is very small, in agreement with several previous studies of hypervalent molecules. The donation of electronic charge from the ligand to metal mainly consists in the interactions of the lone pairs on the donor atoms of the ligands with the s and p valence orbitals of the aluminum. The covalent bonding of the Al with the coordinated ligand is weak, and the interactions between Al and the coordinated ligands are largely ionic. To further explore the geometrical and electronic factors affecting the formation of these pentacoordianted aluminum complexes, we considered the tetracoordinated complex impAlMe2 (imp = N-isopropyl-(3,5-di-tert-butyl)salicylaldimine)), analogous to aeimpAlMe 2, and we investigated the potential energy surface around the aluminum atom corresponding to the approach of NMe3 to the metal center. At the MP2/6-31G(d) level of theory, a weak attraction was revealed only when NMe3 heads toward the metal center through the directions

Pentacoordinated organoaluminum complexes: A computational insight

KAUST Repository

Milione, Stefano; Milano, Giuseppe; Cavallo, Luigi

2012-01-01

The geometry and the electronic structure of a series of organometallic pentacoordinated aluminum complexes bearing tri- or tetradentate N,O-based ligands have been investigated with theoretical methods. The BP86, B3LYP, and M06 functionals reproduce with low accuracy the geometry of the selected complexes. The worst result was obtained for the complex bearing a Schiff base ligand with a pendant donor arm, aeimpAlMe2 (aeimp = N-2-(dimethylamino)ethyl-(3,5-di-tert-butyl)salicylaldimine). In particular, the Al-Namine bond distance was unacceptably overestimated. This failure suggests a reasonably flat potential energy surface with respect to Al-N elongation, indicating a weak interaction with probably a strong component of dispersion forces. MP2 and M06-2X methods led to an acceptable value for the same Al-N distance. Better results were obtained with the addition of the dispersion correction to the hybrid B3LYP functional (B3LYP-D). Natural bond orbital analysis revealed that the contribution of the d orbital to the bonding is very small, in agreement with several previous studies of hypervalent molecules. The donation of electronic charge from the ligand to metal mainly consists in the interactions of the lone pairs on the donor atoms of the ligands with the s and p valence orbitals of the aluminum. The covalent bonding of the Al with the coordinated ligand is weak, and the interactions between Al and the coordinated ligands are largely ionic. To further explore the geometrical and electronic factors affecting the formation of these pentacoordianted aluminum complexes, we considered the tetracoordinated complex impAlMe2 (imp = N-isopropyl-(3,5-di-tert-butyl)salicylaldimine)), analogous to aeimpAlMe 2, and we investigated the potential energy surface around the aluminum atom corresponding to the approach of NMe3 to the metal center. At the MP2/6-31G(d) level of theory, a weak attraction was revealed only when NMe3 heads toward the metal center through the directions

Complex dynamics of our economic life on different scales: insights from search engine query data.

Science.gov (United States)

Preis, Tobias; Reith, Daniel; Stanley, H Eugene

2010-12-28

Search engine query data deliver insight into the behaviour of individuals who are the smallest possible scale of our economic life. Individuals are submitting several hundred million search engine queries around the world each day. We study weekly search volume data for various search terms from 2004 to 2010 that are offered by the search engine Google for scientific use, providing information about our economic life on an aggregated collective level. We ask the question whether there is a link between search volume data and financial market fluctuations on a weekly time scale. Both collective 'swarm intelligence' of Internet users and the group of financial market participants can be regarded as a complex system of many interacting subunits that react quickly to external changes. We find clear evidence that weekly transaction volumes of S&P 500 companies are correlated with weekly search volume of corresponding company names. Furthermore, we apply a recently introduced method for quantifying complex correlations in time series with which we find a clear tendency that search volume time series and transaction volume time series show recurring patterns.

Influence of Cholesterol on the Oxygen Permeability of Membranes: Insight from Atomistic Simulations.

Science.gov (United States)

Dotson, Rachel J; Smith, Casey R; Bueche, Kristina; Angles, Gary; Pias, Sally C

2017-06-06

Cholesterol is widely known to alter the physical properties and permeability of membranes. Several prior works have implicated cell membrane cholesterol as a barrier to tissue oxygenation, yet a good deal remains to be explained with regard to the mechanism and magnitude of the effect. We use molecular dynamics simulations to provide atomic-resolution insight into the influence of cholesterol on oxygen diffusion across and within the membrane. Our simulations show strong overall agreement with published experimental data, reproducing the shapes of experimental oximetry curves with high accuracy. We calculate the upper-limit transmembrane oxygen permeability of a 1-palmitoyl,2-oleoylphosphatidylcholine phospholipid bilayer to be 52 ± 2 cm/s, close to the permeability of a water layer of the same thickness. With addition of cholesterol, the permeability decreases somewhat, reaching 40 ± 2 cm/s at the near-saturating level of 62.5 mol % cholesterol and 10 ± 2 cm/s in a 100% cholesterol mimic of the experimentally observed noncrystalline cholesterol bilayer domain. These reductions in permeability can only be biologically consequential in contexts where the diffusional path of oxygen is not water dominated. In our simulations, cholesterol reduces the overall solubility of oxygen within the membrane but enhances the oxygen transport parameter (solubility-diffusion product) near the membrane center. Given relatively low barriers to passing from membrane to membrane, our findings support hydrophobic channeling within membranes as a means of cellular and tissue-level oxygen transport. In such a membrane-dominated diffusional scheme, the influence of cholesterol on oxygen permeability is large enough to warrant further attention. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Atomistic modeling of the structural components of the blood-brain barrier

Science.gov (United States)

Glukhova, O. E.; Grishina, O. A.; Slepchenkov, M. M.

2015-03-01

Blood-brain barrier, which is a barrage system between the brain and blood vessels, plays a key role in the "isolation" of the brain of unnecessary information, and reduce the "noise" in the interneuron communication. It is known that the barrier function of the BBB strictly depends on the initial state of the organism and changes significantly with age and, especially in developing the "vascular accidents". Disclosure mechanisms of regulation of the barrier function will develop new ways to deliver neurotrophic drugs to the brain in the newborn. The aim of this work is the construction of atomistic models of structural components of the blood-brain barrier to reveal the mechanisms of regulation of the barrier function.

Microscopic theory for coupled atomistic magnetization and lattice dynamics

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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

How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations.

Directory of Open Access Journals (Sweden)

Tarja Äijänen

2014-11-01

Full Text Available Cholesteryl ester transfer protein (CETP mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity and thereby raise high density lipoprotein (HDL-cholesterol and decrease low density lipoprotein (LDL-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site of anacetrapib turns out to reside in the tunnel inside CETP, near the residues surrounding the N-terminal opening. Free energy calculations show that when anacetrapib resides in this area, it hinders the ability of cholesteryl ester to diffuse out from CETP. The simulations further bring out the ability of anacetrapib to regulate the structure-function relationships of phospholipids and helix X, the latter representing the structural region of CETP important to the process of neutral lipid exchange with lipoproteins. Altogether, the simulations propose CETP inhibition to be realized when anacetrapib is transferred into the lipid binding pocket. The novel insight gained in this study has potential use in the development of new molecular agents capable of preventing the progression of cardiovascular diseases.

Atomistic modeling of ion beam induced amorphization in silicon

International Nuclear Information System (INIS)

Pelaz, Lourdes; Marques, Luis A.; Lopez, Pedro; Santos, Ivan; Aboy, Maria; Barbolla, Juan

2005-01-01

Ion beam induced amorphization in Si has attracted significant interest since the beginning of the use of ion implantation for the fabrication of Si devices. Nowadays, a renewed interest in the modeling of amorphization mechanisms at atomic level has arisen due to the use of preamorphizing implants and high dopant implantation doses for the fabrication of nanometric-scale Si devices. In this work, we briefly describe the existing phenomenological and defect-based amorphization models. We focus on the atomistic model we have developed to describe ion beam induced amorphization in Si. In our model, the building block for the amorphous phase is the bond defect or IV pair, whose stability increases with the number of surrounding IV pairs. This feature explains the regrowth behavior of different damage topologies and the kinetics of the crystalline to amorphous transition. The model provides excellent quantitative agreement with experimental results

Atomistic simulations of contact area and conductance at nanoscale interfaces.

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Hu, Xiaoli; Martini, Ashlie

2017-11-09

Atomistic simulations were used to study conductance across the interface between a nanoscale gold probe and a graphite surface with a step edge. Conductance on the graphite terrace was observed to increase with load and be approximately proportional to contact area calculated from the positions of atoms in the interface. The relationship between area and conductance was further explored by varying the position of the contact relative to the location of the graphite step edge. These simulations reproduced a previously-reported current dip at step edges measured experimentally and the trend was explained by changes in both contact area and the distribution of distances between atoms in the interface. The novel approach reported here provides a foundation for future studies of the fundamental relationships between conductance, load and surface topography at the atomic scale.

Atomistic modeling of defect evolution in Si for amorphizing and subamorphizing implants

International Nuclear Information System (INIS)

Lopez, Pedro; Pelaz, Lourdes; Marques, Luis A.; Santos, Ivan; Aboy, Maria; Barbolla, Juan

2004-01-01

Solid phase epitaxial regrowth of pre-amorphizing implants has received significant attention as a method to achieve high dopant activation with minimal diffusion at low implant temperatures and suppress channelling. Therefore, a good understanding of the amorphization and regrowth mechanisms is required in process simulators. We present an atomistic amorphization and recrystallization model that uses the interstitial-vacancy (I-V) pair as a building block to describe the amorphous phase. I-V pairs are locally characterized by the number of neighbouring I-V pairs. This feature captures the damage generation and the dynamical annealing during ion implantation, and also explains the annealing behaviour of amorphous layers and amorphous pockets

Uranium sorption to natural substrates-insights provided by isotope exchange, selective extraction and surface complexation modelling approaches

International Nuclear Information System (INIS)

Waite, T.D.; Payne T.E.; Davis, J.A.

1993-01-01

An extensive experimental program has been conducted over the last three years into the interaction of U(VI) with both single oxides and clays and complex natural substrates from the weathered zone in the vicinity of a uranium ore body in northern Australia. While iron oxides have frequently been considered to account for much of the uptake on such natural substrates, the results of laboratory open-quotes pH edgeclose quotes studies and of isotope exchange and selective extraction studies suggest that other phases must also play a significant role in controlling the partitioning of U(VI) between solid and solution phases. Supporting studies on kaolinite, the dominant clay in this system, provide insight into the most appropriate method of modelling the interaction of U(VI) with these natural substrates. The problems still remaining in adequately describing sorption of radionuclides and trace elements to complex natural substrates are discussed

Mechanistic insights into validoxylamine A 7'-phosphate synthesis by VldE using the structure of the entire product complex.

Directory of Open Access Journals (Sweden)

Michael C Cavalier

Full Text Available The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7'-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of VldE from Streptomyces hygroscopicus subsp. limoneus was determined in apo form, in complex with GDP, in complex with GDP and validoxylamine A 7'-phosphate, and in complex with GDP and trehalose. The structure of VldE with the catalytic site in both an "open" and "closed" conformation is also described. With these structures, the preferred binding of the guanine moiety by VldE, rather than the uracil moiety as seen in OtsA could be explained. The elucidation of the VldE structure in complex with the entirety of its products provides insight into the internal return mechanism by which catalysis occurs with a net retention of the stereochemical configuration of the donated cyclitol.

Atomistic simulations of screw dislocations in bcc tungsten: From core structures and static properties to interaction with vacancies

Energy Technology Data Exchange (ETDEWEB)

Xu, Ke [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Niu, Liang-Liang [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Department of Nuclear Engineering and Radiological Science, University of Michigan, Ann Arbor, MI 48109 (United States); Jin, Shuo, E-mail: jinshuo@buaa.edu.cn [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Shu, Xiaolin [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Xie, Hongxian [School of Mechanical Engineering, Hebei University of Technology, Tianjin 300132 (China); Wang, Lifang; Lu, Guang-Hong [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China)

2017-02-15

Atomistic simulations have been used to investigate the core structures, static properties of isolated 1/2 <1 1 1> screw dislocations, and their interaction with vacancies in bcc tungsten (W) based on three empirical interatomic potentials. Differential displacement maps show that only one embedded atom method potential is able to reproduce the compact non-degenerate core as evidenced by ab initio calculations. The obtained strain energy and stress distribution from atomistic simulations are, in general, consistent with elasticity theory predictions. In particular, one component of the calculated shear stress, which is not present according to elasticity theory, is non-negligible in the core region of our dislocation model. The differences between the results calculated from three interatomic potentials are in details, such as the specific value and the symmetry, but the trend of spatial distributions of static properties in the long range are close to each other. By calculating the binding energies between the dislocations and vacancies, we demonstrate that the dislocations act as vacancy sinks, which may be important for the nucleation and growth of hydrogen bubbles in W under irradiation.

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

Science.gov (United States)

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.

Using Models to Inform Policy: Insights from Modeling the Complexities of Global Polio Eradication

Science.gov (United States)

Thompson, Kimberly M.

Drawing on over 20 years of experience modeling risks in complex systems, this talk will challenge SBP participants to develop models that provide timely and useful answers to critical policy questions when decision makers need them. The talk will include reflections on the opportunities and challenges associated with developing integrated models for complex problems and communicating their results effectively. Dr. Thompson will focus the talk largely on collaborative modeling related to global polio eradication and the application of system dynamics tools. After successful global eradication of wild polioviruses, live polioviruses will still present risks that could potentially lead to paralytic polio cases. This talk will present the insights of efforts to use integrated dynamic, probabilistic risk, decision, and economic models to address critical policy questions related to managing global polio risks. Using a dynamic disease transmission model combined with probabilistic model inputs that characterize uncertainty for a stratified world to account for variability, we find that global health leaders will face some difficult choices, but that they can take actions that will manage the risks effectively. The talk will emphasize the need for true collaboration between modelers and subject matter experts, and the importance of working with decision makers as partners to ensure the development of useful models that actually get used.

Elucidating the atomistic mechanisms underpinning plasticity in Li-Si nanostructures

Science.gov (United States)

Yan, Xin; Gouissem, Afif; Guduru, Pradeep R.; Sharma, Pradeep

2017-10-01

Amorphous lithium-silicon (a-Li-Si), especially in nanostructure form, is an attractive high-capacity anode material for next-generation Li-ion batteries. During cycles of charging and discharging, a-Li-Si undergoes substantive inelastic deformation and exhibits microcracking. The mechanical response to repeated lithiation-delithiation eventually results in the loss of electrical contact and consequent decrease of capacity, thus underscoring the importance of studying the plasticity of a-Li-Si nanostructures. In recent years, a variety of phenomenological continuum theories have been introduced that purport to model plasticity and the electro-chemo-mechanical behavior of a-Li-Si. Unfortunately, the micromechanisms and atomistic considerations underlying plasticity in Li-Si material are not yet fully understood and this impedes the development of physics-based constitutive models. Conventional molecular dynamics, although extensively used to study this material, is grossly inadequate to resolve this matter. As is well known, conventional molecular dynamics simulations can only address phenomena with characteristic time scales of (at most) a microsecond. Accordingly, in such simulations, the mechanical behavior is deduced under conditions of very high strain rates (usually, 108s-1 or even higher). This limitation severely impacts a realistic assessment of rate-dependent effects. In this work, we attempt to circumvent the time-scale bottleneck of conventional molecular dynamics and provide novel insights into the mechanisms underpinning plastic deformation of Li-Si nanostructures. We utilize an approach that allows imposition of slow strain rates and involves the employment of a new and recently developed potential energy surface sampling method—the so-called autonomous basin climbing—to identify the local minima in the potential energy surface. Combined with other techniques, such as nudged elastic band, kinetic Monte Carlo and transition state theory, we assess

Atomistic Simulation of Intrinsic Defects and Trivalent and Tetravalent Ion Doping in Hydroxyapatite

Directory of Open Access Journals (Sweden)

Ricardo D. S. Santos

2014-01-01

Full Text Available Atomistic simulation techniques have been employed in order to investigate key issues related to intrinsic defects and a variety of dopants from trivalent and tetravalent ions. The most favorable intrinsic defect is determined to be a scheme involving calcium and hydroxyl vacancies. It is found that trivalent ions have an energetic preference for the Ca site, while tetravalent ions can enter P sites. Charge compensation is predicted to occur basically via three schemes. In general, the charge compensation via the formation of calcium vacancies is more favorable. Trivalent dopant ions are more stable than tetravalent dopants.

Computer code for the atomistic simulation of lattice defects and dynamics

International Nuclear Information System (INIS)

Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

1980-04-01

This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability

Insight in schizophrenia: a review.

Science.gov (United States)

Dam, Jesper

2006-01-01

The issue of insight in schizophrenia must be assumed to be one of the most important aspects of the clinical examination. Comprehensive studies have shown that between 50% and 80% of all patients suffering from schizophrenia do not believe that they have a disorder. In recent years, poor insight in schizophrenia has been the subject of increasing interest, as manifested in a number of studies discussed in the present review. Some of these studies focus on insight correlated to various parameters such as psychopathology, neuropsychology, clinical relevance and compliance. Other studies refer to more theoretical implications, among these the issue of defining the concept of insight: whether insight can be seen as a "primary" phenomenon in schizophrenia, and whether insight may be graduated, dimensioned or increased. Several authors have developed rating scales in an attempt to obtain a measure for the degree or dimension of insight. Here, the range of parameters employed gives an excellent impression of the complexity of the concept of insight. In the concluding discussion, a phenomenological aspect is brought in, in an attempt to place the concept of insight in relation to disturbances of the self in schizophrenia and to primary symptoms in schizophrenia, amongst these autism.

Critical assessment of Pt surface energy - An atomistic study

Science.gov (United States)

Kim, Jin-Soo; Seol, Donghyuk; Lee, Byeong-Joo

2018-04-01

Despite the fact that surface energy is a fundamental quantity in understanding surface structure of nanoparticle, the results of experimental measurements and theoretical calculations for the surface energy of pure Pt show a wide range of scattering. It is necessary to further ensure the surface energy of Pt to find the equilibrium shape and atomic configuration in Pt bimetallic nanoparticles accurately. In this article, we critically assess and optimize the Pt surface energy using a semi-empirical atomistic approach based on the second nearest-neighbor modified embedded-atom method interatomic potential. That is, the interatomic potential of pure Pt was adjusted in a way that the surface segregation tendency in a wide range of Pt binary alloys is reproduced in accordance with experimental information. The final optimized Pt surface energy (mJ/m2) is 2036 for (100) surface, 2106 for (110) surface, and 1502 for (111) surface. The potential can be utilized to find the equilibrium shape and atomic configuration of Pt bimetallic nanoparticles more accurately.

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

Science.gov (United States)

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.

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

Directory of Open Access Journals (Sweden)

Zhiwei Zhang

2018-05-01

Full Text Available 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.

Mining Login Data for Actionable Student Insight

Science.gov (United States)

Agnihotri, Lalitha; Aghababyan, Ani; Mojarad, Shirin; Riedesel, Mark; Essa, Alfred

2015-01-01

Student login data is a key resource for gaining insight into their learning experience. However, the scale and the complexity of this data necessitate a thorough exploration to identify potential actionable insights, thus rendering it less valuable compared to student achievement data. To compensate for the underestimation of login data…

Microscopic insight into thermodynamics of conformational changes of SAP-SLAM complex in signal transduction cascade

Science.gov (United States)

Samanta, Sudipta; Mukherjee, Sanchita

2017-04-01

The signalling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, associate with SLAM-associated protein (SAP)-related molecules, composed of single SH2 domain architecture. SAP activates Src-family kinase Fyn after SLAM ligation, resulting in a SLAM-SAP-Fyn complex, where, SAP binds the Fyn SH3 domain that does not involve canonical SH3 or SH2 interactions. This demands insight into this SAP mediated signalling cascade. Thermodynamics of the conformational changes are extracted from the histograms of dihedral angles obtained from the all-atom molecular dynamics simulations of this structurally well characterized SAP-SLAM complex. The results incorporate the binding induced thermodynamic changes of individual amino acid as well as the secondary structural elements of the protein and the solvent. Stabilization of the peptide partially comes through a strong hydrogen bonding network with the protein, while hydrophobic interactions also play a significant role where the peptide inserts itself into a hydrophobic cavity of the protein. SLAM binding widens SAP's second binding site for Fyn, which is the next step in the signal transduction cascade. The higher stabilization and less fluctuation of specific residues of SAP in the Fyn binding site, induced by SAP-SLAM complexation, emerge as the key structural elements to trigger the recognition of SAP by the SH3 domain of Fyn. The thermodynamic quantification of the protein due to complexation not only throws deeper understanding in the established mode of SAP-SLAM interaction but also assists in the recognition of the relevant residues of the protein responsible for alterations in its activity.

Atomistic tight-binding theory of excitonic splitting energies in CdX(X = Se, S and Te)/ZnS core/shell nanocrystals

Science.gov (United States)

Sukkabot, Worasak; Pinsook, Udomsilp

2017-01-01

Using the atomistic tight-binding theory (TB) and a configuration interaction description (CI), we numerically compute the excitonic splitting of CdX(X = Se, S and Te)/ZnS core/shell nanocrystals with the objective to explain how types of the core materials and growth shell thickness can provide the detailed manipulation of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting, beneficial for the active application of quantum information. To analyze the splitting of the excitonic states, the optical band gaps, ground-state wave function overlaps and atomistic electron-hole interactions tend to be numerically demonstrated. Based on the atomistic computations, the single-particle and excitonic gaps are mainly reduced with the increasing ZnS shell thickness owing to the quantum confinement. In the range of the higher to lower energies, the order of the single-particle gaps is CdSe/ZnS, CdS/ZnS and CdTe/ZnS core/shell nanocrystals, while one of the excitonic gaps is CdS/ZnS, CdSe/ZnS and CdTe/ZnS core/shell nanocrystals because of the atomistic electron-hole interaction. The strongest electron-hole interactions are mainly observed in CdSe/ZnS core/shell nanocrystals. In addition, the computational results underline that the energies of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting are generally reduced with the increasing ZnS growth shell thickness as described by the trend of the electron-hole exchange interaction. The high-to-low splitting of the excitonic states is demonstrated in CdSe/ZnS, CdTe/ZnS and CdS/ZnS core/shell nanocrystals because of the fashion in the electron-hole exchange interaction and overlaps of the electron-hole wave functions. As the resulting calculations, it is expected that CdS/ZnS core/shell nanocrystals are the best candidates to be the source of entangled photons. Finally, the comprehensive information on the excitonic splitting can enable the use of suitable core

Permutation invariant potential energy surfaces for polyatomic reactions using atomistic neural networks

International Nuclear Information System (INIS)

Kolb, Brian; Zhao, Bin; Guo, Hua; Li, Jun; Jiang, Bin

2016-01-01

The applicability and accuracy of the Behler-Parrinello atomistic neural network method for fitting reactive potential energy surfaces is critically examined in three systems, H + H 2 → H 2 + H, H + H 2 O → H 2 + OH, and H + CH 4 → H 2 + CH 3 . A pragmatic Monte Carlo method is proposed to make efficient choice of the atom-centered mapping functions. The accuracy of the potential energy surfaces is not only tested by fitting errors but also validated by direct comparison in dynamically important regions and by quantum scattering calculations. Our results suggest this method is both accurate and efficient in representing multidimensional potential energy surfaces even when dissociation continua are involved.

Atomistic Simulation of Initiation in Hexanitrostilbene

Science.gov (United States)

Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

2015-06-01

We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Effect of preparation processes and structural insight into the supermolecular system: Bisacodyl and β-cyclodextrin inclusion complex

International Nuclear Information System (INIS)

Li, Shanshan; Zhai, Yuanming; Yan, Jin; Wang, Lili; Xu, Kailin; Li, Hui

2016-01-01

In this study, β-cyclodextrin (β-CD) and bisacodyl were chosen as model host and guest molecule to explore the effect of preparation processes on the physicochemical properties of inclusion complexes (ICs) and to gain an insight into the structure of ICs. The influence of temperature and pH on complexation was studied by multiple temperature–pH phase solubility analysis. The most favorable conformation was predicted by molecular modeling using AutoDock. "1H nuclear magnetic resonance and rotating frame nuclear Overhauser effect spectroscopy further confirmed the structure. Moreover, bisacodyl·β-CD ICs in solid state were successfully prepared via three different procedures (co-crystallization, co-evaporation, and co-grinding) and fully characterized by several solid-state techniques, namely, Fourier transform infrared spectroscopy, X-ray powder diffraction, thermogravimetric analysis, differential scanning calorimetry, solid-state NMR spectroscopy, and scanning electron microscopy. It was found that acid solution and low temperature were unfavorable for formation of bisacodyl·β-CD. The pyridine moiety was suggested to be enclosed in the hydrophobic cavity of β-CD. The complexes prepared using co-crystallization showed properties similar to those prepared using co-evaporation. Moreover, ICs obtained by co-evaporation and co-grinding had higher loading efficiency, water solubility, and dissolution rate than ICs obtained by co-crystallization. - Highlights: • The structure of inclusion complex-bisacodyl·β-CD was determined. • Thermodynamic behaviors of complexation under different conditions were discussed. • Products from three different preparation methods were systemically compared. • Co-crystallization and co-evaporation produced similar complexes. • Co-evaporation and co-grinding had better effects than co-crystallization.

Effect of preparation processes and structural insight into the supermolecular system: Bisacodyl and β-cyclodextrin inclusion complex

Energy Technology Data Exchange (ETDEWEB)

Li, Shanshan [College of Chemical Engineering, Sichuan University, Chengdu 610065 (China); Zhai, Yuanming [Analytical and Testing Center, Sichuan University, Chengdu 610064 (China); Yan, Jin; Wang, Lili; Xu, Kailin [College of Chemical Engineering, Sichuan University, Chengdu 610065 (China); Li, Hui, E-mail: lihuilab@sina.com [College of Chemical Engineering, Sichuan University, Chengdu 610065 (China)

2016-01-01

In this study, β-cyclodextrin (β-CD) and bisacodyl were chosen as model host and guest molecule to explore the effect of preparation processes on the physicochemical properties of inclusion complexes (ICs) and to gain an insight into the structure of ICs. The influence of temperature and pH on complexation was studied by multiple temperature–pH phase solubility analysis. The most favorable conformation was predicted by molecular modeling using AutoDock. {sup 1}H nuclear magnetic resonance and rotating frame nuclear Overhauser effect spectroscopy further confirmed the structure. Moreover, bisacodyl·β-CD ICs in solid state were successfully prepared via three different procedures (co-crystallization, co-evaporation, and co-grinding) and fully characterized by several solid-state techniques, namely, Fourier transform infrared spectroscopy, X-ray powder diffraction, thermogravimetric analysis, differential scanning calorimetry, solid-state NMR spectroscopy, and scanning electron microscopy. It was found that acid solution and low temperature were unfavorable for formation of bisacodyl·β-CD. The pyridine moiety was suggested to be enclosed in the hydrophobic cavity of β-CD. The complexes prepared using co-crystallization showed properties similar to those prepared using co-evaporation. Moreover, ICs obtained by co-evaporation and co-grinding had higher loading efficiency, water solubility, and dissolution rate than ICs obtained by co-crystallization. - Highlights: • The structure of inclusion complex-bisacodyl·β-CD was determined. • Thermodynamic behaviors of complexation under different conditions were discussed. • Products from three different preparation methods were systemically compared. • Co-crystallization and co-evaporation produced similar complexes. • Co-evaporation and co-grinding had better effects than co-crystallization.

Atomistic mechanism of graphene growth on a SiC substrate: Large-scale molecular dynamics simulations based on a new charge-transfer bond-order type potential

Science.gov (United States)

Takamoto, So; Yamasaki, Takahiro; Nara, Jun; Ohno, Takahisa; Kaneta, Chioko; Hatano, Asuka; Izumi, Satoshi

2018-03-01

Thermal decomposition of silicon carbide is a promising approach for the fabrication of graphene. However, the atomistic growth mechanism of graphene remains unclear. This paper describes the development of a new charge-transfer interatomic potential. Carbon bonds with a wide variety of characteristics can be reproduced by the proposed vectorized bond-order term. A large-scale thermal decomposition simulation enables us to observe the continuous growth process of the multiring carbon structure. The annealing simulation reveals the atomistic process by which the multiring carbon structure is transformed to flat graphene involving only six-membered rings. Also, it is found that the surface atoms of the silicon carbide substrate enhance the homogeneous graphene formation.

Quantum mechanical studies of complex ferroelectric perovskites

Science.gov (United States)

Ramer, Nicholas John

In many electronic device applications, there is a need to interconvert electrical energy and other types of energy. Ferroelectric materials, which possess a voltage-dependent polarization, can enable this energy conversion process. Because of the broad interest in ferroelectric materials for these devices, there is a critical research effort, both experimental and theoretical, to understand these materials and aid in the development of materials with improved properties. This thesis presents detailed quantum mechanical investigations of the behavior of a complex ferroelectric perovskite under applied stress. In particular, we have chosen to study the solid solution PbZr1-xTix O3 (PZT). Since the study of ferroelectricity involves understanding both its structural and electronic signatures in materials, it has necessitated the development of a novel theoretical technique which improves the accuracy of the pseudopotentials used in our density functional theory calculations as well as a new method for constructing three-dimensional atomistic responses to small amounts of external stress. To examine the material's behavior under larger amounts of stress, we have studied the behavior of a composition of PZT lying near a structural phase boundary. On either side of the phase boundary, the material is characterized by a different polarization direction and may easily be switched between phases by applying external stress. In addition to stress-induced phase transitions, most ferroelectric materials also have composition dependent phase boundaries. Since different compositions of PZT would require increased computational effort, we have formulated an improved virtual crystal approach that makes tractable the study of the entire composition range. Using this method, we have been able to show for the first time via first-principles calculations, a composition dependent phase transition in a ferroelectric material. This thesis has accomplished three important goals: new

Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

Science.gov (United States)

Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars

2016-06-16

Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration

Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

International Nuclear Information System (INIS)

Seppä, Jeremias; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Lassila, Antti; Reischl, Bernhard; Raiteri, Paolo; Rohl, Andrew L; Nordlund, Kai

2017-01-01

Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation. (paper)

Mechanistic Insights into Validoxylamine A 7'-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex

Energy Technology Data Exchange (ETDEWEB)

Cavalier, Michael C.; Yim, Young-Sun; Asamizu, Shumpei; Neau, David; Almabruk, Khaled H.; Mahmud, Taifo; Lee, Yong-Hwan [Oregon State U.; (Cornell); (LSU)

2013-09-09

The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7'-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of VldE from Streptomyces hygroscopicus subsp. limoneus was determined in apo form, in complex with GDP, in complex with GDP and validoxylamine A 7'-phosphate, and in complex with GDP and trehalose. The structure of VldE with the catalytic site in both an “open” and “closed” conformation is also described. With these structures, the preferred binding of the guanine moiety by VldE, rather than the uracil moiety as seen in OtsA could be explained. The elucidation of the VldE structure in complex with the entirety of its products provides insight into the internal return mechanism by which catalysis occurs with a net retention of the stereochemical configuration of the donated cyclitol.

An Atomistic View on Human Hemoglobin Carbon Monoxide Migration Processes

Science.gov (United States)

Lucas, M. Fátima; Guallar, Víctor

2012-01-01

A significant amount of work has been devoted to obtaining a detailed atomistic knowledge of the human hemoglobin mechanism. Despite this impressive research, to date, the ligand diffusion processes remain unclear and controversial. Using recently developed computational techniques, PELE, we are capable of addressing the ligand migration processes. First, the methodology was tested on myoglobin's CO migration, and the results were compared with the wealth of theoretical and experimental studies. Then, we explored both hemoglobin tense and relaxed states and identified the differences between the α-and β-subunits. Our results indicate that the proximal site, equivalent to the Xe1 cavity in myoglobin, is never visited. Furthermore, strategically positioned residues alter the diffusion processes within hemoglobin's subunits and suggest that multiple pathways exist, especially diversified in the α-globins. A significant dependency of the ligand dynamics on the tertiary structure is also observed. PMID:22385860

Genomic insights into the Saccharomyces sensu stricto complex.

Science.gov (United States)

Borneman, Anthony R; Pretorius, Isak S

2015-02-01

The Saccharomyces sensu stricto group encompasses species ranging from the industrially ubiquitous yeast Saccharomyces cerevisiae to those that are confined to geographically limited environmental niches. The wealth of genomic data that are now available for the Saccharomyces genus is providing unprecedented insights into the genomic processes that can drive speciation and evolution, both in the natural environment and in response to human-driven selective forces during the historical "domestication" of these yeasts for baking, brewing, and winemaking. Copyright © 2015 by the Genetics Society of America.

Local Genetic Correlation Gives Insights into the Shared Genetic Architecture of Complex Traits.

Science.gov (United States)

Shi, Huwenbo; Mancuso, Nicholas; Spendlove, Sarah; Pasaniuc, Bogdan

2017-11-02

Although genetic correlations between complex traits provide valuable insights into epidemiological and etiological studies, a precise quantification of which genomic regions disproportionately contribute to the genome-wide correlation is currently lacking. Here, we introduce ρ-HESS, a technique to quantify the correlation between pairs of traits due to genetic variation at a small region in the genome. Our approach requires GWAS summary data only and makes no distributional assumption on the causal variant effect sizes while accounting for linkage disequilibrium (LD) and overlapping GWAS samples. We analyzed large-scale GWAS summary data across 36 quantitative traits, and identified 25 genomic regions that contribute significantly to the genetic correlation among these traits. Notably, we find 6 genomic regions that contribute to the genetic correlation of 10 pairs of traits that show negligible genome-wide correlation, further showcasing the power of local genetic correlation analyses. Finally, we report the distribution of local genetic correlations across the genome for 55 pairs of traits that show putative causal relationships. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Comparative simulations of microjetting using atomistic and continuous approaches in the presence of viscosity and surface tension

Science.gov (United States)

Durand, O.; Jaouen, S.; Soulard, L.; Heuzé, O.; Colombet, L.

2017-10-01

We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations with systems containing up to 700 × 106 atoms. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and the equation of state is calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with very good agreement the profiles, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes also exhibit a similar fragmentation phenomenology of the metallic liquid sheets ejected, although the fragmentation seed is different. We show in particular, that it depends on the mesh size in the continuous approach.

Atomistic theory of excitonic fine structure in InAs/InP nanowire quantum dot molecules

Science.gov (United States)

Świderski, M.; Zieliński, M.

2017-03-01

Nanowire quantum dots have peculiar electronic and optical properties. In this work we use atomistic tight binding to study excitonic spectra of artificial molecules formed by a double nanowire quantum dot. We demonstrate a key role of atomistic symmetry and nanowire substrate orientation rather than cylindrical shape symmetry of a nanowire and a molecule. In particular for [001 ] nanowire orientation we observe a nonvanishing bright exciton splitting for a quasimolecule formed by two cylindrical quantum dots of different heights. This effect is due to interdot coupling that effectively reduces the overall symmetry, whereas single uncoupled [001 ] quantum dots have zero fine structure splitting. We found that the same double quantum dot system grown on [111 ] nanowire reveals no excitonic fine structure for all considered quantum dot distances and individual quantum dot heights. Further we demonstrate a pronounced, by several orders of magnitude, increase of the dark exciton optical activity in a quantum dot molecule as compared to a single quantum dot. For [111 ] systems we also show spontaneous localization of single particle states in one of nominally identical quantum dots forming a molecule, which is mediated by strain and origins from the lack of the vertical inversion symmetry in [111 ] nanostructures of overall C3 v symmetry. Finally, we study lowering of symmetry due to alloy randomness that triggers nonzero excitonic fine structure and the dark exciton optical activity in realistic nanowire quantum dot molecules of intermixed composition.

