Regional Hydroclimatic Impacts of Contemporary Amazonian Deforestation and Their Spatiotemporal Variability - An Integrated Study Using Remotely Sensed Data and Numerical Tools

NASA Astrophysics Data System (ADS)

Medvigy, D.; Khanna, J.

2016-12-01

The Amazon rainforest has been under deforestation for more than four decades. Recent investigation of the regional hydroclimatic impacts of the past three decades of deforestation has revealed a strong scale-dependence of the atmospheric response to land use change. Contemporary deforestation, affecting spatial scales of a few hundreds of kilometers, has resulted in a spatial redistribution of the local dry season rainfall, with downwind and upwind deforested regions receiving respectively 30% more and 30% less rainfall from the area mean. This phenomenon is attributable to a `dynamical' response of the boundary layer air to a reduction in surface roughness due to deforestation, apparent in both satellite and numerically simulated data. This response is starkly different from a spatially uniform increase in non-precipitating cloudiness triggered by small scale clearings, prevalent in the early phases of deforestation. This study investigates the `generalizability' of the dynamical mechanism to understand its impacts on a continually deforested Amazonia. In particular, we investigate the spatiotemporal variability of the dynamical mechanism. The nature of this investigation demands long time series and large spatial converge datasets of the hydroclimate. As such, satellite imagery of clouds (GridSat) and precipitation (PERSIANN and TRMM) has proven particularly useful in facilitating this analysis. The analysis is further complemented by a reanalysis product (ERA-interim) and numerical simulations (using a variable resolution GCM). Results indicate the presence of the dynamical mechanism during local dry and transition seasons effecting the mean precipitation during this period. Its effect on the transition season precipitation can be important for the local dry season length. The dynamical mechanism also occurs in atmospheric conditions which are otherwise less conducive to thermally triggered convection. Hence, this mechanism, which effects the seasons most important for regional ecology, emerges as a possibly impactful convective triggering mechanism. This study provides context for thinking about the climate of a future, more patchily deforested Amazonia that is more favorable to the dynamical mechanism.

A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation

PubMed Central

Xiao, Li; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray

2014-01-01

A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design. PMID:25404761

Statistical mechanics of self-driven Carnot cycles.

PubMed

Smith, E

1999-10-01

The spontaneous generation and finite-amplitude saturation of sound, in a traveling-wave thermoacoustic engine, are derived as properties of a second-order phase transition. It has previously been argued that this dynamical phase transition, called "onset," has an equivalent equilibrium representation, but the saturation mechanism and scaling were not computed. In this work, the sound modes implementing the engine cycle are coarse-grained and statistically averaged, in a partition function derived from microscopic dynamics on criteria of scale invariance. Self-amplification performed by the engine cycle is introduced through higher-order modal interactions. Stationary points and fluctuations of the resulting phenomenological Lagrangian are analyzed and related to background dynamical currents. The scaling of the stable sound amplitude near the critical point is derived and shown to arise universally from the interaction of finite-temperature disorder, with the order induced by self-amplification.

A novel representation of groundwater dynamics in large-scale land surface modelling

NASA Astrophysics Data System (ADS)

Rahman, Mostaquimur; Rosolem, Rafael; Kollet, Stefan

2017-04-01

Land surface processes are connected to groundwater dynamics via shallow soil moisture. For example, groundwater affects evapotranspiration (by influencing the variability of soil moisture) and runoff generation mechanisms. However, contemporary Land Surface Models (LSM) generally consider isolated soil columns and free drainage lower boundary condition for simulating hydrology. This is mainly due to the fact that incorporating detailed groundwater dynamics in LSMs usually requires considerable computing resources, especially for large-scale applications (e.g., continental to global). Yet, these simplifications undermine the potential effect of groundwater dynamics on land surface mass and energy fluxes. In this study, we present a novel approach of representing high-resolution groundwater dynamics in LSMs that is computationally efficient for large-scale applications. This new parameterization is incorporated in the Joint UK Land Environment Simulator (JULES) and tested at the continental-scale.

Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.

PubMed

Watanabe, Hiroshi C; Kubillus, Maximilian; Kubař, Tomáš; Stach, Robert; Mizaikoff, Boris; Ishikita, Hiroshi

2017-07-21

In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na + , K + , and Ca 2+ solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

Synchronization and Causality Across Time-scales: Complex Dynamics and Extremes in El Niño/Southern Oscillation

NASA Astrophysics Data System (ADS)

Jajcay, N.; Kravtsov, S.; Tsonis, A.; Palus, M.

2017-12-01

A better understanding of dynamics in complex systems, such as the Earth's climate is one of the key challenges for contemporary science and society. A large amount of experimental data requires new mathematical and computational approaches. Natural complex systems vary on many temporal and spatial scales, often exhibiting recurring patterns and quasi-oscillatory phenomena. The statistical inference of causal interactions and synchronization between dynamical phenomena evolving on different temporal scales is of vital importance for better understanding of underlying mechanisms and a key for modeling and prediction of such systems. This study introduces and applies information theory diagnostics to phase and amplitude time series of different wavelet components of the observed data that characterizes El Niño. A suite of significant interactions between processes operating on different time scales was detected, and intermittent synchronization among different time scales has been associated with the extreme El Niño events. The mechanisms of these nonlinear interactions were further studied in conceptual low-order and state-of-the-art dynamical, as well as statistical climate models. Observed and simulated interactions exhibit substantial discrepancies, whose understanding may be the key to an improved prediction. Moreover, the statistical framework which we apply here is suitable for direct usage of inferring cross-scale interactions in nonlinear time series from complex systems such as the terrestrial magnetosphere, solar-terrestrial interactions, seismic activity or even human brain dynamics.

Length-scale dependent mechanical properties of Al-Cu eutectic alloy: Molecular dynamics based model and its experimental verification

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

Tiwary, C. S., E-mail: cst.iisc@gmail.com; Chattopadhyay, K.; Chakraborty, S.

2014-05-28

This paper attempts to gain an understanding of the effect of lamellar length scale on the mechanical properties of two-phase metal-intermetallic eutectic structure. We first develop a molecular dynamics model for the in-situ grown eutectic interface followed by a model of deformation of Al-Al{sub 2}Cu lamellar eutectic. Leveraging the insights obtained from the simulation on the behaviour of dislocations at different length scales of the eutectic, we present and explain the experimental results on Al-Al{sub 2}Cu eutectic with various different lamellar spacing. The physics behind the mechanism is further quantified with help of atomic level energy model for different lengthmore » scale as well as different strain. An atomic level energy partitioning of the lamellae and the interface regions reveals that the energy of the lamellae core are accumulated more due to dislocations irrespective of the length-scale. Whereas the energy of the interface is accumulated more due to dislocations when the length-scale is smaller, but the trend is reversed when the length-scale is large beyond a critical size of about 80 nm.« less

Theoretical approaches for dynamical ordering of biomolecular systems.

PubMed

Okumura, Hisashi; Higashi, Masahiro; Yoshida, Yuichiro; Sato, Hirofumi; Akiyama, Ryo

2018-02-01

Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

DISTURBANCE PATTERNS IN A SOCIO-ECOLOGICAL SYSTEM AT MULTIPLE SCALES

EPA Science Inventory

Ecological systems with hierarchical organization and non-equilibrium dynamics require multiple-scale analyses to comprehend how a system is structured and to formulate hypotheses about regulatory mechanisms. Characteristic scales in real landscapes are determined by, or at least...

Collective dynamics of cell migration and cell rearrangements

NASA Astrophysics Data System (ADS)

Kabla, Alexandre

Understanding multicellular processes such as embryo development or cancer metastasis requires to decipher the contributions of local cell autonomous behaviours and long range interactions with the tissue environment. A key question in this context concerns the emergence of large scale coordination in cell behaviours, a requirement for collective cell migration or convergent extension. I will present a few examples where physical and mechanical aspects play a significant role in driving tissue scale dynamics.

Human seizures self-terminate across spatial scales via a critical transition.

PubMed

Kramer, Mark A; Truccolo, Wilson; Eden, Uri T; Lepage, Kyle Q; Hochberg, Leigh R; Eskandar, Emad N; Madsen, Joseph R; Lee, Jong W; Maheshwari, Atul; Halgren, Eric; Chu, Catherine J; Cash, Sydney S

2012-12-18

Why seizures spontaneously terminate remains an unanswered fundamental question of epileptology. Here we present evidence that seizures self-terminate via a discontinuous critical transition or bifurcation. We show that human brain electrical activity at various spatial scales exhibits common dynamical signatures of an impending critical transition--slowing, increased correlation, and flickering--in the approach to seizure termination. In contrast, prolonged seizures (status epilepticus) repeatedly approach, but do not cross, the critical transition. To support these results, we implement a computational model that demonstrates that alternative stable attractors, representing the ictal and postictal states, emulate the observed dynamics. These results suggest that self-terminating seizures end through a common dynamical mechanism. This description constrains the specific biophysical mechanisms underlying seizure termination, suggests a dynamical understanding of status epilepticus, and demonstrates an accessible system for studying critical transitions in nature.

Scaling behavior of sleep-wake transitions across species

NASA Astrophysics Data System (ADS)

Lo, Chung-Chuan; Chou, Thomas; Ivanov, Plamen Ch.; Penzel, Thomas; Mochizuki, Takatoshi; Scammell, Thomas; Saper, Clifford B.; Stanley, H. Eugene

2003-03-01

Uncovering the mechanisms controlling sleep is a fascinating scientific challenge. It can be viewed as transitions of states of a very complex system, the brain. We study the time dynamics of short awakenings during sleep for three species: humans, rats and mice. We find, for all three species, that wake durations follow a power-law distribution, and sleep durations follow exponential distributions. Surprisingly, all three species have the same power-law exponent for the distribution of wake durations, but the exponential time scale of the distributions of sleep durations varies across species. We suggest that the dynamics of short awakenings are related to species-independent fluctuations of the system, while the dynamics of sleep is related to system-dependent mechanisms which change with species.

Deployment dynamics and control of large-scale flexible solar array system with deployable mast

NASA Astrophysics Data System (ADS)

Li, Hai-Quan; Liu, Xiao-Feng; Guo, Shao-Jing; Cai, Guo-Ping

2016-10-01

In this paper, deployment dynamics and control of large-scale flexible solar array system with deployable mast are investigated. The adopted solar array system is introduced firstly, including system configuration, deployable mast and solar arrays with several mechanisms. Then dynamic equation of the solar array system is established by the Jourdain velocity variation principle and a method for dynamics with topology changes is introduced. In addition, a PD controller with disturbance estimation is designed to eliminate the drift of spacecraft mainbody. Finally the validity of the dynamic model is verified through a comparison with ADAMS software and the deployment process and dynamic behavior of the system are studied in detail. Simulation results indicate that the proposed model is effective to describe the deployment dynamics of the large-scale flexible solar arrays and the proposed controller is practical to eliminate the drift of spacecraft mainbody.

Understanding dislocation mechanics at the mesoscale using phase field dislocation dynamics

PubMed Central

Hunter, A.

2016-01-01

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

Structural modeling of aircraft tires

NASA Technical Reports Server (NTRS)

Clark, S. K.; Dodge, R. N.; Lackey, J. I.; Nybakken, G. H.

1973-01-01

A theoretical and experimental investigation of the feasibility of determining the mechanical properties of aircraft tires from small-scale model tires was accomplished. The theoretical results indicate that the macroscopic static and dynamic mechanical properties of aircraft tires can be accurately determined from the scale model tires although the microscopic and thermal properties of aircraft tires can not. The experimental investigation was conducted on a scale model of a 40 x 12, 14 ply rated, type 7 aircraft tire with a scaling factor of 8.65. The experimental results indicate that the scale model tire exhibited the same static mechanical properties as the prototype tire when compared on a dimensionless basis. The structural modeling concept discussed in this report is believed to be exact for mechanical properties of aircraft tires under static, rolling, and transient conditions.

Population clocks: motor timing with neural dynamics

PubMed Central

Buonomano, Dean V.; Laje, Rodrigo

2010-01-01

An understanding of sensory and motor processing will require elucidation of the mechanisms by which the brain tells time. Open questions relate to whether timing relies on dedicated or intrinsic mechanisms and whether distinct mechanisms underlie timing across scales and modalities. Although experimental and theoretical studies support the notion that neural circuits are intrinsically capable of sensory timing on short scales, few general models of motor timing have been proposed. For one class of models, population clocks, it is proposed that time is encoded in the time-varying patterns of activity of a population of neurons. We argue that population clocks emerge from the internal dynamics of recurrently connected networks, are biologically realistic and account for many aspects of motor timing. PMID:20889368

Disturbance patterns in a socio-ecological system at multiple scales

Treesearch

G. Zurlini; Kurt H. Riitters; N. Zaccarelli; I. Petrosillo; K.B. Jones; L. Rossi

2006-01-01

Ecological systems with hierarchical organization and non-equilibrium dynamics require multiple-scale analyses to comprehend how a system is structured and to formulate hypotheses about regulatory mechanisms. Characteristic scales in real landscapes are determined by, or at least reflect, the spatial patterns and scales of constraining human interactions with the...

NH4+ ad-/desorption in sequencing batch reactors: simulation, laboratory and full-scale studies.

PubMed

Schwitalla, P; Mennerich, A; Austermann-Haun, U; Müller, A; Dorninger, C; Daims, H; Holm, N C; Rönner-Holm, S G E

2008-01-01

Significant NH4-N balance deficits were found during the measurement campaigns for the data collection for dynamic simulation studies at five full-scale sequencing batch reactor (SBR) waste water treatment plants (WWTPs), as well as during subsequent calibrations at the investigated plants. Subsequent lab scale investigations showed high evidence for dynamic, cycle-specific NH4+ ad-/desorption to the activated flocs as one reason for this balance deficit. This specific dynamic was investigated at five full-scale SBR plants for the search of the general causing mechanisms. The general mechanism found was a NH4+ desorption from the activated flocs at the end of the nitrification phase with subsequent nitrification and a chemical NH4+ adsorption at the flocs in the course of the filling phases. This NH4+ ad-/desorption corresponds to an antiparallel K+ ad/-desorption.One reasonable full-scale application was investigated at three SBR plants, a controlled filling phase at the beginning of the sedimentation phase. The results indicate that this kind of filling event must be specifically hydraulic controlled and optimised in order to prevent too high waste water break through into the clear water phase, which will subsequently be discarded. IWA Publishing 2008.

Peridynamic Multiscale Finite Element Methods

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

Costa, Timothy; Bond, Stephen D.; Littlewood, David John

The problem of computing quantum-accurate design-scale solutions to mechanics problems is rich with applications and serves as the background to modern multiscale science research. The prob- lem can be broken into component problems comprised of communicating across adjacent scales, which when strung together create a pipeline for information to travel from quantum scales to design scales. Traditionally, this involves connections between a) quantum electronic structure calculations and molecular dynamics and between b) molecular dynamics and local partial differ- ential equation models at the design scale. The second step, b), is particularly challenging since the appropriate scales of molecular dynamic andmore » local partial differential equation models do not overlap. The peridynamic model for continuum mechanics provides an advantage in this endeavor, as the basic equations of peridynamics are valid at a wide range of scales limiting from the classical partial differential equation models valid at the design scale to the scale of molecular dynamics. In this work we focus on the development of multiscale finite element methods for the peridynamic model, in an effort to create a mathematically consistent channel for microscale information to travel from the upper limits of the molecular dynamics scale to the design scale. In particular, we first develop a Nonlocal Multiscale Finite Element Method which solves the peridynamic model at multiple scales to include microscale information at the coarse-scale. We then consider a method that solves a fine-scale peridynamic model to build element-support basis functions for a coarse- scale local partial differential equation model, called the Mixed Locality Multiscale Finite Element Method. Given decades of research and development into finite element codes for the local partial differential equation models of continuum mechanics there is a strong desire to couple local and nonlocal models to leverage the speed and state of the art of local models with the flexibility and accuracy of the nonlocal peridynamic model. In the mixed locality method this coupling occurs across scales, so that the nonlocal model can be used to communicate material heterogeneity at scales inappropriate to local partial differential equation models. Additionally, the computational burden of the weak form of the peridynamic model is reduced dramatically by only requiring that the model be solved on local patches of the simulation domain which may be computed in parallel, taking advantage of the heterogeneous nature of next generation computing platforms. Addition- ally, we present a novel Galerkin framework, the 'Ambulant Galerkin Method', which represents a first step towards a unified mathematical analysis of local and nonlocal multiscale finite element methods, and whose future extension will allow the analysis of multiscale finite element methods that mix models across scales under certain assumptions of the consistency of those models.« less

Mechanics of a granular skin

NASA Astrophysics Data System (ADS)

Karmakar, Somnath; Sane, Anit; Bhattacharya, S.; Ghosh, Shankar

2017-04-01

Magic sand, a hydrophobic toy granular material, is widely used in popular science instructions because of its nonintuitive mechanical properties. A detailed study of the failure of an underwater column of magic sand shows that these properties can be traced to a single phenomenon: the system self-generates a cohesive skin that encapsulates the material inside. The skin, consisting of pinned air-water-grain interfaces, shows multiscale mechanical properties: they range from contact-line dynamics in the intragrain roughness scale, to plastic flow at the grain scale, all the way to sample-scale mechanical responses. With decreasing rigidity of the skin, the failure mode transforms from brittle to ductile (both of which are collective in nature) to a complete disintegration at the single-grain scale.