Protocols for atomistic modeling of water uptake into zeolite crystals for thermal storage and other applications

International Nuclear Information System (INIS)

Fasano, Matteo; Borri, Daniele; Chiavazzo, Eliodoro; Asinari, Pietro

2016-01-01

Highlights: • Numerical protocols for modeling water adsorption and infiltration into zeolite. • A priori screening of new materials for heat storage and desalination is possible. • Water uptake isotherms for bridging atomistic and engineering scales. - Abstract: We report numerical protocols for describing the water uptake process into microporous materials, with special emphasis on zeolite crystals. A better understanding and more predictive tools of the latter process are critical for a number of modern engineering applications, ranging from the optimization of loss free and compact thermal storage plants up to more efficient separation processes. Water sorption (and desorption) is indeed the key physical phenomenon to consider when designing several heat storage cycles, whereas water infiltration is to be studied when concerned with sieving through microporous materials for manufacturing selective membranes (e.g. water desalination by reverse osmosis). Despite the two quite different applications above, in this article we make an effort for illustrating a comprehensive numerical framework for predicting the engineering performances of microporous materials, based on detailed atomistic models. Thanks to the nowadays spectacular progresses in synthesizing an ever increasing number of new materials with desired properties such as zeolite with various concentrations of hydrophilic defects, we believe that the reported tools can possibly guide engineers in choosing and optimizing innovative materials for (thermal) engineering applications in the near future.

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

Energy Technology Data Exchange (ETDEWEB)

Chu, Manh-Hung; Tian, Liang; Chaker, Ahmad; Skopin, Evgenii; Cantelli, Valentina; Ouled, Toufik; Boichot, Raphaël; Crisci, Alexandre; Lay, Sabine; Richard, Marie-Ingrid; Thomas, Olivier; Deschanvres, Jean-Luc; Renevier, Hubert; Fong, Dillon; Ciatto, Gianluca

2017-03-20

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 and 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.

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

Science.gov (United States)

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 modeling of dropwise condensation

Energy Technology Data Exchange (ETDEWEB)

Sikarwar, B. S., E-mail: bssikarwar@amity.edu; Singh, P. L. [Department of Mechanical Engineering, Amity University Uttar Pradesh, Noida (India); Muralidhar, K.; Khandekar, S. [Department of Mechanical Engineering, IIT Kanpur (India)

2016-05-23

The basic aim of the atomistic modeling of condensation of water is to determine the size of the stable cluster and connect phenomena occurring at atomic scale to the macroscale. In this paper, a population balance model is described in terms of the rate equations to obtain the number density distribution of the resulting clusters. The residence time is taken to be large enough so that sufficient time is available for all the adatoms existing in vapor-phase to loose their latent heat and get condensed. The simulation assumes clusters of a given size to be formed from clusters of smaller sizes, but not by the disintegration of the larger clusters. The largest stable cluster size in the number density distribution is taken to be representative of the minimum drop radius formed in a dropwise condensation process. A numerical confirmation of this result against predictions based on a thermodynamic model has been obtained. Results show that the number density distribution is sensitive to the surface diffusion coefficient and the rate of vapor flux impinging on the substrate. The minimum drop radius increases with the diffusion coefficient and the impinging vapor flux; however, the dependence is weak. The minimum drop radius predicted from thermodynamic considerations matches the prediction of the cluster model, though the former does not take into account the effect of the surface properties on the nucleation phenomena. For a chemically passive surface, the diffusion coefficient and the residence time are dependent on the surface texture via the coefficient of friction. Thus, physical texturing provides a means of changing, within limits, the minimum drop radius. The study reveals that surface texturing at the scale of the minimum drop radius does not provide controllability of the macro-scale dropwise condensation at large timescales when a dynamic steady-state is reached.

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

Science.gov (United States)

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

Permutation invariant potential energy surfaces for polyatomic reactions using atomistic neural networks

Energy Technology Data Exchange (ETDEWEB)

Kolb, Brian [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Zhao, Bin; Guo, Hua, E-mail: hguo@unm.edu [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Li, Jun [School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331 (China); Jiang, Bin [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

2016-06-14

The applicability and accuracy of the Behler-Parrinello atomistic neural network method for fitting reactive potential energy surfaces is critically examined in three systems, H + H{sub 2} → H{sub 2} + H, H + H{sub 2}O → H{sub 2} + OH, and H + CH{sub 4} → H{sub 2} + CH{sub 3}. A pragmatic Monte Carlo method is proposed to make efficient choice of the atom-centered mapping functions. The accuracy of the potential energy surfaces is not only tested by fitting errors but also validated by direct comparison in dynamically important regions and by quantum scattering calculations. Our results suggest this method is both accurate and efficient in representing multidimensional potential energy surfaces even when dissociation continua are involved.

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-08-15

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

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

Science.gov (United States)

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

2015-08-01

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

Thermodynamics of grain boundary premelting in alloys. II. Atomistic simulation

International Nuclear Information System (INIS)

Williams, P.L.; Mishin, Y.

2009-01-01

We apply the semi-grand-canonical Monte Carlo method with an embedded-atom potential to study grain boundary (GB) premelting in Cu-rich Cu-Ag alloys. The Σ5 GB chosen for this study becomes increasingly disordered near the solidus line while its local chemical composition approaches the liquidus composition at the same temperature. This behavior indicates the formation of a thin layer of the liquid phase in the GB when the grain composition approaches the solidus. The thickness of the liquid layer remains finite and the GB can be overheated/oversaturated to metastable states slightly above the solidus. The premelting behavior found by the simulations is qualitatively consistent with the phase-field model of the same binary system presented in Part I of this work [Mishin Y, Boettinger WJ, Warren JA, McFadden GB. Acta Mater, in press]. Although this agreement is encouraging, we discuss several problems arising when atomistic simulations are compared with phase-field modeling.

Atomistic simulation of MgO nanowires subject to electromagnetic wave

International Nuclear Information System (INIS)

Wang, Xianqiao; Lee, James D

2010-01-01

This work is concerned with the application of atomistic field theory (AFT) in modeling and simulation of polarizable materials under an electromagnetic (EM) field. AFT enables us to express an atomic scale local property of a multi-element crystalline (which has more than one kind of atom in the unit cell) system in terms of the distortions of lattice cells and the rearrangement of atoms within the lattice cell, thereby making AFT suitable to fully reproduce both acoustic and optical branches in phonon dispersion relations. Due to the applied EM field, the inhomogeneous motions of discrete atoms in the polarizable crystal give rise to the rearrangement of microstructure and polarization. The AFT and its corresponding finite element implementation are briefly introduced. Single-crystal MgO nanowires under an EM field is modeled and simulated. The numerical results have demonstrated that AFT can serve as a tool to analyze the electromagnetic phenomena of multi-element crystal materials at micro/nano-level within a field framework

Ash'arite's atomistic conception of the physical world: A restatement

International Nuclear Information System (INIS)

Pozi, Firdaus; Othman, Mohd Yusof; Mohamed, Faizal

2013-01-01

Atomism plays an important role in the history of human thought. It can be traced back from Democritus atomos in the 500 BC to particle physics and quantum theory in the 21 st century. However, as it being rejected and developed in the course of history of science, it still brings the fundamental question that perplexes physicists. It gives the views that the world is eternal; that the laws of nature is immutable and eternal therefore all phenomena can be determined through the laws and that there is no reality behind the quantum world. In this paper, we shall briefly describe all these three views on the nature of the physical world or universe and this include on the nature of matter. Then, we shall explain our stand on those conceptions based on the Ash'arites atomistic conception of the physical world. We hope this paper can shed a light on several fundamental issues in the conception of the universe and gives the proper response to them

Modelling of radiation induced segregation in austenitic Fe alloys at the atomistic level

International Nuclear Information System (INIS)

Piochaud, Jean-Baptiste

2013-01-01

In pressurized water reactors, under irradiation internal structures are subject of irradiation assisted stress corrosion cracking which is influenced by radiation induced segregation (RIS). In this work RIS of 316 stainless steels is modelled considering a model ternary Fe-10Ni-20Cr alloy. For this purpose we have built an Fe-Ni-Cr pair interaction model to simulate RIS at the atomistic level using an atomistic kinetic Monte Carlo approach. The pair interactions have been deduced from density functional theory (DFT) data available in the pure fcc systems but also from DFT calculations we have performed in the Fe-10Ni-20Cr target alloy. Point defect formation energies were calculated and found to depend strongly on the local environment of the defect. As a consequence, a rather good estimation of these energies can be obtained from the knowledge of the number and respective positions of the Ni and Cr atoms in the vicinity of the defect. This work shows that a model based only on interaction parameters between elements positioned in perfect lattice sites (solute atoms and vacancy) cannot capture alone both the thermodynamic and the kinetic aspect of RIS. A more accurate of estimating the barriers encountered by the diffusing species is required than the one used in our model, which has to depend on the saddle point environment. This study therefore shows thus the need to estimate point defect migration energies using the DFT approach to calibrate a model that can be used in the framework of atomic kinetic Monte Carlo simulations. We also found that the reproduction by our pair interaction model of DFT data for the self-interstitial atoms was found to be incompatible with the modelling of RIS under electron irradiation. (author)

Tilts, dopants, vacancies and non-stoichiometry: Understanding and designing the properties of complex solid oxide perovskites from first principles

Science.gov (United States)

Bennett, Joseph W.

Perovskite oxides of formula ABO3 have a wide range of structural, electrical and mechanical properties, making them vital materials for many applications, such as catalysis, ultrasound machines and communication devices. Perovskite solid solutions with high piezoelectric response, such as ferroelectrics, are of particular interest as they can be employed as sensors in SONAR devices. Ferroelectric materials are unique in that their chemical and electrical properties can be non-invasively and reversibly changed, by switching the bulk polarization. This makes ferroelectrics useful for applications in non-volatile random access memory (NVRAM) devices. Perovskite solid solutions with a lower piezoelectric response than ferroelectrics are important for communication technology, as they function well as electroceramic capacitors. Also of interest is how these materials act as a component in a solid oxide fuel cell, as they can function as an efficient source of energy. Altering the chemical composition of these solid oxide materials offers an opportunity to change the desired properties of the final ceramic, adding a degree of flexibility that is advantageous for a variety of applications. These solid oxides are complex, sometimes disordered systems that are a challenge to study experimentally. However, as it is their complexity which produces favorable properties, highly accurate modeling which captures the essential features of the disordered structure is necessary to explain the behavior of current materials and predict favorable compositions for new materials. Methodological improvements and faster computer speeds have made first-principles and atomistic calculations a viable tool for understanding these complex systems. Offering a combination of accuracy and computational speed, the density functional theory (DFT) approach can reveal details about the microscopic structure and interactions of complex systems. Using DFT and a combination of principles from both

Sodium montmorillonite/amine-containing drugs complexes: new insights on intercalated drugs arrangement into layered carrier material.

Directory of Open Access Journals (Sweden)

Murilo L Bello

Full Text Available Layered drug delivery carriers are current targets of nanotechnology studies since they are able to accommodate pharmacologically active substances and are effective at modulating drug release. Sodium montmorillonite (Na-MMT is a clay that has suitable properties for developing new pharmaceutical materials due to its high degree of surface area and high capacity for cation exchange. Therefore Na-MMT is a versatile material for the preparation of new drug delivery systems, especially for slow release of protonable drugs. Herein, we describe the intercalation of several amine-containing drugs with Na-MMT so we can derive a better understanding of how these drugs molecules interact with and distribute throughout the Na-MMT interlayer space. Therefore, for this purpose nine sodium montmorillonite/amine-containing drugs complexes (Na-MMT/drug were prepared and characterized. In addition, the physicochemical properties of the drugs molecules in combination with different experimental conditions were assessed to determine how these factors influenced experimental outcomes (e.g. increase of the interlayer spacing versus drugs arrangement and orientation. We also performed a molecular modeling study of these amine-containing drugs associated with different Na-MMT/drug complex models to analyze the orientation and arrangement of the drugs molecules in the complexes studied. Six amine-containing drugs (rivastigmine, doxazosin, 5-fluorouracil, chlorhexidine, dapsone, nystatin were found to successfully intercalate Na-MMT. These findings provide important insights on the interlayer aspect of the molecular systems formed and may contribute to produce more efficient drug delivery nanosystems.

Phonon dispersion and thermal conductivity of nanocrystal superlattices using three-dimensional atomistic models

International Nuclear Information System (INIS)

Zanjani, Mehdi B.; Lukes, Jennifer R.

2014-01-01

A computational study of thermal conductivity and phonon dispersion of gold nanocrystal superlattices is presented. Phonon dispersion curves, reported here for the first time from combined molecular dynamics and lattice dynamics calculations, show multiple phononic band gaps and consist of many more dispersion branches than simple atomic crystals. Fully atomistic three dimensional molecular dynamics calculations of thermal conductivity using the Green Kubo method are also performed for the first time on these materials. Thermal conductivity is observed to increase for increasing nanocrystal core size and decrease for increasing surface ligand density. Our calculations predict values in the range 0.1–1 W/m K that are consistent with reported experimental results

Managing Complex Dynamical Systems

Science.gov (United States)

Cox, John C.; Webster, Robert L.; Curry, Jeanie A.; Hammond, Kevin L.

2011-01-01

Management commonly engages in a variety of research designed to provide insight into the motivation and relationships of individuals, departments, organizations, etc. This paper demonstrates how the application of concepts associated with the analysis of complex systems applied to such data sets can yield enhanced insights for managerial action.

Irradiation-induced void evolution in iron: A phase-field approach with atomistic derived parameters

International Nuclear Information System (INIS)

Wang Yuan-Yuan; Ding Jian-Hua; Huang Shao-Song; Zhao Ji-Jun; Liu Wen-Bo; Ke Xiao-Qin; Wang Yun-Zhi; Zhang Chi

2017-01-01

A series of material parameters are derived from atomistic simulations and implemented into a phase field (PF) model to simulate void evolution in body-centered cubic (bcc) iron subjected to different irradiation doses at different temperatures. The simulation results show good agreement with experimental observations — the porosity as a function of temperature varies in a bell-shaped manner and the void density monotonically decreases with increasing temperatures; both porosity and void density increase with increasing irradiation dose at the same temperature. Analysis reveals that the evolution of void number and size is determined by the interplay among the production, diffusion and recombination of vacancy and interstitial. (paper)

Atomistic spin dynamics simulations on Mn-doped GaAs and CuMn

Energy Technology Data Exchange (ETDEWEB)

Hellsvik, Johan, E-mail: johan.hellsvik@fysik.uu.s [Department of Physics and Materials Science, Uppsala University, Box 530, SE-751 21 Uppsala (Sweden)

2010-01-01

The magnetic dynamical behavior of two random alloys have been investigated in atomistic spin dynamics (ASD) simulations. For both materials, magnetic exchange parameters calculated with first principles electronic structure methods were used. From experiments it is well known that CuMn is a highly frustrated magnetic system and a good manifestation of a Heisenberg spin glass. In our ASD simulations the behavior of the autocorrelation function indicate spin glass behavior. The diluted magnetic semiconductor (DMS) Mn-doped GaAs is engineered with hopes of high enough Curie temperatures to operate in spintronic devices. Impurities such as As antisites and Mn interstitials change the exhange couplings from being mainly ferromagnetic to also have antiferromagnetic components. We explore how the resulting frustration affects the magnetization dynamics for a varying rate of As antisites.

First insights into circulating Mycobacterium tuberculosis complex lineages and drug resistance in Guinea

Science.gov (United States)

Ejo, Mebrat; Gehre, Florian; Barry, Mamadou Dian; Sow, Oumou; Bah, Nene Mamata; Camara, Mory; Bah, Boubacar; Uwizeye, Cecile; Nduwamahoro, Elie; Fissette, Kristina; Rijk, Pim De; Merle, Corinne; Olliaro, Piero; Burgos, Marcos; Lienhardt, Christian; Rigouts, Leen; de Jong, Bouke C.

2015-01-01

In this study we assessed first-line anti-tuberculosis drug resistance and the genotypic distribution of Mycobacterium tuberculosis complex (MTBC) isolates that had been collected from consecutive new tuberculosis patients enrolled in two clinical trials conducted in Guinea between 2005 and 2010. Among the total 359 MTBC strains that were analyzed in this study, 22.8% were resistant to at least one of the first line anti-tuberculosis drugs, including 2.5% multidrug resistance and 17.5% isoniazid resistance, with or without other drugs. In addition, further characterization of isolates from a subset of the two trials (n = 184) revealed a total of 80 different spoligotype patterns, 29 “orphan” and 51 shared patterns. We identified the six major MTBC lineages of human relevance, with predominance of the Euro-American lineage. In total, 132 (71.7%) of the strains were genotypically clustered, and further analysis (using the DESTUS model) suggesting significantly faster spread of LAM10_CAM family (p = 0.00016). In conclusion, our findings provide a first insight into drug resistance and the population structure of the MTBC in Guinea, with relevance for public health scientists in tuberculosis control programs. PMID:26004194

Scalable and portable visualization of large atomistic datasets

Science.gov (United States)

Sharma, Ashish; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2004-10-01

A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms. Program summaryTitle of program: Atomsviewer Catalogue identifier: ADUM Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUM Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics card Operating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5 Programming languages used: C++, C and OpenGL Memory required to execute with typical data: 1 gigabyte of RAM High speed storage required: 60 gigabytes No. of lines in the distributed program including test data, etc.: 550 241 No. of bytes in the distributed program including test data, etc.: 6 258 245 Number of bits in a word: Arbitrary Number of processors used: 1 Has the code been vectorized or parallelized: No Distribution format: tar gzip file Nature of physical problem: Scientific visualization of atomic systems Method of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data

Atomistic Force Field for Pyridinium-Based Ionic Liquids: Reliable Transport Properties

DEFF Research Database (Denmark)

Voroshylova, I. V.; Chaban, V. V.

2014-01-01

Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)......Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis......(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cationanion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove...... and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia LopesPadua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids....

An atomistic analysis of the interface mobility in a massive transformation

International Nuclear Information System (INIS)

Bos, C.; Sommer, F.; Mittemeijer, E.J.

2005-01-01

A new multi-lattice kinetic Monte Carlo method has been used for an atomistic study on the interpretation of the interface mobility parameter for a massive face-centred cubic (fcc) to body-centred cubic (bcc) transformation in a single element system. For lateral growth of bcc in a system with an fcc(111)//bcc(110) and fcc[112-bar ]//bcc[001-bar ] interface orientation the overall activation energy for the interface mobility parameter is governed by energetically unfavourable atomic jumps. The atoms on the fcc lattice often cannot jump directly to bcc lattice sites because neighbouring atoms block the empty bcc sites. By single unfavourable jumps and by groups of unfavourable jumps a path from fcc to bcc is created. The necessity of these unfavourable jumps leads to an overall activation energy considerably larger than the activation energy barrier for a single atomic jump

Heteroleptic Copper(I) Complexes of "Scorpionate" Bis-pyrazolyl Carboxylate Ligand with Auxiliary Phosphine as Potential Anticancer Agents: An Insight into Cytotoxic Mode.

Science.gov (United States)

Khan, Rais Ahmad; Usman, Mohammad; Dhivya, Rajakumar; Balaji, Perumalsamy; Alsalme, Ali; AlLohedan, Hamad; Arjmand, Farukh; AlFarhan, Khalid; Akbarsha, Mohammad Abdulkader; Marchetti, Fabio; Pettinari, Claudio; Tabassum, Sartaj

2017-03-24

New copper(I) complexes [CuCl(PPh 3 )(L)] (1: L = L A  = 4-carboxyphenyl)bis(3,5-dimethylpyrazolyl)methane; (2: L = L B  = 3-carboxyphenyl)bis(3,5-dimethylpyrazolyl)methane) were prepared and characterised by elemental analysis and various spectroscopic techniques such as FT-IR, NMR, UV-Vis, and ESI-MS. The molecular structures of complexes 1 and 2 were analyzed by theoretical B3LYP/DFT method. Furthermore, in vitro DNA binding studies were carried out to check the ability of complexes 1 and 2 to interact with native calf thymus DNA (CT-DNA) using absorption titration, fluorescence quenching and circular dichroism, which is indicative of more avid binding of the complex 1. Moreover, DNA mobility assay was also conducted to study the concentration-dependent cleavage pattern of pBR322 DNA by complex 1, and the role of ROS species to have a mechanistic insight on the cleavage pattern, which ascertained substantial roles by both hydrolytic and oxidative pathways. Additionally, we analyzed the potential of the interaction of complex 1 with DNA and enzyme (Topo I and II) with the aid of molecular modeling. Furthermore, cytotoxic activity of complex 1 was tested against HepG2 cancer cell lines. Thus, the potential of the complex 1 is promising though further in vivo investigations may be required before subjecting it to clinical trials.

Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code

Energy Technology Data Exchange (ETDEWEB)

Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

1980-04-01

This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability.

Adsorption studies of alcohol molecules on monolayer MoS_2 nanosheet—A first-principles insights

International Nuclear Information System (INIS)

Nagarajan, V.; Chandiramouli, R.

2017-01-01

Highlights: • The adsorption of methanol, ethanol & 1-propanol on MoS_2 nanosheet are studied. • The PDOS & band structure confirms adsorption of alcohol vapors on MoS_2 nanosheet. • The adsorption of 1-propanol vapor on MoS_2 nanosheet is more favorable. • The alcohol molecules adsorption on MoS_2 nanosheet is explored in atomistic level. - Abstract: The electronic and adsorption properties of three different alcohol molecules namely methanol, ethanol and 1-propanol vapors on MoS_2 nanosheet is investigated using DFT method. The structural stability of MoS_2 nanosheet is ascertained with formation energy. The adsorption properties of alcohol molecules on MoS_2 base material is discussed in terms of average energy gap variation, Mulliken charge transfer, energy band gap and adsorption energy. The prominent adsorption sites of methanol, ethanol and 1-propanol vapors on MoS_2 nanosheet are studied in atomistic level. The projected density of states (PDOS) spectrum gives the clear insights on the electronic properties of MoS_2 nanosheet. The PDOS and energy band structure confirmed the adsorption of alcohol vapors on MoS_2 nanosheet. The variation in the band structure and PDOS is noticed upon adsorption of methanol, ethanol and 1-propanol molecules on MoS_2 nanosheet. The PDOS spectrum also reveals the variation in peak maxima owing to transfer of electron between alcohol molecules and MoS_2 base material. The adsorption of 1-propanol vapor on MoS_2 nanosheet is observed to be more favorable than other alcohol molecules. The findings confirm that monolayer MoS_2 nanosheet can be used to detect the presence of alcohol vapors in the environment.

Atomistic minimal model for estimating profile of electrodeposited nanopatterns

Science.gov (United States)

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.

Atomistic Tight-Binding Theory of Electron-Hole Exchange Interaction in Morphological Evolution of CdSe/ZnS Core/Shell Nanodisk to CdSe/ZnS Core/Shell Nanorod

Directory of Open Access Journals (Sweden)

Worasak Sukkabot

2016-01-01

Full Text Available Based on the atomistic tight-binding theory (TB and a configuration interaction (CI description, the electron-hole exchange interaction in the morphological transformation of CdSe/ZnS core/shell nanodisk to CdSe/ZnS core/shell nanorod is described with the aim of understanding the impact of the structural shapes on the change of the electron-hole exchange interaction. Normally, the ground hole states confined in typical CdSe/ZnS core/shell nanocrystals are of heavy hole-like character. However, the atomistic tight-binding theory shows that a transition of the ground hole states from heavy hole-like to light hole-like contribution with the increasing aspect ratios of the CdSe/ZnS core/shell nanostructures is recognized. According to the change in the ground-state hole characters, the electron-hole exchange interaction is also significantly altered. To do so, optical band gaps, ground-state electron character, ground-state hole character, oscillation strengths, ground-state coulomb energies, ground-state exchange energies, and dark-bright (DB excitonic splitting (stoke shift are numerically demonstrated. These atomistic computations obviously show the sensitivity with the aspect ratios. Finally, the alteration in the hole character has a prominent effect on dark-bright (DB excitonic splitting.

Novel insights in agent-based complex automated negotiation

CERN Document Server

Lopez-Carmona, Miguel; Ito, Takayuki; Zhang, Minjie; Bai, Quan; Fujita, Katsuhide

2014-01-01

This book focuses on all aspects of complex automated negotiations, which are studied in the field of autonomous agents and multi-agent systems. This book consists of two parts. I: Agent-Based Complex Automated Negotiations, and II: Automated Negotiation Agents Competition. The chapters in Part I are extended versions of papers presented at the 2012 international workshop on Agent-Based Complex Automated Negotiation (ACAN), after peer reviews by three Program Committee members. Part II examines in detail ANAC 2012 (The Third Automated Negotiating Agents Competition), in which automated agents that have different negotiation strategies and are implemented by different developers are automatically negotiated in the several negotiation domains. ANAC is an international competition in which automated negotiation strategies, submitted by a number of universities and research institutes across the world, are evaluated in tournament style. The purpose of the competition is to steer the research in the area of bilate...

Natural sciences in the focus IV. Foundations of atomistics, quantum mechanics, and chemistry; Naturwissenschaften im Fokus IV. Grundlagen der Atomistik, Quantenmechanik und Chemie

Energy Technology Data Exchange (ETDEWEB)

Petersen, Christian

2017-07-01

The following topics are dealt with: The electronic structure of the atom, the structure of the atomic nucleus together with radioactive decays, fission, and fusion, the elementary particles together with the standard model, the atomistic foundations of chemistrytogether with the binding types, and inorganic and organic chemistry. (HSI)

Compression deformation of WC: atomistic description of hard ceramic material

Science.gov (United States)

Feng, Qing; Song, Xiaoyan; Liu, Xuemei; Liang, Shuhua; Wang, Haibin; Nie, Zuoren

2017-11-01

The deformation characteristics of WC, as a typical hard ceramic material, were studied on the nanoscale using atomistic simulations for both the single-crystal and polycrystalline forms under uniaxial compression. In particular, the effects of crystallographic orientation, grain boundary coordination and grain size on the origin of deformation were investigated. The deformation behavior of the single-crystal and polycrystalline WC both depend strongly on the orientation towards the loading direction. The grain boundaries play a significant role in the deformation coordination and the potential high fracture toughness of the nanocrystalline WC. In contrast to conventional knowledge of ceramics, maximum strength was obtained at a critical grain size corresponding to the turning point from a Hall-Petch to an inverse Hall-Petch relationship. For this the mechanism of the combined effect of dislocation motion within grains and the coordination of stress concentration at the grain boundaries were proposed. The present work has moved forward our understanding of plastic deformability and the possibility of achieving a high strength of nanocrystalline ceramic materials.

Atomistic description of large nanostructures based on III-nitride semiconductors

Energy Technology Data Exchange (ETDEWEB)

Molina-Sanchez, Alejandro; Garcia-Cristobal, Alberto; Cantarero, Andres [Instituto de Ciencia de Materiales de la Universidad de Valencia (Spain); Terentjevs, Aleksandrs; Cicero, Giancarlo [Physics and Materials Science and Chemical Engineering Departments, Politecnico di Torino (Italy)

2010-07-01

Semiconductor nanocolumns exhibiting a growth without dislocations and high crystalline quality are of great interest in nanotechnology applications. Specifically, InN-based nanocolumns are good candidates to develop multi-junction solar cells due to their small gap, 0.67 eV, and the possibility of alloying with other nitrides (as GaN and AlN) to cover the entire solar spectrum. A proper description of optical properties of the nanostructures described above can start with an atomistic treatment of the electronic structure in order to keep the essential geometry and symmetry of the objects. Unfortunately, the best description realized with ab initio electronic structure software is strongly limited by the nanocolumn diameter to a few nanometers. By using a combination of ab initio and empirical tight-binding methods, we can connect the quality of the first principles calculations (performed with the Espresso code), with the versatility of an empirical approach. Once we have an ab initio quality parameter set for the empirical tight-binding code, we can study larger nanostructures with this approach, reducing the computation time in orders of magnitude.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Atomistic computer simulations of FePt nanoparticles. Thermodynamic and kinetic properties

Energy Technology Data Exchange (ETDEWEB)

Mueller, M.

2007-12-20

In the present dissertation, a hierarchical multiscale approach for modeling FePt nanoparticles by atomistic computer simulations is developed. By describing the interatomic interactions on different levels of sophistication, various time and length scales can be accessed. Methods range from static quantum-mechanic total-energy calculations of small periodic systems to simulations of whole particles over an extended time by using simple lattice Hamiltonians. By employing these methods, the energetic and thermodynamic stability of non-crystalline multiply twinned FePt nanoparticles is investigated. Subsequently, the thermodynamics of the order-disorder transition in FePt nanoparticles is analyzed, including the influence of particle size, composition and modified surface energies by different chemical surroundings. In order to identify processes that reduce or enhance the rate of transformation from the disordered to the ordered state, the kinetics of the ordering transition in FePt nanoparticles is finally investigated by assessing the contributions of surface and volume diffusion. (orig.)

3D atomistic studies of fatigue behaviour of edge crack (0 0 1) in bcc iron loaded in mode i and II

Czech Academy of Sciences Publication Activity Database

Machová, Anna; Pokluda, J.; Uhnáková, Alena; Hora, Petr

2014-01-01

Roč. 66, September (2014), s. 11-19 ISSN 0142-1123 R&D Projects: GA ČR(CZ) GAP108/10/0698 Institutional support: RVO:61388998 Keywords : fatigue crack growth * bcc iron * 3D atomistic simulations * molecular dynamics Subject RIV: JQ - Machines ; Tools Impact factor: 2.275, year: 2014 www.elsevier.com/locate/ijfatigue

Adsorption studies of alcohol molecules on monolayer MoS{sub 2} nanosheet—A first-principles insights

Energy Technology Data Exchange (ETDEWEB)

Nagarajan, V.; Chandiramouli, R., E-mail: rcmoulii@gmail.com

2017-08-15

Highlights: • The adsorption of methanol, ethanol & 1-propanol on MoS{sub 2} nanosheet are studied. • The PDOS & band structure confirms adsorption of alcohol vapors on MoS{sub 2} nanosheet. • The adsorption of 1-propanol vapor on MoS{sub 2} nanosheet is more favorable. • The alcohol molecules adsorption on MoS{sub 2} nanosheet is explored in atomistic level. - Abstract: The electronic and adsorption properties of three different alcohol molecules namely methanol, ethanol and 1-propanol vapors on MoS{sub 2} nanosheet is investigated using DFT method. The structural stability of MoS{sub 2} nanosheet is ascertained with formation energy. The adsorption properties of alcohol molecules on MoS{sub 2} base material is discussed in terms of average energy gap variation, Mulliken charge transfer, energy band gap and adsorption energy. The prominent adsorption sites of methanol, ethanol and 1-propanol vapors on MoS{sub 2} nanosheet are studied in atomistic level. The projected density of states (PDOS) spectrum gives the clear insights on the electronic properties of MoS{sub 2} nanosheet. The PDOS and energy band structure confirmed the adsorption of alcohol vapors on MoS{sub 2} nanosheet. The variation in the band structure and PDOS is noticed upon adsorption of methanol, ethanol and 1-propanol molecules on MoS{sub 2} nanosheet. The PDOS spectrum also reveals the variation in peak maxima owing to transfer of electron between alcohol molecules and MoS{sub 2} base material. The adsorption of 1-propanol vapor on MoS{sub 2} nanosheet is observed to be more favorable than other alcohol molecules. The findings confirm that monolayer MoS{sub 2} nanosheet can be used to detect the presence of alcohol vapors in the environment.

Embracing uncertainty, managing complexity: applying complexity thinking principles to transformation efforts in healthcare systems.

Science.gov (United States)

Khan, Sobia; Vandermorris, Ashley; Shepherd, John; Begun, James W; Lanham, Holly Jordan; Uhl-Bien, Mary; Berta, Whitney

2018-03-21

Complexity thinking is increasingly being embraced in healthcare, which is often described as a complex adaptive system (CAS). Applying CAS to healthcare as an explanatory model for understanding the nature of the system, and to stimulate changes and transformations within the system, is valuable. A seminar series on systems and complexity thinking hosted at the University of Toronto in 2016 offered a number of insights on applications of CAS perspectives to healthcare that we explore here. We synthesized topics from this series into a set of six insights on how complexity thinking fosters a deeper understanding of accepted ideas in healthcare, applications of CAS to actors within the system, and paradoxes in applications of complexity thinking that may require further debate: 1) a complexity lens helps us better understand the nebulous term "context"; 2) concepts of CAS may be applied differently when actors are cognizant of the system in which they operate; 3) actor responses to uncertainty within a CAS is a mechanism for emergent and intentional adaptation; 4) acknowledging complexity supports patient-centred intersectional approaches to patient care; 5) complexity perspectives can support ways that leaders manage change (and transformation) in healthcare; and 6) complexity demands different ways of implementing ideas and assessing the system. To enhance our exploration of key insights, we augmented the knowledge gleaned from the series with key articles on complexity in the literature. Ultimately, complexity thinking acknowledges the "messiness" that we seek to control in healthcare and encourages us to embrace it. This means seeing challenges as opportunities for adaptation, stimulating innovative solutions to ensure positive adaptation, leveraging the social system to enable ideas to emerge and spread across the system, and even more important, acknowledging that these adaptive actions are part of system behaviour just as much as periods of stability are. By

Quantum Calculations of Electron Tunneling in Respiratory Complex III.

Science.gov (United States)

Hagras, Muhammad A; Hayashi, Tomoyuki; Stuchebrukhov, Alexei A

2015-11-19

The most detailed and comprehensive to date study of electron transfer reactions in the respiratory complex III of aerobic cells, also known as bc1 complex, is reported. In the framework of the tunneling current theory, electron tunneling rates and atomistic tunneling pathways between different redox centers were investigated for all electron transfer reactions comprising different stages of the proton-motive Q-cycle. The calculations reveal that complex III is a smart nanomachine, which under certain conditions undergoes conformational changes gating electron transfer, or channeling electrons to specific pathways. One-electron tunneling approximation was adopted in the tunneling calculations, which were performed using hybrid Broken-Symmetry (BS) unrestricted DFT/ZINDO levels of theory. The tunneling orbitals were determined using an exact biorthogonalization scheme that uniquely separates pairs of tunneling orbitals with small overlaps out of the remaining Franck-Condon orbitals with significant overlap. Electron transfer rates in different redox pairs show exponential distance dependence, in agreement with the reported experimental data; some reactions involve coupled proton transfer. Proper treatment of a concerted two-electron bifurcated tunneling reaction at the Q(o) site is given.

Modelling and simulation of superalloys. Book of abstracts

Energy Technology Data Exchange (ETDEWEB)

Rogal, Jutta; Hammerschmidt, Thomas; Drautz, Ralf (eds.)

2014-07-01

Superalloys are multi-component materials with complex microstructures that offer unique properties for high-temperature applications. The complexity of the superalloy materials makes it particularly challenging to obtain fundamental insight into their behaviour from the atomic structure to turbine blades. Recent advances in modelling and simulation of superalloys contribute to a better understanding and prediction of materials properties and therefore offer guidance for the development of new alloys. This workshop will give an overview of recent progress in modelling and simulation of materials for superalloys, with a focus on single crystal Ni-base and Co-base alloys. Topics will include electronic structure methods, atomistic simulations, microstructure modelling and modelling of microstructural evolution, solidification and process simulation as well as the modelling of phase stability and thermodynamics.

Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation.

Directory of Open Access Journals (Sweden)

Shane E Gordon

2016-03-01

Full Text Available Dihydrodipicolinate synthase (DHDPS catalyzes the first committed step in the diaminopimelate pathway of bacteria, yielding amino acids required for cell wall and protein biosyntheses. The essentiality of the enzyme to bacteria, coupled with its absence in humans, validates DHDPS as an antibacterial drug target. Conventional drug design efforts have thus far been unsuccessful in identifying potent DHDPS inhibitors. Here, we make use of contemporary molecular dynamics simulation and Markov state models to explore the interactions between DHDPS from the human pathogen Staphylococcus aureus and its cognate substrate, pyruvate. Our simulations recover the crystallographic DHDPS-pyruvate complex without a priori knowledge of the final bound structure. The highly conserved residue Arg140 was found to have a pivotal role in coordinating the entry of pyruvate into the active site from bulk solvent, consistent with previous kinetic reports, indicating an indirect role for the residue in DHDPS catalysis. A metastable binding intermediate characterized by multiple points of intermolecular interaction between pyruvate and key DHDPS residue Arg140 was found to be a highly conserved feature of the binding trajectory when comparing alternative binding pathways. By means of umbrella sampling we show that these binding intermediates are thermodynamically metastable, consistent with both the available experimental data and the substrate binding model presented in this study. Our results provide insight into an important enzyme-substrate interaction in atomistic detail that offers the potential to be exploited for the discovery of more effective DHDPS inhibitors and, in a broader sense, dynamic protein-drug interactions.

The politics of insight.

Science.gov (United States)

Salvi, Carola; Cristofori, Irene; Grafman, Jordan; Beeman, Mark

2016-01-01

Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insight and analytic problem-solving, are reliable and are associated with two different neural circuits. In our research we found that participants self-identifying with distinct political orientations demonstrated differences in problem-solving strategy. Liberals solved significantly more problems via insight instead of in a step-by-step analytic fashion. Our findings extend previous observations that self-identified political orientations reflect differences in cognitive styles. More specifically, we show that type of political orientation is associated with problem-solving strategy. The data converge with previous neurobehavioural and cognitive studies indicating a link between cognitive style and the psychological mechanisms that mediate political beliefs.

The politics of insight

Science.gov (United States)

Salvi, Carola; Cristofori, Irene; Grafman, Jordan; Beeman, Mark

2016-01-01

Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insight and analytic problem-solving, are reliable and are associated with two different neural circuits. In our research we found that participants self-identifying with distinct political orientations demonstrated differences in problem-solving strategy. Liberals solved significantly more problems via insight instead of in a step-by-step analytic fashion. Our findings extend previous observations that self-identified political orientations reflect differences in cognitive styles. More specifically, we show that type of political orientation is associated with problem-solving strategy. The data converge with previous neurobehavioural and cognitive studies indicating a link between cognitive style and the psychological mechanisms that mediate political beliefs. PMID:26810954

Gaining insight into the physics of dynamic atomic force microscopy in complex environments using the VEDA simulator

Science.gov (United States)

Kiracofe, Daniel; Melcher, John; Raman, Arvind

2012-01-01

Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often contrary to what is known in air or vacuum environments. Mathematical simulations have proven to be an effective tool in providing physical insight into these non-intuitive systems. In this article we describe recent developments in the VEDA (virtual environment for dynamic AFM) simulator, which is a suite of freely available, open-source simulation tools that are delivered through the cloud computing cyber-infrastructure of nanoHUB (www.nanohub.org). Here we describe three major developments. First, simulations in liquid environments are improved by enhancements in the modeling of cantilever dynamics, excitation methods, and solvation shell forces. Second, VEDA is now able to simulate many new advanced modes of operation (bimodal, phase-modulation, frequency-modulation, etc.). Finally, nineteen different tip-sample models are available to simulate the surface physics of a wide variety different material systems including capillary, specific adhesion, van der Waals, electrostatic, viscoelasticity, and hydration forces. These features are demonstrated through example simulations and validated against experimental data, in order to provide insight into practical problems in dynamic AFM.

De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers

Energy Technology Data Exchange (ETDEWEB)

Nakano, A; Kalia, R K; Nomura, K; Sharma, A; Vashishta, P; Shimojo, F; van Duin, A; Goddard, III, W A; Biswas, R; Srivastava, D; Yang, L H

2006-09-04

We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and geographically distributed clusters. In this framework, high-end chemically reactive and non-reactive molecular dynamics (MD) simulations explore a wide solution space to discover microscopic mechanisms that govern macroscopic material properties, into which highly accurate quantum mechanical (QM) simulations are embedded to validate the discovered mechanisms and quantify the uncertainty of the solution. The framework includes an embedded divide-and-conquer (EDC) algorithmic framework for the design of linear-scaling simulation algorithms with minimal bandwidth complexity and tight error control. The EDC framework also enables adaptive hierarchical simulation with automated model transitioning assisted by graph-based event tracking. A tunable hierarchical cellular decomposition parallelization framework then maps the O(N) EDC algorithms onto Petaflops computers, while achieving performance tunability through a hierarchy of parameterized cell data/computation structures, as well as its implementation using hybrid Grid remote procedure call + message passing + threads programming. High-end computing platforms such as IBM BlueGene/L, SGI Altix 3000 and the NSF TeraGrid provide an excellent test grounds for the framework. On these platforms, we have achieved unprecedented scales of quantum-mechanically accurate and well validated, chemically reactive atomistic simulations--1.06 billion-atom fast reactive force-field MD and 11.8 million-atom (1.04 trillion grid points) quantum-mechanical MD in the framework of the EDC density functional theory on adaptive multigrids--in addition to 134 billion-atom non-reactive space-time multiresolution MD, with the parallel efficiency as high as 0.998 on 65,536 dual-processor BlueGene/L nodes. We have also achieved an automated execution of hierarchical QM

Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores

Science.gov (United States)

Yang, Guomin; Neretnieks, Ivars; Holmboe, Michael

2017-08-01

During the last four decades, numerous studies have been directed to the swelling smectite-rich clays in the context of high-level radioactive waste applications and waste-liners for contaminated sites. The swelling properties of clay mineral particles arise due to hydration of the interlayer cations and the diffuse double layers formed near the negatively charged montmorillonite (MMT) surfaces. To accurately study the cation hydration in the interlayer nanopores of MMT, solvent-solute and solvent-clay surface interactions (i.e., the solvation effects and the shape effects) on the atomic level should be taken into account, in contrast to many recent electric double layer based methodologies using continuum models. Therefore, in this research we employed fully atomistic simulations using classical molecular dynamics (MD) simulations, the software package GROMACS along with the CLAYFF forcefield and the SPC/E water model. We present the ion distributions and the deformation of the hydrated coordination structures, i.e., the hydration shells of Na+ and Ca2+ in the interlayer, respectively, for MMT in the first-layer, the second-layer, the third-layer, the fourth-layer, and the fifth-layer (1W, 2W, 3W, 4W, and 5W) hydrate states. Our MD simulations show that Na+ in Na-MMT nanopores have an affinity to the ditrigonal cavities of the clay layers and form transient inner-sphere complexes at about 3.8 Å from clay midplane at water contents less than the 5W hydration state. However, these phenomena are not observed in Ca-MMT regardless of swelling states. For Na-MMT, each Na+ is coordinated to four water molecules and one oxygen atom of the clay basal-plane in the first hydration shell at the 1W hydration state, and with five to six water molecules in the first hydration shell within a radius of 3.1 Å at all higher water contents. In Ca-MMT, however each Ca2+ is coordinated to approximately seven water molecules in the first hydration shell at the 1W hydration state and

Atomistic modelling of diffusional phase transformations with elastic strain

International Nuclear Information System (INIS)

Mason, D R; Rudd, R E; Sutton, A P

2004-01-01

Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Atomic interactions are modelled by Finnis-Sinclair potentials constructed for these simulations. Vacancy diffusion is modelled by comparing the energies of trial states, where the system is partially relaxed for each trial state. No special requirements are made about the description of atomic interactions, making our approach suitable for more fundamentally based models such as tight binding if sufficient computational resources are available. Only a limited precision is required for the energy of each trial state, determined by the value of k B T. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r 3 , it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centred on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice

The politics of insight

OpenAIRE

Salvi, Carola; Cristofori, Irene; Grafman, Jordan; Beeman, Mark

2016-01-01

Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insig...

Free-energy landscape of protein oligomerization from atomistic simulations

Science.gov (United States)

Barducci, Alessandro; Bonomi, Massimiliano; Prakash, Meher K.; Parrinello, Michele

2013-01-01

In the realm of protein–protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage. PMID:24248370

Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations

DEFF Research Database (Denmark)

Kaszuba, K.; Postila, P. A.; Cramariuc, O.

2013-01-01

studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular...... interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic...

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

Directory of Open Access Journals (Sweden)

Pavel V. Komarov

2013-09-01

Full Text Available 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.

An atomistic study of the deformation behavior of tungsten nanowires

Energy Technology Data Exchange (ETDEWEB)

Xu, Shuozhi [University of California, California NanoSystems Institute, Santa Barbara, CA (United States); Su, Yanqing [University of California, Department of Mechanical Engineering, Santa Barbara, CA (United States); Chen, Dengke [Georgia Institute of Technology, GWW School of Mechanical Engineering, Atlanta, GA (United States); Li, Longlei [Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA (United States)

2017-12-15

Large-scale atomistic simulations are performed to study tensile and compressive left angle 112 right angle loading of single-crystalline nanowires in body-centered cubic tungsten (W). Effects of loading mode, wire cross-sectional shape, wire size, strain rate, and crystallographic orientations of the lateral surfaces are explored. Uniaxial deformation of a W bulk single crystal is also investigated for reference. Our results reveal a strong tension-compression asymmetry in both the stress-strain response and the deformation behavior due to different yielding/failure modes: while the nanowires fail by brittle fracture under tensile loading, they yield by nucleation of dislocations from the wire surface under compressive loading. It is found that (1) nanowires have a higher strength than the bulk single crystal; (2) with a cross-sectional size larger than 10 nm, there exists a weak dependence of strength on wire size; (3) when the wire size is equal to or smaller than 10 nm, nanowires buckle under compressive loading; (4) the cross-sectional shape, strain rate, and crystallographic orientations of the lateral surfaces affect the strength and the site of defect initiation but not the overall deformation behavior. (orig.)

Edge dislocations in dicalcium silicates: Experimental observations and atomistic analysis

International Nuclear Information System (INIS)

Shahsavari, Rouzbeh; Chen, Lu; Tao, Lei

2016-01-01

Understanding defects and influence of dislocations on dicalcium silicates (Ca 2 SiO 4 ) is a challenge in cement science. We report a high-resolution transmission electron microscopy image of edge dislocations in Ca 2 SiO 4 , followed by developing a deep atomic understanding of the edge dislocation-mediated properties of five Ca 2 SiO 4 polymorphs. By decoding the interplay between core dislocation energies, core structures, and nucleation rate of reactivity, we find that γ-C2S and α-C2S polymorphs are the most favorable polymorphs for dislocations in Ca 2 SiO 4 , mainly due to their large pore channels which take away majority of the distortions imposed by edge dislocations. Furthermore, in the context of edge dislocation, while α-C2S represents the most active polymorph for reactivity and crystal growth, β-C2S represents the most brittle polymorph suitable for grinding. This work is the first report on the atomistic-scale analysis of edge dislocation-mediated properties of Ca 2 SiO 4 and may open up new opportunities for tuning fracture and reactivity processes of Ca 2 SiO 4 and other cement components.

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

Science.gov (United States)

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.

Interwell Connectivity Evaluation Using Injection and Production Fluctuation Data

Science.gov (United States)

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

Atomistic simulation of CO 2 solubility in poly(ethylene oxide) oligomers

KAUST Repository

Hong, Bingbing

2013-10-02

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(CH 2CH2O)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 Henrys constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henrys constant. Dependence of the calculated Henrys constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. © 2013 Taylor & Francis.

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

KAUST Repository

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-01-01

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. © 2013 The Royal Society of Chemistry.

MEANS 2: Microstructure- and Micromechanism-Sensitive Property Models for Advanced Turbine Disk and Blade Systems

National Research Council Canada - National Science Library

Pollock, Tresa M; Mills, Michael J

2008-01-01

.... A model for the novel microtwinning regime. Modeling at the ab initio, atomistic and phase field levels is providing insight into the activation parameters associated with the observed deformation mechanisms...

New insights into the stereochemical requirements of the bradykinin B2 receptor antagonists binding

Science.gov (United States)

Lupala, Cecylia S.; Gomez-Gutierrez, Patricia; Perez, Juan J.

2016-01-01

Bradykinin (BK) is a member of the kinin family, released in response to inflammation, trauma, burns, shock, allergy and some cardiovascular diseases, provoking vasodilatation and increased vascular permeability among other effects. Their actions are mediated through at least two G-protein coupled receptors, B1 a receptor up-regulated during inflammation episodes or tissue trauma and B2 that is constitutively expressed in a variety of cell types. The goal of the present work is to carry out a structure-activity study of BK B2 antagonism, taking into account the stereochemical features of diverse non-peptide antagonists and the way these features translate into ligand anchoring points to complementary regions of the receptor, through the analysis of the respective ligand-receptor complex. For this purpose an atomistic model of the BK B2 receptor was built by homology modeling and subsequently refined embedded in a lipid bilayer by means of a 600 ns molecular dynamics trajectory. The average structure from the last hundred nanoseconds of the molecular dynamics trajectory was energy minimized and used as model of the receptor for docking studies. For this purpose, a set of compounds with antagonistic profile, covering maximal diversity were selected from the literature. Specifically, the set of compounds include Fasitibant, FR173657, Anatibant, WIN64338, Bradyzide, CHEMBL442294, and JSM10292. Molecules were docked into the BK B2 receptor model and the corresponding complexes analyzed to understand ligand-receptor interactions. The outcome of this study is summarized in a 3D pharmacophore that explains the observed structure-activity results and provides insight into the design of novel molecules with antagonistic profile. To prove the validity of the pharmacophore hypothesized a virtual screening process was also carried out. The pharmacophore was used as query to identify new hits using diverse databases of molecules. The results of this study revealed a set of new

Prediction of irradiation induced microstructures in the AgCu model alloy using a multiscale method coupling atomistic and phase field modelling

OpenAIRE

Demange, Gilles; Pontikis, Vassilis; Lunéville, Laurence; Simeone, David

2016-01-01

In this work, a multiscale approach based on phase field was developed to simulate the microstructure's evolution under irradiation in binary systems, from atomic to microstructural scale. For that purpose, an efficient numerical scheme was developed. In the case of AgCu alloy under Krypton ions irradiation, phenomenological parameters were computed using atomistic methods, as a function of the temperature and the irradiation flux. As a result, we predicted the influence of the irradiation fl...

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

Science.gov (United States)

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.

Study of the embedded atom method of atomistic calculations for metals and alloys

International Nuclear Information System (INIS)

Johnson, R.A.

1990-10-01

Two projects were completed in the past year. The stability of a series of binary alloys was calculated using the embedded-atom method (EAM) with an analytic form for two-body potentials derived previously. Both disordered alloys and intermetallic compounds with the L1 0 and L1 2 structures were studied. The calculated heats of solution of alloys of Cu, Ag, Au, Ni, and Pt were satisfactory, while results for alloys containing Pd were too high. Atomistic calculations using the EAM were also carried out for point defects in hcp metals. By comparison with results in the literature, it was found that many body effects from the EAM significantly alter predicted physical properties of hcp metals. For example, the EAM calculations yield anisotropic vacancy diffusion with greater vacancy mobility in the basal plane, and imply that diffusion will start at a lower fraction of the melting temperature

Atomistic studies of cation transport in tetragonal ZrO2 during zirconium corrosion

International Nuclear Information System (INIS)

Bai, Xian-Ming; Zhang, Yongfeng; Tonks, Michael R.

2015-01-01

Zirconium alloys are the major fuel cladding materials in current reactors. The water-side corrosion is a significant degradation mechanism of these alloys. During corrosion, the transport of oxidizing species in zirconium dioxide (ZrO 2 ) determines the corrosion kinetics. Previously, it has been argued that the outward diffusion of cations is important for forming protective oxides. In this work, the migration of Zr defects in tetragonal ZrO 2 is studied with temperature accelerated dynamics and molecular dynamics simulations. The results show that Zr interstitials have anisotropic diffusion and migrate preferentially along the [001] or c direction in tetragonal ZrO 2 . The compressive stresses can increase the Zr interstitial migration barrier significantly. The migration of Zr interstitials at a grain boundary is much slower than in a bulk oxide. The implications of these atomistic simulation results in the Zr corrosion are discussed. (authors)

Atomistic study of lipid membranes containing chloroform: looking for a lipid-mediated mechanism of anesthesia.

Directory of Open Access Journals (Sweden)

Ramon Reigada

Full Text Available The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic and carbon tetrachloride (non-anesthetic. Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.

Structural insights into SUN-KASH complexes across the nuclear envelope

Institute of Scientific and Technical Information of China (English)

Wenjia Wang; Zhaocai Zhou; Zhubing Shi; Shi Jiao; Cuicui Chen; Huizhen Wang; Guoguang Liu; Qiang Wang; Yun Zhao; Mark I Greene

2012-01-01

Linker of the nucleoskeleton and the cytoskeleton (LINC) complexes are composed of SUN and KASH domaincontaining proteins and bridge the inner and outer membranes of the nuclear envelope.LINC complexes play critical roles in nuclear positioning,cell polarization and cellular stiffness.Previously,we reported the homotrimeric structure of human SUN2.We have now determined the crystal structure of the human SUN2-KASH complex.In the complex structure,the SUN domain homotrimer binds to three independent "hook"-like KASH peptides.The overall conformation of the SUN domain in the complex closely resembles the SUN domain in its apo state.A major conformational change involves the AA'-loop of KASH-bound SUN domain,which rearranges to form a mini β-sheet that interacts with the KASH peptide.The PPPT motif of the KASH domain fits tightly into a hydrophobic pocket on the homotrimeric interface of the SUN domain,which we termed the BI-pocket.Moreover,two adjacent protomers of the SUN domain homotrimer sandwich the KASH domain by hydrophobic interaction and hydrogen bonding.Mutations of these binding sites disrupt or reduce the association between the SUN and KASH domains in vitro.In addition,transfection of wild-type,but not mutant,SUN2 promotes cell migration in Ovcar-3 cells.These results provide a structural model of the LINC complex,which is essential for additional study of the physical and functional coupling between the cytoplasm and the nucleoplasm.

Investigation of the removing process of cathode material in micro-EDM using an atomistic-continuum model

International Nuclear Information System (INIS)

Guo, Jianwen; Zhang, Guojun; Huang, Yu; Ming, Wuyi; Liu, Min; Huang, Hao

2014-01-01

Highlights: • An atomistic-continuum computational simulation model for single-discharge micro-EDM process of Cu cathode is constructed. • Cathode material is removed mainly in the form of single atoms or small clusters in micro-EDM. • Electric action leads to the formation of peaks on the surface of crater. • Removing process of cathode material under the hybrid action combining the thermal action and the electric action is studied, and the strength of either action needed for material to remove is much reduced. - Abstract: In micro-electrical discharge machining (micro-EDM), the discharge duration is ultra-short, and both the electric action and the thermal action by the discharge channel play important roles in the removing process of cathode material. However, in most researches on the machining mechanism of micro-EDM, only the thermal action is concerned. In this article, a combined atomistic-continuum modeling method in which the two-temperature model and the molecular dynamics simulation model are integrated is used to construct the simulation model for cathode in single-discharge micro-EDM process. With this simulation model, removing processes of Cu cathode material in micro-EDM under pure thermal action, pure electric action and the combination of them are investigated in a simulative way. By analyzing evolutions of temperature, stress and micro-structure of material as well as the dynamical behaviors of material in the removing process, mechanisms of the cathode material removal and crater formation are revealed. In addition, the removing process of cathode material under the combination of pure thermal action and pure electric action is compared with those under the two pure actions respectively to analyze the interactive effect between the thermal action and the electric action

Can matter and spirit be mediated through language? Some insights ...

African Journals Online (AJOL)

Neuroscience utilises insights from the theory of complex systems to attempt to understand how perception, thought and self-awareness can arise as a consequence of the complex system that is the brain. However, already at the height of the Enlightenment, a contemporary and critic of Immanuel Kant, Johann Georg ...

Mining sensor data from complex systems

NARCIS (Netherlands)

Vespier, Ugo

2015-01-01

Today, virtually everything, from natural phenomena to complex artificial and physical systems, can be measured and the resulting information collected, stored and analyzed in order to gain new insight. This thesis shows how complex systems often exhibit diverse behavior at different temporal

Exploring the limits of cooperative phenomena using complex plasmas

International Nuclear Information System (INIS)

Schwabe, M.; Zhdanov, S.; Ivlev, A. V.; Thomas, H. M.; Morfill, G. E.

2011-01-01

With the advancing miniaturization of technological applications, processes on the mesoscale become increasingly important. This is the scale where the individual movement of particles transforms into cooperative behavior-behavior that cannot be explained by investigating the motion of individual particles alone.Complex plasmas are ideally suited to study the limits of cooperative behavior. The time scales of the dynamics of the microparticles embedded in the plasma are such that their movement can be fully resolved, and an investigation on the atomistic (kinetic) level is possible. In addition, complex plasmas can be considered a model system for ordinary fluids: The internal microparticle dynamics is basically undamped and is characterized by the similarity parameters matching those of other fluids. This similarity does not break down even at small scales: For instance, in [2], microparticle droplets comprised of only a few 1000-10000 particles were examined. In these experiments, the Weber number (the ratio of inertia to surface tension forces) matches that of falling water drops. As another example, the onset of a Rayleigh-Taylor instability in a complex plasma can be described by the ordinary dispersion relation, even at scales of only few particle layers. This allows investigating the 'nanoscale' of fluid flows, and, hence, the limits of cooperative behavior.

Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

Science.gov (United States)

Anwar, Muhammad Ayaz; Choi, Sangdun

2017-03-01

Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations.

Atomistic study of drag, surface and inertial effects on edge dislocations in face-centered cubic metals

International Nuclear Information System (INIS)

Bitzek, Erik; Gumbsch, Peter

2004-01-01

Atomistic simulations of an accelerating edge dislocation were carried out to study the effects of drag and inertia. Using an embedded atom potential for nickel, the Peierls stress, the effective mass and the drag coefficient of an edge dislocation were determined for different temperatures and stresses in a simple slab geometry. The effect of {1 1 1} surfaces on an intersecting edge dislocation were studied by appropriately cutting the slab. A dislocation intersecting a surface step was used as a model system to demonstrate the importance of inertial effects for dynamically overcoming short range obstacles. Significant effects were found even at room temperature. A simple model based on the dislocation-obstacle interaction energies was used to describe the findings

Atomistic simulations of the yielding of gold nanowires

International Nuclear Information System (INIS)

Diao Jiankuai; Gall, Ken; Dunn, Martin L.; Zimmerman, Jonathan A.

2006-01-01

We performed atomistic simulations to study the effect of free surfaces on the yielding of gold nanowires. Tensile surface stresses on the surfaces of the nanowires cause them to contract along the length with respect to the bulk face-centered cubic lattice and induce compressive stress in the interior. When the cross-sectional area of a nanowire is less than 2.45 nm x 2.45 nm, the wire yields under its surface stresses. Under external forces and surface stresses, nanowires yield via the nucleation and propagation of the {1 1 1} partial dislocations. The magnitudes of the tensile and compressive yield stress of nanowires increase and decrease, respectively, with a decrease of the wire width. The magnitude of the tensile yield stress is much larger than that of the compressive yield stress for small nanowires, while for small nanowires, tensile and compressive yield stresses have similar magnitudes. The critical resolved shear stress (RSS) by external forces depends on wire width, orientation and loading condition (tension vs. compression). However, the critical RSS in the interior of the nanowires, which is exerted by both the external force and the surface-stress-induced compressive stress, does not change significantly with wire width for same orientation and same loading condition, and can thus serve as a 'local' criterion. This local criterion is invoked to explain the observed size dependence of yield behavior and tensile/compressive yield stress asymmetry, considering surface stress effects and different slip systems active in tensile and compressive yielding

Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides

International Nuclear Information System (INIS)

Ogawa, Hiroshi

2015-01-01

Highlights: • Hydrogen–dislocation interaction was simulated by molecular dynamics method. • Different distribution of H atoms were observed at edge and screw dislocation. • Planner distribution of hydrogen may be caused by partialized edge dislocation. • Hydrogen diffusivity was reduced in both edge and screw dislocation models. • Pipe diffusion was observed for edge dislocation but not for screw dislocation. - Abstract: Kinetics of interstitial hydrogen atoms near dislocation cores were analyzed by atomistic simulation. Classical molecular dynamics method was applied to model structures of edge and screw dislocations in α-phase vanadium hydride. Simulation showed that hydrogen atoms aggregate near dislocation cores. The spatial distribution of hydrogen has a planner shape at edge dislocation due to dislocation partialization, and a cylindrical shape at screw dislocation. Simulated self-diffusion coefficients of hydrogen atoms in dislocation models were a half- to one-order lower than that of dislocation-free model. Arrhenius plot of self-diffusivity showed slightly different activation energies for edge and screw dislocations. Directional dependency of hydrogen diffusion near dislocation showed high and low diffusivity along edge and screw dislocation lines, respectively, hence so called ‘pipe diffusion’ possibly occur at edge dislocation but does not at screw dislocation

Atomistic Simulations of Small-scale Materials Tests of Nuclear Materials

International Nuclear Information System (INIS)

Shin, Chan Sun; Jin, Hyung Ha; Kwon, Jun Hyun

2012-01-01

Degradation of materials properties under neutron irradiation is one of the key issues affecting the lifetime of nuclear reactors. Evaluating the property changes of materials due to irradiations and understanding the role of microstructural changes on mechanical properties are required for ensuring reliable and safe operation of a nuclear reactor. However, high dose of neuron irradiation capabilities are rather limited and it is difficult to discriminate various factors affecting the property changes of materials. Ion beam irradiation can be used to investigate radiation damage to materials in a controlled way, but has the main limitation of small penetration depth in the length scale of micro meters. Over the past decade, the interest in the investigations of size-dependent mechanical properties has promoted the development of various small-scale materials tests, e.g. nanoindentation and micro/nano-pillar compression tests. Small-scale materials tests can address the issue of the limitation of small penetration depth of ion irradiation. In this paper, we present small-scale materials tests (experiments and simulation) which are applied to study the size and irradiation effects on mechanical properties. We have performed molecular dynamics simulations of nanoindentation and nanopillar compression tests. These atomistic simulations are expected to significantly contribute to the investigation of the fundamental deformation mechanism of small scale irradiated materials

Modelling phase separation in Fe-Cr system using different atomistic kinetic Monte Carlo techniques

International Nuclear Information System (INIS)

Castin, N.; Bonny, G.; Terentyev, D.; Lavrentiev, M.Yu.; Nguyen-Manh, D.

2011-01-01

Atomistic kinetic Monte Carlo (AKMC) simulations were performed to study α-α' phase separation in Fe-Cr alloys. Two different energy models and two approaches to estimate the local vacancy migration barriers were used. The energy models considered are a two-band model Fe-Cr potential and a cluster expansion, both fitted to ab initio data. The classical Kang-Weinberg decomposition, based on the total energy change of the system, and an Artificial Neural Network (ANN), employed as a regression tool were used to predict the local vacancy migration barriers 'on the fly'. The results are compared with experimental thermal annealing data and differences between the applied AKMC approaches are discussed. The ability of the ANN regression method to accurately predict migration barriers not present in the training list is also addressed by performing cross-check calculations using the nudged elastic band method.

Making Sustainable Energy Choices: Insights on the Energy/Water/Land Nexus

Energy Technology Data Exchange (ETDEWEB)

2014-10-01

This periodic publication summarizes insights from the body of NREL analysis work. In this issue of Analysis Insights, we examine the implications of our energy choices on water, land use, climate, developmental goals, and other factors. Collectively, NREL's work helps policymakers and investors understand and evaluate energy choices within the complex web of connections, or nexus, between energy, water, and land.

Atomistic modeling of nanowires, small-scale fatigue damage in cast magnesium, and materials for MEMS

Energy Technology Data Exchange (ETDEWEB)

Dunn, Martin L. [Univ. of Colorado, Boulder, CO (United States); Talmage, Mellisa J. [Univ. of Colorado, Boulder, CO (United States); McDowell, David L. [Georgia Inst. of Technology, Atlanta, GA (United States); West, Neil [Univ. of Colorado, Boulder, CO (United States); Gullett, Philip Michael [Mississippi State Univ., Mississippi State, MS (United States); Miller, David C. [Univ. of Colorado, Boulder, CO (United States); Spark, Kevin [Univ. of Colorado, Boulder, CO (United States); Diao, Jiankuai [Univ. of Colorado, Boulder, CO (United States); Horstemeyer, Mark F. [Mississippi State Univ., Mississippi State, MS (United States); Zimmerman, Jonathan A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gall, K. [Georgia Inst. of Technology, Atlanta, GA (United States)

2006-10-01

Lightweight and miniaturized weapon systems are driving the use of new materials in design such as microscale materials and ultra low-density metallic materials. Reliable design of future weapon components and systems demands a thorough understanding of the deformation modes in these materials that comprise the components and a robust methodology to predict their performance during service or storage. Traditional continuum models of material deformation and failure are not easily extended to these new materials unless microstructural characteristics are included in the formulation. For example, in LIGA Ni and Al-Si thin films, the physical size is on the order of microns, a scale approaching key microstructural features. For a new potential structural material, cast Mg offers a high stiffness-to-weight ratio, but the microstructural heterogeneity at various scales requires a structure-property continuum model. Processes occurring at the nanoscale and microscale develop certain structures that drive material behavior. The objective of the work presented in this report was to understand material characteristics in relation to mechanical properties at the nanoscale and microscale in these promising new material systems. Research was conducted primarily at the University of Colorado at Boulder to employ tightly coupled experimentation and simulation to study damage at various material size scales under monotonic and cyclic loading conditions. Experimental characterization of nano/micro damage will be accomplished by novel techniques such as in-situ environmental scanning electron microscopy (ESEM), 1 MeV transmission electron microscopy (TEM), and atomic force microscopy (AFM). New simulations to support experimental efforts will include modified embedded atom method (MEAM) atomistic simulations at the nanoscale and single crystal micromechanical finite element simulations. This report summarizes the major research and development accomplishments for the LDRD project

An adhesive contact mechanics formulation based on atomistically induced surface traction

Energy Technology Data Exchange (ETDEWEB)

Fan, Houfu [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States); Ren, Bo [Livermore Software Technology Corporation, 7374 Las Positas Road, Livermore, CA 94551 (United States); Li, Shaofan, E-mail: shaofan@berkeley.edu [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States)

2015-12-01

In this work, we have developed a novel multiscale computational contact formulation based on the generalized Derjuguin approximation for continua that are characterized by atomistically enriched constitutive relations in order to study macroscopic interaction between arbitrarily shaped deformable continua. The proposed adhesive contact formulation makes use of the microscopic interaction forces between individual particles in the interacting bodies. In particular, the double-layer volume integral describing the contact interaction (energy, force vector, matrix) is converted into a double-layer surface integral through a mathematically consistent approach that employs the divergence theorem and a special partitioning technique. The proposed contact model is formulated in the nonlinear continuum mechanics framework and implemented using the standard finite element method. With no large penalty constant, the stiffness matrix of the system will in general be well-conditioned, which is of great significance for quasi-static analysis. Three numerical examples are presented to illustrate the capability of the proposed method. Results indicate that with the same mesh configuration, the finite element computation based on the surface integral approach is faster and more accurate than the volume integral based approach. In addition, the proposed approach is energy preserving even in a very long dynamic simulation.

Nucleation of ripplocations through atomistic modeling of surface nanoindentation in graphite

Science.gov (United States)

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 aspects of ductile responses of cubic silicon carbide during nanometric cutting.

Science.gov (United States)

Goel, Saurav; Luo, Xichun; Reuben, Robert L; Rashid, Waleed Bin

2011-11-11

Cubic silicon carbide (SiC) is an extremely hard and brittle material having unique blend of material properties which makes it suitable candidate for microelectromechanical systems and nanoelectromechanical systems applications. Although, SiC can be machined in ductile regime at nanoscale through single-point diamond turning process, the root cause of the ductile response of SiC has not been understood yet which impedes significant exploitation of this ceramic material. In this paper, molecular dynamics simulation has been carried out to investigate the atomistic aspects of ductile response of SiC during nanometric cutting process. Simulation results show that cubic SiC undergoes sp3-sp2 order-disorder transition resulting in the formation of SiC-graphene-like substance with a growth rate dependent on the cutting conditions. The disorder transition of SiC causes the ductile response during its nanometric cutting operations. It was further found out that the continuous abrasive action between the diamond tool and SiC causes simultaneous sp3-sp2 order-disorder transition of diamond tool which results in graphitization of diamond and consequent tool wear.

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

Science.gov (United States)

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.

How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations

DEFF Research Database (Denmark)

Aijanen, T.; Koivuniemi, A.; Javanainen, M.

2014-01-01

Cholesteryl ester transfer protein (CETP) mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides) and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity...... and thereby raise high density lipoprotein (HDL)-cholesterol and decrease low density lipoprotein (LDL)-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics...... simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site...

Scaling up complex interventions: insights from a realist synthesis.

Science.gov (United States)

Willis, Cameron D; Riley, Barbara L; Stockton, Lisa; Abramowicz, Aneta; Zummach, Dana; Wong, Geoff; Robinson, Kerry L; Best, Allan

2016-12-19

Preventing chronic diseases, such as cancer, cardiovascular disease and diabetes, requires complex interventions, involving multi-component and multi-level efforts that are tailored to the contexts in which they are delivered. Despite an increasing number of complex interventions in public health, many fail to be 'scaled up'. This study aimed to increase understanding of how and under what conditions complex public health interventions may be scaled up to benefit more people and populations.A realist synthesis was conducted and discussed at an in-person workshop involving practitioners responsible for scaling up activities. Realist approaches view causality through the linkages between changes in contexts (C) that activate mechanisms (M), leading to specific outcomes (O) (CMO configurations). To focus this review, three cases of complex interventions that had been successfully scaled up were included: Vibrant Communities, Youth Build USA and Pathways to Education. A search strategy of published and grey literature related to each case was developed, involving searches of relevant databases and nominations from experts. Data extracted from included documents were classified according to CMO configurations within strategic themes. Findings were compared and contrasted with guidance from diffusion theory, and interpreted with knowledge users to identify practical implications and potential directions for future research.Four core mechanisms were identified, namely awareness, commitment, confidence and trust. These mechanisms were activated within two broad scaling up strategies, those of renewing and regenerating, and documenting success. Within each strategy, specific actions to change contexts included building partnerships, conducting evaluations, engaging political support and adapting funding models. These modified contexts triggered the identified mechanisms, leading to a range of scaling up outcomes, such as commitment of new communities, changes in relevant

Structural insight into the UNC-45–myosin complex

DEFF Research Database (Denmark)

Fratev, Filip; Jonsdottir, Svava Osk; Pajeva, Ilza

2013-01-01

The UNC-45 chaperone protein interacts with and affects the folding, stability, and the ATPase activity of myosins. It plays a critical role in the cardiomyopathy development and in the breast cancer tumor growth. Here we propose the first structural model of the UNC-45–myosin complex using various...... is mainly stabilized by electrostatic interactions. Remarkably, the contact surface area is similar to that of the myosinactin complex. A significant interspecies difference in the myosin binding epitope is observed. Our results reveal the structural basis of MYH7 exons 15–16 hypertrophic cardiomyopathy...... mutations and provide directions for drug targeting. © 2013 Wiley Periodicals, Inc....

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

DEFF Research Database (Denmark)

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

2012-01-01

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

Insights into the catalytic mechanism of dehydrogenase BphB: A quantum mechanics/molecular mechanics study.