Plasticity-mediated collapse and recrystallization in hollow copper nanowires: a molecular dynamics simulation.

PubMed

Dutta, Amlan; Raychaudhuri, Arup Kumar; Saha-Dasgupta, Tanusri

2016-01-01

We study the thermal stability of hollow copper nanowires using molecular dynamics simulation. We find that the plasticity-mediated structural evolution leads to transformation of the initial hollow structure to a solid wire. The process involves three distinct stages, namely, collapse, recrystallization and slow recovery. We calculate the time scales associated with different stages of the evolution process. Our findings suggest a plasticity-mediated mechanism of collapse and recrystallization. This contradicts the prevailing notion of diffusion driven transport of vacancies from the interior to outer surface being responsible for collapse, which would involve much longer time scales as compared to the plasticity-based mechanism.

Shear banding leads to accelerated aging dynamics in a metallic glass

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

Küchemann, Stefan; Liu, Chaoyang; Dufresne, Eric M.

Traditionally, strain localization in metallic glasses is related to the thickness of the shear defect, which is confined to the nanometer scale. In this study, using site-specific x-ray photon correlation spectroscopy (XPCS), we reveal significantly accelerated relaxation dynamics around a shear band in a metallic glass at a length scale that is orders of magnitude larger than the defect itself. The relaxation time in the shear-band vicinity is up to ten-times smaller compared to the as-cast matrix, and the relaxation dynamics occurs in a characteristic three-stage aging response that manifests itself in the temperature-dependent shape parameter known from classical stretchedmore » exponential relaxation dynamics of disordered materials. We demonstrate that the time-dependent correlation functions describing the aging at different temperatures can be captured and collapsed using simple scaling functions. Finally, these insights highlight how an ubiquitous nano-scale strain-localization mechanism in metallic glasses leads to a fundamental change of the relaxation dynamics at the mesoscale.« less

Shear banding leads to accelerated aging dynamics in a metallic glass

DOE PAGES

Küchemann, Stefan; Liu, Chaoyang; Dufresne, Eric M.; ...

2018-01-11

Traditionally, strain localization in metallic glasses is related to the thickness of the shear defect, which is confined to the nanometer scale. In this study, using site-specific x-ray photon correlation spectroscopy (XPCS), we reveal significantly accelerated relaxation dynamics around a shear band in a metallic glass at a length scale that is orders of magnitude larger than the defect itself. The relaxation time in the shear-band vicinity is up to ten-times smaller compared to the as-cast matrix, and the relaxation dynamics occurs in a characteristic three-stage aging response that manifests itself in the temperature-dependent shape parameter known from classical stretchedmore » exponential relaxation dynamics of disordered materials. We demonstrate that the time-dependent correlation functions describing the aging at different temperatures can be captured and collapsed using simple scaling functions. Finally, these insights highlight how an ubiquitous nano-scale strain-localization mechanism in metallic glasses leads to a fundamental change of the relaxation dynamics at the mesoscale.« less

In situ atomic scale mechanical microscopy discovering the atomistic mechanisms of plasticity in nano-single crystals and grain rotation in polycrystalline metals.

PubMed

Han, Xiaodong; Wang, Lihua; Yue, Yonghai; Zhang, Ze

2015-04-01

In this review, we briefly introduce our in situ atomic-scale mechanical experimental technique (ASMET) for transmission electron microscopy (TEM), which can observe the atomic-scale deformation dynamics of materials. This in situ mechanical testing technique allows the deformation of TEM samples through a simultaneous double-tilt function, making atomic-scale mechanical microscopy feasible. This methodology is generally applicable to thin films, nanowires (NWs), tubes and regular TEM samples to allow investigation of the dynamics of mechanically stressed samples at the atomic scale. We show several examples of this technique applied to Pt and Cu single/polycrystalline specimens. The in situ atomic-scale observation revealed that when the feature size of these materials approaches the nano-scale, they often exhibit "unusual" deformation behaviours compared to their bulk counterparts. For example, in Cu single-crystalline NWs, the elastic-plastic transition is size-dependent. An ultra-large elastic strain of 7.2%, which approaches the theoretical elasticity limit, can be achieved as the diameter of the NWs decreases to ∼6 nm. The crossover plasticity transition from full dislocations to partial dislocations and twins was also discovered as the diameter of the single-crystalline Cu NWs decreased. For Pt nanocrystals (NC), the long-standing uncertainties of atomic-scale plastic deformation mechanisms in NC materials (grain size G less than 15 nm) were clarified. For larger grains with G<∼10 nm, we frequently observed movements and interactions of cross-grain full dislocations. For G between 6 and 10 nm, stacking faults resulting from partial dislocations become more frequent. For G<∼6 nm, the plasticity mechanism transforms from a mode of cross-grain dislocation to a collective grain rotation mechanism. This grain rotation process is mediated by grain boundary (GB) dislocations with the assistance of GB diffusion and shuffling. These in situ atomic-scale images provide a direct demonstration that grain rotation, through the evolution of the misorientation angle between neighbouring grains, can be quantitatively assessed by the dislocation content within the grain boundaries. In combination with the revolutionary Cs-corrected sub-angstrom imaging technologies developed by Urban et al., the opportunities for experimental mechanics at the atomic scale are emerging. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Decorrelation of the static and dynamic length scales in hard-sphere glass formers.

PubMed

Charbonneau, Patrick; Tarjus, Gilles

2013-04-01

We show that, in the equilibrium phase of glass-forming hard-sphere fluids in three dimensions, the static length scales tentatively associated with the dynamical slowdown and the dynamical length characterizing spatial heterogeneities in the dynamics unambiguously decorrelate. The former grow at a much slower rate than the latter when density increases. This observation is valid for the dynamical range that is accessible to computer simulations, which roughly corresponds to that accessible in colloidal experiments. We also find that, in this same range, no one-to-one correspondence between relaxation time and point-to-set correlation length exists. These results point to the coexistence of several relaxation mechanisms in the dynamically accessible regime of three-dimensional hard-sphere glass formers.

The dynamics of oceanic fronts. I - The Gulf Stream

NASA Technical Reports Server (NTRS)

Kao, T. W.

1980-01-01

The establishment and maintenance of the mean hydrographic properties of large-scale density fronts in the upper ocean is considered. The dynamics is studied by posing an initial value problem starting with a near-surface discharge of buoyant water with a prescribed density deficit into an ambient stationary fluid of uniform density; full time dependent diffusion and Navier-Stokes equations are then used with constant eddy diffusion and viscosity coefficients, together with a constant Coriolis parameter. Scaling analysis reveals three independent scales of the problem including the radius of deformation of the inertial length, buoyancy length, and diffusive length scales. The governing equations are then suitably scaled and the resulting normalized equations are shown to depend on the Ekman number alone for problems of oceanic interest. It is concluded that the mean Gulf Stream dynamics can be interpreted in terms of a solution of the Navier-Stokes and diffusion equations, with the cross-stream circulation responsible for the maintenance of the front; this mechanism is suggested for the maintenance of the Gulf Stream dynamics.