Science.gov (United States)

Zhang, Ruiming; Shi, Xiangli; Sun, Yanhui; Zhang, Qingzhu; Wang, Wenxing

2018-05-17

The present study delineated the dehydrogenation mechanism of cis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDBPH) and cis-2,3-dihydro-2,3-dihydroxy-4,4'-dichlorobiphenyl (2,3-DD-4,4'-DBPH) by Pandoraea pnomenusa strain B-356 cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (BphB) in atomistic detail. The enzymatic process was investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Five different snapshots were extracted and calculated, which revealed that the Boltzmann-weighted average barriers of 2,3-DDBPH and 2,3-DD-4,4'-DBPH dehydrogenation processes are 10.7 and 11.5 kcal mol -1 , respectively. The established dehydrogenation mechanism provides new insight into the degradation processes of other chlorinated 2,3-DDBPH. In addition to Asn115, Ser142, and Lys149, the importance of Ile 89, Asn143, Pro184, Met 187, Thr189, and Lue 191 during the dehydrogenation process of 2,3-DDBPH and 2,3-DD-4,4'-DBPH were also highlighted to search for promising mutation targets for improving the catalytic efficiency of BphB. Copyright © 2018. Published by Elsevier Ltd.

An Insight into Pedicularis cheilanthifolia Schrenk Complex (Scrophulariaceae

Directory of Open Access Journals (Sweden)

Arti Garg

2009-09-01

Full Text Available The taxonomy complexity of Pedicularis cheilanthifolia Schrenk along with its three varieties viz. var. cheilanthifolia, var. purpurea (Pennell Tsoong ex Garg and var. albida (Pennell Tsoong is elucidated and resolved. Key to varieties, morphology, distribution, phenology and ecology is provided to differentiate the varieties. Diagnostic morphological characters supported the transfer of P. purpurea (Pennel Tsoong to P. cheilanthifolia, hence the new combination is made.

Excitation energy transfer in natural photosynthetic complexes and chlorophyll trefoils: hole-burning and single complex/trefoil spectroscopic studies

Energy Technology Data Exchange (ETDEWEB)

Ryszard Jankowiak, Kansas State University, Department of Chemistry, CBC Bldg., Manhattan KS, 66505; Phone: (785) 532-6785

2012-09-12

In this project we studied both natural photosynthetic antenna complexes and various artificial systems (e.g. chlorophyll (Chl) trefoils) using high resolution hole-burning (HB) spectroscopy and excitonic calculations. Results obtained provided more insight into the electronic (excitonic) structure, inhomogeneity, electron-phonon coupling strength, vibrational frequencies, and excitation energy (or electron) transfer (EET) processes in several antennas and reaction centers. For example, our recent work provided important constraints and parameters for more advanced excitonic calculations of CP43, CP47, and PSII core complexes. Improved theoretical description of HB spectra for various model systems offers new insight into the excitonic structure and composition of low-energy absorption traps in very several antenna protein complexes and reaction centers. We anticipate that better understanding of HB spectra obtained for various photosynthetic complexes and their simultaneous fits with other optical spectra (i.e. absorption, emission, and circular dichroism spectra) provides more insight into the underlying electronic structures of these important biological systems. Our recent progress provides a necessary framework for probing the electronic structure of these systems via Hole Burning Spectroscopy. For example, we have shown that the theoretical description of non-resonant holes is more restrictive (in terms of possible site energies) than those of absorption and emission spectra. We have demonstrated that simultaneous description of linear optical spectra along with HB spectra provides more realistic site energies. We have also developed new algorithms to describe both nonresonant and resonant hole-burn spectra using more advanced Redfield theory. Simultaneous description of various optical spectra for complex biological system, e.g. artificial antenna systems, FMO protein complexes, water soluble protein complexes, and various mutants of reaction centers

Study of local currents in low dimension materials using complex injecting potentials

Science.gov (United States)

He, Shenglai; Covington, Cody; Varga, Kálmán

2018-04-01

A complex potential is constructed to inject electrons into the conduction band, mimicking electron currents in nanoscale systems. The injected electrons are time propagated until a steady state is reached. The local current density can then be calculated to show the path of the conducting electrons on an atomistic level. The method allows for the calculation of the current density vectors within the medium as a function of energy of the conducting electron. Using this method, we investigate the electron pathway of graphene nanoribbons in various structures, molecular junctions, and black phosphorus nanoribbons. By analyzing the current flow through the structures, we find strong dependence on the structural geometry and the energy of the injected electrons. This method may be of general use in the study of nano-electronic materials and interfaces.

Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations.

Science.gov (United States)

Paul, Fabian; Noé, Frank; Weikl, Thomas R

2018-03-27

Unstructured proteins and peptides typically fold during binding to ligand proteins. A challenging problem is to identify the mechanism and kinetics of these binding-induced folding processes in experiments and atomistic simulations. In this Article, we present a detailed picture for the folding of the inhibitor peptide PMI into a helix during binding to the oncoprotein fragment 25-109 Mdm2 obtained from atomistic, explicit-water simulations and Markov state modeling. We find that binding-induced folding of PMI is highly parallel and can occur along a multitude of pathways. Some pathways are induced-fit-like with binding occurring prior to PMI helix formation, while other pathways are conformational-selection-like with binding after helix formation. On the majority of pathways, however, binding is intricately coupled to folding, without clear temporal ordering. A central feature of these pathways is PMI motion on the Mdm2 surface, along the binding groove of Mdm2 or over the rim of this groove. The native binding groove of Mdm2 thus appears as an asymmetric funnel for PMI binding. Overall, binding-induced folding of PMI does not fit into the classical picture of induced fit or conformational selection that implies a clear temporal ordering of binding and folding events. We argue that this holds in general for binding-induced folding processes because binding and folding events in these processes likely occur on similar time scales and do exhibit the time-scale separation required for temporal ordering.

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

Science.gov (United States)

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) .

Insight to structural subsite recognition in plant thiol protease-inhibitor complexes : Understanding the basis of differential inhibition and the role of water

Directory of Open Access Journals (Sweden)

Mukhopadhayay Bishnu P

2001-09-01

Full Text Available Abstract Background This work represents an extensive MD simulation / water-dynamics studies on a series of complexes of inhibitors (leupeptin, E-64, E-64-C, ZPACK and plant cysteine proteases (actinidin, caricain, chymopapain, calotropin DI of papain family to understand the various interactions, water binding mode, factors influencing it and the structural basis of differential inhibition. Results The tertiary structure of the enzyme-inhibitor complexes were built by visual interactive modeling and energy minimization followed by dynamic simulation of 120 ps in water environment. DASA study with and without the inhibitor revealed the potential subsite residues involved in inhibition. Though the interaction involving main chain atoms are similar, critical inspection of the complexes reveal significant differences in the side chain interactions in S2-P2 and S3-P3 pairs due to sequence differences in the equivalent positions of respective subsites leading to differential inhibition. Conclusion The key finding of the study is a conserved site of a water molecule near oxyanion hole of the enzyme active site, which is found in all the modeled complexes and in most crystal structures of papain family either native or complexed. Conserved water molecules at the ligand binding sites of these homologous proteins suggest the structural importance of the water, which changes the conventional definition of chemical geometry of inhibitor binding domain, its shape and complimentarity. The water mediated recognition of inhibitor to enzyme subsites (Pn...H2O....Sn of leupeptin acetyl oxygen to caricain, chymopapain and calotropinDI is an additional information and offer valuable insight to potent inhibitor design.

Atomistic Kinetic Monte Carlo studies of microchemical evolutions driven by diffusion processes under irradiation

Science.gov (United States)

Soisson, F.; Becquart, C. S.; Castin, N.; Domain, C.; Malerba, L.; Vincent, E.

2010-11-01

Atomistic Kinetic Monte Carlo (AKMC) simulations are a powerful tool to study the microstructural and microchemical evolution of alloys controlled by diffusion processes, under irradiation and during thermal ageing. In the framework of the FP6 Perfect program, two main approaches have been applied to binary and multicomponent iron based alloys. The first one is based on a diffusion model which takes into account vacancy and self-interstitial jumps, using simple rigid lattice approximation and broken-bond models to compute the point-defect jump frequencies. The corresponding parameters are fitted on ab initio calculations of a few typical configurations and migration barriers. The second method uses empirical potentials to compute a much larger number of migration barriers, including atomic relaxations, and Artificial Intelligence regression methods to predict the other ones. It is somewhat less rapid than the first one, but significantly more than simulations using "on-the-fly" calculations of all the barriers. We review here the recent advances and perspectives concerning these techniques.

Atomistic Kinetic Monte Carlo studies of microchemical evolutions driven by diffusion processes under irradiation

International Nuclear Information System (INIS)

Soisson, F.; Becquart, C.S.; Castin, N.; Domain, C.; Malerba, L.; Vincent, E.

2010-01-01

Atomistic Kinetic Monte Carlo (AKMC) simulations are a powerful tool to study the microstructural and microchemical evolution of alloys controlled by diffusion processes, under irradiation and during thermal ageing. In the framework of the FP6 Perfect program, two main approaches have been applied to binary and multicomponent iron based alloys. The first one is based on a diffusion model which takes into account vacancy and self-interstitial jumps, using simple rigid lattice approximation and broken-bond models to compute the point-defect jump frequencies. The corresponding parameters are fitted on ab initio calculations of a few typical configurations and migration barriers. The second method uses empirical potentials to compute a much larger number of migration barriers, including atomic relaxations, and Artificial Intelligence regression methods to predict the other ones. It is somewhat less rapid than the first one, but significantly more than simulations using 'on-the-fly' calculations of all the barriers. We review here the recent advances and perspectives concerning these techniques.

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

Science.gov (United States)

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.

Atomistic simulation of fatigue in face centred cubic metals

International Nuclear Information System (INIS)

Fan, Zhengxuan

2016-01-01

Fatigue is one of the major damage mechanisms of metals. It is characterized by strong environmental effects and wide lifetime dispersions which must be better understood. Different face centred cubic metals, al, Cu, Ni, and Ag are analyzed. The mechanical behaviour of surface steps naturally created by the glide of dislocations subjected to cyclic loading is examined using molecular dynamics simulations in vacuum and in air for Cu and Ni. an atomistic reconstruction phenomenon is observed at these surface steps which can induce strong irreversibility. Three different mechanisms of reconstruction are defined. Surface slip irreversibility under cyclic loading is analyzed. all surface steps are intrinsically irreversible under usual fatigue laboratory loading amplitude without the arrival of opposite sign dislocations on direct neighbor plane.With opposite sign dislocations on non direct neighbour planes, irreversibility cumulates cycle by cycle and a micro-notch is produced whose depth gradually increases.Oxygen environment affects the surface (first stage of oxidation) but does not lead to higher irreversibility as it has no major influence on the different mechanisms linked to surface relief evolution.a rough estimation of surface irreversibility is carried out for pure edge dislocations in persistent slip bands in so-called wavy materials. It gives an irreversibility fraction between 0.5 and 0.75 in copper in vacuum and in air, in agreement with recent atomic force microscopy measurements.Crack propagation mechanisms are simulated in inert environment. Cracks can propagate owing to the irreversibility of generated dislocations because of their mutual interactions up to the formation of dislocation junctions. (author) [fr

Radiation damage in Fe-Cr alloys: Atomistic studies

International Nuclear Information System (INIS)

Terentyev, Dmitry; Malerba, Lorenzo; Bonny, Giovanni; Castin, Nicolas

2009-01-01

High-Cr ferritic-martensitic steels are the most promising candidate structural materials for future advanced fission reactors, as well as for fusion systems, due to their better thermomechanical properties and higher radiation resistance as compared to austenitic steels. The performance of these steels, especially under irradiation, appears to be largely determined by the Cr content. For instance, the current choice of steel compositions around ∼9 wt% Cr is mainly based on the observation of a local minimum in the ductile-brittle transition temperature shift at this composition. On the other hand, reduced void swelling is observed between 3 and 12 wt% Cr. The origin of these and other Cr-dependent effects remained unexplained for a long time, thereby calling for a physical modelling effort addressing these questions. In this presentation, an overview is given on the effort made in recent years to construct a whole modelling framework, from ab initio to dislocations, to provide explanations to the above-mentioned issues. Ab initio calculations combined to the development of the interatomic potentials capable of grasping key features of Cr atoms embedded in perfect and defected Fe matrix, were required. Primary damage, defect migration, Cr mass transport, phase separation, Cr-defect segregation and dislocation-defect interactions could then be studied using fully atomistic approaches. Our research shows that many of the effects of Cr content on the behaviour of these alloys under irradiation can be attributed to the only recently highlighted high solubility of Cr in Fe (∼10 wt%), below which, in addition, Cr atoms tend to order. The presentation will clarify how this aspect, combined with the high affinity between Cr atoms and self-interstitials defects, influences and partly explain both microstructure evolution and mechanical behaviour of high-Cr steels under irradiation. (author)

Insights from LGI1 and CASPR2 potassium channel complex autoantibody subtyping.

Science.gov (United States)

Klein, Christopher J; Lennon, Vanda A; Aston, Paula A; McKeon, Andrew; O'Toole, Orna; Quek, Amy; Pittock, Sean J

2013-02-01

To determine, in patients identified as seropositive for neuronal voltage-gated potassium channel (VGKC) complex autoantibodies, the spectrum of clinical presentations and frequency of leucine-rich glioma-inactivated protein 1 (LGI1) and contactin-associated protein-like 2 (CASPR2) as defined antigenic neuronal targets in the VGKC macromolecular complex. Retrospective cohort study. Clinical practice, Mayo Clinic Neuroimmunology Laboratory and Department of Neurology. A total of 54 853 patients were evaluated, of whom 1992 were found to be VGKC complex IgG positive. From June 1, 2008, to June 30, 2010, comprehensive service serologic evaluation performed on 54853 patients with unexplained neurologic symptoms identified 1992 patients (4%) who were positive for VGKC complex IgG (values ≥ 0.03 nmol/L). Among 316 seropositive patients evaluated clinically at our institution, 82 (26%) were seropositive for LGI1 IgG and/or CASPR2 IgG. Of these 82 patients, 27% had low (0.03-0.09 nmol/L), 51% had medium (0.10-0.99 nmol/L), and 22% had high (≥ 1.00 nmol/L) VGKC complex IgG values. Leucine-rich glioma-inactivated protein 1 IgG positivity was associated with higher VGKC complex IgG values (PVGKC complex IgG values and varying LGI1 IgG and CASPR2 IgG specificities. The frequent occurrence of LGI1 IgG and CASPR2 IgG in serum samples with low and medium VGKC complex IgG values supports the clinical significance of low values in clinical evaluation. Additional antigenic components of VGKC macromolecular complexes remain to be defined.

Conventional and phenomics characterization provides insight into the diversity and relationships of hypervariable scarlet (Solanum aethiopicum L. and gboma (S. macrocarpon L. eggplant complexes

Directory of Open Access Journals (Sweden)

Mariola ePlazas

2014-07-01

Full Text Available Scarlet (Solanum aethiopicum and gboma (S. macrocarpon eggplants are major vegetable crops in sub-Saharan Africa. Together with their respective wild ancestors (S. anguivi and S. dasyphyllum and intermediate cultivated-wild forms they constitute the so-called scarlet and gboma eggplant complexes. We used conventional descriptors and the high-throughput phenomics tool Tomato Analyzer for characterizing 63 accessions of the scarlet eggplant complex, including the four S. aethiopicum cultivar groups (Aculeatum, Gilo, Kumba, and Shum, Intermediate S. aethiopicum-S. anguivi forms, and S. anguivi, and 12 cultivated and wild accessions of the gboma eggplant complex. A large diversity was found between both complexes, showing that they are very well differentiated from each other. Within the scarlet eggplant complex, many significant differences were also found among cultivar groups, but more differences were found for fruit traits evaluated with Tomato Analyzer than with conventional descriptors. In particular, Tomato Analyzer phenomics characterization was useful for distinguishing small fruited groups (Shum, Intermediate, and S. anguivi, as well as groups for which few or no significant differences were observed for plant traits. Multivariate principal components analysis (PCA separated well all groups, except the Intermediate group which plotted between S. anguivi and small fruited S. aethiopicum accessions. For the gboma eggplant complex, S. dasyphyllum was clearly distinguished from S. macrocarpon and an important diversity was found in the latter. The results have shown that both complexes are hypervariable and have provided insight into their diversity and relationships. The information obtained has important implications for the conservation and management of genetic resources as well as for the selection and breeding of both scarlet and gboma eggplants.

Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

Science.gov (United States)

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.

Ash'arite's atomistic conception of the physical world: A restatement

Energy Technology Data Exchange (ETDEWEB)

Pozi, Firdaus; Othman, Mohd Yusof [School of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia and Institute of Islam Hadhari, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan (Malaysia); Mohamed, Faizal [School of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan (Malaysia)

2013-11-27

Atomism plays an important role in the history of human thought. It can be traced back from Democritus atomos in the 500 BC to particle physics and quantum theory in the 21{sup st} century. However, as it being rejected and developed in the course of history of science, it still brings the fundamental question that perplexes physicists. It gives the views that the world is eternal; that the laws of nature is immutable and eternal therefore all phenomena can be determined through the laws and that there is no reality behind the quantum world. In this paper, we shall briefly describe all these three views on the nature of the physical world or universe and this include on the nature of matter. Then, we shall explain our stand on those conceptions based on the Ash'arites atomistic conception of the physical world. We hope this paper can shed a light on several fundamental issues in the conception of the universe and gives the proper response to them.

Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys

International Nuclear Information System (INIS)

Djurabekova, F.G.; Domingos, R.; Cerchiara, G.; Castin, N.; Vincent, E.; Malerba, L.

2007-01-01

Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed

Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys

Energy Technology Data Exchange (ETDEWEB)

Djurabekova, F.G. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Domingos, R. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Cerchiara, G. [Department of Nuclear and Production Engineering, University of Pisa (Italy); Castin, N. [Catholic University of Louvain-la-Neuve (Belgium); Vincent, E. [LMPGM UMR-8517, University of Lille I, Villeneuve d' Ascq (France); Malerba, L. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium)]. E-mail: lmalerba@sckcen.be

2007-02-15

Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed.

From empirical to ab initio: transferable potentials in the atomistic simulation of amorphous carbons

International Nuclear Information System (INIS)

Marks, N.A.; Goringe, C.M.; McKenzie, D.R.; McCulloch, D.G.; Royal Melbourne Institute of Technology University, Melbourne, VIC

2000-01-01

Full text: Silicon is often described as the prototype covalent material, and when it comes to developing atomistic models this situation is well described by the sentiment that 'everything works for silicon'. The same cannot be said for carbon though, where the interaction potential has always proved problematical, be it with empirical, tight-binding or ab initio methods. Thus far the most decisive contributions to understanding amorphous carbon networks have come from ab initio simulations using the Car-Parrinello method, where the fully quantum treatment of the valence electrons has provided unexpected insight into the local structure. However such first principles calculations are restricted spatially and temporally to systems with approximately 100 atoms and times of order one picosecond. There is therefore demand for less expensive techniques capable of resolving important questions whose solution can only to found with larger simulations running for longer times. In the case of tetrahedral amorphous carbon, such issues include the release of compressive stress through annealing, the origin of graphitic surface layers and the nature of the film growth process and thermal spike. Against this background tight-binding molecular dynamics has emerged as a popular alternative to first principles methods, and our group has an ongoing program to understand film growth using one of the efficient variants of tight-binding. Another direction of research is a new empirical potential based on the Environment Dependent Interaction Potential (EDIP) recently developed for silicon. The EDIP approach represents a promising direction for empirical potentials through its use of ab initio data to motivate the functional form as well as the more conventional parametrisation. By inverting ab initio cohesive energy curves the authors of EDIP arrived at a pair potential expression which reduces to the well-known Stillinger-Weber form at integer coordination, while providing

The Complexity of Indirect Translation

DEFF Research Database (Denmark)

Wenjie, L. I.

2017-01-01

its complex nature, and thus determined that many facets of ITr remain to be studied. The present article will try to encompass the complexity of ITr by looking into the reasons for translating indirectly, the challenge of finding out mediating texts (MTs), indirectness in both translation...... of which have been translated and interpreted indirectly through major languages like English, will be employed as examples. Hopefully, this study will offer more insights into the nature of translation as a social activity and raise further interests in studying translation as a complex phenomenon....

Unraveling interrelationships among psychopathology symptoms, cognitive domains and insight dimensions in chronic schizophrenia.

Science.gov (United States)

Xavier, Rose Mary; Pan, Wei; Dungan, Jennifer R; Keefe, Richard S E; Vorderstrasse, Allison

2018-03-01

Insight in schizophrenia is long known to have a complex relationship with psychopathology symptoms and cognition. However, very few studies have examined models that explain these interrelationships. In a large sample derived from the NIMH Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) schizophrenia trial (N=1391), we interrogated these interrelationships for potential causal pathways using structural equation modeling. Using the NIMH consensus model, latent variables were constructed for psychopathology symptom dimensions, including positive, negative, disorganized, excited and depressed from the Positive and Negative Syndrome Scale (PANSS) items. Neurocognitive variables were created from five predefined domains of working memory, verbal memory, reasoning, vigilance and processing speed. Illness insight and treatment insight were tested using latent variables constructed from the Illness and Treatment Attitude Questionnaire (ITAQ). Disorganized symptoms had the strongest effect on insight. Illness insight mediated the relationship of positive, depressed, and disorganized symptoms with treatment insight. Neurocognition mediated the relationship between disorganized and treatment insight and depressed symptoms and treatment insight. There was no effect of negative symptoms on either illness insight or treatment insight. Taken together, our results indicate overlapping and unique relational paths for illness and treatment insight dimensions, which could suggest differences in causal mechanisms and potential interventions to improve insight. Copyright © 2017 Elsevier B.V. All rights reserved.

Insight, psychopathology, explanatory models and outcome of schizophrenia in India: a prospective 5-year cohort study

Directory of Open Access Journals (Sweden)

Johnson Shanthi

2012-09-01

Full Text Available Abstract Background The sole focus of models of insight on bio-medical perspectives to the complete exclusion of local, non-medical and cultural constructs mandates review. This study attempted to investigate the impact of insight, psychopathology, explanatory models of illness on outcome of first episode schizophrenia. Method Patients diagnosed to have DSM IV schizophrenia (n = 131 were assessed prospectively for insight, psychopathology, explanatory models of illness at baseline, 6, 12 and 60 months using standard instruments. Multiple linear and logistic regression and generalized estimating equations (GEE were employed to assess predictors of outcome. Results We could follow up 95 (72.5% patients. Sixty-five of these patients (68.4% achieved remission. There was a negative relationship between psychosis rating and insight scores. Urban residence, fluctuating course of the initial illness, and improvement in global functioning at 6 months and lower psychosis rating at 12 months were significantly related to remission at 5 years. Insight scores, number of non-medical explanatory models and individual explanatory models held during the later course of the illness were significantly associated with outcome. Analysis of longitudinal data using GEE showed that women, rural residence, insight scores and number of non-medical explanatory models of illness held were significantly associated with BPRS scores during the study period. Conclusions Insight, the disease model and the number of non-medical model positively correlated with improvement in psychosis arguing for a complex interaction between the culture, context and illness variables. These finding argue that insight and explanatory models are secondary to psychopathology, course and outcome of the illness. The awareness of mental illness is a narrative act in which people make personal sense of the many challenges they face. The course and outcome of the illness, cultural context

Neurosurgical implications of Carney complex.

Science.gov (United States)

Watson, J C; Stratakis, C A; Bryant-Greenwood, P K; Koch, C A; Kirschner, L S; Nguyen, T; Carney, J A; Oldfield, E H

2000-03-01

The authors present their neurosurgical experience with Carney complex. Carney complex, characterized by spotty skin pigmentation, cardiac myxomas, primary pigmented nodular adrenocortical disease, pituitary tumors, and nerve sheath tumors (NSTs), is a recently described, rare, autosomal-dominant familial syndrome that is relatively unknown to neurosurgeons. Neurosurgery is required to treat pituitary adenomas and a rare NST, the psammomatous melanotic schwannoma (PMS), in patients with Carney complex. Cushing's syndrome, a common component of the complex, is caused by primary pigmented nodular adrenocortical disease and is not secondary to an adrenocorticotropic hormone-secreting pituitary adenoma. The authors reviewed 14 cases of Carney complex, five from the literature and nine from their own experience. Of the 14 pituitary adenomas recognized in association with Carney complex, 12 developed growth hormone (GH) hypersecretion (producing gigantism in two patients and acromegaly in 10), and results of immunohistochemical studies in one of the other two were positive for GH. The association of PMSs with Carney complex was established in 1990. Of the reported tumors, 28% were associated with spinal nerve sheaths. The spinal tumors occurred in adults (mean age 32 years, range 18-49 years) who presented with pain and radiculopathy. These NSTs may be malignant (10%) and, as with the cardiac myxomas, are associated with significant rates of morbidity and mortality. Because of the surgical comorbidity associated with cardiac myxoma and/or Cushing's syndrome, recognition of Carney complex has important implications for perisurgical patient management and family screening. Study of the genetics of Carney complex and of the biological abnormalities associated with the tumors may provide insight into the general pathobiological abnormalities associated with the tumors may provide insight into the general pathobiological features of pituitary adenomas and NSTs.

Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations

DEFF Research Database (Denmark)

Franova, M. D.; Vattulainen, I.; Ollila, O. H. S.

2014-01-01

The lateral pressure profile of lipid bilayers has gained a lot of attention, since changes in the pressure profile have been suggested to shift the membrane protein conformational equilibrium. This relation has been mostly studied with theoretical methods, especially with molecular dynamics....../monomer fluorescence ratio has been assumed to represent the lateral pressure in the location of the pyrene moieties. Here, we consider the validity of this assumption through atomistic molecular dynamics simulations in a DOPC (dioleoylphosphatidylcholine) membrane, which hosts di-pyr-PC probes with different acyl...... simulations, since established methods to measure the lateral pressure profile experimentally have not been available. The only experiments that have attempted to gauge the lateral pressure profile have been done by using di-pyrenyl-phosphatidylcholine (di-pyr-PC) probes. In these experiments, the excimer...

Structural insights into the p97-Ufd1-Npl4 complex

Science.gov (United States)

Pye, Valerie E.; Beuron, Fabienne; Keetch, Catherine A.; McKeown, Ciaran; Robinson, Carol V.; Meyer, Hemmo H.; Zhang, Xiaodong; Freemont, Paul S.

2007-01-01

p97/VCP (Cdc48 in yeast) is an essential and abundant member of the AAA+ family of ATPases and is involved in a number of diverse cellular pathways through interactions with different adaptor proteins. The two most characterized adaptors for p97 are p47 and the Ufd1 (ubiquitin fusion degradation 1)-Npl4 (nuclear protein localization 4) complex. p47 directs p97 to membrane fusion events and has been shown to be involved in protein degradation. The Ufd1-Npl4 complex directs p97 to an essential role in endoplasmic reticulum-associated degradation and an important role in mitotic spindle disassembly postmitosis. Here we describe the structural features of the Ufd1-Npl4 complex and its interaction with p97 with the aid of EM and other biophysical techniques. The Ufd1-Npl4 heterodimer has an elongated bilobed structure that is ≈80 × 30 Å in dimension. One Ufd1-Npl4 heterodimer is shown to interact with one p97 hexamer to form the p97-Ufd1-Npl4 complex. The Ufd1-Npl4 heterodimer emanates from one region on the periphery of the N-D1 plane of the p97 hexamer. Intriguingly, the p97-p47 and the p97-Ufd1-Npl4 complexes are significantly different in stoichiometry, symmetry, and quaternary arrangement, reflecting their specific actions and their ability to interact with additional cofactors that cooperate with p97 in diverse cellular pathways. PMID:17202270

Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations

DEFF Research Database (Denmark)

Heikkila, E.; Martinez-Seara, H.; Gurtovenko, A. A.

2014-01-01

Despite being chemically inert as a bulk material, nanoscale gold can pose harmful side effects to living organisms. In particular, cationic Au nanoparticles (AuNP+) of 2 nm diameter or less permeate readily through plasma membranes and induce cell death. We report atomistic simulations of cationic...... to be governed by cooperative effects where AuNP+, counterions, water, and the two membrane leaflets all contribute. On the extracellular side, we find that the nanoparticle has to cross a free energy barrier of about 5 k(B)T prior forming a stable contact with the membrane. This results in a rearrangement...

Ion specific correlations in bulk and at biointerfaces

International Nuclear Information System (INIS)

Kalcher, I; Horinek, D; Netz, R R; Dzubiella, J

2009-01-01

Ion specific effects are ubiquitous in any complex colloidal or biological fluid in bulk or at interfaces. The molecular origins of these 'Hofmeister effects' are not well understood and their theoretical description poses a formidable challenge to the modeling and simulation community. On the basis of the combination of atomistically resolved molecular dynamics (MD) computer simulations and statistical mechanics approaches, we present a few selected examples of specific electrolyte effects in bulk, at simple neutral and charged interfaces, and on a short α-helical peptide. The structural complexity in these strongly Coulomb-correlated systems is highlighted and analyzed in the light of available experimental data. While in general the comparison of MD simulations to experiments often lacks quantitative agreement, mostly because molecular force fields and coarse-graining procedures remain to be optimized, the consensus as regards trends provides important insights into microscopic hydration and binding mechanisms.

Ion specific correlations in bulk and at biointerfaces.

Science.gov (United States)

Kalcher, I; Horinek, D; Netz, R R; Dzubiella, J

2009-10-21

Ion specific effects are ubiquitous in any complex colloidal or biological fluid in bulk or at interfaces. The molecular origins of these 'Hofmeister effects' are not well understood and their theoretical description poses a formidable challenge to the modeling and simulation community. On the basis of the combination of atomistically resolved molecular dynamics (MD) computer simulations and statistical mechanics approaches, we present a few selected examples of specific electrolyte effects in bulk, at simple neutral and charged interfaces, and on a short α-helical peptide. The structural complexity in these strongly Coulomb-correlated systems is highlighted and analyzed in the light of available experimental data. While in general the comparison of MD simulations to experiments often lacks quantitative agreement, mostly because molecular force fields and coarse-graining procedures remain to be optimized, the consensus as regards trends provides important insights into microscopic hydration and binding mechanisms.

An Atomistic Modeling Study of Alloying Element Impurity Element, and Transmutation Products on the cohesion of A Nickel E5 {001} Twist Grain Boundary

International Nuclear Information System (INIS)

Young, G.A. Jr.; Najafabadi, R.; Strohmayer, W.; Baldrey, D.G.; Hamm, B.; Harris, J.; Sticht, J.; Wimmer, E.

2003-01-01

Atomistic modeling methods were employed to investigate the effects of impurity elements on the metallurgy, irradiation embrittlement, and environmentally assisted cracking of nickel-base alloys exposed to nuclear environments. Calculations were performed via ab initio atomistic modeling methods to ensure the accuracy and reliability of the results. A Griffith-type fracture criterion was used to quantitatively assess the effect of elements or element pairs on the grain boundary cohesive strength. In order of most embrittling to most strengthening, the elements are ranked as: He, Li, S, H, C, Zr, P, Fe, Mn, Nb, Cr, and B. Helium is strongly embrittling (-2.04 eV/atom lowering of the Griffith energy), phosphorus has little effect on the grain boundary (0.1 eV/atom), and boron offers appreciable strengthening (1.03 eV/atom increase in the Griffith energy). Calculations for pairs of elements (H-Li, H-B, H-C, H-P, and H-S) show little interaction on the grain boundary cohesive energy, so that for the conditions studied, linear superposition of elemental effects is a good approximation. These calculations help explain metallurgical effects (e.g. why boron can strengthen grain boundaries), irradiation embrittlement (e.g. how boron transmutation results in grain boundary embrittlement), as well as how grain boundary impurity elements can affect environmentally assisted cracking (i.e. low temperature crack propagation and stress corrosion cracking) of nickel-base alloys

New insight into the ternary complexes of uranyl carbonate in seawater.

Science.gov (United States)

Beccia, M R; Matara-Aho, M; Reeves, B; Roques, J; Solari, P L; Monfort, M; Moulin, C; Den Auwer, C

2017-11-01

Uranium is naturally present in seawater at trace levels and may in some cases be present at higher concentrations, due to anthropogenic nuclear activities. Understanding uranium speciation in seawater is thus essential for predicting and controlling its behavior in this specific environmental compartment and consequently, its possible impact on living organisms. The carbonato calcic complex Ca 2 UO 2 (CO 3 ) 3 was previously identified as the main uranium species in natural seawater, together with CaUO 2 (CO 3 ) 3 2- . In this work, we further investigate the role of the alkaline earth cation in the structure of the ternary uranyl-carbonate complexes. For this purpose, artificial seawater, free of Mg 2+ and Ca 2+ , using Sr 2+ as a spectroscopic probe was prepared. Combining TRLIF and EXAFS spectroscopy, together with DFT and theoretical thermodynamic calculations, evidence for the presence of Sr alkaline earth counter ion in the complex structure can be asserted. Furthermore, data suggest that when Ca 2+ is replaced by Sr 2+ , SrUO 2 (CO 3 ) 3 2- is the main complex in solution and it occurs with the presence of at least one monodentate carbonate in the uranyl coordination sphere. Copyright © 2017 Elsevier Ltd. All rights reserved.

Anharmonic phonon-phonon scattering modeling of three-dimensional atomistic transport: An efficient quantum treatment

Science.gov (United States)

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.

Atomistic modeling of zirconium hydride precipitation: methodology for deriving a tight-binding potential

International Nuclear Information System (INIS)

Dufresne, Alice

2014-01-01

The zirconium-hydrogen system is of nuclear safety interest, as the hydride precipitation leads to the cladding embrittlement, which is made of zirconium-based alloys. The cladding is the first safety barrier confining the radioactive products: its integrity shall be kept during the entire fuel-assemblies life, in reactor, including accidental situation, and post-operation (transport and storage). Many uncertainties remain regarding the hydrides precipitation kinetics and the local stress impact on their precipitation. The atomic scale modeling of this system would bring clarifications on the relevant mechanisms. The usual atomistic modeling methods are based on thermo-statistic approaches, whose precision and reliability depend on the interatomic potential used. However, there was no potential allowing a rigorous study of the Zr-H system. The present work has indeed addressed this issue: a new tight-binding potential for zirconium hydrides modeling is now available. Moreover, this thesis provides a detailed manual for deriving such potentials accounting for spd hybridization, and fitted here on DFT results. This guidebook has be written in light of modeling a pure transition metal followed by a metal-covalent coupling (metallic carbides, nitrides and silicides). (author)

Multiscale modeling of dislocation processes in BCC tantalum: bridging atomistic and mesoscale simulations

International Nuclear Information System (INIS)

Yang, L H; Tang, M; Moriarty, J A

2001-01-01

Plastic deformation in bcc metals at low temperatures and high-strain rates is controlled by the motion of a/2 screw dislocations, and understanding the fundamental atomistic processes of this motion is essential to develop predictive multiscale models of crystal plasticity. The multiscale modeling approach presented here for bcc Ta is based on information passing, where results of simulations at the atomic scale are used in simulations of plastic deformation at mesoscopic length scales via dislocation dynamics (DD). The relevant core properties of a/2 screw dislocations in Ta have been obtained using quantum-based interatomic potentials derived from model generalized pseudopotential theory and an ab-initio data base together with an accurate Green's-function simulation method that implements flexible boundary conditions. In particular, the stress-dependent activation enthalpy for the lowest-energy kink-pair mechanism has been calculated and fitted to a revealing analytic form. This is the critical quantity determining dislocation mobility in the DD simulations, and the present activation enthalpy is found to be in good agreement with the previous empirical form used to explain the temperature dependence of the yield stress

Organometallic neptunium(III) complexes.

Science.gov (United States)

Dutkiewicz, Michał S; Farnaby, Joy H; Apostolidis, Christos; Colineau, Eric; Walter, Olaf; Magnani, Nicola; Gardiner, Michael G; Love, Jason B; Kaltsoyannis, Nikolas; Caciuffo, Roberto; Arnold, Polly L

2016-08-01

Studies of transuranic organometallic complexes provide a particularly valuable insight into covalent contributions to the metal-ligand bonding, in which the subtle differences between the transuranium actinide ions and their lighter lanthanide counterparts are of fundamental importance for the effective remediation of nuclear waste. Unlike the organometallic chemistry of uranium, which has focused strongly on U(III) and has seen some spectacular advances, that of the transuranics is significantly technically more challenging and has remained dormant. In the case of neptunium, it is limited mainly to Np(IV). Here we report the synthesis of three new Np(III) organometallic compounds and the characterization of their molecular and electronic structures. These studies suggest that Np(III) complexes could act as single-molecule magnets, and that the lower oxidation state of Np(II) is chemically accessible. In comparison with lanthanide analogues, significant d- and f-electron contributions to key Np(III) orbitals are observed, which shows that fundamental neptunium organometallic chemistry can provide new insights into the behaviour of f-elements.

Organometallic neptunium(III) complexes

Science.gov (United States)

Dutkiewicz, Michał S.; Farnaby, Joy H.; Apostolidis, Christos; Colineau, Eric; Walter, Olaf; Magnani, Nicola; Gardiner, Michael G.; Love, Jason B.; Kaltsoyannis, Nikolas; Caciuffo, Roberto; Arnold, Polly L.

2016-08-01

Studies of transuranic organometallic complexes provide a particularly valuable insight into covalent contributions to the metal-ligand bonding, in which the subtle differences between the transuranium actinide ions and their lighter lanthanide counterparts are of fundamental importance for the effective remediation of nuclear waste. Unlike the organometallic chemistry of uranium, which has focused strongly on UIII and has seen some spectacular advances, that of the transuranics is significantly technically more challenging and has remained dormant. In the case of neptunium, it is limited mainly to NpIV. Here we report the synthesis of three new NpIII organometallic compounds and the characterization of their molecular and electronic structures. These studies suggest that NpIII complexes could act as single-molecule magnets, and that the lower oxidation state of NpII is chemically accessible. In comparison with lanthanide analogues, significant d- and f-electron contributions to key NpIII orbitals are observed, which shows that fundamental neptunium organometallic chemistry can provide new insights into the behaviour of f-elements.

Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Orlowski, A.; St-Pierre, J. F.; Magarkar, A.

2011-01-01

We used atomistic simulations to study the membrane-bound form of catechol-O-methyltransferase (MB-COMT). In particular we investigated the 26-residue transmembrane a-helical segment of MB-COMT together with the 24-residue fragment that links the transmembrane component to the main protein unit...... that was not included in our model. In numerous independent simulations we observed the formation of a salt bridge between ARC 27 and GLU40. The salt bridge closed the flexible loop that formed in the linker and kept it in the vicinity of the membrane-water interface. All simulations supported this conclusion...... that the linker has a clear affinity for the interface and preferentially arranges its residues to reside next to the membrane, without a tendency to relocate into the water phase. Furthermore, an extensive analysis of databases for sequences of membrane proteins that have a single transmembrane helical segment...

Complexity, Connections, and Soul-Work

Science.gov (United States)

Bloch, Deborah P.

2008-01-01

Organizational theory and personal behaviors are both shaped by contemporary thinking and theories regarding spirituality, history, and the order, shape, and direction of modern culture. Complexity theory, discussed in this article, offers some helpful insights into appreciating the relationships and connections often overlooked in today's…

Degenerate Ising model for atomistic simulation of crystal-melt interfaces

Energy Technology Data Exchange (ETDEWEB)

Schebarchov, D., E-mail: Dmitri.Schebarchov@gmail.com [University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Schulze, T. P., E-mail: schulze@math.utk.edu [Department of Mathematics, University of Tennessee, Knoxville, Tennessee 37996-1300 (United States); Hendy, S. C. [The MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6140 (New Zealand); Department of Physics, University of Auckland, Auckland 1010 (New Zealand)

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) lattices 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.

Degenerate Ising model for atomistic simulation of crystal-melt interfaces

International Nuclear Information System (INIS)

Schebarchov, D.; Schulze, T. P.; Hendy, S. C.

2014-01-01

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) lattices 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

Molecular dynamic simulation of the self-assembly of DAP12-NKG2C activating immunoreceptor complex.

Directory of Open Access Journals (Sweden)

Peng Wei

Full Text Available The DAP12-NKG2C activating immunoreceptor complex is one of the multisubunit transmembrane protein complexes in which ligand-binding receptor chains assemble with dimeric signal-transducing modules through non-covalent associations in their transmembrane (TM domains. In this work, both coarse grained and atomistic molecular dynamic simulation methods were applied to investigate the self-assembly dynamics of the transmembrane domains of the DAP12-NKG2C activating immunoreceptor complex. Through simulating the dynamics of DAP12-NKG2C TM heterotrimer and point mutations, we demonstrated that a five-polar-residue motif including: 2 Asps and 2 Thrs in DAP12 dimer, as well as 1 Lys in NKG2C TM plays an important role in the assembly structure of the DAP12-NKG2C TM heterotrimer. Furthermore, we provided clear evidences to exclude the possibility that another NKG2C could stably associate with the DAP12-NKG2C heterotrimer. Based on the simulation results, we proposed a revised model for the self-assembly of DAP12-NKG2C activating immunoreceptor complex, along with a plausible explanation for the association of only one NKG2C with a DAP12 dimer.

Intraparticulate Metal Speciation Analysis of Soft Complexing Nanoparticles. The Intrinsic Chemical Heterogeneity of Metal-Humic Acid Complexes

DEFF Research Database (Denmark)

Town, R. M.; van Leeuwen, Herman P.

2016-01-01

ion condensation potential for higher valency counterions within the intraparticulate double layer zone of the soft NP. The approach offers new insights into the intrinsic heterogeneity of the HA. complexes, as revealed by the intraparticulate speciation as a function of the true degree of inner......-sphere complexation, theta(M). The ensuing intrinsic heterogeneity parameters, Gamma, for CdHA and CuHA complexes are in very good agreement with those obtained from dynamic electrochemical stripping chronopotentiometric measurements. The overall intraparticulate metal ion speciation is found to depend on theta...

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

Science.gov (United States)

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.

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations.

Science.gov (United States)

Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo

2016-01-21

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.

New insights into the evolutionary history of biological nitrogen fixation

Directory of Open Access Journals (Sweden)

Eric eBoyd

2013-08-01

Full Text Available Nitrogenase, which catalyzes the ATP-dependent reduction of dinitrogen (N2 to ammonia (NH3, accounts for roughly half of the bioavailable nitrogen supporting extant life. The fundamental requirement for fixed forms of nitrogen for life on Earth, both at present and in the past, has led to broad and significant interest in the origin and evolution of this fundamental biological process. One key question is whether the limited availability of fixed nitrogen was a factor in life’s origin or whether there were ample sources of fixed nitrogen produced by abiotic processes or delivered through the weathering of bolide impact materials to support this early life. If the latter, the key questions become what were the characteristics of the environment that precipitated the evolution of this oxygen sensitive process, when did this occur, and how was its subsequent evolutionary history impacted by the advent of oxygenic photosynthesis and the rise of oxygen in the Earth’s biosphere. Since the availability of fixed sources of nitrogen capable of supporting early life is difficult to glean from the geologic record, there are limited means to get direct insights into these questions. Indirect insights, however, can be gained by deep phylogenetic studies of nitrogenase structural gene products and additional gene products involved in the biosynthesis of the complex metal-containing prosthetic groups associated with this enzyme complex. Insights gained from such studies, as reviewed herein, challenge traditional models for the evolution of biological nitrogen fixation and provide the basis for the development of new conceptual models that explain the stepwise evolution of this highly complex and life sustaining process.

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Science.gov (United States)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Insight in paranoia: The role of experiential avoidance and internalized stigma.

Science.gov (United States)

Valiente, Carmen; Provencio, Maria; Espinosa, Regina; Duque, Almudena; Everts, Franziska

2015-05-01

Evidence suggests that insight in psychosis has been related to treatment adherence, recovery and good prognosis, but also to depression, low self-esteem, and diminished quality of life. Thus, insight might not be advantageous under all circumstances. Internalized-stigma (i.e. self-acceptance of stigmatizing images of illness) and experiential avoidance (i.e. unwillingness to experience negative private events) have been proposed as moderating variables between insight, and psychological health variables and/or distress. We investigated the patterns of association of insight with satisfaction with life, self-esteem, depression, anxiety and psychotic psychopathology as moderated by self-stigmatizing beliefs and experiential avoidance, in a sample of 47 participants with persecutory beliefs and diagnosed with schizophrenia or other psychotic disorder. Moderation analyses confirm the importance of internalized-stigma and experiential avoidance. The presence of insight was associated with more depression when there were high levels of self-stigma. Whereas, the absence of insight was associated with a greater life satisfaction when there were high levels of experiential avoidance. To summarize, our results help understand the complex relationship between insight, psychological health variables and emotional distress, pointing to a differential pattern of moderation for negative and positive outcomes. We discuss the implications of these results for research and treatment of paranoia. Copyright © 2015 Elsevier B.V. All rights reserved.

Thinking in complexity the complex dynamics of matter, mind, and mankind

CERN Document Server

Mainzer, Klaus

1994-01-01

The theory of nonlinear complex systems has become a successful and widely used problem-solving approach in the natural sciences - from laser physics, quantum chaos and meteorology to molecular modeling in chemistry and computer simulations of cell growth in biology In recent times it has been recognized that many of the social, ecological and political problems of mankind are also of a global, complex and nonlinear nature And one of the most exciting topics of present scientific and public interest is the idea that even the human mind is governed largely by the nonlinear dynamics of complex systems In this wide-ranging but concise treatment Prof Mainzer discusses, in nontechnical language, the common framework behind these endeavours Special emphasis is given to the evolution of new structures in natural and cultural systems and it is seen clearly how the new integrative approach of complexity theory can give new insights that were not available using traditional reductionistic methods

An insight into the complex prion-prion interaction network in the budding yeast Saccharomyces cerevisiae.

Science.gov (United States)

Du, Zhiqiang; Valtierra, Stephanie; Li, Liming

2014-01-01

The budding yeast Saccharomyces cerevisiae is a valuable model system for studying prion-prion interactions as it contains multiple prion proteins. A recent study from our laboratory showed that the existence of Swi1 prion ([SWI(+)]) and overproduction of Swi1 can have strong impacts on the formation of 2 other extensively studied yeast prions, [PSI(+)] and [PIN(+)] ([RNQ(+)]) (Genetics, Vol. 197, 685-700). We showed that a single yeast cell is capable of harboring at least 3 heterologous prion elements and these prions can influence each other's appearance positively and/or negatively. We also showed that during the de novo [PSI(+)] formation process upon Sup35 overproduction, the aggregation patterns of a preexisting inducer ([RNQ(+)] or [SWI(+)]) can undergo significant remodeling from stably transmitted dot-shaped aggregates to aggregates that co-localize with the newly formed Sup35 aggregates that are ring/ribbon/rod- shaped. Such co-localization disappears once the newly formed [PSI(+)] prion stabilizes. Our finding provides strong evidence supporting the "cross-seeding" model for prion-prion interactions and confirms earlier reports that the interactions among different prions and their prion proteins mostly occur at the initiation stages of prionogenesis. Our results also highlight a complex prion interaction network in yeast. We believe that elucidating the mechanism underlying the yeast prion-prion interaction network will not only provide insight into the process of prion de novo generation and propagation in yeast but also shed light on the mechanisms that govern protein misfolding, aggregation, and amyloidogenesis in higher eukaryotes.

Complex land systems: the need for long time perspectives to assess their future

DEFF Research Database (Denmark)

Dearing,, John A.; Braimoh, Ademola K.; Reenberg, Anette

2010-01-01

) temporal perspectives on complex system behavior that can provide insights through both analog and evolutionary approaches. Analogs are useful in generating typologies of generic system behavior, whereas evolutionary assessments provide insight into site-specific system properties. Four dimensions...

The application of graph theoretical analysis to complex networks in the brain

NARCIS (Netherlands)

Reijneveld, Jaap C.; Ponten, Sophie C.; Berendse, Henk W.; Stam, Cornelis J.

2007-01-01

Considering the brain as a complex network of interacting dynamical systems offers new insights into higher level brain processes such as memory, planning, and abstract reasoning as well as various types of brain pathophysiology. This viewpoint provides the opportunity to apply new insights in

Insight in schizophrenia spectrum disorders: relationship with behavior, mood and perceived quality of life, underlying causes and emerging treatments.

Science.gov (United States)

Lysaker, Paul H; Pattison, Michelle L; Leonhardt, Bethany L; Phelps, Scott; Vohs, Jenifer L

2018-02-01

Poor insight in schizophrenia is prevalent across cultures and phases of illness. In this review, we examine the recent research on the relationship of insight with behavior, mood and perceived quality of life, on its complex roots, and on the effects of existing and emerging treatments. This research indicates that poor insight predicts poorer treatment adherence and therapeutic alliance, higher symptom severity and more impaired community function, while good insight predicts a higher frequency of depression and demoralization, especially when coupled with stigma and social disadvantage. This research also suggests that poor insight may arise in response to biological, experiential, neuropsychological, social-cognitive, metacognitive and socio-political factors. Studies of the effects of existing and developing treatments indicate that they may influence insight. In the context of earlier research and historical models, these findings support an integrative model of poor insight. This model suggests that insight requires the integration of information about changes in internal states, external circumstances, others' perspectives and life trajectory as well as the multifaceted consequences and causes of each of those changes. One implication is that treatments should, beyond providing education, seek to assist persons with schizophrenia to integrate the broad range of complex and potentially deeply painful experiences which are associated with mental illness into their own personally meaningful, coherent and adaptive picture. © 2018 World Psychiatric Association.

Correlation between self-diffusion in Si and the migration mechanisms of vacancies and self-interstitials: An atomistic study

International Nuclear Information System (INIS)

Posselt, M.; Gao, F.; Bracht, H.

2008-01-01

The migration of point defects in silicon and the corresponding atomic mobility are investigated by comprehensive classical molecular-dynamics simulations using the Stillinger-Weber potential and the Tersoff potential. In contrast to most of the previous studies both the point defect diffusivity and the self-diffusion coefficient per defect are calculated separately so that the diffusion-correlation factor can be determined. Simulations with both the Stillinger-Weber and the Tersoff potential show that vacancy migration is characterized by the transformation of the tetrahedral vacancy to the split vacancy and vice versa and the diffusion-correlation factor f V is about 0.5. This value was also derived by the statistical diffusion theory under the assumption of the same migration mechanism. The mechanisms of self-interstitial migration are more complex. The detailed study, including a visual analysis and investigations with the nudged elastic band method, reveals a variety of transformations between different self-interstitial configurations. Molecular-dynamics simulations using the Stillinger-Weber potential show that the self-interstitial migration is dominated by a dumbbell mechanism, whereas in the case of the Tersoff potential the interstitialcy mechanism prevails. The corresponding values of the correlation factor f I are different, namely, 0.59 and 0.69 for the dumbbell and the interstitialcy mechanisms, respectively. The latter value is nearly equal to that obtained by the statistical theory which assumes the interstitialcy mechanism. Recent analysis of experimental results demonstrated that in the framework of state-of-the-art diffusion and reaction models the best interpretation of point defect data can be given by assuming f I ≅0.6. The comparison with the present atomistic study leads to the conclusion that the self-interstitial migration in Si should be governed by a dumbbell mechanism

Lack of FTSH4 Protease Affects Protein Carbonylation, Mitochondrial Morphology, and Phospholipid Content in Mitochondria of Arabidopsis: New Insights into a Complex Interplay.

Science.gov (United States)

Smakowska, Elwira; Skibior-Blaszczyk, Renata; Czarna, Malgorzata; Kolodziejczak, Marta; Kwasniak-Owczarek, Malgorzata; Parys, Katarzyna; Funk, Christiane; Janska, Hanna

2016-08-01

FTSH4 is one of the inner membrane-embedded ATP-dependent metalloproteases in mitochondria of Arabidopsis (Arabidopsis thaliana). In mutants impaired to express FTSH4, carbonylated proteins accumulated and leaf morphology was altered when grown under a short-day photoperiod, at 22°C, and a long-day photoperiod, at 30°C. To provide better insight into the function of FTSH4, we compared the mitochondrial proteomes and oxyproteomes of two ftsh4 mutants and wild-type plants grown under conditions inducing the phenotypic alterations. Numerous proteins from various submitochondrial compartments were observed to be carbonylated in the ftsh4 mutants, indicating a widespread oxidative stress. One of the reasons for the accumulation of carbonylated proteins in ftsh4 was the limited ATP-dependent proteolytic capacity of ftsh4 mitochondria, arising from insufficient ATP amount, probably as a result of an impaired oxidative phosphorylation (OXPHOS), especially complex V. In ftsh4, we further observed giant, spherical mitochondria coexisting among normal ones. Both effects, the increased number of abnormal mitochondria and the decreased stability/activity of the OXPHOS complexes, were probably caused by the lower amount of the mitochondrial membrane phospholipid cardiolipin. We postulate that the reduced cardiolipin content in ftsh4 mitochondria leads to perturbations within the OXPHOS complexes, generating more reactive oxygen species and less ATP, and to the deregulation of mitochondrial dynamics, causing in consequence the accumulation of oxidative damage. © 2016 American Society of Plant Biologists. All Rights Reserved.

Pedagogy of complex relationality exploring complexity theory, neuro-phenomenology, and attentiveness for education

Science.gov (United States)

Khattar, Randa

What do the new sciences of complex relationality offer education? This work draws on complexity theory, neurological understandings of biology and phenomenology, and attentiveness to study what the new sciences might offer education and the possibilities of a pedagogical understanding of embodied knowing. Complexity theory provides understandings of local-global relationality, self-organization, far-from-equilibrium conditions, and emergent dynamics that are important for describing pedagogical relationality. In itself, however, complexity theory is lacking an attention to issues of embodiment that respond directly to an ethical understanding of relationality. Phenomenology provides important views on the human experience of perception, for example, Merleau-Ponty's, whose research opens up possibilities for embodiment and attentiveness. At the level of pedagogical practice, I will pose, following biologists Humberto Maturana and Francisco Varela's autopoietic self-making understanding of life, that attentiveness perspectives, which have been largely absent from western pedagogical theory and practice, are crucial to promoting embodied knowing for education. Maturana and Varela's autopoietic perspective offers an embodied understanding of living---and therefore education---which opens up necessary attentive spaces to listen to one another in non judgmental awareness in the present moment of experience. I offer insights into a relationally complex conception of education drawing on this biological and autopoietically-grounded framework. These insights are framed in the context of five clusters of relations: (1) emergence, far-from-equilibrium, and local-global relationality; (2) autopoietic autonomy, structural determination and sensory-motor coupling; (3) triggering perturbations, structural plasticity, and autopoietic organization; (4) knowing as adequate action, domains of interaction, and blind spots; and (5) attentiveness and responsive relationality. Four

Atomistic structure of cobalt-phosphate nanoparticles for catalytic water oxidation.

Science.gov (United States)

Hu, Xiao Liang; Piccinin, Simone; Laio, Alessandro; Fabris, Stefano

2012-12-21

Solar-driven water splitting is a key photochemical reaction that underpins the feasible and sustainable production of solar fuels. An amorphous cobalt-phosphate catalyst (Co-Pi) based on earth-abundant elements has been recently reported to efficiently promote water oxidation to protons and dioxygen, a main bottleneck for the overall process. The structure of this material remains largely unknown. We here exploit ab initio and classical atomistic simulations combined with metadynamics to build a realistic and statistically meaningful model of Co-Pi nanoparticles. We demonstrate the emergence and stability of molecular-size ordered crystallites in nanoparticles initially formed by a disordered Co-O network and phosphate groups. The stable crystallites consist of bis-oxo-bridged Co centers that assemble into layered structures (edge-sharing CoO(6) octahedra) as well as in corner- and face-sharing cubane units. These layered and cubane motifs coexist in the crystallites, which always incorporate disordered phosphate groups at the edges. Our computational nanoparticles, although limited in size to ~1 nm, can contain more than one crystallite and incorporate up to 18 Co centers in the cubane/layered structures. The crystallites are structurally stable up to high temperatures. We simulate the extended X-ray absorption fine structure (EXAFS) of our nanoparticles. Those containing several complete and incomplete cubane motifs-which are believed to be essential for the catalytic activity-display a very good agreement with the experimental EXAFS spectra of Co-Pi grains. We propose that the crystallites in our nanoparticles are reliable structural models of the Co-Pi catalyst surface. They will be useful to reveal the origin of the catalytic efficiency of these novel water-oxidation catalysts.

Modeling Double Subjectivity for Gaining Programmable Insights: Framing the Case of Uber

Directory of Open Access Journals (Sweden)

Loretta Henderson Cheeks

2017-09-01

Full Text Available The Internet is the premier platform that enable the emergence of new technologies. Online news is unstructured narrative text that embeds facts, frames, and amplification that can influence society attitudes about technology adoption. Online news sources are carriers of voluminous amounts of news for reaching significantly large audience and have no geographical or time boundaries. The interplay of complex and dynamical forces among authors and readers allow for progressive emergent and latent properties to exhibit. Our concept of “Double subjectivity” provides a new paradigm for exploring complementary programmable insights of deeply buried meanings in a system. The ability to understand internal embeddedness in a large collection of related articles are beyond the reach of existing computational tools, and are hence left to human readers with unscalable results. This paper uncovers the potential to utilize advanced machine learning in a new way to automate the understanding of implicit structures and their associated latent meanings to give an early human-level insight into emergent technologies, with a concrete example of “Uber”. This paper establishes the new concept of double subjectivity as an instrument for large-scale machining of unstructured text and introduces a social influence model for the discovery of distinct pathways into emerging technology, and hence an insight. The programmable insight reveals early spatial and temporal opinion shift monitoring in complex networks in a structured way for computational treatment and visualization.

A Long-Range Electric Field Solver for Molecular Dynamics Based on Atomistic-to-Continuum Modeling.

Science.gov (United States)

Templeton, Jeremy A; Jones, Reese E; Lee, Jonathan W; Zimmerman, Jonathan A; Wong, Bryan M

2011-06-14

Understanding charge transport processes at a molecular level is currently hindered by a lack of appropriate models for incorporating nonperiodic, anisotropic electric fields in molecular dynamics (MD) simulations. In this work, we develop a model for including electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and the algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. Our model represents the electric potential on a FE mesh satisfying a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagate to each atom through modified forces. The method is verified using simulations where analytical solutions are known or comparisons can be made to existing techniques. In addition, a calculation of a salt water solution in a silicon nanochannel is performed to demonstrate the method in a target scientific application in which ions are attracted to charged surfaces in the presence of electric fields and interfering media.

Insights into the Halogen Oxidative Addition Reaction to Dinuclear Gold(I) Di(NHC) Complexes

KAUST Repository

Baron, Marco

2016-06-14

Gold(I) dicarbene complexes [Au2(MeIm-Y-ImMe)2](PF6)2(Y=CH2(1), (CH2)2(2), (CH2)4(4), MeIm=1-methylimidazol-2-ylidene) react with iodine to give the mixed-valence complex [Au(MeIm-CH2-ImMe)2AuI2](PF6)2(1 aI) and the gold(III) complexes [Au2I4(MeIm-Y-ImMe)2](PF6)2(2 cIand 4 cI). Reaction of complexes 1 and 2 with an excess of ICl allows the isolation of the tetrachloro gold(III) complexes [Au2Cl4(MeIm-CH2-ImMe)2](PF6)2(1 cCl) and [Au2Cl4(MeIm-(CH2)2-ImMe)2](Cl)2(2 cCl-Cl) (as main product); remarkably in the case of complex 2, the X-ray molecular structure of the crystals also shows the presence of I-Au-Cl mixed-sphere coordination. The same type of coordination has been observed in the main product of the reaction of complexes 3 or 4 with ICl. The study of the reactivity towards the oxidative addition of halogens to a large series of dinuclear bis(dicarbene) gold(I) complexes has been extended and reviewed. The complexes react with Cl2, Br2and I2to give the successive formation of the mixed-valence gold(I)/gold(III) n aXand gold(III) n cX(excluding compound 1 cI) complexes. However, complex 3 affords with Cl2and Br2the gold(II) complex 3 bX[Au2X2(MeIm-(CH2)3-ImMe)2](PF6)2(X=Cl, Br), which is the predominant species over compound 3 cXeven in the presence of free halogen. The observed different relative stabilities of the oxidised complexes of compounds 1 and 3 have also been confirmed by DFT calculations. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design and Use of a Learning Object for Finding Complex Polynomial Roots

Science.gov (United States)

Benitez, Julio; Gimenez, Marcos H.; Hueso, Jose L.; Martinez, Eulalia; Riera, Jaime

2013-01-01

Complex numbers are essential in many fields of engineering, but students often fail to have a natural insight of them. We present a learning object for the study of complex polynomials that graphically shows that any complex polynomials has a root and, furthermore, is useful to find the approximate roots of a complex polynomial. Moreover, we…

In situ observations of the atomistic mechanisms of Ni catalyzed low temperature graphene growth.

Science.gov (United States)

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.

Structural and functional insights into the malaria parasite moving junction complex.

Directory of Open Access Journals (Sweden)

Brigitte Vulliez-Le Normand

Full Text Available Members of the phylum Apicomplexa, which include the malaria parasite Plasmodium, share many features in their invasion mechanism in spite of their diverse host cell specificities and life cycle characteristics. The formation of a moving junction (MJ between the membranes of the invading apicomplexan parasite and the host cell is common to these intracellular pathogens. The MJ contains two key parasite components: the surface protein Apical Membrane Antigen 1 (AMA1 and its receptor, the Rhoptry Neck Protein (RON complex, which is targeted to the host cell membrane during invasion. In particular, RON2, a transmembrane component of the RON complex, interacts directly with AMA1. Here, we report the crystal structure of AMA1 from Plasmodium falciparum in complex with a peptide derived from the extracellular region of PfRON2, highlighting clear specificities of the P. falciparum RON2-AMA1 interaction. The receptor-binding site of PfAMA1 comprises the hydrophobic groove and a region that becomes exposed by displacement of the flexible Domain II loop. Mutations of key contact residues of PfRON2 and PfAMA1 abrogate binding between the recombinant proteins. Although PfRON2 contacts some polymorphic residues, binding studies with PfAMA1 from different strains show that these have little effect on affinity. Moreover, we demonstrate that the PfRON2 peptide inhibits erythrocyte invasion by P. falciparum merozoites and that this strong inhibitory potency is not affected by AMA1 polymorphisms. In parallel, we have determined the crystal structure of PfAMA1 in complex with the invasion-inhibitory peptide R1 derived by phage display, revealing an unexpected structural mimicry of the PfRON2 peptide. These results identify the key residues governing the interactions between AMA1 and RON2 in P. falciparum and suggest novel approaches to antimalarial therapeutics.

COMPLEX PROMOTIONSIN RETAIL

Directory of Open Access Journals (Sweden)

O. Yusupova

2015-10-01

Full Text Available Complex promotions used by retailers introduce to the consumers several rules that must be satisfied in order to get some benefits and usually refer to multiple products (e.g. “buy two, get one free”. Rules of complex promotions can be quite sophisticated and complicated themselves. Since diversity of complex promotions limited only by marketers’ imagination we can observe broad variety of promotions’ rules and representa¬tions of those rules in retailers’ commercials. Such diversification makes no good for fellow scientist who’s trying to sort all type of promotions into the neatly organized classification. Although we can simple add every single set of rules offered by retailers as a separate form of sales promotion it seems not to be the best way of dealing with such a problem. The better way is to realize that mechanisms underlying that variety of promotions are basically the same, namely changes in demand or quantity demanded. Those two concepts alone provide powerful insight into classification of complex promotions and allow us to comprehend the variety of promotions offered by marketers nowadays.

Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

Science.gov (United States)

Martin, Daniel R.; Matyushov, Dmitry V.

2015-04-01

Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ˜0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

International Nuclear Information System (INIS)

Martin, Daniel R.; Matyushov, Dmitry V.

2015-01-01

Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc 1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins

Defects and impurities in silicon materials an introduction to atomic-level silicon engineering

CERN Document Server

Langouche, Guido

2015-01-01

This book emphasizes the importance of the fascinating atomistic insights into the defects and the impurities as well as the dynamic behaviors in silicon materials, which have become more directly accessible over the past 20 years. Such progress has been made possible by newly developed experimental methods, first principle theories, and computer simulation techniques. The book is aimed at young researchers, scientists, and technicians in related industries. The main purposes are to provide readers with 1) the basic physics behind defects in silicon materials, 2) the atomistic modeling as well as the characterization techniques related to defects and impurities in silicon materials, and 3) an overview of the wide range of the research fields involved.

Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, Kaushik; Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

2016-05-28

The noncovalent interaction between protein and DNA is responsible for regulating the genetic activities in living organisms. The most critical issue in this problem is to understand the underlying driving force for the formation and stability of the complex. To address this issue, we have performed atomistic molecular dynamics simulations of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein (FBP) complexed with two single-stranded DNA (ss-DNA) oligomers in aqueous media. Attempts have been made to calculate the individual components of the net entropy change for the complexation process by adopting suitable statistical mechanical approaches. Our calculations reveal that translational, rotational, and configurational entropy changes of the protein and the DNA components have unfavourable contributions for this protein-DNA association process and such entropy lost is compensated by the entropy gained due to the release of hydration layer water molecules. The free energy change corresponding to the association process has also been calculated using the Free Energy Perturbation (FEP) method. The free energy gain associated with the KH4–DNA complex formation has been found to be noticeably higher than that involving the formation of the KH3–DNA complex.

Solid-state NMR spectroscopy on complex biomolecules

NARCIS (Netherlands)

Renault, M.A.M.; Cukkemane, A.A.; Baldus, M.

2010-01-01

Biomolecular applications of NMR spectroscopy are often merely associated with soluble molecules or magnetic resonance imaging. However, since the late 1970s, solid-state NMR (ssNMR) spectroscopy has demonstrated its ability to provide atomic-level insight into complex biomolecular systems ranging

The influence of trifluoromethyl groups on the miscibility of fluorinated alcohols with water : A molecular dynamics simulation study of 1,1,1-trifluoropropan-2-ol in aqueous solution

NARCIS (Netherlands)

Fioroni, M.; Burger, K.; Mark, A.E.; Roccatano, D

2003-01-01

1,1,1-Trifluoro-propan-2-ol (TFIP) alcohol has been used to study the influence of trifluoromethyl groups (CF3) on the physicochemical properties of fluorinated organic molecules. TFIP contains both a CF3 and a methyl (CH3) group. An atomistic study of TFIP thus can provide insight into the behavior

Primary care physician insights into a typology of the complex patient in primary care.

Science.gov (United States)

Loeb, Danielle F; Binswanger, Ingrid A; Candrian, Carey; Bayliss, Elizabeth A

2015-09-01

Primary care physicians play unique roles caring for complex patients, often acting as the hub for their care and coordinating care among specialists. To inform the clinical application of new models of care for complex patients, we sought to understand how these physicians conceptualize patient complexity and to develop a corresponding typology. We conducted qualitative in-depth interviews with internal medicine primary care physicians from 5 clinics associated with a university hospital and a community health hospital. We used systematic nonprobabilistic sampling to achieve an even distribution of sex, years in practice, and type of practice. The interviews were analyzed using a team-based participatory general inductive approach. The 15 physicians in this study endorsed a multidimensional concept of patient complexity. The physicians perceived patients to be complex if they had an exacerbating factor-a medical illness, mental illness, socioeconomic challenge, or behavior or trait (or some combination thereof)-that complicated care for chronic medical illnesses. This perspective of primary care physicians caring for complex patients can help refine models of complexity to design interventions or models of care that improve outcomes for these patients. © 2015 Annals of Family Medicine, Inc.

Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association.

Science.gov (United States)

Rawle, Rachel A; Hamerly, Timothy; Tripet, Brian P; Giannone, Richard J; Wurch, Louie; Hettich, Robert L; Podar, Mircea; Copié, Valerie; Bothner, Brian

2017-09-01

Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted 'omics' analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized using interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis-N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. This multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis-N. equitans association. Our study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

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.

Distinct pattern of cerebral blood flow alterations specific to schizophrenics experiencing auditory verbal hallucinations with and without insight: a pilot study.

Science.gov (United States)

Jing, Rixing; Huang, Jiangjie; Jiang, Deguo; Lin, Xiaodong; Ma, Xiaolei; Tian, Hongjun; Li, Jie; Zhuo, Chuanjun

2018-01-23

Schizophrenia is associated with widespread and complex cerebral blood flow (CBF) disturbance. Auditory verbal hallucinations (AVH) and insight are the core symptoms of schizophrenia. However, to the best of our knowledge, very few studies have assessed the CBF characteristics of the AVH suffered by schizophrenic patients with and without insight. Based on our previous findings, Using a 3D pseudo-continuous ASL (pcASL) technique, we investigated the differences in AVH-related CBF alterations in schizophrenia patients with and without insight. We used statistical parametric mapping (SPM8) and statistical non-parametric mapping (SnPM13) to perform the fMRI analysis. We found that AVH-schizophrenia patients without insight showed an increased CBF in the left temporal pole and a decreased CBF in the right middle frontal gyrus when compared to AVH-schizophrenia patients with insight. Our novel findings suggest that AVH-schizophrenia patients without insight possess a more complex CBF disturbance. Simultaneously, our findings also incline to support the idea that the CBF aberrant in some specific brain regions may be the common neural basis of insight and AVH. Our findings support the mostly current hypotheses regarding AVH to some extent. Although our findings come from a small sample, it provide the evidence that indicate us to conduct a larger study to thoroughly explore the mechanisms of schizophrenia, especially the core symptoms of AVHs and insight.

Quantitative risk assessment: is more complex always better? Simple is not stupid and complex is not always more correct.

Science.gov (United States)

Zwietering, Marcel H

2009-08-31

In quantitative risk assessments a large variety of complexities can be found, from simple and deterministic to very extensive and stochastic. This publication advocates that both simple and complex approaches have their value and should be done in parallel. The simple analysis gives much insight and can help to detect main factors and potential errors in the complex analysis. Extensive analysis with increased complexity suggests better precision but might not increase the accuracy, due to the uncertainty in the additional parameters. However, complex analysis supplies more confidence in certain phenomena and might also increase insight. This is shown with two examples. The first is the effectiveness of sampling plans for powdered infant formula, for factories operating at various levels of contamination. The results of a simple determination, an analysis including a within batch variability and an analysis including both within batch and between batch variability will be compared. The last approach has as advantage that apart from determining the probability of rejection of a batch, it can determine also the reduction of the health risk in the population following a certain sampling plan; it is more complex but it also does bring additional information. However the conclusions still contain large uncertainty, due to the difficulty of obtaining realistic values of the within batch and between batch variability. The second example is dose-response relations comparing the exponential model (one parameter), the beta-Poisson model (two parameters) and the Weibull-gamma model (three parameters). The conclusion is not that simple is best, but that simple is not stupid, and provides valuable information. Complex, on the other hand, is not always by definition more correct, but also does have its merits.

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

Science.gov (United States)

Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;

Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc{sub 1} complex

Energy Technology Data Exchange (ETDEWEB)

Martin, Daniel R.; Matyushov, Dmitry V., E-mail: dmitrym@asu.edu [Department of Physics and Department of Chemistry and Biochemistry, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287 (United States)

2015-04-28

Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc{sub 1} bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

Role of hydrogen on the incipient crack tip deformation behavior in α-Fe: An atomistic perspective

Science.gov (United States)

Adlakha, I.; Solanki, K. N.

2018-01-01

A crack tip in α-Fe presents a preferential trap site for hydrogen, and sufficient concentration of hydrogen can change the incipient crack tip deformation response, causing a transition from a ductile to a brittle failure mechanism for inherently ductile alloys. In this work, the effect of hydrogen segregation around the crack tip on deformation in α-Fe was examined using atomistic simulations and the continuum based Rice-Thompson criterion for various modes of fracture (I, II, and III). The presence of a hydrogen rich region ahead of the crack tip was found to cause a decrease in the critical stress intensity factor required for incipient deformation for various crack orientations and modes of fracture examined here. Furthermore, the triaxial stress state ahead of the crack tip was found to play a crucial role in determining the effect of hydrogen on the deformation behavior. Overall, the segregation of hydrogen atoms around the crack tip enhanced both dislocation emission and cleavage behavior suggesting that hydrogen has a dual role during the deformation in α-Fe.