Spontaneous scale-free structure in adaptive networks with synchronously dynamical linking

NASA Astrophysics Data System (ADS)

Yuan, Wu-Jie; Zhou, Jian-Fang; Li, Qun; Chen, De-Bao; Wang, Zhen

2013-08-01

Inspired by the anti-Hebbian learning rule in neural systems, we study how the feedback from dynamical synchronization shapes network structure by adding new links. Through extensive numerical simulations, we find that an adaptive network spontaneously forms scale-free structure, as confirmed in many real systems. Moreover, the adaptive process produces two nontrivial power-law behaviors of deviation strength from mean activity of the network and negative degree correlation, which exists widely in technological and biological networks. Importantly, these scalings are robust to variation of the adaptive network parameters, which may have meaningful implications in the scale-free formation and manipulation of dynamical networks. Our study thus suggests an alternative adaptive mechanism for the formation of scale-free structure with negative degree correlation, which means that nodes of high degree tend to connect, on average, with others of low degree and vice versa. The relevance of the results to structure formation and dynamical property in neural networks is briefly discussed as well.

Competing Thermodynamic and Dynamic Factors Select Molecular Assemblies on a Gold Surface

NASA Astrophysics Data System (ADS)

Haxton, Thomas K.; Zhou, Hui; Tamblyn, Isaac; Eom, Daejin; Hu, Zonghai; Neaton, Jeffrey B.; Heinz, Tony F.; Whitelam, Stephen

2013-12-01

Controlling the self-assembly of surface-adsorbed molecules into nanostructures requires understanding physical mechanisms that act across multiple length and time scales. By combining scanning tunneling microscopy with hierarchical ab initio and statistical mechanical modeling of 1,4-substituted benzenediamine (BDA) molecules adsorbed on a gold (111) surface, we demonstrate that apparently simple nanostructures are selected by a subtle competition of thermodynamics and dynamics. Of the collection of possible BDA nanostructures mechanically stabilized by hydrogen bonding, the interplay of intermolecular forces, surface modulation, and assembly dynamics select at low temperature a particular subset: low free energy oriented linear chains of monomers and high free energy branched chains.

Bosonic-seesaw portal dark matter

NASA Astrophysics Data System (ADS)

Ishida, Hiroyuki; Matsuzaki, Shinya; Yamaguchi, Yuya

2017-10-01

We discuss a new type of Higgs-portal dark matter (DM) production mechanism, called the bosonic-seesaw portal (BSP) scenario. The BS provides the dynamical origin of the electroweak symmetry breaking, triggered by mixing between the elementary Higgs and a composite Higgs generated by a new-color strong dynamics, hypercolor (HC). At the HC strong coupling scale, the classical-scale invariance assumed in the model is dynamically broken, as well as the "chiral" symmetry present in the HC sector. In addition to the composite Higgs, HC baryons emerge to potentially be stable because of the unbroken HC baryon number symmetry. Hence the lightest HC baryon can be a DM candidate. Of interest in the present scenario is that HC pions can be as heavy as the HC baryon due to the possibly enhanced explicit "chiral"-breaking effect triggered after the BS mechanism, so the HC baryon pair cannot annihilate into HC pions. As in the standard setup of the freeze-in scenario, it is assumed that the DM was never in the thermal equilibrium, which ends up with no thermal abundance. It is then the non-thermal BSP process that crucially comes into the game below the HC scale: the HC baryon significantly couples to the standard-model Higgs via the BS mechanism, and can non-thermally be produced from the thermal plasma below the HC scale, which turns out to allow the TeV mass scale for the composite baryonic DM, much smaller than the generic bound placed in the conventional thermal freeze-out scenario, to account for the observed relic abundance. Thus the DM can closely be related to the mechanism of the electroweak symmetry breaking.

Dynamic structural disorder in supported nanoscale catalysts

NASA Astrophysics Data System (ADS)

Rehr, J. J.; Vila, F. D.

2014-04-01

We investigate the origin and physical effects of "dynamic structural disorder" (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

Buckling Causes Nonlinear Dynamics of Filamentous Viruses Driven through Nanopores.

PubMed

McMullen, Angus; de Haan, Hendrick W; Tang, Jay X; Stein, Derek

2018-02-16

Measurements and Langevin dynamics simulations of filamentous viruses driven through solid-state nanopores reveal a superlinear rise in the translocation velocity with driving force. The mobility also scales with the length of the virus in a nontrivial way that depends on the force. These dynamics are consequences of the buckling of the leading portion of a virus as it emerges from the nanopore and is put under compressive stress by the viscous forces it encounters. The leading tip of a buckled virus stalls and this reduces the total viscous drag force. We present a scaling theory that connects the solid mechanics to the nonlinear dynamics of polyelectrolytes translocating nanopores.

Buckling Causes Nonlinear Dynamics of Filamentous Viruses Driven through Nanopores

NASA Astrophysics Data System (ADS)

McMullen, Angus; de Haan, Hendrick W.; Tang, Jay X.; Stein, Derek

2018-02-01

Measurements and Langevin dynamics simulations of filamentous viruses driven through solid-state nanopores reveal a superlinear rise in the translocation velocity with driving force. The mobility also scales with the length of the virus in a nontrivial way that depends on the force. These dynamics are consequences of the buckling of the leading portion of a virus as it emerges from the nanopore and is put under compressive stress by the viscous forces it encounters. The leading tip of a buckled virus stalls and this reduces the total viscous drag force. We present a scaling theory that connects the solid mechanics to the nonlinear dynamics of polyelectrolytes translocating nanopores.

Towards an eco-phylogenetic framework for infectious disease ecology.

PubMed

Fountain-Jones, Nicholas M; Pearse, William D; Escobar, Luis E; Alba-Casals, Ana; Carver, Scott; Davies, T Jonathan; Kraberger, Simona; Papeş, Monica; Vandegrift, Kurt; Worsley-Tonks, Katherine; Craft, Meggan E

2018-05-01

Identifying patterns and drivers of infectious disease dynamics across multiple scales is a fundamental challenge for modern science. There is growing awareness that it is necessary to incorporate multi-host and/or multi-parasite interactions to understand and predict current and future disease threats better, and new tools are needed to help address this task. Eco-phylogenetics (phylogenetic community ecology) provides one avenue for exploring multi-host multi-parasite systems, yet the incorporation of eco-phylogenetic concepts and methods into studies of host pathogen dynamics has lagged behind. Eco-phylogenetics is a transformative approach that uses evolutionary history to infer present-day dynamics. Here, we present an eco-phylogenetic framework to reveal insights into parasite communities and infectious disease dynamics across spatial and temporal scales. We illustrate how eco-phylogenetic methods can help untangle the mechanisms of host-parasite dynamics from individual (e.g. co-infection) to landscape scales (e.g. parasite/host community structure). An improved ecological understanding of multi-host and multi-pathogen dynamics across scales will increase our ability to predict disease threats. © 2017 Cambridge Philosophical Society.

Pore-Scale Investigation on Stress-Dependent Characteristics of Granular Packs and Their Impact on Multiphase Fluid Distribution

NASA Astrophysics Data System (ADS)

Torrealba, V.; Karpyn, Z.; Yoon, H.; Hart, D. B.; Klise, K. A.

2013-12-01

The pore-scale dynamics that govern multiphase flow under variable stress conditions are not well understood. This lack of fundamental understanding limits our ability to quantitatively predict multiphase flow and fluid distributions in natural geologic systems. In this research, we focus on pore-scale, single and multiphase flow properties that impact displacement mechanisms and residual trapping of non-wetting phase under varying stress conditions. X-ray micro-tomography is used to image pore structures and distribution of wetting and non-wetting fluids in water-wet synthetic granular packs, under dynamic load. Micro-tomography images are also used to determine structural features such as medial axis, surface area, and pore body and throat distribution; while the corresponding transport properties are determined from Lattice-Boltzmann simulations performed on lattice replicas of the imaged specimens. Results are used to investigate how inter-granular deformation mechanisms affect fluid displacement and residual trapping at the pore-scale. This will improve our understanding of the dynamic interaction of mechanical deformation and fluid flow during enhanced oil recovery and geologic CO2 sequestration. 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. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Effects of friction on forced two-dimensional Navier-Stokes turbulence.