Atomistic simulations of thermal transport in Si and SiGe based materials: From bulk to nanostructures

Science.gov (United States)

Savic, Ivana; Mingo, Natalio; Donadio, Davide; Galli, Giulia

2010-03-01

It has been recently proposed that Si and SiGe based nanostructured materials may exhibit low thermal conductivity and overall promising properties for thermoelectric applications. Hence there is a considerable interest in developing accurate theoretical and computational methods which can help interpret recent measurements, identify the physical origin of the reduced thermal conductivity, as well as shed light on the interplay between disorder and nanostructuring in determining a high figure of merit. In this work, we investigate the capability of an atomistic Green's function method [1] to describe phonon transport in several types of Si and SiGe based systems: amorphous Si, SiGe alloys, planar and nanodot Si/SiGe multilayers. We compare our results with experimental data [2,3], and with the findings of molecular dynamics simulations and calculations based on the Boltzmann transport equation. [1] I. Savic, N. Mingo, and D. A. Stewart, Phys. Rev. Lett. 101, 165502 (2008). [2] S.-M. Lee, D. G. Cahill, and R. Venkatasubramanian, Appl. Phys. Lett. 70, 2957 (1997). [3] G. Pernot et al., submitted.

Function theory of several complex variables

CERN Document Server

Krantz, Steven G

2001-01-01

The theory of several complex variables can be studied from several different perspectives. In this book, Steven Krantz approaches the subject from the point of view of a classical analyst, emphasizing its function-theoretic aspects. He has taken particular care to write the book with the student in mind, with uniformly extensive and helpful explanations, numerous examples, and plentiful exercises of varying difficulty. In the spirit of a student-oriented text, Krantz begins with an introduction to the subject, including an insightful comparison of analysis of several complex variables with th

Molecular Level Design Principle behind Optimal Sizes of Photosynthetic LH2 Complex: Taming Disorder through Cooperation of Hydrogen Bonding and Quantum Delocalization.

Science.gov (United States)

Jang, Seogjoo; Rivera, Eva; Montemayor, Daniel

2015-03-19

The light harvesting 2 (LH2) antenna complex from purple photosynthetic bacteria is an efficient natural excitation energy carrier with well-known symmetric structure, but the molecular level design principle governing its structure-function relationship is unknown. Our all-atomistic simulations of nonnatural analogues of LH2 as well as those of a natural LH2 suggest that nonnatural sizes of LH2-like complexes could be built. However, stable and consistent hydrogen bonding (HB) between bacteriochlorophyll and the protein is shown to be possible only near naturally occurring sizes, leading to significantly smaller disorder than for nonnatural ones. Extensive quantum calculations of intercomplex exciton transfer dynamics, sampled for a large set of disorder, reveal that taming the negative effect of disorder through a reliable HB as well as quantum delocalization of the exciton is a critical mechanism that makes LH2 highly functional, which also explains why the natural sizes of LH2 are indeed optimal.

Interpretation of stream programs: characterizing type 2 polynomial time complexity

OpenAIRE

Férée , Hugo; Hainry , Emmanuel; Hoyrup , Mathieu; Péchoux , Romain

2010-01-01

International audience; We study polynomial time complexity of type 2 functionals. For that purpose, we introduce a first order functional stream language. We give criteria, named well-founded, on such programs relying on second order interpretation that characterize two variants of type 2 polynomial complexity including the Basic Feasible Functions (BFF). These charac- terizations provide a new insight on the complexity of stream programs. Finally, we adapt these results to functions over th...

Bio-Signal Complexity Analysis in Epileptic Seizure Monitoring: A Topic Review

Directory of Open Access Journals (Sweden)

Zhenning Mei

2018-05-01

Full Text Available Complexity science has provided new perspectives and opportunities for understanding a variety of complex natural or social phenomena, including brain dysfunctions like epilepsy. By delving into the complexity in electrophysiological signals and neuroimaging, new insights have emerged. These discoveries have revealed that complexity is a fundamental aspect of physiological processes. The inherent nonlinearity and non-stationarity of physiological processes limits the methods based on simpler underlying assumptions to point out the pathway to a more comprehensive understanding of their behavior and relation with certain diseases. The perspective of complexity may benefit both the research and clinical practice through providing novel data analytics tools devoted for the understanding of and the intervention about epilepsies. This review aims to provide a sketchy overview of the methods derived from different disciplines lucubrating to the complexity of bio-signals in the field of epilepsy monitoring. Although the complexity of bio-signals is still not fully understood, bundles of new insights have been already obtained. Despite the promising results about epileptic seizure detection and prediction through offline analysis, we are still lacking robust, tried-and-true real-time applications. Multidisciplinary collaborations and more high-quality data accessible to the whole community are needed for reproducible research and the development of such applications.

Calculation of phonon dispersion in carbon nanotubes using a continuum-atomistic finite element approach

Directory of Open Access Journals (Sweden)

Michael J. Leamy

2011-12-01

Full Text Available Dispersion calculations are presented for cylindrical carbon nanotubes using a manifold-based continuum-atomistic finite element formulation combined with Bloch analysis. The formulated finite elements allow any (n,m chiral nanotube, or mixed tubes formed by periodically-repeating heterojunctions, to be examined quickly and accurately using only three input parameters (radius, chiral angle, and unit cell length and a trivial structured mesh, thus avoiding the tedious geometry generation and energy minimization tasks associated with ab initio and lattice dynamics-based techniques. A critical assessment of the technique is pursued to determine the validity range of the resulting dispersion calculations, and to identify any dispersion anomalies. Two small anomalies in the dispersion curves are documented, which can be easily identified and therefore rectified. They include difficulty in achieving a zero energy point for the acoustic twisting phonon, and a branch veering in nanotubes with nonzero chiral angle. The twisting mode quickly restores its correct group velocity as wavenumber increases, while the branch veering is associated with a rapid exchange of eigenvectors at the veering point, which also lessens its impact. By taking into account the two noted anomalies, accurate predictions of acoustic and low-frequency optical branches can be achieved out to the midpoint of the first Brillouin zone.

First insights into the evolutionary history of the Davallia repens complex

NARCIS (Netherlands)

Chen, C.-W.; Ngan, L.T.; Hidayat, A.; Evangelista, L.; Nooteboom, H.P.; Chiou, W.-L.

2014-01-01

Davallia repens and its close relatives have been identified as a species complex in this study because of the existence of continuously morphological variation. To decipher its evolutionary history, integrated methodologies were applied in this study including morphology, cytology, reproductive

Theory of mind correlates with clinical insight but not cognitive insight in patients with schizophrenia.

Science.gov (United States)

Zhang, Qi; Li, Xu; Parker, Giverny J; Hong, Xiao-Hong; Wang, Yi; Lui, Simon S Y; Neumann, David L; Cheung, Eric F C; Shum, David H K; Chan, Raymond C K

2016-03-30

Research on the relationship between insight and social cognition, in particular Theory of Mind (ToM), in schizophrenia has yielded mixed findings to date. Very few studies, however, have assessed both clinical insight and cognitive insight when examining their relationships with ToM in schizophrenia. The current study thus investigated the relationship between clinical insight, cognitive insight, and ToM in a sample of 56 patients with schizophrenia and 30 healthy controls. Twenty-seven patients were classified as low in clinical insight according to their scores on the 'insight' item (G12) of the Positive and Negative Syndrome Scale (PANSS). Moreover, cognitive insight and ToM were assessed with the Beck Cognitive Insight Scale (BCIS) and the Yoni task, respectively. The results indicated that patients with poor clinical insight performed worse on tasks of second-order cognitive and affective ToM, while the ToM performance of patients with high clinical insight was equivalent to that of healthy controls. Furthermore, while clinical insight was correlated with ToM and clinical symptoms, cognitive insight did not correlate with clinical insight, ToM, or clinical symptoms. Clinical insight thus appears to be an important factor related to ToM in schizophrenia. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Chaperone-client complexes: A dynamic liaison

Science.gov (United States)

Hiller, Sebastian; Burmann, Björn M.

2018-04-01

Living cells contain molecular chaperones that are organized in intricate networks to surveil protein homeostasis by avoiding polypeptide misfolding, aggregation, and the generation of toxic species. In addition, cellular chaperones also fulfill a multitude of alternative functionalities: transport of clients towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver clients towards proteolysis machineries. Until recently, the only available source of atomic resolution information for virtually all chaperones were crystal structures of their client-free, apo-forms. These structures were unable to explain details of the functional mechanisms underlying chaperone-client interactions. The difficulties to crystallize chaperones in complexes with clients arise from their highly dynamic nature, making solution NMR spectroscopy the method of choice for their study. With the advent of advanced solution NMR techniques, in the past few years a substantial number of structural and functional studies on chaperone-client complexes have been resolved, allowing unique insight into the chaperone-client interaction. This review summarizes the recent insights provided by advanced high-resolution NMR-spectroscopy to understand chaperone-client interaction mechanisms at the atomic scale.

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

2015-07-28

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

Insights into the Halogen Oxidative Addition Reaction to Dinuclear Gold(I) Di(NHC) Complexes

KAUST Repository

Baron, Marco; Tubaro, Cristina; Basato, Marino; Isse, Abdirisak Ahmed; Gennaro, Armando; Cavallo, Luigi; Graiff, Claudia; Dolmella, Alessandro; Falivene, Laura; Caporaso, Lucia

2016-01-01

Gold(I) dicarbene complexes [Au2(MeIm-Y-ImMe)2](PF6)2(Y=CH2(1), (CH2)2(2), (CH2)4(4), MeIm=1-methylimidazol-2-ylidene) react with iodine to give the mixed-valence complex [Au(MeIm-CH2-ImMe)2AuI2](PF6)2(1 aI) and the gold(III) complexes [Au2I4(Me

Multiscale Modeling of UHTC: Thermal Conductivity

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Aryl-NHC-group 13 trimethyl complexes: structural, stability and bonding insights

KAUST Repository

Wu, Melissa M.; Gill, Arran M.; Yunpeng, Lu; Yongxin, Li; Ganguly, Rakesh; Falivene, Laura; Garcí a, Felipe

2016-01-01

Treatment of aromatic N-substituted N-heterocyclic carbenes (NHCs) with trimethyl-gallium and -indium yielded the new Lewis acid-base adducts, IMes·GaMe3 (1), SIMes·GaMe3 (2), IPr·GaMe3 (3), SIPr·GaMe3 (4), IMes·InMe3 (5), SIMes·InMe3 (6), IPr·InMe3 (7), and SIPr·InMe3 (8), with all complexes being identified by X-ray diffraction, IR, and multinuclear NMR analyses. Complex stability was found to be largely dependent on the nature of the constituent NHC ligands. Percent buried volume (%VBur) and topographic steric map analyses were employed to quantify and elucidate the observed trends. Additionally, a detailed bond snapping energy (BSE) decomposition analysis focusing on both steric and orbital interactions of the M-NHC bond (M = Al, Ga and In) has been performed.

Aryl-NHC-group 13 trimethyl complexes: structural, stability and bonding insights

KAUST Repository

Wu, Melissa M.

2016-12-14

Treatment of aromatic N-substituted N-heterocyclic carbenes (NHCs) with trimethyl-gallium and -indium yielded the new Lewis acid-base adducts, IMes·GaMe3 (1), SIMes·GaMe3 (2), IPr·GaMe3 (3), SIPr·GaMe3 (4), IMes·InMe3 (5), SIMes·InMe3 (6), IPr·InMe3 (7), and SIPr·InMe3 (8), with all complexes being identified by X-ray diffraction, IR, and multinuclear NMR analyses. Complex stability was found to be largely dependent on the nature of the constituent NHC ligands. Percent buried volume (%VBur) and topographic steric map analyses were employed to quantify and elucidate the observed trends. Additionally, a detailed bond snapping energy (BSE) decomposition analysis focusing on both steric and orbital interactions of the M-NHC bond (M = Al, Ga and In) has been performed.

Bifunctional (cyclopentadienone)iron-tricarbonyl complexes: Synthesis, computational studies and application in reductive amination

KAUST Repository

Moulin, Solenne

2013-11-15

Reductive amination under hydrogen pressure is a valuable process in organic chemistry to access amine derivatives from aldehydes or ketones. Knölker\\'s complex has been shown to be an efficient iron catalyst in this reaction. To determine the influence of the substituents on the cyclopentadienone ancillary ligand, a series of modified Knölker\\'s complexes was synthesised and fully characterised. These complexes were also transformed into their analogous acetonitrile iron-dicarbonyl complexes. Catalytic activities of these complexes were evaluated and compared in a model reaction. The scope of this reaction is also reported. For mechanistic insights, deuterium-labelling experiments and DFT calculations were undertaken and are also presented. Festival of amination: Two series of modified Knölker\\'s complexes were synthesised and applied in the reductive amination of various carbonyl derivatives with primary or secondary amines (see scheme, TIPS = triisopropylsilyl). For a mechanistic insight, deuterium-labelling experiments and DFT calculations were undertaken and are also presented. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Insight into the structures and stabilities of Tc and Re DMSA complexes: A computational study

International Nuclear Information System (INIS)

Blanco González, Alejandro; Hernández Valdés, Daniel; García Fleitas, Ariel; Rodríguez Riera, Zalua; Jáuregui Haza, Ulises

2016-01-01

Meso-2,3-dimercaptosuccinic acid (DMSA) is used in nuclear medicine as ligand for preparation of radiopharmaceuticals for diagnostic and therapy. DMSA has been the subject of numerous investigations during the past three decades and new and significant information of the chemistry and pharmacology of DMSA complexes have emerged. In comparison to other ligands, the structure of some DMSA complexes is unclear up today. The structures and applications of DMSA complexes are strictly dependent on the chemical conditions of their preparation, especially pH and the ratio of components. A computational study of M-DMSA (M = Tc, Re) complexes has been performed using density functional theory. Different isomers for M(V) and M(III) complexes were study. The pH influence over ligand structures was taken into account and the solvent effect was evaluated using an implicit solvation model. The fully optimized complex syn-endo Re(V)-DMSA shows a geometry similar to the X-ray data and was used to validate the methodology. Moreover, new alternative structures for the renal agent 99mTc(III)-DMSA were proposed and computationally studied. For two complex structures, a larger stability respect to that proposed in the literature was obtained. Furthermore, Tc(V)-DMSA complexes are more stable than the Tc(III)-DMSA proposed structures. In general, Re complexes are more stables than the corresponding Tc ones. (author)

Border detection in complex networks

International Nuclear Information System (INIS)

Travencolo, Bruno A N; Viana, Matheus Palhares; Costa, Luciano da Fontoura

2009-01-01

One important issue implied by the finite nature of real-world networks regards the identification of their more external (border) and internal nodes. The present work proposes a formal and objective definition of these properties, founded on the recently introduced concept of node diversity. It is shown that this feature does not exhibit any relevant correlation with several well-established complex networks measurements. A methodology for the identification of the borders of complex networks is described and illustrated with respect to theoretical (geographical and knitted networks) as well as real-world networks (urban and word association networks), yielding interesting results and insights in both cases.

Argon defect complexes in low energy Ar irradiated molybdenum

International Nuclear Information System (INIS)

Veen, A. van; Buters, W.T.M.; Kolk, G.J. van der; Caspers, L.M.; Armstrong, T.R.

1982-01-01

Thermal desorption spectrometry has been used to study the defects created in Mo irradiated along the direction with Ar ions ranging in energy from 0.1 to 2 keV. In addition to monitoring the release of the implanted Ar, additional information has been obtained by decoration of the defects with low energy helium and subsequent monitoring of the helium release. The studies show evidence that the Ar can be trapped in both substitutional sites and in a configuration in which the Ar is associated with vacancies (ArVsub(n), n >= 2). Most of the Ar implanted at high energy is released at approx. equal to 1500 K by thermal vacancy assisted diffusion. Argon trapped closer to the surface is released at lower temperatures via at least three different surface related release mechanisms. Additional results are presented on the interaction of self interstitial atoms (introduced by 100 eV Xe bombardment) with the Ar defects. Substitutional Ar is found to convert to interstitial Ar which seems to be mobile at room temperature. The Ar-vacancy complexes are found to be reduced to substitutional Ar. The results of atomistic calculations of the release mechanisms will also be presented. (orig.)

Large scale atomistic approaches to thermal transport and phonon scattering in nanostructured materials

Science.gov (United States)

Savic, Ivana

2012-02-01

Decreasing the thermal conductivity of bulk materials by nanostructuring and dimensionality reduction, or by introducing some amount of disorder represents a promising strategy in the search for efficient thermoelectric materials [1]. For example, considerable improvements of the thermoelectric efficiency in nanowires with surface roughness [2], superlattices [3] and nanocomposites [4] have been attributed to a significantly reduced thermal conductivity. In order to accurately describe thermal transport processes in complex nanostructured materials and directly compare with experiments, the development of theoretical and computational approaches that can account for both anharmonic and disorder effects in large samples is highly desirable. We will first summarize the strengths and weaknesses of the standard atomistic approaches to thermal transport (molecular dynamics [5], Boltzmann transport equation [6] and Green's function approach [7]) . We will then focus on the methods based on the solution of the Boltzmann transport equation, that are computationally too demanding, at present, to treat large scale systems and thus to investigate realistic materials. We will present a Monte Carlo method [8] to solve the Boltzmann transport equation in the relaxation time approximation [9], that enables computation of the thermal conductivity of ordered and disordered systems with a number of atoms up to an order of magnitude larger than feasible with straightforward integration. We will present a comparison between exact and Monte Carlo Boltzmann transport results for small SiGe nanostructures and then use the Monte Carlo method to analyze the thermal properties of realistic SiGe nanostructured materials. This work is done in collaboration with Davide Donadio, Francois Gygi, and Giulia Galli from UC Davis.[4pt] [1] See e.g. A. J. Minnich, M. S. Dresselhaus, Z. F. Ren, and G. Chen, Energy Environ. Sci. 2, 466 (2009).[0pt] [2] A. I. Hochbaum et al, Nature 451, 163 (2008).[0pt

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

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

Hofman, G.L. [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States); Bozzolo, G., E-mail: guille_bozzolo@yahoo.com [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States); Mosca, H.O. [Gerencia de Investigaciones y Aplicaciones, CNEA, Av. Gral Paz 1499, B165KNA, San Martin, Buenos Aires (Argentina); Yacout, A.M. [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States)

2011-07-15

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.

Atomistic modeling of metal surfaces under electric fields: direct coupling of electric fields to a molecular dynamics algorithm

CERN Document Server

Djurabekova, Flyura; Pohjonen, Aarne; Nordlund, Kai

2011-01-01

The effect of electric fields on metal surfaces is fairly well studied, resulting in numerous analytical models developed to understand the mechanisms of ionization of surface atoms observed at very high electric fields, as well as the general behavior of a metal surface in this condition. However, the derivation of analytical models does not include explicitly the structural properties of metals, missing the link between the instantaneous effects owing to the applied field and the consequent response observed in the metal surface as a result of an extended application of an electric field. In the present work, we have developed a concurrent electrodynamic–molecular dynamic model for the dynamical simulation of an electric-field effect and subsequent modification of a metal surface in the framework of an atomistic molecular dynamics (MD) approach. The partial charge induced on the surface atoms by the electric field is assessed by applying the classical Gauss law. The electric forces acting on the partially...

Prediction of point-defect migration energy barriers in alloys using artificial intelligence for atomistic kinetic Monte Carlo applications

Energy Technology Data Exchange (ETDEWEB)

Castin, N. [Structural Materials Group, Nuclear Materials Science Institute, Studiecentrum voor Kerneenergie Centre d' etude de l' energie nucleaire (SCK CEN), Boeretang 200, B-2400 Mol (Belgium); Universite Libre de Bruxelles (ULB), Physique des Solides Irradies et Nanostructures (PSIN), CP234 Boulevard du triomphe, Brussels (Belgium); Malerba, L. [Structural Materials Group, Nuclear Materials Science Institute, Studiecentrum voor Kerneenergie Centre d' etude de l' energie nucleaire (SCK CEN), Boeretang 200, B-2400 Mol (Belgium)], E-mail: lmalerba@sckcen.be

2009-09-15

We significantly improved a previously proposed method to take into account chemical and also relaxation effects on point-defect migration energy barriers, as predicted by an interatomic potential, in a rigid lattice atomistic kinetic Monte Carlo simulation. Examples of energy barriers are rigorously calculated, including chemical and relaxation effects, as functions of the local atomic configuration, using a nudged elastic bands technique. These examples are then used to train an artificial neural network that provides the barriers on-demand during the simulation for each configuration encountered by the migrating defect. Thanks to a newly developed training method, the configuration can include a large number of neighbour shells, thereby properly including also strain effects. Satisfactory results have been obtained when the configuration includes different chemical species only. The problems encountered in the extension of the method to configurations including any number of point-defects are stated and solutions to tackle them are sketched.

Structural insights into RNA processing by the human RISC-loading complex.

Science.gov (United States)

Wang, Hong-Wei; Noland, Cameron; Siridechadilok, Bunpote; Taylor, David W; Ma, Enbo; Felderer, Karin; Doudna, Jennifer A; Nogales, Eva

2009-11-01

Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Dicer and the RNA-binding protein TRBP to form a RISC-loading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and miRNAs from Dicer to AGO2. Here, using single-particle EM analysis, we show that human Dicer has an L-shaped structure. The RLC Dicer's N-terminal DExH/D domain, located in a short 'base branch', interacts with TRBP, whereas its C-terminal catalytic domains in the main body are proximal to AGO2. A model generated by docking the available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction suggests a mechanism for siRNA transfer from Dicer to AGO2.

Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

Energy Technology Data Exchange (ETDEWEB)

Abdur, Rob; Gerlits, Oksana O.; Gan, Jianhua; Jiang, Jiansheng; Salon, Jozef; Kovalevsky, Andrey Y.; Chumanevich, Alexander A.; Weber, Irene T.; Huang, Zhen, E-mail: huang@gsu.edu [Georgia State University, Atlanta, GA 30303 (United States)

2014-02-01

Selenium-derivatized oligonucleotides may facilitate phase determination and high-resolution structure determination for protein–nucleic acid crystallography. The Se atom-specific mutagenesis (SAM) strategy may also enhance the study of nuclease catalysis. The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.

Insight Is Not in the Problem: Investigating Insight in Problem Solving across Task Types.

Science.gov (United States)

Webb, Margaret E; Little, Daniel R; Cropper, Simon J

2016-01-01

The feeling of insight in problem solving is typically associated with the sudden realization of a solution that appears obviously correct (Kounios et al., 2006). Salvi et al. (2016) found that a solution accompanied with sudden insight is more likely to be correct than a problem solved through conscious and incremental steps. However, Metcalfe (1986) indicated that participants would often present an inelegant but plausible (wrong) answer as correct with a high feeling of warmth (a subjective measure of closeness to solution). This discrepancy may be due to the use of different tasks or due to different methods in the measurement of insight (i.e., using a binary vs. continuous scale). In three experiments, we investigated both findings, using many different problem tasks (e.g., Compound Remote Associates, so-called classic insight problems, and non-insight problems). Participants rated insight-related affect (feelings of Aha-experience, confidence, surprise, impasse, and pleasure) on continuous scales. As expected we found that, for problems designed to elicit insight, correct solutions elicited higher proportions of reported insight in the solution compared to non-insight solutions; further, correct solutions elicited stronger feelings of insight compared to incorrect solutions.

Are Model Transferability And Complexity Antithetical? Insights From Validation of a Variable-Complexity Empirical Snow Model in Space and Time

Science.gov (United States)

Lute, A. C.; Luce, Charles H.

2017-11-01

The related challenges of predictions in ungauged basins and predictions in ungauged climates point to the need to develop environmental models that are transferable across both space and time. Hydrologic modeling has historically focused on modelling one or only a few basins using highly parameterized conceptual or physically based models. However, model parameters and structures have been shown to change significantly when calibrated to new basins or time periods, suggesting that model complexity and model transferability may be antithetical. Empirical space-for-time models provide a framework within which to assess model transferability and any tradeoff with model complexity. Using 497 SNOTEL sites in the western U.S., we develop space-for-time models of April 1 SWE and Snow Residence Time based on mean winter temperature and cumulative winter precipitation. The transferability of the models to new conditions (in both space and time) is assessed using non-random cross-validation tests with consideration of the influence of model complexity on transferability. As others have noted, the algorithmic empirical models transfer best when minimal extrapolation in input variables is required. Temporal split-sample validations use pseudoreplicated samples, resulting in the selection of overly complex models, which has implications for the design of hydrologic model validation tests. Finally, we show that low to moderate complexity models transfer most successfully to new conditions in space and time, providing empirical confirmation of the parsimony principal.

Insights into functional-group-tolerant polymerization catalysis with phosphine-sulfonamide palladium (II) complexes

KAUST Repository

Jian, Zhongbao

2014-12-08

Two series of cationic palladium(II) methyl complexes {[(2-MeOC6H4)2PC6H4SO2NHC6H3(2,6-R1,R2)]PdMe}2[A]2 (X1+-A: R1=R2=H: H1+-A; R1=R2=CH(CH3)2: DIPP1+-A; R1=H, R2=CF3: CF31+-A; A=BF4 or SbF6) and neutral palladium(II) methyl complexes {[(2-MeOC6H4)2PC6H4SO2NC6H3(2,6-R1,R2)]PdMe(L)} (X1-acetone: L=acetone; X1-dmso: L=dimethyl sulfoxide; X1-pyr: L=pyridine) chelated by a phosphine-sulfonamide were synthesized and fully characterized. Stoichiometric insertion of methyl acrylate (MA) into all complexes revealed that a 2,1 regiochemistry dominates in the first insertion of MA. Subsequently, for the cationic complexes X1+-A, β-H elimination from the 2,1-insertion product X2+-AMA-2,1 is overwhelmingly favored over a second MA insertion to yield two major products X4+-AMA-1,2 and X5+-AMA. By contrast, for the weakly coordinated neutral complexes X1-acetone and X1-dmso, a second MA insertion of the 2,1-insertion product X2MA-2,1 is faster than β-H elimination and gives X3MA as major products. For the strongly coordinated neutral complexes X1-pyr, no second MA insertion and no β-H elimination (except for DIPP2-pyrMA-2,1) were observed for the 2,1-insertion product X2-pyrMA-2,1. The cationic complexes X1+-A exhibited high catalytic activities for ethylene dimerization, affording butenes (C4) with a high selectivity of up to 97.7% (1-butene: 99.3%). Differences in activities and selectivities suggest that the phosphine-sulfonamide ligands remain coordinated to the metal center in a bidentate fashion in the catalytically active species. By comparison, the neutral complexes X1-acetone, X1-dmso, and X1-pyr showed very low activity towards ethylene to give traces of oligomers. DFT analyses taking into account the two possible coordination modes (O or N) of the sulfonamide ligand for the cationic system CF31+ suggested that the experimentally observed high activity in ethylene dimerization is the result of a facile first ethylene insertion into the O-coordinated PdMe isomer and

Unified analysis of ensemble and single-complex optical spectral data from light-harvesting complex-2 chromoproteins for gaining deeper insight into bacterial photosynthesis

Science.gov (United States)

Pajusalu, Mihkel; Kunz, Ralf; Rätsep, Margus; Timpmann, Kõu; Köhler, Jürgen; Freiberg, Arvi

2015-11-01

Bacterial light-harvesting pigment-protein complexes are very efficient at converting photons into excitons and transferring them to reaction centers, where the energy is stored in a chemical form. Optical properties of the complexes are known to change significantly in time and also vary from one complex to another; therefore, a detailed understanding of the variations on the level of single complexes and how they accumulate into effects that can be seen on the macroscopic scale is required. While experimental and theoretical methods exist to study the spectral properties of light-harvesting complexes on both individual complex and bulk ensemble levels, they have been developed largely independently of each other. To fill this gap, we simultaneously analyze experimental low-temperature single-complex and bulk ensemble optical spectra of the light-harvesting complex-2 (LH2) chromoproteins from the photosynthetic bacterium Rhodopseudomonas acidophila in order to find a unique theoretical model consistent with both experimental situations. The model, which satisfies most of the observations, combines strong exciton-phonon coupling with significant disorder, characteristic of the proteins. We establish a detailed disorder model that, in addition to containing a C2-symmetrical modulation of the site energies, distinguishes between static intercomplex and slow conformational intracomplex disorders. The model evaluations also verify that, despite best efforts, the single-LH2-complex measurements performed so far may be biased toward complexes with higher Huang-Rhys factors.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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 [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)

2015-05-21

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Study of the embedded atom method of atomistic calculations for metals and alloys: Progress report, March 1, 1987-February 28, 1988

International Nuclear Information System (INIS)

Johnson, R.A.

1987-11-01

The relationships between the physical input and output of the Embedded Atom Method (EAM) used in atomistic calculations for metals and alloys and the model functions and parameters are being investigated. An analytic fcc EAM model has been derived based on short range approximations to the input functions in EAM and has been studied both analytically and numerically for the fcc lattice. This model has been extended to longer ranges and applied to both fcc and hcp metals. The correspondence between models based on density functional theory (EAM), tight binding methods, and effective medium theory has been reported. The reasons for difficulty in applying EAM to bcc metals is under study and a new form of alloy potential which retains general properties of pure metal potentials has been developed. 8 refs

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

Science.gov (United States)

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.

Thermally activated magnetization reversal in monatomic magnetic chains on surfaces studied by classical atomistic spin-dynamics simulations

International Nuclear Information System (INIS)

Bauer, David S G; Mavropoulos, Phivos; Bluegel, Stefan; Lounis, Samir

2011-01-01

We analyse the spontaneous magnetization reversal of supported monatomic chains of finite length due to thermal fluctuations via atomistic spin-dynamics simulations. Our approach is based on the integration of the Landau-Lifshitz equation of motion of a classical spin Hamiltonian in the presence of stochastic forces. The associated magnetization lifetime is found to obey an Arrhenius law with an activation barrier equal to the domain wall energy in the chain. For chains longer than one domain wall width, the reversal is initiated by nucleation of a reversed magnetization domain primarily at the chain edge followed by a subsequent propagation of the domain wall to the other edge in a random-walk fashion. This results in a linear dependence of the lifetime on the chain length, if the magnetization correlation length is not exceeded. We studied chains of uniaxial and triaxial anisotropy and found that a triaxial anisotropy leads to a reduction of the magnetization lifetime due to a higher reversal attempt rate, even though the activation barrier is not changed.

Insights into functional-group-tolerant polymerization catalysis with phosphine-sulfonamide palladium(II) complexes.

Science.gov (United States)

Jian, Zhongbao; Falivene, Laura; Wucher, Philipp; Roesle, Philipp; Caporaso, Lucia; Cavallo, Luigi; Göttker-Schnetmann, Inigo; Mecking, Stefan

2015-01-26

Two series of cationic palladium(II) methyl complexes {[(2-MeOC6 H4 )2 PC6 H4 SO2 NHC6 H3 (2,6-R(1) ,R(2) )]PdMe}2 [A]2 ((X) 1(+) -A: R(1) =R(2) =H: (H) 1(+) -A; R(1) =R(2) =CH(CH3 )2 : (DIPP) 1(+) -A; R(1) =H, R(2) =CF3 : (CF3) 1(+) -A; A=BF4 or SbF6 ) and neutral palladium(II) methyl complexes {[(2-MeOC6 H4 )2 PC6 H4 SO2 NC6 H3 (2,6-R(1) ,R(2) )]PdMe(L)} ((X) 1-acetone: L=acetone; (X) 1-dmso: L=dimethyl sulfoxide; (X) 1-pyr: L=pyridine) chelated by a phosphine-sulfonamide were synthesized and fully characterized. Stoichiometric insertion of methyl acrylate (MA) into all complexes revealed that a 2,1 regiochemistry dominates in the first insertion of MA. Subsequently, for the cationic complexes (X) 1(+) -A, β-H elimination from the 2,1-insertion product (X) 2(+) -AMA-2,1 is overwhelmingly favored over a second MA insertion to yield two major products (X) 4(+) -AMA-1,2 and (X) 5(+) -AMA . By contrast, for the weakly coordinated neutral complexes (X) 1-acetone and (X) 1-dmso, a second MA insertion of the 2,1-insertion product (X) 2MA-2,1 is faster than β-H elimination and gives (X) 3MA as major products. For the strongly coordinated neutral complexes (X) 1-pyr, no second MA insertion and no β-H elimination (except for (DIPP) 2-pyrMA-2,1 ) were observed for the 2,1-insertion product (X) 2-pyrMA-2,1 . The cationic complexes (X) 1(+) -A exhibited high catalytic activities for ethylene dimerization, affording butenes (C4 ) with a high selectivity of up to 97.7 % (1-butene: 99.3 %). Differences in activities and selectivities suggest that the phosphine-sulfonamide ligands remain coordinated to the metal center in a bidentate fashion in the catalytically active species. By comparison, the neutral complexes (X) 1-acetone, (X) 1-dmso, and (X) 1-pyr showed very low activity towards ethylene to give traces of oligomers. DFT analyses taking into account the two possible coordination modes (O or N) of the sulfonamide ligand for the cationic system (CF3) 1(+) suggested

Solute effects on edge dislocation pinning in complex alpha-Fe alloys

Science.gov (United States)

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.

Ultrafast Charge Photogeneration in MEH-PPV Charge-Transfer Complexes

NARCIS (Netherlands)

Bakulin, Artem A.; Paraschuk, Dmitry Yu; Pshenichnikov, Maxim S.; van Loosdrecht, Paul H. M.; Corkum, P; DeSilvestri, S; Nelson, KA; Riedle, E; Schoenlein, RW

2009-01-01

Visible-pump - IR-probe spectroscopy is used to study the ultrafast charge dynamics in MEH-PPV based charge-transfer complexes and donor-acceptor blends. Transient anisotropy of the polymer polaron band provides invaluable insights into excitation localisation and charge-transfer pathways.

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

Science.gov (United States)

Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D.

2016-08-01

This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

Directory of Open Access Journals (Sweden)

Thomas M. Vlasic

2016-08-01

Full Text Available This work uses density functional theory (DFT to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane, at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

Energy Technology Data Exchange (ETDEWEB)

Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D., E-mail: alejandro.rey@mcgill.ca [Department of Chemical Engineering, McGill University, Montreal H3A 0C5 (Canada)

2016-08-15

This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

Plutonium(IV) complexation by diglycolamide ligands - coordination chemistry insight into TODGA-based actinide separations

NARCIS (Netherlands)

Reilly, S.D.; Gaunt, A.J.; Scott, B.L.; Modolo, G.; Iqbal, M.; Verboom, Willem; Sarsfield, M.J.

2012-01-01

Complexation of Pu(IV) with TMDGA, TEDGA, and TODGA diglycolamide ligands was followed by vis-NIR spectroscopy. A crystal structure determination reveals that TMDGA forms a 1:3 homoleptic Pu(IV) complex with the nitrate anions forced into the outer coordination sphere

A method of integration of atomistic simulations and continuum mechanics by collecting of dynamical systems with dimensional reduction

International Nuclear Information System (INIS)

Kaczmarek, J.