PubMed

Blackbourn, Luke A K; Tran, Chuong V

2011-10-01

Large-scale dissipation mechanisms have been routinely employed in numerical simulations of two-dimensional turbulence to absorb energy at large scales, presumably mimicking the quasisteady picture of Kraichnan in an unbounded fluid. Here, "side effects" of such a mechanism--mechanical friction--on the small-scale dynamics of forced two-dimensional Navier-Stokes turbulence are elaborated by both theoretical and numerical analysis. Given a positive friction coefficient α, viscous dissipation of enstrophy has been known to vanish in the inviscid limit ν→0. This effectively renders the scale-neutral friction the only mechanism responsible for enstrophy dissipation in that limit. The resulting dynamical picture is that the classical enstrophy inertial range becomes a dissipation range in which the dissipation of enstrophy by friction mainly occurs. For each α>0, there exists a critical viscosity ν(c), which depends on physical parameters, separating the regimes of predominant viscous and frictional dissipation of enstrophy. It is found that ν(c)=[η'(1/3)/(Ck(f)(2))]exp[-η'(1/3)/(Cα)], where η' is half the enstrophy injection rate, k(f) is the forcing wave number, and C is a nondimensional constant (the Kraichnan-Batchelor constant). The present results have important theoretical and practical implications. Apparently, mechanical friction is a poor choice in numerical attempts to address fundamental issues concerning the direct enstrophy transfer in two-dimensional Navier-Stokes turbulence. Furthermore, as relatively strong friction naturally occurs on the surfaces and at lateral boundaries of experimental fluids as well as at the interfaces of shallow layers in geophysical fluid models, the frictional effects discussed in this study are crucial in understanding the dynamics of these systems.

Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions.

PubMed

Buchenberg, Sebastian; Schaudinnus, Norbert; Stock, Gerhard

2015-03-10

Biomolecules exhibit structural dynamics on a number of time scales, including picosecond (ps) motions of a few atoms, nanosecond (ns) local conformational transitions, and microsecond (μs) global conformational rearrangements. Despite this substantial separation of time scales, fast and slow degrees of freedom appear to be coupled in a nonlinear manner; for example, there is theoretical and experimental evidence that fast structural fluctuations are required for slow functional motion to happen. To elucidate a microscopic mechanism of this multiscale behavior, Aib peptide is adopted as a simple model system. Combining extensive molecular dynamics simulations with principal component analysis techniques, a hierarchy of (at least) three tiers of the molecule's free energy landscape is discovered. They correspond to chiral left- to right-handed transitions of the entire peptide that happen on a μs time scale, conformational transitions of individual residues that take about 1 ns, and the opening and closing of structure-stabilizing hydrogen bonds that occur within tens of ps and are triggered by sub-ps structural fluctuations. Providing a simple mechanism of hierarchical dynamics, fast hydrogen bond dynamics is found to be a prerequisite for the ns local conformational transitions, which in turn are a prerequisite for the slow global conformational rearrangement of the peptide. As a consequence of the hierarchical coupling, the various processes exhibit a similar temperature behavior which may be interpreted as a dynamic transition.

Micromechanics of sea ice gouge in shear zones

NASA Astrophysics Data System (ADS)

Sammonds, Peter; Scourfield, Sally; Lishman, Ben

2015-04-01

The deformation of sea ice is a key control on the Arctic Ocean dynamics. Shear displacement on all scales is an important deformation process in the sea cover. Shear deformation is a dominant mechanism from the scale of basin-scale shear lineaments, through floe-floe interaction and block sliding in ice ridges through to the micro-scale mechanics. Shear deformation will not only depend on the speed of movement of ice surfaces but also the degree that the surfaces have bonded during thermal consolidation and compaction. Recent observations made during fieldwork in the Barents Sea show that shear produces a gouge similar to a fault gouge in a shear zone in the crust. A range of sizes of gouge are exhibited. The consolidation of these fragments has a profound influence on the shear strength and the rate of the processes involved. We review experimental results in sea ice mechanics from mid-scale experiments, conducted in the Hamburg model ship ice tank, simulating sea ice floe motion and interaction and compare these with laboratory experiments on ice friction done in direct shear, and upscale to field measurement of sea ice friction and gouge deformation made during experiments off Svalbard. We find that consolidation, fragmentation and bridging play important roles in the overall dynamics and fit the model of Sammis and Ben-Zion, developed for understanding the micro-mechanics of rock fault gouge, to the sea ice problem.

Dynamics of oxygen ordering in YBa2CU3O6+x studied by neutron and high-energy synchrotron x-ray diffiaction.

NASA Astrophysics Data System (ADS)

Frello, T.; Andersen, N. H.; Madsen, J.; Ka¨ll, M.; von Zimmermann, M.; Schmidt, O.; Poulsen, H. F.; Schneider, J. R.; Wolf, Th.

1997-08-01

The dynamics of the ortho-II oxygen structure in a high purity YBa 2Cu 3O 6+ x single crystal with x=0.50 has been studied by neutron and by X-ray diffraction with a photon energy of 100 keV. Our data show that the oxygen order develops on two different time-scales, one of the order of seconds and a much slower of the order of weeks and months. The mechanism dominating the slow time-scale is related to oxygen diffusion, while the fast mechanism may result from a temperature-dependent change in the average oxygen chain length.

Computational study of 3-D hot-spot initiation in shocked insensitive high-explosive

NASA Astrophysics Data System (ADS)

Najjar, F. M.; Howard, W. M.; Fried, L. E.; Manaa, M. R.; Nichols, A., III; Levesque, G.

2012-03-01

High-explosive (HE) material consists of large-sized grains with micron-sized embedded impurities and pores. Under various mechanical/thermal insults, these pores collapse generating hightemperature regions leading to ignition. A hydrodynamic study has been performed to investigate the mechanisms of pore collapse and hot spot initiation in TATB crystals, employing a multiphysics code, ALE3D, coupled to the chemistry module, Cheetah. This computational study includes reactive dynamics. Two-dimensional high-resolution large-scale meso-scale simulations have been performed. The parameter space is systematically studied by considering various shock strengths, pore diameters and multiple pore configurations. Preliminary 3-D simulations are undertaken to quantify the 3-D dynamics.

Plasticity-mediated collapse and recrystallization in hollow copper nanowires: a molecular dynamics simulation

PubMed Central

Raychaudhuri, Arup Kumar; Saha-Dasgupta, Tanusri

2016-01-01

Summary We study the thermal stability of hollow copper nanowires using molecular dynamics simulation. We find that the plasticity-mediated structural evolution leads to transformation of the initial hollow structure to a solid wire. The process involves three distinct stages, namely, collapse, recrystallization and slow recovery. We calculate the time scales associated with different stages of the evolution process. Our findings suggest a plasticity-mediated mechanism of collapse and recrystallization. This contradicts the prevailing notion of diffusion driven transport of vacancies from the interior to outer surface being responsible for collapse, which would involve much longer time scales as compared to the plasticity-based mechanism. PMID:26977380

Dynamical Dark Matter from thermal freeze-out

NASA Astrophysics Data System (ADS)

Dienes, Keith R.; Fennick, Jacob; Kumar, Jason; Thomas, Brooks

2018-03-01

In the Dynamical Dark-Matter (DDM) framework, the dark sector comprises a large number of constituent dark particles whose individual masses, lifetimes, and cosmological abundances obey specific scaling relations with respect to each other. In particular, the most natural versions of this framework tend to require a spectrum of cosmological abundances which scale inversely with mass, so that dark-sector states with larger masses have smaller abundances. Thus far, DDM model-building has primarily relied on nonthermal mechanisms for abundance generation such as misalignment production, since these mechanisms give rise to abundances that have this property. By contrast, the simplest versions of thermal freeze-out tend to produce abundances that increase, rather than decrease, with the mass of the dark-matter component. In this paper, we demonstrate that there exist relatively simple modifications of the traditional thermal freeze-out mechanism which "flip" the resulting abundance spectrum, producing abundances that scale inversely with mass. Moreover, we demonstrate that a far broader variety of scaling relations between lifetimes, abundances, and masses can emerge through thermal freeze-out than through the nonthermal mechanisms previously considered for DDM ensembles. The results of this paper thus extend the DDM framework into the thermal domain and essentially allow us to "design" our resulting DDM ensembles at will in order to realize a rich array of resulting dark-matter phenomenologies.

Heating and Large Scale Dynamics of the Solar Corona

NASA Technical Reports Server (NTRS)

Schnack, Dalton D.

2000-01-01

The effort was concentrated in the areas: coronal heating mechanism, unstructured adaptive grid algorithms, numerical modeling of magnetic reconnection in the MRX experiment: effect of toroidal magnetic field and finite pressure, effect of OHMIC heating and vertical magnetic field, effect of dynamic MESH adaption.