2002-01-01

Elementary processes responsible for phenomena in material are frequently related to scale close to atomic one. Therefore atomistic simulations are important for material sciences. On the other hand continuum mechanics is widely applied in mechanics of materials. It seems inevitable that both methods will gradually integrate. A multiscale method of integration of these approaches called collection of dynamical systems with dimensional reduction is introduced in this work. The dimensional reduction procedure realizes transition between various scale models from an elementary dynamical system (EDS) to a reduced dynamical system (RDS). Mappings which transform variables and forces, skeletal dynamical system (SDS) and a set of approximation and identification methods are main components of this procedure. The skeletal dynamical system is a set of dynamical systems parameterized by some constants and has variables related to the dimensionally reduced model. These constants are identified with the aid of solutions of the elementary dynamical system. As a result we obtain a dimensionally reduced dynamical system which describes phenomena in an averaged way in comparison with the EDS. Concept of integration of atomistic simulations with continuum mechanics consists in using a dynamical system describing evolution of atoms as an elementary dynamical system. Then, we introduce a continuum skeletal dynamical system within the dimensional reduction procedure. In order to construct such a system we have to modify a continuum mechanics formulation to some degree. Namely, we formalize scale of averaging for continuum theory and as a result we consider continuum with finite-dimensional fields only. Then, realization of dimensional reduction is possible. A numerical example of realization of the dimensional reduction procedure is shown. We consider a one dimensional chain of atoms interacting by Lennard-Jones potential. Evolution of this system is described by an elementary

How to make a complex story understandable. Communication on nitrogen

International Nuclear Information System (INIS)

Bleeker, A.; Hensen, A.; Erisman, J.W.

2011-01-01

Understanding is the first step towards solving the nitrogen problem. Various applications have been developed to gain insight in the complex interactions between the nitrogen cycle and the social-economic and environmental aspects. Experience has learned that many users have not only gained a clearer picture of the urgency and complexity of the problem; now they also have options for dealing with the nitrogen problem. [nl

Atomistic tight-binding computations of the structural and optical properties of CdTe/CdX (X=S and Se)/ZnS core/shell/shell nanocrystals

Science.gov (United States)

Sukkabot, Worasak

2018-05-01

A study of CdTe/CdX (X=S and Se)/ZnS core/shell/shell nanocrystals is carried out using atomistic tight-binding theory and the configuration interaction method to provide information for applications in bioimaging, biolabeling, display devices and near-infrared electronic instruments. The calculations yield the dependences of the internal and external passivated shells on the natural behaviours of CdTe/CdX (X=S and Se)/ZnS core/shell/shell nanocrystals. The reduction of the optical band gaps is observed with increasing numbers of monolayers in the external ZnS shell due to quantum confinement. Interestingly, the optical band gaps of CdTe/CdS/ZnS core/shell/shell nanocrystals are greater than those of CdTe/CdSe/ZnS core/shell/shell nanocrystals. In the presence of an external ZnS-coated shell, electron-hole wave function overlaps, oscillation strengths, ground-state exchange energies and Stokes shift are improved, whereas ground-state coulomb energies and fine-structure splitting are reduced. The oscillation strengths, Stokes shift and fine-structure splitting are reduced with the increase in external ZnS shell thickness. The oscillation strengths, Stokes shift and fine-structure splitting of CdTe/CdS/ZnS core/shell/shell nanocrystals are larger than those of CdTe/CdSe/ZnS core/shell/shell nanocrystals. Reduction of the atomistic electron-hole interactions is observed with increasing external ZnS shell size. The strong electron-hole interactions are more probed in CdTe/CdS/ZnS core/shell/shell nanocrystals than in CdTe/CdSe/ZnS core/shell/shell nanocrystals.

Phylogenetic relationships in the Festuca-Lolium complex (Loliinae; Poaceae: New insights from chloroplast sequences

Directory of Open Access Journals (Sweden)

Yajuan Cheng

2016-07-01

Full Text Available The species within the Lolium/Festuca grass complex have dispersed and colonized large areas of temperate global grasslands both naturally and by human intervention. The species within this grass complex represent some of the most important grass species both for amenity and agricultural use worldwide. There has been renewed interest by grass breeders in producing hybrid combinations between these species and several countries now market Festulolium varieties as a combination of genes from both genera. The two genera have been differentiated by their inflorescence structure, but controversy has surrounded the taxonomic classification of the Lolium-Festuca complex species for several decades. In order to better understand the complexities within the Lolium/Festuca complex and their genetic background, the phylogeny of important examplers from the Lolium-Festuca complex were reconstructed. In total 40 taxa representing the Festuca and Lolium species with Vulpia myuros and Brachypodium distachyon as outgroups were sampled, using two noncoding intergenic spacers (trnQ-rps16, trnH-psbA and one coding gene (rbcL. Maximum parsimony (MP, Bayesian inference (BI analyses based on each partition and combined plastid DNA dataset, and median-jointing network analysis were employed. The outcomes strongly suggested that the subgen. Schedonorus has a close relationship to Lolium, and it is also proposed to move the sect. Leucopoa from subgen. Leucopoa to Subgen. Schedonorus and to separate sect. Breviaristatae from the subgen. Leucopoa. We found that F. californica could be a lineage of hybrid origin because of its intermediate placement between the broad-leaved and fine-leaved clade.

Insight in seasonal affective disorder.

Science.gov (United States)

Ghaemi, S N; Sachs, G S; Baldassano, C F; Truman, C J

1997-01-01

Lack of insight complicates the evaluation and treatment of patients with psychotic and affective disorders. No studies of insight in seasonal affective disorder (SAD) have been reported. Thirty patients with SAD diagnosed by the Structured Clinical Interview for DSM-III-R but no other axis I conditions were treated short-term with light-therapy. Insight was measured with the Scale to Assess Unawareness of Mental Disorder (SUMD) as modified by the authors to assess the self-report of insight into depressive symptoms. Increasing scores (1 to 5) indicated increasing unawareness of illness (i.e., less insight). SAD patients displayed a moderate amount of insight when depressed (mean SUMD score, 2.5). When recovered, they showed no significant change in insight into past depressive symptoms (mean SUMD score, 2.8). Greater insight into current depressive symptoms correlated with more depressive symptoms on the Hamilton Rating Scale for Depression score ([HRSD] r = .35, P depressive symptoms that does not change after recovery, a result in agreement with studies of insight in psychosis and mania. Further, in SAD, increased severity of illness may be associated with increased insight into depressive symptoms, consistent with the hypothesis of depressive realism.

Quantum Electron Tunneling in Respiratory Complex I1

Science.gov (United States)

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A.

2014-01-01

We have simulated the atomistic details of electronic wiring of all Fe/S clusters in complex I, a key enzyme in the respiratory electron transport chain. The tunneling current theory of many-electron systems is applied to the broken-symmetry (BS) states of the protein at the ZINDO level. One-electron tunneling approximation is found to hold in electron tunneling between the anti-ferromagnetic binuclear and tetranuclear Fe/S clusters with moderate induced polarization of the core electrons. Calculated tunneling energy is about 3 eV higher than Fermi level in the band gap of the protein, which supports that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of electron transport chain. Resulting electron tunneling pathways consist of up to three key contributing protein residues between neighboring Fe/S clusters. A distinct signature of the wave properties of electrons is observed as quantum interferences when multiple tunneling pathways exist. In N6a-N6b, electron tunnels along different pathways depending on the involved BS states, suggesting possible fluctuations of the tunneling pathways driven by the local protein environment. The calculated distance dependence of the electron transfer rates with internal water molecules included are in good agreement with a reported phenomenological relation. PMID:21495666

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

Science.gov (United States)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.

Science.gov (United States)

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.

Molecular Simulations of Cyclic Loading Behavior of Carbon Nanotubes Using the Atomistic Finite Element Method

Directory of Open Access Journals (Sweden)

Jianfeng Wang

2009-01-01

Full Text Available The potential applications of carbon nanotubes (CNT in many engineered bionanomaterials and electromechanical devices have imposed an urgent need on the understanding of the fatigue behavior and mechanism of CNT under cyclic loading conditions. To date, however, very little work has been done in this field. This paper presents the results of a theoretical study on the behavior of CNT subject to cyclic tensile and compressive loads using quasi-static molecular simulations. The Atomistic Finite Element Method (AFEM has been applied in the study. It is shown that CNT exhibited extreme cyclic loading resistance with yielding strain and strength becoming constant within limited number of loading cycles. Viscoelastic behavior including nonlinear elasticity, hysteresis, preconditioning (stress softening, and large strain have been observed. Chiral symmetry was found to have appreciable effects on the cyclic loading behavior of CNT. Mechanisms of the observed behavior have been revealed by close examination of the intrinsic geometric and mechanical features of tube structure. It was shown that the accumulated residual defect-free morphological deformation was the primary mechanism responsible for the cyclic failure of CNT, while the bond rotating and stretching experienced during loading/unloading played a dominant role on the strength, strain and modulus behavior of CNT.

Situation awareness and workload in complex tactical environments

NARCIS (Netherlands)

Veltman, J.A.

1999-01-01

The paper provides an example of a method to get insight into workload changes over time, executed tasks and situation awareness (SA) in complex task environments. The method is applied to measure the workload of a helicopter crew. The method has three components: 1) task analysis, 2) video

Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455.

Science.gov (United States)

Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng

2016-01-01

Aberrant FGFR4 signaling has been documented abundantly in various human cancers. The majority of FGFR inhibitors display significantly reduced potency toward FGFR4 compared to FGFR1-3. However, LY2874455 has similar inhibition potency for FGFR1-4 with IC50 less than 6.4 nM. To date, there is no published crystal structure of LY2874455 in complex with any kinase. To better understand the pan-FGFR selectivity of LY2874455, we have determined the crystal structure of the FGFR4 kinase domain bound to LY2874455 at a resolution of 2.35 Å. LY2874455, a type I inhibitor for FGFR4, binds to the ATP-binding pocket of FGFR4 in a DFG-in active conformation with three hydrogen bonds and a number of van der Waals contacts. After alignment of the kinase domain sequence of 4 FGFRs, and superposition of the ATP binding pocket of 4 FGFRs, our structural analyses reveal that the interactions of LY2874455 to FGFR4 are largely conserved in 4 FGFRs, explaining at least partly, the broad inhibitory activity of LY2874455 toward 4 FGFRs. Consequently, our studies reveal new insights into the pan-FGFR selectivity of LY2874455 and provide a structural basis for developing novel FGFR inhibitors that target FGFR1-4 broadly.

Polycomb complexes and silencing mechanisms

DEFF Research Database (Denmark)

Lund, Anders H; van Lohuizen, Maarten

2004-01-01

Advances in the past couple of years have brought important new knowledge on the mechanisms by which Polycomb-group proteins regulate gene expression and on the consequences of their actions. The discovery of histone methylation imprints specific for Polycomb and Trithorax complexes has provided...... mechanistic insight on how this ancient epigenetic memory system acts to repress and indicates that it may share mechanistic aspects with other silencing and genome-protective processes, such as RNA interference....

Insights into functional-group-tolerant polymerization catalysis with phosphine-sulfonamide palladium (II) complexes

KAUST Repository

Jian, Zhongbao; Falivene, Laura; Wucher, Philipp; Roesle, Philipp; Caporaso, Lucia; Cavallo, Luigi; Gç ttker-Schnetmann, Inigo; Mecking, Stefan

2014-01-01

Two series of cationic palladium(II) methyl complexes {[(2-MeOC6H4)2PC6H4SO2NHC6H3(2,6-R1,R2)]PdMe}2[A]2 (X1+-A: R1=R2=H: H1+-A; R1=R2=CH(CH3)2: DIPP1+-A; R1=H, R2=CF3: CF31+-A; A=BF4 or SbF6) and neutral palladium(II) methyl complexes {[(2-MeOC6H4

Mechanisms of recognition and binding of α-TTP to the plasma membrane by multi-scale molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Christos eLamprakis

2015-07-01

Full Text Available We used multiple sets of simulations both at the atomistic and coarse-grained level of resolution, to investigate interaction and binding of α-tochoperol transfer protein (α-TTP to phosphatidylinositol phosphate lipids (PIPs. Our calculations indicate that enrichment of membranes with such lipids facilitate membrane anchoring. Atomistic models suggest that PIP can be incorporated into the binding cavity of α-TTP and therefore confirm that such protein can work as lipid exchanger between the endosome and the plasma membrane. Comparison of the atomistic models of the α-TTP / PIPs complex with membrane-bound α-TTP revealed different roles for the various basic residues composing the basic patch that is key for the protein / ligand interaction. Such residues are of critical importance as several point mutations at their position lead to severe forms of ataxia with vitamin E deficiency (AVED phenotypes. Specifically, R221 is main residue responsible for the stabilisation of the complex. R68 and R192 exchange strong interactions in the protein or in the membrane complex only, suggesting that the two residues alternate contact formation, thus facilitating lipid flipping from the membrane into the protein cavity during the lipid exchange process. Finally, R59 shows weaker interactions with PIPs anyway with a clear preference for specific phosphorylation positions, hinting a role in early membrane selectivity for the protein. Altogether, our simulations reveal significant aspects at the atomistic scale of interactions of α-TTP with the plasma membrane and with PIP, providing clarifications on the mechanism of intracellular vitamin E trafficking and helping establishing the role of key residue for the functionality of α-TTP.

Exploring the reducing role of boron: added insights from theory.

Science.gov (United States)

Dangat, Yuvraj; Vanka, Kumar

2016-04-14

Carbon-carbon coupling in CO molecules is a challenging proposition, and very few main group complexes have been shown to effect this process. A recently reported triply bonded diboryne system (1) is notable for coupling four CO molecules to produce a (bis)boralactone species. The current full quantum chemical computational investigation with density functional theory (DFT) provides important insights into the nature of the CO coupling process by triply bonded diboryne systems. The complete reaction pathway leading to the formation of the (bis)boralactone has been determined. Factors that make this system so successful in coupling CO groups have been elucidated, and pertinent issues, such as why the coupling process stops after four CO additions, have been explored. Also, importantly, insights have been gained through the natural bond orbital (NBO) analysis into how the back-donation from diboryne activates CO.

Interaction of amyloid inhibitor proteins with amyloid beta peptides: insight from molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Payel Das

Full Text Available Knowledge of the detailed mechanism by which proteins such as human αB- crystallin and human lysozyme inhibit amyloid beta (Aβ peptide aggregation is crucial for designing treatment for Alzheimer's disease. Thus, unconstrained, atomistic molecular dynamics simulations in explicit solvent have been performed to characterize the Aβ17-42 assembly in presence of the αB-crystallin core domain and of lysozyme. Simulations reveal that both inhibitor proteins compete with inter-peptide interaction by binding to the peptides during the early stage of aggregation, which is consistent with their inhibitory action reported in experiments. However, the Aβ binding dynamics appear different for each inhibitor. The binding between crystallin and the peptide monomer, dominated by electrostatics, is relatively weak and transient due to the heterogeneous amino acid distribution of the inhibitor surface. The crystallin-bound Aβ oligomers are relatively long-lived, as they form more extensive contact surface with the inhibitor protein. In contrast, a high local density of arginines from lysozyme allows strong binding with Aβ peptide monomers, resulting in stable complexes. Our findings not only illustrate, in atomic detail, how the amyloid inhibitory mechanism of human αB-crystallin, a natural chaperone, is different from that of human lysozyme, but also may aid de novo design of amyloid inhibitors.

Characterization of the interaction forces in a drug carrier complex of doxorubicin with a drug-binding peptide.

Science.gov (United States)

Gocheva, Gergana; Ilieva, Nina; Peneva, Kalina; Ivanova, Anela

2018-04-01

Polypeptide-based materials are used as building blocks for drug delivery systems aimed at toxicity decrease in chemotherapeutics. A molecular-level approach is adopted for investigating the non-covalent interactions between doxorubicin and a recently synthesized drug-binging peptide as a key part of a system for delivery to neoplastic cells. Molecular dynamics simulations in aqueous solution at room and body temperature are applied to investigate the structure and the binding modes within the drug-peptide complex. The tryptophans are outlined as the main chemotherapeutic adsorption sites, and the importance of their placement in the peptide sequence is highlighted. The drug-peptide binging energy is evaluated by density functional theory calculations. Principal component analysis reveals comparable importance of several types of interaction for the binding strength. π-Stacking is dominant, but other factors are also significant: intercalation, peptide backbone stacking, electrostatics, dispersion, and solvation. Intra- and intermolecular H-bonding also stabilizes the complexes. The influence of solvent molecules on the binding energy is mild. The obtained data characterize the drug-to-peptide attachment as a mainly attractive collective process with interactions spanning a broad range of values. These results explain with atomistic detail the experimentally registered doxorubicin-binging ability of the peptide and outline the complex as a prospective carrying unit that can be employed in design of drug delivery systems. © 2017 John Wiley & Sons A/S.

Impaired insight into illness and cognitive insight in schizophrenia spectrum disorders: Resting state functional connectivity

Science.gov (United States)

Gerretsen, Philip; Menon, Mahesh; Mamo, David C.; Fervaha, Gagan; Remington, Gary; Pollock, Bruce G.; Graff-Guerrero, Ariel

2015-01-01

Background Impaired insight into illness (clinical insight) in schizophrenia has negative effects on treatment adherence and clinical outcomes. Schizophrenia is described as a disorder of disrupted brain connectivity. In line with this concept, resting state networks (RSNs) appear differentially affected in persons with schizophrenia. Therefore, impaired clinical, or the related construct of cognitive insight (which posits that impaired clinical insight is a function of metacognitive deficits), may reflect alterations in RSN functional connectivity (fc). Based on our previous research, which showed that impaired insight into illness was associated with increased left hemisphere volume relative to right, we hypothesized that impaired clinical insight would be associated with increased connectivity in the DMN with specific left hemisphere brain regions. Methods Resting state MRI scans were acquired for participants with schizophrenia or schizoaffective disorder (n = 20). Seed-to-voxel and ROI-to-ROI fc analyses were performed using the CONN-fMRI fc toolbox v13 for established RSNs. Clinical and cognitive insight were measured with the Schedule for the Assessment of Insight—Expanded Version and Beck Cognitive Insight Scale, respectively, and included as the regressors in fc analyses. Results As hypothesized, impaired clinical insight was associated with increased connectivity in the default mode network (DMN) with the left angular gyrus, and also in the self-referential network (SRN) with the left insula. Cognitive insight was associated with increased connectivity in the dorsal attention network (DAN) with the right inferior frontal cortex (IFC) and left anterior cingulate cortex (ACC). Conclusion Increased connectivity in DMN and SRN with the left angular gyrus and insula, respectively, may represent neural correlates of impaired clinical insight in schizophrenia spectrum disorders, and is consistent with the literature attributing impaired insight to left

Stearic acid spin labels in lipid bilayers :  insight through atomistic simulations

NARCIS (Netherlands)

Stimson, L.M.; Dong, L.; Karttunen, M.E.J.; Wisniewska, A.; Dutka, M.; Róg, T.

2007-01-01

Spin-labeled stearic acid species are commonly used for electron paramagnetic resonance (EPR) studies of cell membranes to investigate phase transitions, fluidity, and other physical properties. In this paper, we use large-scale molecular dynamics simulations to investigate the position and behavior

Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry

DEFF Research Database (Denmark)

Petersen, Michael; Madsen, Jeppe B; Jørgensen, Thomas J D

2017-01-01

activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations...... are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1......Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen...

Proofs that Develop Insight

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Weber, Keith

2010-01-01

Many mathematics educators have noted that mathematicians do not only read proofs to gain conviction but also to obtain insight. The goal of this article is to discuss what this insight is from mathematicians' perspective. Based on interviews with nine research-active mathematicians, two sources of insight are discussed. The first is reading a…

Insights to regenerate materials: learning from nature

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García-Aznar, J. M.; Valero, C.; Gómez-Benito, M. J.; Javierre, E.

2016-08-01

Self-healing materials, both biological and engineered, integrate the ability to repair themselves and recover their functionality using the resources inherently available to them. Although significant advances have been made, in recent years, for the design of different concepts of self-healing materials, this work aims to provide some insights into how living materials are able to regenerate or heal when a fracture or injury occurs. The main sensors that regulate this adaptive and regenerative behavior are the cells. These are able to sense the mechanical alterations in their surroundings and regulate their activity in order to remove dead tissue and/or create new tissue. Therefore, understanding how cells are able to regenerate tissues under complex and multiphysics conditions can define the biomimetics guidelines to heal through inert or traditional engineering materials. In this work, we present a combination of experiments and different kinds of multiscale and multiphysics models in order to understand how mechanics regulate some mechanisms at cell and tissue level. This combination of results aims to gain insight into the development of novel strategies for self-healing materials, mimicking the behavior induced by cells and biological tissues.

AN INSIGHT INTO STAKEHOLDER-LED CSR COMMUNICATION

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Olesia Mihai

2012-11-01

Full Text Available Although companies have always been engaged in communicating strategically with the main stakeholders, recent developments have shown that the corporate communication function has been redefined as a complex activity of communicating with both internal and external stakeholders. The authors use stakeholder theory to provide insight into CSR on-line communication by analyzing the content available to the general public of three major Romanian companies. The analysis shows that Romanian companies have adopted mainly the engagement rhetoric, one of the explanations being the fact that many domestic stakeholders still fail to understand the key role of CSR in developing corporate identity and reputation via on-line communication.

Structural and dynamical effects induced by the anticancer drug topotecan on the human topoisomerase I - DNA complex.

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Giordano Mancini

Full Text Available BACKGROUND: Human topoisomerase I catalyzes the relaxation of DNA supercoils in fundamental cell processes like transcription, replication and chromosomal segregation. It is the only target of the camptothecin family of anticancer drugs. Among these, topotecan has been used to treat lung and ovarian carcinoma for several years. Camptothecins reversibly binds to the covalent intermediate DNA-enzyme, stabilizing the cleavable complex and reducing the religation rate. The stalled complex then collides with the progression of the replication fork, producing lethal double strand DNA breaks and eventually cell death. METHODOLOGY/PRINCIPAL FINDINGS: Long lasting molecular dynamics simulations of the DNA-topoisomerase I binary complex and of the DNA-topoisomerase-topotecan ternary complex have been performed and compared. The conformational space sampled by the binary complex is reduced by the presence of the drug, as observed by principal component and cluster analyses. This conformational restraint is mainly due to the reduced flexibility of residues 633-643 (the region connecting the linker to the core domain that causes an overall mobility loss in the ternary complex linker domain. During the simulation, DNA/drug stacking interactions are fully maintained, and hydrogen bonds are maintained with the enzyme. Topotecan keeps the catalytic residue Lys532 far from the DNA, making it unable to participate to the religation reaction. Arg364 is observed to interact with both the B and E rings of topotecan with two stable direct hydrogen bonds. An interesting constrain exerted by the protein on the geometrical arrangement of topotecan is also observed. CONCLUSIONS/SIGNIFICANCE: Atomistic-scale understanding of topotecan interactions with the DNA-enzyme complex is fundamental to the explaining of its poisonous effect and of the drug resistance observed in several single residue topoisomerase mutants. We observed significant alterations due to topotecan in

The GARP complex is required for cellular sphingolipid homeostasis

DEFF Research Database (Denmark)

Fröhlich, Florian; Petit, Constance; Kory, Nora

2015-01-01

(GARP) complex, which functions in endosome-to-Golgi retrograde vesicular transport, as a critical player in sphingolipid homeostasis. GARP deficiency leads to accumulation of sphingolipid synthesis intermediates, changes in sterol distribution, and lysosomal dysfunction. A GARP complex mutation...... analogous to a VPS53 allele causing progressive cerebello-cerebral atrophy type 2 (PCCA2) in humans exhibits similar, albeit weaker, phenotypes in yeast, providing mechanistic insights into disease pathogenesis. Inhibition of the first step of de novo sphingolipid synthesis is sufficient to mitigate many...

Illness Insight and Recovery: How Important is Illness Insight in Peoples’ Recovery Process?

DEFF Research Database (Denmark)

Korsbek, Lisa

2013-01-01

. Sources Used:The writing is based on research literature related to illness insight and on personal recovery experiences.Conclusions and Implications for Practice: It is helpful to consider the integration of the issue of illness insight when addressing the questions and consequences of diagnosis......Topic: This account reflects on the topic of illness insight and recovery. Purpose: The purpose of the account is to clarify our understanding about the importance of illness insight in peoples’ recovery process, especially when relating the question of illness insight to the question of identity......, and to assist individuals to work through the false analogy between illness and identity while supporting the transformation from patient to person. It is also necessary for clinicians to develop a clear understanding of peoples’ actual needs and gain more knowledge about peoples’ own views and experiences...

Breaking the hydrophobicity of the MscL pore: insights into a charge-induced gating mechanism.

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Balasubramanian Chandramouli

Full Text Available The mechanosensitive channel of large conductance (MscL is a protein that responds to membrane tension by opening a transient pore during osmotic downshock. Due to its large pore size and functional reconstitution into lipid membranes, MscL has been proposed as a promising artificial nanovalve suitable for biotechnological applications. For example, site-specific mutations and tailored chemical modifications have shown how MscL channel gating can be triggered in the absence of tension by introducing charged residues at the hydrophobic pore level. Recently, engineered MscL proteins responsive to stimuli like pH or light have been reported. Inspired by experiments, we present a thorough computational study aiming at describing, with atomistic detail, the artificial gating mechanism and the molecular transport properties of a light-actuated bacterial MscL channel, in which a charge-induced gating mechanism has been enabled through the selective cleavage of photo-sensitive alkylating agents. Properties such as structural transitions, pore dimension, ion flux and selectivity have been carefully analyzed. Besides, the effects of charge on alternative sites of the channel with respect to those already reported have been addressed. Overall, our results provide useful molecular insights into the structural events accompanying the engineered MscL channel gating and the interplay of electrostatic effects, channel opening and permeation properties. In addition, we describe how the experimentally observed ionic current in a single-subunit charged MscL mutant is obtained through a hydrophobicity breaking mechanism involving an asymmetric inter-subunit motion.

Cognitive insight: A systematic review.

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Van Camp, L S C; Sabbe, B G C; Oldenburg, J F E

2017-07-01

Cognitive insight is the ability to re-evaluate thoughts and beliefs in order to make thoughtful conclusions. It differs from clinical insight, as it focuses on more general metacognitive processes. Therefore, it could be relevant to diverse disorders and non-clinical subjects. There is a growing body of research on cognitive insight in individuals with and without psychosis. This review has summarised the current state of the art regarding this topic. We conclude that while cognitive insight in its current form seems valid for use in individuals with psychosis, it is less so for individuals without psychosis. Additionally, higher cognitive insight not always leads to better psychological functioning. For instance, higher levels of self-reflection are often associated with depressive mood. We therefore recommend the sub-components of cognitive insight to be studied separately. Also, it is unclear what position cognitive insight takes within the spectrum of metacognitive processes and how it relates to other self-related concepts that have been defined previously in literature. Combining future and past research on cognitive insight and its analogue concepts will help in the formation of a uniform definition that fits all subjects discussed here. Copyright © 2017. Published by Elsevier Ltd.

Insights into the Intramolecular Properties of η6-Arene-Ru-Based Anticancer Complexes Using Quantum Calculations

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Adebayo A. Adeniyi

2013-01-01

Full Text Available The factors that determine the stability and the effects of noncovalent interaction on the η6-arene ruthenium anticancer complexes are determined using DFT method. The intramolecular and intra-atomic properties were computed for two models of these half-sandwich ruthenium anticancer complexes and their respective hydrated forms. The results showed that the stability of these complexes depends largely on the network of hydrogen bonds (HB, strong nature of charge transfer, polarizability, and electrostatic energies that exist within the complexes. The hydrogen bonds strength was found to be related to the reported anticancer activities and the activation of the complexes by hydration. The metal–ligand bonds were found to be closed shell systems that are characterised by high positive Laplacian values of electron density. Two of the complexes are found to be predominantly characterised by LMCT while the other two are predominately characterised by MLCT.

Intuition, insight, and the right hemisphere: Emergence of higher sociocognitive functions

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Simon M McCrea

2010-03-01

Full Text Available Simon M McCreaDepartments of Neurology and Neuroophthalmology, University of British Columbia, Vancouver, British Columbia, CanadaAbstract: Intuition is the ability to understand immediately without conscious reasoning and is sometimes explained as a ‘gut feeling’ about the rightness or wrongness of a person, place, situation, temporal episode or object. In contrast, insight is the capacity to gain accurate and a deep understanding of a problem and it is often associated with movement beyond existing paradigms. Examples include Darwin, Einstein and Freud’s theories of natural selection, relativity, or the unconscious; respectively. Many cultures name these concepts and acknowledge their value, and insight is recognized as particularly characteristic of eminent achievements in the arts, sciences and politics. Considerable data suggests that these two concepts are more related than distinct, and that a more distributed intuitive network may feed into a predominately right hemispheric insight-based functional neuronal architecture. The preparation and incubation stages of insight may rely on the incorporation of domain-specific automatized expertise schema associated with intuition. In this manuscript the neural networks associated with intuition and insight are reviewed. Case studies of anomalous subjects with ability–achievement discrepancies are summarized. This theoretical review proposes the prospect that atypical localization of cognitive modules may enhance intuitive and insightful functions and thereby explain individual achievement beyond that expected by conventionally measured intelligence tests. A model and theory of intuition and insight’s neuroanatomical basis is proposed which could be used as a starting point for future research and better understanding of the nature of these two distinctly human and highly complex poorly understood abilities.Keywords: intuition, insight, nonverbal decoding, nonverbal sequencing

Losing the boxes: fragmentation as a source of system complexity

CSIR Research Space (South Africa)

Baumbach, J

2015-09-01

Full Text Available . This paper, which looks at systems containing people, argues that the use of transdisciplinary approaches will aid in the insight and comprehension of complex problems. It will also be shown that the inclusion of subjective and inter-subjective system aspects...

Complexity, cognition and the city

CERN Document Server

Portugali, Juval

2011-01-01

Complexity, Cognition and the City aims at a deeper understanding of urbanism, while invoking, on an equal footing, the contributions both the hard and soft sciences have made, and are still making, when grappling with the many issues and facets of regional planning and dynamics. In this work, the author goes beyond merely seeing the city as a self-organized, emerging pattern of some collective interaction between many stylized urban "agents" – he makes the crucial step of attributing cognition to his agents and thus raises, for the first time, the question on how to deal with a complex system composed of many interacting complex agents in clearly defined settings. Accordingly, the author eventually addresses issues of practical relevance for urban planners and decision makers. The book unfolds its message in a largely nontechnical manner, so as to provide a broad interdisciplinary readership with insights, ideas, and other stimuli to encourage further research – with the twofold aim of further pushing ba...

Emergence: Complexity Pedagogy in Action

Science.gov (United States)

Jonas-Simpson, Christine

2015-01-01

Many educators are looking for new ways to engage students and each other in order to enrich curriculum and the teaching-learning process. We describe an example of how we enacted teaching-learning approaches through the insights of complexity thinking, an approach that supports the emergence of new possibilities for teaching-learning in the classroom and online. Our story begins with an occasion to meet with 10 nursing colleagues in a three-hour workshop using four activities that engaged learning about complexity thinking and pedagogy. Guiding concepts for the collaborative workshop were nonlinearity, distributed decision-making, divergent thinking, self-organization, emergence, and creative exploration. The workshop approach considered critical questions to spark our collective inquiry. We asked, “What is emergent learning?” and “How do we, as educators and learners, engage a community so that new learning surfaces?” We integrated the arts, creative play, and perturbations within a complexity approach. PMID:25838945

Quantum-Chemical Insights into the Self-Assembly of Carbon-Based Supramolecular Complexes

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Joaquín Calbo

2018-01-01

Full Text Available Understanding how molecular systems self-assemble to form well-organized superstructures governed by noncovalent interactions is essential in the field of supramolecular chemistry. In the nanoscience context, the self-assembly of different carbon-based nanoforms (fullerenes, carbon nanotubes and graphene with, in general, electron-donor molecular systems, has received increasing attention as a means of generating potential candidates for technological applications. In these carbon-based systems, a deep characterization of the supramolecular organization is crucial to establish an intimate relation between supramolecular structure and functionality. Detailed structural information on the self-assembly of these carbon-based nanoforms is however not always accessible from experimental techniques. In this regard, quantum chemistry has demonstrated to be key to gain a deep insight into the supramolecular organization of molecular systems of high interest. In this review, we intend to highlight the fundamental role that quantum-chemical calculations can play to understand the supramolecular self-assembly of carbon-based nanoforms through a limited selection of supramolecular assemblies involving fullerene, fullerene fragments, nanotubes and graphene with several electron-rich π-conjugated systems.

Visualizing the complex functions and mechanisms of the anaphase promoting complex/cyclosome (APC/C)

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Alfieri, Claudio; Zhang, Suyang

2017-01-01

The anaphase promoting complex or cyclosome (APC/C) is a large multi-subunit E3 ubiquitin ligase that orchestrates cell cycle progression by mediating the degradation of important cell cycle regulators. During the two decades since its discovery, much has been learnt concerning its role in recognizing and ubiquitinating specific proteins in a cell-cycle-dependent manner, the mechanisms governing substrate specificity, the catalytic process of assembling polyubiquitin chains on its target proteins, and its regulation by phosphorylation and the spindle assembly checkpoint. The past few years have witnessed significant progress in understanding the quantitative mechanisms underlying these varied APC/C functions. This review integrates the overall functions and properties of the APC/C with mechanistic insights gained from recent cryo-electron microscopy (cryo-EM) studies of reconstituted human APC/C complexes. PMID:29167309

Dreaming and insight

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Edwards, Christopher L.; Ruby, Perrine M.; Malinowski, Josie E.; Bennett, Paul D.; Blagrove, Mark T.

2013-01-01

This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years). Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996) therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams (ATD). The need to distinguish “aha” experiences as a result of discovering a waking life source for part of a dream, from “aha” experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared. PMID:24550849

The drug-eluting resorbable magnesium vascular scaffold in complex coronary bifurcations: insights from an in vivo multimodality imaging study.

Science.gov (United States)

Bennett, Johan; Vanhaverbeke, Maarten; Vanden Driessche, Nina; Hiltrop, Nick; Adriaenssens, Tom; Desmet, Walter; Sinnaeve, Peter; Dubois, Christophe

2018-04-20

This acute in vivo study sought to provide insights regarding the feasibility of performing complex bifurcation stenting with Magmaris magnesium alloy bioresorbable scaffolds (Biotronik, Bulach, Switzerland). Twenty-five New Zealand White rabbits underwent stenting of non-diseased aorto-iliac bifurcations with the Magmaris using provisional (PS; n=5), culotte (n=6), modified T (n=6), or T and protrusion (TAP, n=8) stenting techniques. Angiography, optical coherence tomography and micro-computed tomography were performed. Angiographic results were good without evidence of side branch (SB) compromise. In 9/25 procedures, strut fractures were identified with minimal luminal compromise in two cases. PS opened the SB optimally without evidence of scaffold compromise. Culotte resulted in complete bifurcation coverage and good scaffold expansion; single strut fractures were present in three out of six and double fractures in one out of six procedures. Modified T and TAP resulted in complete bifurcation coverage, minimal neocarina double-strut layers and good expansion. In two out of six modified T procedures, strut fractures were present with SB scaffold deformity present in an additional two out of six procedures. In three out of eight TAP procedures, strut fractures were present without compromising overall scaffold integrity. Bifurcation stenting using Magmaris appears feasible. PS with additional TAP whenever needed seems a reasonable approach. Whenever a two-stent technique is planned, TAP appears most favourable whilst modified T and culotte stenting should probably be avoided.

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

Energy Technology Data Exchange (ETDEWEB)

Gray, Alan [The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom); Harlen, Oliver G. [University of Leeds, Leeds LS2 9JT (United Kingdom); Harris, Sarah A., E-mail: s.a.harris@leeds.ac.uk [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Leeds, Leeds LS2 9JT (United Kingdom); Khalid, Syma; Leung, Yuk Ming [University of Southampton, Southampton SO17 1BJ (United Kingdom); Lonsdale, Richard [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg (Germany); Mulholland, Adrian J. [University of Bristol, Bristol BS8 1TS (United Kingdom); Pearson, Arwen R. [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Hamburg, Hamburg (Germany); Read, Daniel J.; Richardson, Robin A. [University of Leeds, Leeds LS2 9JT (United Kingdom); The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom)

2015-01-01

The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. 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.