Realistic Modeling of Multi-Scale MHD Dynamics of the Solar Atmosphere

NASA Technical Reports Server (NTRS)

Kitiashvili, Irina; Mansour, Nagi N.; Wray, Alan; Couvidat, Sebastian; Yoon, Seokkwan; Kosovichev, Alexander

2014-01-01

Realistic 3D radiative MHD simulations open new perspectives for understanding the turbulent dynamics of the solar surface, its coupling to the atmosphere, and the physical mechanisms of generation and transport of non-thermal energy. Traditionally, plasma eruptions and wave phenomena in the solar atmosphere are modeled by prescribing artificial driving mechanisms using magnetic or gas pressure forces that might arise from magnetic field emergence or reconnection instabilities. In contrast, our 'ab initio' simulations provide a realistic description of solar dynamics naturally driven by solar energy flow. By simulating the upper convection zone and the solar atmosphere, we can investigate in detail the physical processes of turbulent magnetoconvection, generation and amplification of magnetic fields, excitation of MHD waves, and plasma eruptions. We present recent simulation results of the multi-scale dynamics of quiet-Sun regions, and energetic effects in the atmosphere and compare with observations. For the comparisons we calculate synthetic spectro-polarimetric data to model observational data of SDO, Hinode, and New Solar Telescope.

Long-time atomistic dynamics through a new self-adaptive accelerated molecular dynamics method

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

Gao, N.; Yang, L.; Gao, F.

2017-02-27

A self-adaptive accelerated molecular dynamics method is developed to model infrequent atomic- scale events, especially those events that occur on a rugged free-energy surface. Key in the new development is the use of the total displacement of the system at a given temperature to construct a boost-potential, which is slowly increased to accelerate the dynamics. The temperature is slowly increased to accelerate the dynamics. By allowing the system to evolve from one steady-state con guration to another by overcoming the transition state, this self-evolving approach makes it possible to explore the coupled motion of species that migrate on vastly differentmore » time scales. The migrations of single vacancy (V) and small He-V clusters, and the growth of nano-sized He-V clusters in Fe for times in the order of seconds are studied by this new method. An interstitial- assisted mechanism is rst explored for the migration of a helium-rich He-V cluster, while a new two-component Ostwald ripening mechanism is suggested for He-V cluster growth.« less

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

PubMed Central

Schöneberg, Johannes; Noé, Frank

2013-01-01

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics. PMID:24040218

Dynamical ocean-atmospheric drivers of floods and droughts

NASA Astrophysics Data System (ADS)

Perdigão, Rui A. P.; Hall, Julia

2014-05-01

The present study contributes to a better depiction and understanding of the "facial expression" of the Earth in terms of dynamical ocean-atmospheric processes associated to both floods and droughts. For this purpose, the study focuses on nonlinear dynamical and statistical analysis of ocean-atmospheric mechanisms contributing to hydrological extremes, broadening the analytical hydro-meteorological perspective of floods and hydrological droughts to driving mechanisms and feedbacks at the global scale. In doing so, the analysis of the climate-related causality of hydrological extremes is not limited to the synoptic situation in the region where the events take place. Rather, it goes further in the train of causality, peering into dynamical interactions between planetary-scale ocean and atmospheric processes that drive weather regimes and influence the antecedent and event conditions associated to hydrological extremes. In order to illustrate the approach, dynamical ocean-atmospheric drivers are investigated for a selection of floods and droughts. Despite occurring in different regions with different timings, common underlying mechanisms are identified for both kinds of hydrological extremes. For instance, several analysed events are seen to have resulted from a large-scale atmospheric situation consisting on standing planetary waves encircling the northern hemisphere. These correspond to wider vortices locked in phase, resulting in wider and more persistent synoptic weather patterns, i.e. with larger spatial and temporal coherence. A standing train of anticyclones and depressions thus encircled the mid and upper latitudes of the northern hemisphere. The stationary regime of planetary waves occurs when the mean eastward zonal flow decreases up to a point in which it no longer exceeds the westward phase propagation of the Rossby waves produced by the latitude-varying Coriolis effect. The ocean-atmospheric causes for this behaviour and consequences on hydrological extremes are investigated and the findings supported with spatiotemporal geostatistical analysis and nonlinear geophysical models. Overall, the study provides a three-fold contribution to the research on hydrological extremes: Firstly, it improves their physical attribution by better understanding the dynamical reasons behind the meteorological drivers. Secondly, it brings out fundamental early warning signs for potential hydrological extremes, by bringing out global ocean-atmospheric features that manifest themselves much earlier than the regional weather patterns. Thirdly, it provides tools for addressing and understanding hydrological regime changes at wider spatiotemporal scales, by providing links to planetary-scale dynamical processes that play a crucial role in multi-decadal global climate variability.

Probing the non-equilibrium force fluctuation spectrum of actomyosin cortices in vivo

NASA Astrophysics Data System (ADS)

Tan, Tzer Han; Swartz, Zachary; Keren, Kinneret; Fakhri, Nikta

Mechanics of the cortex govern the shape of animal cells, and its dynamics underlie cell migration, cytokinesis and embryogenesis. The molecular players involved are largely known, yet it is unclear how their collective dynamics give rise to large scale behavior. This is mostly due to the lack of experimental tools to probe the spatially varying active mechanical properties of the cortex. Here, we introduce a novel technique based on fluorescent single walled carbon nanotubes to generate non-equilibrium force fluctuation spectrum of actomysion cortices in starfish oocytes. The quantitative measurements combined with a theoretical model reveal the role of stress organization in active mechanics and dynamics of the cortex.

Aggrecan nanoscale solid-fluid interactions are a primary determinant of cartilage dynamic mechanical properties.

PubMed

Nia, Hadi Tavakoli; Han, Lin; Bozchalooi, Iman Soltani; Roughley, Peter; Youcef-Toumi, Kamal; Grodzinsky, Alan J; Ortiz, Christine

2015-03-24

Poroelastic interactions between interstitial fluid and the extracellular matrix of connective tissues are critical to biological and pathophysiological functions involving solute transport, energy dissipation, self-stiffening and lubrication. However, the molecular origins of poroelasticity at the nanoscale are largely unknown. Here, the broad-spectrum dynamic nanomechanical behavior of cartilage aggrecan monolayer is revealed for the first time, including the equilibrium and instantaneous moduli and the peak in the phase angle of the complex modulus. By performing a length scale study and comparing the experimental results to theoretical predictions, we confirm that the mechanism underlying the observed dynamic nanomechanics is due to solid-fluid interactions (poroelasticity) at the molecular scale. Utilizing finite element modeling, the molecular-scale hydraulic permeability of the aggrecan assembly was quantified (kaggrecan = (4.8 ± 2.8) × 10(-15) m(4)/N·s) and found to be similar to the nanoscale hydraulic permeability of intact normal cartilage tissue but much lower than that of early diseased tissue. The mechanisms underlying aggrecan poroelasticity were further investigated by altering electrostatic interactions between the molecule's constituent glycosaminoglycan chains: electrostatic interactions dominated steric interactions in governing molecular behavior. While the hydraulic permeability of aggrecan layers does not change across species and age, aggrecan from adult human cartilage is stiffer than the aggrecan from newborn human tissue.

Scale-invariance underlying the logistic equation and its social applications

NASA Astrophysics Data System (ADS)

Hernando, A.; Plastino, A.

2013-01-01

On the basis of dynamical principles we i) advance a derivation of the Logistic Equation (LE), widely employed (among multiple applications) in the simulation of population growth, and ii) demonstrate that scale-invariance and a mean-value constraint are sufficient and necessary conditions for obtaining it. We also generalize the LE to multi-component systems and show that the above dynamical mechanisms underlie a large number of scale-free processes. Examples are presented regarding city-populations, diffusion in complex networks, and popularity of technological products, all of them obeying the multi-component logistic equation in an either stochastic or deterministic way.

Endocytic reawakening of motility in jammed epithelia

NASA Astrophysics Data System (ADS)

Malinverno, Chiara; Corallino, Salvatore; Giavazzi, Fabio; Bergert, Martin; Li, Qingsen; Leoni, Marco; Disanza, Andrea; Frittoli, Emanuela; Oldani, Amanda; Martini, Emanuele; Lendenmann, Tobias; Deflorian, Gianluca; Beznoussenko, Galina V.; Poulikakos, Dimos; Ong, Kok Haur; Uroz, Marina; Trepat, Xavier; Parazzoli, Dario; Maiuri, Paolo; Yu, Weimiao; Ferrari, Aldo; Cerbino, Roberto; Scita, Giorgio

2017-05-01

Dynamics of epithelial monolayers has recently been interpreted in terms of a jamming or rigidity transition. How cells control such phase transitions is, however, unknown. Here we show that RAB5A, a key endocytic protein, is sufficient to induce large-scale, coordinated motility over tens of cells, and ballistic motion in otherwise kinetically arrested monolayers. This is linked to increased traction forces and to the extension of cell protrusions, which align with local velocity. Molecularly, impairing endocytosis, macropinocytosis or increasing fluid efflux abrogates RAB5A-induced collective motility. A simple model based on mechanical junctional tension and an active cell reorientation mechanism for the velocity of self-propelled cells identifies regimes of monolayer dynamics that explain endocytic reawakening of locomotion in terms of a combination of large-scale directed migration and local unjamming. These changes in multicellular dynamics enable collectives to migrate under physical constraints and may be exploited by tumours for interstitial dissemination.

Disruption of sheet-like structures in Alfvénic turbulence by magnetic reconnection

NASA Astrophysics Data System (ADS)

Mallet, A.; Schekochihin, A. A.; Chandran, B. D. G.

2017-07-01

We propose a mechanism whereby the intense, sheet-like structures naturally formed by dynamically aligning Alfvénic turbulence are destroyed by magnetic reconnection at a scale \\hat{λ }_D, larger than the dissipation scale predicted by models of intermittent, dynamically aligning turbulence. The reconnection process proceeds in several stages: first, a linear tearing mode with N magnetic islands grows and saturates, and then the X-points between these islands collapse into secondary current sheets, which then reconnect until the original structure is destroyed. This effectively imposes an upper limit on the anisotropy of the structures within the perpendicular plane, which means that at scale \\hat{λ }_D the turbulent dynamics change: at scales larger than \\hat{λ }_D, the turbulence exhibits scale-dependent dynamic alignment and a spectral index approximately equal to -3/2, while at scales smaller than \\hat{λ }_D, the turbulent structures undergo a succession of disruptions due to reconnection, limiting dynamic alignment, steepening the effective spectral index and changing the final dissipation scale. The scaling of \\hat{λ }_D with the Lundquist (magnetic Reynolds) number S_{L_\\perp } depends on the order of the statistics being considered, and on the specific model of intermittency; the transition between the two regimes in the energy spectrum is predicted at approximately \\hat{λ }_D˜ S_{L_\\perp }^{-0.6}. The spectral index below \\hat{λ }_D is bounded between -5/3 and -2.3. The final dissipation scale is at \\hat{λ }_{η ,∞}˜ S_{L_\\perp }^{-3/4}, the same as the Kolmogorov scale arising in theories of turbulence that do not involve scale-dependent dynamic alignment.

Statistical persistence of air pollutants (O3,SO2,NO2 and PM10) in Mexico City

NASA Astrophysics Data System (ADS)

Meraz, M.; Rodriguez, E.; Femat, R.; Echeverria, J. C.; Alvarez-Ramirez, J.

2015-06-01

The rescaled range (R / S) analysis was used for analyzing the statistical persistence of air pollutants in Mexico City. The air-pollution time series consisted of hourly observations of ozone, nitrogen dioxide, sulfur dioxide and particulate matter obtained at the Mexico City downtown monitoring station during 1999-2014. The results showed that long-range persistence is not a uniform property over a wide range of time scales, from days to months. In fact, although the air pollutant concentrations exhibit an average persistent behavior, environmental (e.g., daily and yearly) and socio-economic (e.g., daily and weekly) cycles are reflected in the dependence of the persistence strength as quantified in terms of the Hurst exponent. It was also found that the Hurst exponent exhibits time variations, with the ozone and nitrate oxide concentrations presenting some regularity, such as annual cycles. The persistence dynamics of the pollutant concentrations increased during the rainy season and decreased during the dry season. The time and scale dependences of the persistence properties provide some insights in the mechanisms involved in the internal dynamics of the Mexico City atmosphere for accumulating and dissipating dangerous air pollutants. While in the short-term individual pollutants dynamics seems to be governed by specific mechanisms, in the long-term (for monthly and higher scales) meteorological and seasonal mechanisms involved in atmospheric recirculation seem to dominate the dynamics of all air pollutant concentrations.

Mechanisms of change in cognitive therapy for major depressive disorder in the community mental health setting.

PubMed

Crits-Christoph, Paul; Gallop, Robert; Diehl, Caroline K; Yin, Seohyun; Gibbons, Mary Beth Connolly

2017-06-01

This study examined the relation of change in theory-relevant cognitive variables to depressive symptom change over the course of cognitive therapy, as well as the specificity of change mechanisms to cognitive therapy as compared with dynamic therapy. There were 237 adult outpatients who were randomized to either cognitive (n = 119) or dynamic (n = 118) therapy for major depressive disorder in a community mental health setting. Assessments of compensatory skills (Ways of Responding Community Version and Self-Report Version), dysfunctional attitudes (Dysfunctional Attitudes Scale), and depressogenic schemas (Psychological Distance Scaling Task) were obtained at baseline and months 1, 2, and 5 following baseline. Primary outcome was measured using the Hamilton Rating Scale for Depression. Across both therapy conditions, change in all 3 cognitive domains was associated with concurrent change in depressive symptoms. After controlling for other cognitive variables, increased interconnectedness of the positive achievement-related schema was significantly associated with concurrent symptom change in cognitive (rp = .26, p < .001) but not dynamic therapy (rp = .08, p = .29). Increases in positive compensatory skills were associated with subsequent change in depressive symptoms in cognitive therapy (rp = -.36, p = .003), but not in dynamic therapy (rp = .11, p = .386). Results provide support for the compensatory skills model of cognitive therapy (CT) within a community mental health setting. Additional research is necessary to understand other possible mechanisms of change in CT in the community setting. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Unified force-level theory of multiscale transient localization and emergent elasticity in polymer solutions and melts

NASA Astrophysics Data System (ADS)

Dell, Zachary E.; Schweizer, Kenneth S.

A unified, microscopic, theoretical understanding of polymer dynamics in concentrated liquids from segmental to macromolecular scales remains an open problem. We have formulated a statistical mechanical theory for this problem that explicitly accounts for intra- and inter-molecular forces at the Kuhn segment level. The theory is self-consistently closed at the level of a matrix of dynamical second moments of a tagged chain. Two distinct regimes of isotropic transient localization are predicted. In semidilute solutions, weak localization is predicted on a mesoscopic length scale between segment and chain scales which is a power law function of the invariant packing length. This is consistent with the breakdown of Rouse dynamics and the emergence of entanglements. The chain structural correlations in the dynamically arrested state are also computed. In dense melts, strong localization is predicted on a scale much smaller than the segment size which is weakly dependent on chain connectivity and signals the onset of glassy dynamics. Predictions of the dynamic plateau shear modulus are consistent with the known features of emergent rubbery and glassy elasticity. Generalizations to treat the effects of chemical crosslinking and physical bond formation in polymer gels are possible.

Time Scale Hierarchies in the Functional Organization of Complex Behaviors

PubMed Central

Perdikis, Dionysios; Huys, Raoul; Jirsa, Viktor K.

2011-01-01

Traditional approaches to cognitive modelling generally portray cognitive events in terms of ‘discrete’ states (point attractor dynamics) rather than in terms of processes, thereby neglecting the time structure of cognition. In contrast, more recent approaches explicitly address this temporal dimension, but typically provide no entry points into cognitive categorization of events and experiences. With the aim to incorporate both these aspects, we propose a framework for functional architectures. Our approach is grounded in the notion that arbitrary complex (human) behaviour is decomposable into functional modes (elementary units), which we conceptualize as low-dimensional dynamical objects (structured flows on manifolds). The ensemble of modes at an agent’s disposal constitutes his/her functional repertoire. The modes may be subjected to additional dynamics (termed operational signals), in particular, instantaneous inputs, and a mechanism that sequentially selects a mode so that it temporarily dominates the functional dynamics. The inputs and selection mechanisms act on faster and slower time scales then that inherent to the modes, respectively. The dynamics across the three time scales are coupled via feedback, rendering the entire architecture autonomous. We illustrate the functional architecture in the context of serial behaviour, namely cursive handwriting. Subsequently, we investigate the possibility of recovering the contributions of functional modes and operational signals from the output, which appears to be possible only when examining the output phase flow (i.e., not from trajectories in phase space or time). PMID:21980278

Emergence, evolution and scaling of online social networks.