Understanding complex urban systems multidisciplinary approaches to modeling

CERN Document Server

Gurr, Jens; Schmidt, J

2014-01-01

Understanding Complex Urban Systems takes as its point of departure the insight that the challenges of global urbanization and the complexity of urban systems cannot be understood – let alone ‘managed’ – by sectoral and disciplinary approaches alone. But while there has recently been significant progress in broadening and refining the methodologies for the quantitative modeling of complex urban systems, in deepening the theoretical understanding of cities as complex systems, or in illuminating the implications for urban planning, there is still a lack of well-founded conceptual thinking on the methodological foundations and the strategies of modeling urban complexity across the disciplines. Bringing together experts from the fields of urban and spatial planning, ecology, urban geography, real estate analysis, organizational cybernetics, stochastic optimization, and literary studies, as well as specialists in various systems approaches and in transdisciplinary methodologies of urban analysis, the volum...

Giant electrocaloric response in the prototypical Pb(Mg,Nb)O3 relaxor ferroelectric from atomistic simulations

Science.gov (United States)

Jiang, Zhijun; Nahas, Y.; Prokhorenko, S.; Prosandeev, S.; Wang, D.; Íñiguez, Jorge; Bellaiche, L.

2018-03-01

An atomistic effective Hamiltonian is used to investigate electrocaloric (EC) effects of Pb (Mg1 /3Nb2 /3) O3 relaxor ferroelectrics in its ergodic regime, and subject to electric fields applied along the pseudocubic [111] direction. Such a Hamiltonian qualitatively reproduces (i) the electric field-versus-temperature phase diagram, including the existence of a critical point where first-order and second-order transitions meet each other; and (ii) a giant EC response near such a critical point. It also reveals that such giant response around this critical point is microscopically induced by field-induced percolation of polar nanoregions. Moreover, it is also found that, for any temperature above the critical point, the EC coefficient-versus-electric-field curve adopts a maximum (and thus larger electrocaloric response too), that can be well described by the general Landau-like model proposed by Jiang et al., [Phys. Rev. B 96, 014114 (2017)], 10.1103/PhysRevB.96.014114, and that is further correlated with specific microscopic features related to dipoles lying along different rhombohedral directions. Furthermore, for temperatures being at least 40 K higher than the critical temperature, the (electric field, temperature) line associated with this maximal EC coefficient is below both the Widom line and the line representing percolation of polar nanoregions.

From big data to deep insight in developmental science.

Science.gov (United States)

Gilmore, Rick O

2016-01-01

The use of the term 'big data' has grown substantially over the past several decades and is now widespread. In this review, I ask what makes data 'big' and what implications the size, density, or complexity of datasets have for the science of human development. A survey of existing datasets illustrates how existing large, complex, multilevel, and multimeasure data can reveal the complexities of developmental processes. At the same time, significant technical, policy, ethics, transparency, cultural, and conceptual issues associated with the use of big data must be addressed. Most big developmental science data are currently hard to find and cumbersome to access, the field lacks a culture of data sharing, and there is no consensus about who owns or should control research data. But, these barriers are dissolving. Developmental researchers are finding new ways to collect, manage, store, share, and enable others to reuse data. This promises a future in which big data can lead to deeper insights about some of the most profound questions in behavioral science. © 2016 The Authors. WIREs Cognitive Science published by Wiley Periodicals, Inc.

Catalytic Hydroamination of Alkynes and Norbornene with Neutral and Cationic Tantalum Imido Complexes

Science.gov (United States)

Anderson, Laura L.; Arnold, John; Bergman, Robert G.

2005-01-01

Several tantalum imido complexes have been synthesized and shown to efficiently catalyze the hydroamination of internal and terminal alkynes. An unusual hydroamination/hydroarylation reaction of norbornene catalyzed by a highly electrophilic cationic tantalum imido complex is also reported. Factors affecting catalyst activity and selectivity are discussed along with mechanistic insights gained from stoichiometric reactions. PMID:15255680

Landscape-Scale Disturbance: Insights into the Complexity of Catchment Hydrology in the Mountaintop Removal Mining Region of the Eastern United States

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Andrew J. Miller

2016-07-01

Full Text Available Few land disturbances impact watersheds at the scale and extent of mountaintop removal mining (MTM. This practice removes forests, soils and bedrock to gain access to underground coal that results in likely permanent and wholesale changes that impact catchment hydrology, geochemistry and ecosystem health. MTM is the dominant driver of land cover changes in the central Appalachian Mountains region of the United States, converting forests to mine lands and burying headwater streams. Despite its dominance on the landscape, determining the hydrological impacts of MTM is complicated by underground coal mines that significantly alter groundwater hydrology. To provide insight into how coal mining impacts headwater catchments, we compared the hydrologic responses of an MTM and forested catchment using event rainfall-runoff analysis, modeling and isotopic approaches. Despite similar rainfall characteristics, hydrology in the two catchments differed in significant ways, but both catchments demonstrated threshold-mediated hydrologic behavior that was attributed to transient storage and the release of runoff from underground mines. Results suggest that underground mines are important controls for runoff generation in both obviously disturbed and seemingly undisturbed catchments and interact in uncertain ways with disturbance from MTM. This paper summarizes our results and demonstrates the complexity of catchment hydrology in the MTM region.

Structure and tectonic evolution of the southwestern Trinidad dome, Escambray complex, Central Cuba: Insights into deformation in an accretionary wedge

Science.gov (United States)

Despaigne-Díaz, Ana Ibis; García Casco, Antonio; Cáceres Govea, Dámaso; Wilde, Simon A.; Millán Trujillo, Guillermo

2017-10-01

The Trinidad dome, Escambray complex, Cuba, forms part of an accretionary wedge built during intra-oceanic subduction in the Caribbean from the Late Cretaceous to Cenozoic. The structure reflects syn-subduction exhumation during thickening of the wedge, followed by extension. Field mapping, metamorphic and structural analysis constrain the tectonic evolution into five stages. Three ductile deformation events (D1, D2 and D3) are related to metamorphism in a compressional setting and formation of several nappes. D1 subduction fabrics are only preserved as relict S1 foliation and rootless isoclinal folds strongly overprinted by the main S2 foliation. The S2 foliation is parallel to sheared serpentinised lenses that define tectonic contacts, suggesting thrust stacks and underthrusting at mantle depths. Thrusting caused an inverted metamorphic structure with higher-grade on top of lower-grade nappes. Exhumation started during D2 when the units were incorporated into the growing accretionary wedge along NNE-directed thrust faults and was accompanied by substantial decompression and cooling. Folding and thrusting continued during D3 and marks the transition from ductile to brittle-ductile conditions at shallower crustal levels. The D4-5 events are related to extension and contributed to the final exhumation (likely as a core complex). D4 is associated with a regional spaced S4 cleavage, late open folds, and numerous extension veins, whereas D5 is recorded by normal and strike-slip faults affecting all nappes. The P-t path shows rapid exhumation during D2 and slower rates during D3 when the units were progressively incorporated into the accretionary prism. The domal shape formed in response to tectonic denudation assisted by normal faulting and erosion at the surface during the final stages of structural development. These results support tectonic models of SW subduction of the Proto-Caribbean crust under the Caribbean plate during the latest Cretaceous and provide

Chemometric and Statistical Analyses of ToF-SIMS Spectra of Increasingly Complex Biological Samples

Energy Technology Data Exchange (ETDEWEB)

Berman, E S; Wu, L; Fortson, S L; Nelson, D O; Kulp, K S; Wu, K J

2007-10-24

Characterizing and classifying molecular variation within biological samples is critical for determining fundamental mechanisms of biological processes that will lead to new insights including improved disease understanding. Towards these ends, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to examine increasingly complex samples of biological relevance, including monosaccharide isomers, pure proteins, complex protein mixtures, and mouse embryo tissues. The complex mass spectral data sets produced were analyzed using five common statistical and chemometric multivariate analysis techniques: principal component analysis (PCA), linear discriminant analysis (LDA), partial least squares discriminant analysis (PLSDA), soft independent modeling of class analogy (SIMCA), and decision tree analysis by recursive partitioning. PCA was found to be a valuable first step in multivariate analysis, providing insight both into the relative groupings of samples and into the molecular basis for those groupings. For the monosaccharides, pure proteins and protein mixture samples, all of LDA, PLSDA, and SIMCA were found to produce excellent classification given a sufficient number of compound variables calculated. For the mouse embryo tissues, however, SIMCA did not produce as accurate a classification. The decision tree analysis was found to be the least successful for all the data sets, providing neither as accurate a classification nor chemical insight for any of the tested samples. Based on these results we conclude that as the complexity of the sample increases, so must the sophistication of the multivariate technique used to classify the samples. PCA is a preferred first step for understanding ToF-SIMS data that can be followed by either LDA or PLSDA for effective classification analysis. This study demonstrates the strength of ToF-SIMS combined with multivariate statistical and chemometric techniques to classify increasingly complex biological samples

New Insights into the Role of Pb-BHA Complexes in the Flotation of Tungsten Minerals

Science.gov (United States)

Yue, Tong; Han, Haisheng; Hu, Yuehua; Sun, Wei; Li, Xiaodong; Liu, Runqing; Gao, Zhiyong; Wang, Li; Chen, Pan; Zhang, Chenyang; Tian, Mengjie

2017-11-01

Lead ions (lead nitrate) were introduced to modify the surface properties of tungsten minerals, effectively improving the floatability, with benzohydroxamic acid (BHA) serving as the collector. Flotation tests indicated that Pb-BHA complexes were the active species responsible for flotation of the tungsten minerals. The developed Pb-BHA complexes and the novel flotation process effectively increased the recovery of scheelite and wolframite, simplified the technological process, and led to reduced costs. Fourier transform infrared spectra data showed the presence of adsorbed Pb-BHA complexes on the surface of the minerals. The characteristic peaks of BHA shifted by a considerable extent, indicating that chemical adsorption plays an important role in the flotation process. Zeta potential results confirmed physical adsorption of the positively charged Pb-BHA complexes on the mineral surfaces. The synergistic effect between chemical and physical adsorption facilitated the maximum flotation recovery of scheelite and wolframite.

Two Discrete RuCp* (Cp*=Pentamethylcyclopentadienyl) Binding Modes of N-Confused Porphyrins: Peripheral π Complex and Sitting Atop Ruthenocenophane Complex by Skeletal Transformation.

Science.gov (United States)

Yamamoto, Takaaki; Mitsuno, Koki; Mori, Shigeki; Itoyama, Shuhei; Shiota, Yoshihito; Yoshizawa, Kazunari; Ishida, Masatoshi; Furuta, Hiroyuki

2018-05-07

Complexation of a RuCp* cation with N-confused tetraarylporphyrins (NCPs) forms directly bound ruthenium(II) pentamethylcyclopentadienyl (Cp*) π-complex on a specific meso-aryl group (e.g., phenyl) neighboring peripheral imino nitrogen of NCPs in high yields. In contrast, in the case of NCPs bearing bulky meso-substituents (e.g., 3,5-di-tert-butylphenyl), new ruthenocenophane-like complex embedded on an N-confused calix[4]phyrin was formed through multiple C-H bond activation of methyl groups of Cp* ligand. The mechanistic insight into the formation of the ruthenocenophane was derived from DFT calculations. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

In situ XAS of the solvothermal decomposition of dithiocarbamate complexes

NARCIS (Netherlands)

Islam, H.-U.; Roffey, A.; Hollingsworth, N.; Catlow, R.; Wolthers, M.; de Leeuw, N.H.; Bras, W.; Sankar, G.; Hogarth, G.

2012-01-01

An in situ XAS study of the solvothermal decomposition of iron and nickel dithiocarbamate complexes was performed in order to gain understanding of the decomposition mechanisms. This work has given insight into the steps involved in the decomposition, showing variation in reaction pathways between

Insights from gas and water chemistry on the geothermal system of the Domuyo volcanic complex (Patagonia, Argentina)

Science.gov (United States)

Tassi, F.; Liccioli, C.; Chiodini, G.; Agusto, M.; Caselli, A. T.; Caliro, S.; Vaselli, O.; Pecoraino, G.

2015-12-01

This study focuses on the geochemistry of geothermal fluids discharging from the western flank of the Domuyo volcanic complex (Argentina), which is hosted within an extensional basins that interrupts the Andes at latitudes comprises between 35° and 39°S. The analytical results of gas and water samples collected during three sampling campaigns (2013, 2014 and 2015) are presented and discussed in order to: i) evaluate the equilibrium temperature(s) of the main fluid reservoir, ii) provide information on the origin of the fluid discharges and the secondary processes controlling their chemistry. Geothermometry based on the chemical composition of thermal waters indicates a maximum equilibrium temperature of 220 °C. This temperature, coupled with the measured amount of discharged Cl, suggest that the total energy released from this system is 1.1±0.2 GW. Atmospheric gases from a thick shallow aquifer contaminate most gas emissions, masking the chemical features of the deep fluid component, with the only exception of a jet fumarole located at 3,000 m a.s.l. (Bramadora). The H2O-CO2-CH4-H2-CO-C3H6-C3H8 composition of this gas emission was used to construct a geochemical conceptual model showing that the hydrothermal reservoir is liquid-dominated and thermally stratified, with temperatures ranging from 180 to 270 °C. The helium isotopic ratios (up to 6.8 Ra) and the δ13C-CO2 values (from -7.05 to -7.75 ‰ V-PDB) indicate that mantle degassing represents the dominant primary source for this dormant volcano. These results highlight the huge potential of this system as energy resource for the region. Accordingly, the regional authorities have recently planned and approved an investigation project aimed to provide further insights into the fluid geochemistry and the geostructural assessment in this promising area.

Crystal Structure of the Herpesvirus Nuclear Egress Complex Provides Insights into Inner Nuclear Membrane Remodeling

NARCIS (Netherlands)

Zeev-Ben-Mordehai, Tzviya; Weberruss, Marion; Lorenz, Michael; Cheleski, Juliana; Hellberg, Teresa; Whittle, Cathy; El Omari, Kamel; Vasishtan, Daven; Dent, Kyle C.; Harlos, Karl; Franzke, Kati; Hagen, Christoph; Klupp, Barbara G.; Antonin, Wolfram; Mettenleiter, Thomas C.; Gruenewald, Kay

2015-01-01

Although nucleo-cytoplasmic transport is typically mediated through nuclear pore complexes, herpesvirus capsids exit the nucleus via a unique vesicular pathway. Together, the conserved herpesvirus proteins pUL31 and pUL34 form the heterodimeric nuclear egress complex (NEC), which, in turn, mediates

Mechanism-based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight

DEFF Research Database (Denmark)

Rajabi, Nima; Auth, Marina; Troelsen, Kathrin Rentzius

2017-01-01

to date. We provide rationalization of the mode of binding by solving co-crystal structures of selected inhibitors in complex with both human and zebrafish SIRT5, which provide insight for future optimization of inhibitors with more "drug-like" properties. Importantly, enzyme kinetic evaluation revealed...

Phase behaviour of macromolecular liquid crystalline materials. Computational studies at the molecular level

International Nuclear Information System (INIS)

Stimson, Lorna M.

2003-01-01

Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a single dendrimer molecule in the gas phase at the atomistic level, semi-atomistic molecular dynamics of a single molecule in liquid crystalline solvents and a coarse-grained molecular dynamics study of the dendrimer in the bulk. The coarse-grained model has been developed and parameterized using the results of the atomistic and semi-atomistic work. The single molecule studies showed that the liquid crystalline dendrimer was able to change its structure by conformational changes in the flexible chains that link the mesogenic groups to the core. Structural change was seen under the application of a mean field ordering potential in the gas phase, and in the presence of liquid crystalline solvents. No liquid crystalline phases were observed for the bulk phase studies of the coarse-grained model. However, when the length of the mesogenic units was increased there was some evidence for microphase separation in these systems. (author)

What are System Dynamics Insights?

OpenAIRE

Stave, K.; Zimmermann, N. S.; Kim, H.

2016-01-01

This paper explores the concept of system dynamics insights. In our field, the term “insight” is generally understood to mean dynamic insight, that is, a deep understanding about the relationship between structure and behavior. We argue this is only one aspect of the range of insights possible from system dynamics activities, and describe a broader range of potential system dynamics insights. We also propose an initial framework for discussion that relates different types of system dynamics a...

Structure of an APC3-APC16 complex: Insights into assembly of the Anaphase Promoting Complex/Cyclosome

OpenAIRE

Yamaguchi, Masaya; Yu, Shanshan; Qiao, Renping; Weissmann, Florian; Miller, Darcie J.; VanderLinden, Ryan; Brown, Nicholas G.; Frye, Jeremiah J.; Peters, Jan-Michael; Schulman, Brenda A.

2014-01-01

The Anaphase Promoting Complex/Cyclosome (APC/C) is a massive E3 ligase that controls mitosis by catalyzing ubiquitination of key cell cycle regulatory proteins. The APC/C assembly contains two subcomplexes: the “Platform” centers around a cullin-RING-like E3 ligase catalytic core; the “Arc Lamp” is a hub that mediates transient association with regulators and ubiquitination substrates. The Arc Lamp contains the small subunits APC16, CDC26, and APC13, and tetratricopeptide repeat (TPR) protei...

Imaging morphogenesis: technological advances and biological insights.

Science.gov (United States)

Keller, Philipp J

2013-06-07

Morphogenesis, the development of the shape of an organism, is a dynamic process on a multitude of scales, from fast subcellular rearrangements and cell movements to slow structural changes at the whole-organism level. Live-imaging approaches based on light microscopy reveal the intricate dynamics of this process and are thus indispensable for investigating the underlying mechanisms. This Review discusses emerging imaging techniques that can record morphogenesis at temporal scales from seconds to days and at spatial scales from hundreds of nanometers to several millimeters. To unlock their full potential, these methods need to be matched with new computational approaches and physical models that help convert highly complex image data sets into biological insights.

Multiple Problem-Solving Strategies Provide Insight into Students' Understanding of Open-Ended Linear Programming Problems

Science.gov (United States)

Sole, Marla A.

2016-01-01

Open-ended questions that can be solved using different strategies help students learn and integrate content, and provide teachers with greater insights into students' unique capabilities and levels of understanding. This article provides a problem that was modified to allow for multiple approaches. Students tended to employ high-powered, complex,…

Pathophysiology of Degenerative Mitral Regurgitation: New 3-Dimensional Imaging Insights.

Science.gov (United States)

Antoine, Clemence; Mantovani, Francesca; Benfari, Giovanni; Mankad, Sunil V; Maalouf, Joseph F; Michelena, Hector I; Enriquez-Sarano, Maurice

2018-01-01

Despite its high prevalence, little is known about mechanisms of mitral regurgitation in degenerative mitral valve disease apart from the leaflet prolapse itself. Mitral valve is a complex structure, including mitral annulus, mitral leaflets, papillary muscles, chords, and left ventricular walls. All these structures are involved in physiological and pathological functioning of this valvuloventricular complex but up to now were difficult to analyze because of inherent limitations of 2-dimensional imaging. The advent of 3-dimensional echocardiography, computed tomography, and cardiac magnetic resonance imaging overcoming these limitations provides new insights into mechanistic analysis of degenerative mitral regurgitation. This review will detail the contribution of quantitative and qualitative dynamic analysis of mitral annulus and mitral leaflets by new imaging methods in the understanding of degenerative mitral regurgitation pathophysiology. © 2018 American Heart Association, Inc.

Insights into aquatic toxicities of the antibiotics oxytetracycline and ciprofloxacin in the presence of metal: Complexation versus mixture

International Nuclear Information System (INIS)

Zhang Yu; Cai Xiyun; Lang Xianming; Qiao Xianliang; Li Xuehua; Chen Jingwen

2012-01-01

Co-contamination of ligand-like antibiotics (e.g., tetracyclines and quinolones) and heavy metals prevails in the environment, and thus the complexation between them is involved in environmental risks of antibiotics. To understand toxicological significance of the complex, effects of metal coordination on antibiotics' toxicity were investigated. The complexation of two antibiotics, oxytetracycline and ciprofloxacin, with three heavy metals, copper, zinc, and cadmium, was verified by spectroscopic techniques. The antibiotics bound metals via multiple coordination sites and rendered a mixture of various complexation speciations. Toxicity analysis indicated that metal coordination did modify the toxicity of the antibiotics and that antibiotic, metal, and their complex acted primarily as concentration addition. Comparison of EC 50 values revealed that the complex commonly was highest toxic and predominately correlated in toxicity to the mixture. Finally, environmental scenario analysis demonstrated that ignoring complexation would improperly classify environmental risks of the antibiotics. - Highlights: ► The complex of antibiotic with metal is a mixture of various complexation modes. ► Antibiotic and metal act as various combined interactions when their complexation is ignored. ► Antibiotic, metal, and their complex act as concentration addition interaction. ► Complex commonly is the highest toxicant. ► Neglecting complexation renders improper classification of risks for antibiotics. - Antibiotic, heavy metal and their complex act primarily as concentration addition interaction and the complex commonly is highest toxic.

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

Science.gov (United States)

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.

Complexities in barrier island response to sea level rise: Insights from numerical model experiments, North Carolina Outer Banks

Science.gov (United States)

Moore, Laura J.; List, Jeffrey H.; Williams, S. Jeffress; Stolper, David

2010-09-01

.g., previous slopes, sediment budgets, etc.) in determining migration trajectories and therefore how a barrier island will respond to sea level rise. Although simple analytical calculations may predict barrier response in simplified coastal environments (e.g., constant slope, constant sea level rise rate, etc.), our model experiments demonstrate that morphological-behavior modeling is necessary to provide critical insights regarding changes that may occur in environments having complex geometries, especially when multiple parameters change simultaneously.

Complexities in barrier island response to sea level rise: Insights from numerical model experiments, North Carolina Outer Banks

Science.gov (United States)

Moore, Laura J.; List, Jeffrey H.; Williams, S. Jeffress; Stolper, David

2010-01-01

.g., previous slopes, sediment budgets, etc.) in determining migration trajectories and therefore how a barrier island will respond to sea level rise. Although simple analytical calculations may predict barrier response in simplified coastal environments (e.g., constant slope, constant sea level rise rate, etc.), our model experiments demonstrate that morphological-behavior modeling is necessary to provide critical insights regarding changes that may occur in environments having complex geometries, especially when multiple parameters change simultaneously.

Insights gained from NRC research investigations at the Maxey Flats LLW SLB facility

International Nuclear Information System (INIS)

O'Donnell, E.

1983-01-01

The NRC funded program of research at Maxey Flats was done to assist an Agreement State in assessing the performance of the site. That program has yielded both site specific insights and generic insights which are likely to be useful in licensing future sites. They are as follows: Site Specific Insights: (1) The principal pathway of water entry into burial trenches at Maxey Flats is through the trench caps. (2) Sampling of vegetation, soils, and streams adjoining the site indicates that the small but measureable amounts of radionuclides found offsite were from surface runoff or the site evaporator. (3) There is limited onsite subsurface movement of radionuclides where open fractures intersect burial trenches. Generic Insights: (1) Tritium in the plant transpiration stream appears useful for mapping trench boundaries. (2) Trees offer a promising means of monitoring subsurface radionuclide movement in fractured rocks of low permeability. (3) Complexing with EDTA appears to be a potentially important mechanism that increases mobility of such radionuclides as Co-60, Pu-238, Am-241, and Sr-90. (4) Changes in soil solution chemistry encountered as leachate moves from trenches generally reduce the solubility of migrating radionuclides. (5) Agronomic management techniques appear promising as a means to control deep water percolation through waste burial trench caps. 18 references

The morphology and distribution of submerged reefs in the Maui-Nui Complex, Hawaii: New insights into their evolution since the Early Pleistocene

Science.gov (United States)

Faichney, Iain D.E.; Webster, James M.; Clague, David A.; Kelley, Chris; Applegate, Bruce; Moore, James G.

2009-01-01

Reef drowning and backstepping have long been recognised as reef responses to sea-level rise on subsiding margins. During the Late Pleistocene (~500–14 ka) Hawaiian reefs grew in response to rapid subsidence and 120 m 100 kyr sea-level cycles, with recent work on the submerged drowned reefs around the big island of Hawaii, and in other locations from the last deglacial, providing insight into reef development under these conditions. In contrast, reefs of the Early Pleistocene (~1.8–0.8 Ma) remain largely unexplored despite developing in response to significantly different 60–70 m 41 kyr sea-level cycles. The Maui-Nui Complex (MNC — forming the islands of Maui, Molokai, Lanai and Kahoolawe), provides a natural laboratory to study reef evolution throughout this time period as recent data indicate the reefs grew from 1.1 to 0.5 Ma. We use new high resolution bathymetric and backscatter data as well as sub-bottom profiling seismic data and field observations from ROV and submersible dives to make a detailed analysis of reef morphology and structure around the MNC. We focus specifically on the south-central region of the complex that provides the best reef exposure and find that the morphology of the reefs varies both regionally and temporally within this region. Barrier and pinnacle features dominate the steeper margins in the north of the study area whilst broad backstepping of the reefs is observed in the south. Within the Au'au channel in the central region between the islands, closely spaced reef and karst morphology indicates repeated subaerial exposure. We propose that this variation in the morphology and structure of the reefs within the MNC has been controlled by three main factors; the subsidence rate of the complex, the amplitude and period of eustatic sea-level cycles, and the slope and continuity of the basement substrate. We provide a model of reef development within the MNC over the last 1.2 Ma highlighting the effect that the interaction

Insights into aquatic toxicities of the antibiotics oxytetracycline and ciprofloxacin in the presence of metal: Complexation versus mixture

Energy Technology Data Exchange (ETDEWEB)

Yu, Zhang [Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024 (China); Cai Xiyun, E-mail: xiyuncai@dlut.edu.cn [Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024 (China); Xianming, Lang [Liaoning Academy of Environmental Sciences, Shenyang 110031 (China); Xianliang, Qiao; Xuehua, Li; Jingwen, Chen [Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024 (China)

2012-07-15

Co-contamination of ligand-like antibiotics (e.g., tetracyclines and quinolones) and heavy metals prevails in the environment, and thus the complexation between them is involved in environmental risks of antibiotics. To understand toxicological significance of the complex, effects of metal coordination on antibiotics' toxicity were investigated. The complexation of two antibiotics, oxytetracycline and ciprofloxacin, with three heavy metals, copper, zinc, and cadmium, was verified by spectroscopic techniques. The antibiotics bound metals via multiple coordination sites and rendered a mixture of various complexation speciations. Toxicity analysis indicated that metal coordination did modify the toxicity of the antibiotics and that antibiotic, metal, and their complex acted primarily as concentration addition. Comparison of EC{sub 50} values revealed that the complex commonly was highest toxic and predominately correlated in toxicity to the mixture. Finally, environmental scenario analysis demonstrated that ignoring complexation would improperly classify environmental risks of the antibiotics. - Highlights: Black-Right-Pointing-Pointer The complex of antibiotic with metal is a mixture of various complexation modes. Black-Right-Pointing-Pointer Antibiotic and metal act as various combined interactions when their complexation is ignored. Black-Right-Pointing-Pointer Antibiotic, metal, and their complex act as concentration addition interaction. Black-Right-Pointing-Pointer Complex commonly is the highest toxicant. Black-Right-Pointing-Pointer Neglecting complexation renders improper classification of risks for antibiotics. - Antibiotic, heavy metal and their complex act primarily as concentration addition interaction and the complex commonly is highest toxic.

Insight, Cognitive Insight and Sociodemographic Features in Obsessive Compulsive Disorder Presenting with Reactive and Autogeneus Features

Directory of Open Access Journals (Sweden)

Katre ÇAMLI

2012-03-01

Full Text Available Objective: The aim of the present study was to test hypothesis that obsessive compulsive disorder (OCD patients who have autogenous obsessions and reactive obsessions show different sociodemographic and clinical characteristics with different insight and cognitive insight levels. Method: Sixty-one patients diagnosed as OCD according to the Structured Clinical Interview for DSM-III-R (SCID-I are recruited. 31 patients had reactive obsessions and 30 had autogenous obsessions. The sociodemographic characteristics of patients and the symptomatology were evaluated using psychiatric scales including SCID-I, Yale Brown Obsessive- Compulsive Scale (YBOCS, Yale Brown Obsessive-Compulsive Scale-Symptom Checklist (YBOCS-SC and Beck Insight Scale. Results: The percentage of women in reactive obsessive group was higher and also this group had significantly less antipsychotic medication prescribed than the autogenous obsessive group. No significant difference was found for the other demographic variables. No significant difference was identified for the Beck Insight Self-Reflectiveness subscale but for the Self-Certainty subscale, reactive obsessives had higher scores. Although there was no significant difference for the composit index points, which is the subtraction of the two subscales, the p value was close to the limit. On the other hand YBOCS item- 11 scores which evaluates insight were higher in autogenous obsessives meaning low levels of insight. Conclusion: For the sociodemographic and clinical characteristics; there was no significant difference between the groups except gender distribution and antipsychotic medication. Our data about insight seems inconsistent but insight and cognitive insight can be different entities which show different levels of insight. Further investigation with different obsession types is needed.

The Association of Insight and Change in Insight with Clinical Symptoms in Depressed Inpatients.

Science.gov (United States)

He, Hongbo; Chang, Qing; Ma, Yarong

2018-04-25

Lack of insight has been extensively studied and was found to be adversely correlated with impaired treatment compliance and worse long term clinical outcomes among patients with schizophrenia, while not much is known about this phenonmenon in patients with severe depression. To explore the correlates of insight and its relation to symptom changes among the most seriously ill patients with affective disorders, those who require hospitalization. Patients hospitalized in a large psychiatric hospital in south China with either major depressive disorder (MDD)(N=55) or bipolar depression (BD) (N=85) based on ICD-10 diagnostic criteria were assessed with the Insight and Treatment Attitudes Questionnaire (ITAQ) one week after admission and at the time of discharge. Clinical symptoms were measured at the same time with the Hamilton Rating Scale for Depression (HAMD-17) and the Depression subscale of the Symptom Check list-90 (SCL-90). Length of stay (LOS), duration of illness, duration of untreated mood disorder, number of previous episodes of depression and previous admissions for depression were documented during interviews with patients and their families and from a review of medical records. Bivariate correlations and multiple regression analysis were used to examine the relationship of sociodemographic characteristics, clinical symptomatology and clinical history, to insight at the time of admission. The relationships between change in clinical symptoms and change in insight from admission to discharge were also examined. Stepwise multiple regression models suggested that any previous admissions for depression and higher anxiety factor scores on the HAMD-17 are significant independent predictors of insight accounting for 22.9% of the variance. Multiple regression analysis residual change scores (change scores adjusted for baseline values) on the ITAQ showed that improved insight over average stays of 51 days were inversely related to the residual psychomotor

Information geometric methods for complexity

Science.gov (United States)

Felice, Domenico; Cafaro, Carlo; Mancini, Stefano

2018-03-01

Research on the use of information geometry (IG) in modern physics has witnessed significant advances recently. In this review article, we report on the utilization of IG methods to define measures of complexity in both classical and, whenever available, quantum physical settings. A paradigmatic example of a dramatic change in complexity is given by phase transitions (PTs). Hence, we review both global and local aspects of PTs described in terms of the scalar curvature of the parameter manifold and the components of the metric tensor, respectively. We also report on the behavior of geodesic paths on the parameter manifold used to gain insight into the dynamics of PTs. Going further, we survey measures of complexity arising in the geometric framework. In particular, we quantify complexity of networks in terms of the Riemannian volume of the parameter space of a statistical manifold associated with a given network. We are also concerned with complexity measures that account for the interactions of a given number of parts of a system that cannot be described in terms of a smaller number of parts of the system. Finally, we investigate complexity measures of entropic motion on curved statistical manifolds that arise from a probabilistic description of physical systems in the presence of limited information. The Kullback-Leibler divergence, the distance to an exponential family and volumes of curved parameter manifolds, are examples of essential IG notions exploited in our discussion of complexity. We conclude by discussing strengths, limits, and possible future applications of IG methods to the physics of complexity.

Adsorption and pathways of single atomistic processes on NbN (0 0 1) and (1 1 1) surfaces: A first-principle study

International Nuclear Information System (INIS)

Ren, Yuan; Liu, Xuejie; Tan, Xin; Sun, Shiyang; Wei, Huai; Lu, Feng

2014-01-01

Highlights: • We investigate the behaviors of Nb, Si, N atom on NbN(0 0 1) and (1 1 1) surfaces. • The adsorption and diffusion of single atom on NbN(0 0 1) and (1 1 1) were calculated by DFT. • The potential energy surface of single atom on NbN(0 0 1) and (1 1 1) surfaces were investigated. • The diffusion process of single on NbN(0 0 1) and (1 1 1) were calculated by nudged elastic band. - Abstract: The adsorption and pathway processes of atomistic Nb, Si, and N at high-symmetry sites on NbN (0 0 1) and (1 1 1) surfaces were studied using first-principle method, which is based on the density functional theory. This investigation presents some of the results obtained. The potential energy surface (PES) was obtained by calculating the adsorption of Nb, Si, and N atoms on NbN (0 0 1). The most energetic site for the Nb atom adsorbed on NbN(0 0 1) was the site ‘on-top of face–center cubic’ (HL), whereas those for N and Si were both at the site ‘between TopN and HL’ (TopN-HL). The minimum energy paths of the single atom on NbN (0 0 1) surface diffusion were obtained using the PES calculation results. The Nb and Si atoms were diffused from the TopN to the HL position. The N atom was diffused from the TopNb, whereas the TopN–HL to HL position. The diffusion energies of the Nb, Si, and N atoms on the NbN (0 0 1) surface were 0.32, 0.69, and 1.32 eV, respectively. The pathways of the atomistic diffusion involved the diffusion of atoms from the FCC to the HCP site on the NbN (1 1 1) surface. The results showed that the diffusion energy of Si on the Nb layer was smaller than that on the N layer. Si and N can easily form stable structures while bonding on the N layer. Moreover, Si atoms can stabilize the activity of N atoms while promoting the spread of Nb atoms during deposition

Genetic correlates of insight in schizophrenia.

Science.gov (United States)

Xavier, Rose Mary; Vorderstrasse, Allison; Keefe, Richard S E; Dungan, Jennifer R

2018-05-01

Insight in schizophrenia is clinically important as it is associated with several adverse outcomes. Genetic contributions to insight are unknown. We examined genetic contributions to insight by investigating if polygenic risk scores (PRS) and candidate regions were associated with insight. Schizophrenia case-only analysis of the Clinical Antipsychotics Trials of Intervention Effectiveness trial. Schizophrenia PRS was constructed using Psychiatric Genomics Consortium (PGC) leave-one out GWAS as discovery data set. For candidate regions, we selected 105 schizophrenia-associated autosomal loci and 11 schizophrenia-related oligodendrocyte genes. We used regressions to examine PRS associations and set-based testing for candidate analysis. We examined data from 730 subjects. Best-fit PRS at p-threshold of 1e-07 was associated with total insight (R 2 =0.005, P=0.05, empirical P=0.054) and treatment insight (R 2 =0.005, P=0.048, empirical P=0.048). For models that controlled for neurocognition, PRS significantly predicted treatment insight but at higher p-thresholds (0.1 to 0.5) but did not survive correction. Patients with highest polygenic burden had 5.9 times increased risk for poor insight compared to patients with lowest burden. PRS explained 3.2% (P=0.002, empirical P=0.011) of variance in poor insight. Set-based analyses identified two variants associated with poor insight- rs320703, an intergenic variant (within-set P=6e-04, FDR P=0.046) and rs1479165 in SOX2-OT (within-set P=9e-04, FDR P=0.046). To the best of our knowledge, this is the first study examining genetic basis of insight. We provide evidence for genetic contributions to impaired insight. Relevance of findings and necessity for replication are discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Reaction-diffusion controlled growth of complex structures

Science.gov (United States)

Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna

2013-03-01

Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support