PubMed

Wang, Le-Zhi; Huang, Zi-Gang; Rong, Zhi-Hai; Wang, Xiao-Fan; Lai, Ying-Cheng

2014-01-01

Online social networks have become increasingly ubiquitous and understanding their structural, dynamical, and scaling properties not only is of fundamental interest but also has a broad range of applications. Such networks can be extremely dynamic, generated almost instantaneously by, for example, breaking-news items. We investigate a common class of online social networks, the user-user retweeting networks, by analyzing the empirical data collected from Sina Weibo (a massive twitter-like microblogging social network in China) with respect to the topic of the 2011 Japan earthquake. We uncover a number of algebraic scaling relations governing the growth and structure of the network and develop a probabilistic model that captures the basic dynamical features of the system. The model is capable of reproducing all the empirical results. Our analysis not only reveals the basic mechanisms underlying the dynamics of the retweeting networks, but also provides general insights into the control of information spreading on such networks.

Identifying and correcting non-Markov states in peptide conformational dynamics

NASA Astrophysics Data System (ADS)

Nerukh, Dmitry; Jensen, Christian H.; Glen, Robert C.

2010-02-01

Conformational transitions in proteins define their biological activity and can be investigated in detail using the Markov state model. The fundamental assumption on the transitions between the states, their Markov property, is critical in this framework. We test this assumption by analyzing the transitions obtained directly from the dynamics of a molecular dynamics simulated peptide valine-proline-alanine-leucine and states defined phenomenologically using clustering in dihedral space. We find that the transitions are Markovian at the time scale of ≈50 ps and longer. However, at the time scale of 30-40 ps the dynamics loses its Markov property. Our methodology reveals the mechanism that leads to non-Markov behavior. It also provides a way of regrouping the conformations into new states that now possess the required Markov property of their dynamics.

Dynamics of relaxed inflation

NASA Astrophysics Data System (ADS)

Tangarife, Walter; Tobioka, Kohsaku; Ubaldi, Lorenzo; Volansky, Tomer

2018-02-01

The cosmological relaxation of the electroweak scale has been proposed as a mechanism to address the hierarchy problem of the Standard Model. A field, the relaxion, rolls down its potential and, in doing so, scans the squared mass parameter of the Higgs, relaxing it to a parametrically small value. In this work, we promote the relaxion to an inflaton. We couple it to Abelian gauge bosons, thereby introducing the necessary dissipation mechanism which slows down the field in the last stages. We describe a novel reheating mechanism, which relies on the gauge-boson production leading to strong electro-magnetic fields, and proceeds via the vacuum production of electron-positron pairs through the Schwinger effect. We refer to this mechanism as Schwinger reheating. We discuss the cosmological dynamics of the model and the phenomenological constraints from CMB and other experiments. We find that a cutoff close to the Planck scale may be achieved. In its minimal form, the model does not generate sufficient curvature perturbations and additional ingredients, such as a curvaton field, are needed.

OTEC riser cable model and prototype testing

NASA Astrophysics Data System (ADS)

Kurt, J. P.; Schultz, J. A.; Roblee, L. H. S.

1981-12-01

Two different OTEC riser cables have been developed to span the distance between a floating OTEC power plant and the ocean floor. The major design concerns for a riser cable in the dynamic OTEC environment are fatigue, corrosion, and electrical/mechanical aging of the cable components. The basic properties of the cable materials were studied through tests on model cables and on samples of cable materials. Full-scale prototype cables were manufactured and were tested to measure their electrical and mechanical properties and performance. The full-scale testing was culminated by the electrical/mechanical fatigue test, which exposes full-scale cables to simultaneous tension, bending and electrical loads, all in a natural seawater environment.

Shear banding leads to accelerated aging dynamics in a metallic glass

NASA Astrophysics Data System (ADS)

Küchemann, Stefan; Liu, Chaoyang; Dufresne, Eric M.; Shin, Jeremy; Maaß, Robert

2018-01-01

Traditionally, strain localization in metallic glasses is related to the thickness of the shear defect, which is confined to the nanometer scale. Using site-specific x-ray photon correlation spectroscopy, we reveal significantly accelerated relaxation dynamics around a shear band in a metallic glass at a length scale that is orders of magnitude larger than the defect itself. The relaxation time in the shear-band vicinity is up to ten times smaller compared to the as-cast matrix, and the relaxation dynamics occurs in a characteristic three-stage aging response that manifests itself in the temperature-dependent shape parameter known from classical stretched exponential relaxation dynamics of disordered materials. We demonstrate that the time-dependent correlation functions describing the aging at different temperatures can be captured and collapsed using simple scaling functions. These insights highlight how a ubiquitous nanoscale strain-localization mechanism in metallic glasses leads to a fundamental change of the relaxation dynamics at the mesoscale.

Drivers of forest cover dynamics in smallholder farming systems: the case of northwestern Vietnam.

PubMed

Jadin, Isaline; Vanacker, Veerle; Hoang, Huong Thi Thu

2013-04-01

The national-scale forest recovery of Vietnam started in the early 1990s and is associated with a shift from net deforestation to net reforestation. Large disparities in forest cover dynamics are, however, observed at the local scale. This study aims to unravel the mechanisms driving forest cover change for a mountainous region located in northwest Vietnam. Statistical analyses were used to explore the association between forest cover change and household characteristics. In Sa Pa district, deforestation rates are decreasing, but forest degradation continues at similar rates. Deforestation is not necessarily associated with impoverished ethnic communities or high levels of subsistence farming, and the largest forest cover dynamics are found in villages with the best socio-economic conditions. Our empirical study does not provide strong evidence of a dominant role of agriculture in forest cover dynamics. It shows that empirical studies on local-scale forest dynamics remain important to unravel the complexity of human-environment interactions.

Graphene Statistical Mechanics

NASA Astrophysics Data System (ADS)

Bowick, Mark; Kosmrlj, Andrej; Nelson, David; Sknepnek, Rastko

2015-03-01

Graphene provides an ideal system to test the statistical mechanics of thermally fluctuating elastic membranes. The high Young's modulus of graphene means that thermal fluctuations over even small length scales significantly stiffen the renormalized bending rigidity. We study the effect of thermal fluctuations on graphene ribbons of width W and length L, pinned at one end, via coarse-grained Molecular Dynamics simulations and compare with analytic predictions of the scaling of width-averaged root-mean-squared height fluctuations as a function of distance along the ribbon. Scaling collapse as a function of W and L also allows us to extract the scaling exponent eta governing the long-wavelength stiffening of the bending rigidity. A full understanding of the geometry-dependent mechanical properties of graphene, including arrays of cuts, may allow the design of a variety of modular elements with desired mechanical properties starting from pure graphene alone. Supported by NSF grant DMR-1435794

Research on Formation Mechanism of Dynamic Response and Residual Stress of Sheet Metal Induced by Laser Shock Wave

NASA Astrophysics Data System (ADS)

Feng, Aixin; Cao, Yupeng; Wang, Heng; Zhang, Zhengang

2018-01-01

In order to reveal the quantitative control of the residual stress on the surface of metal materials, the relevant theoretical and experimental studies were carried out to investigate the dynamic response of metal thin plates and the formation mechanism of residual stress induced by laser shock wave. In this paper, the latest research trends on the surface residual stress of laser shock processing technology were elaborated. The main progress of laser shock wave propagation mechanism and dynamic response, laser shock, and surface residual stress were discussed. It is pointed out that the multi-scale characterization of laser and material, surface residual stress and microstructure change is a new hotspot in laser shock strengthening technology.

Feedforward and feedback frequency-dependent interactions in a large-scale laminar network of the primate cortex.

PubMed

Mejias, Jorge F; Murray, John D; Kennedy, Henry; Wang, Xiao-Jing

2016-11-01

Interactions between top-down and bottom-up processes in the cerebral cortex hold the key to understanding attentional processes, predictive coding, executive control, and a gamut of other brain functions. However, the underlying circuit mechanism remains poorly understood and represents a major challenge in neuroscience. We approached this problem using a large-scale computational model of the primate cortex constrained by new directed and weighted connectivity data. In our model, the interplay between feedforward and feedback signaling depends on the cortical laminar structure and involves complex dynamics across multiple (intralaminar, interlaminar, interareal, and whole cortex) scales. The model was tested by reproducing, as well as providing insights into, a wide range of neurophysiological findings about frequency-dependent interactions between visual cortical areas, including the observation that feedforward pathways are associated with enhanced gamma (30 to 70 Hz) oscillations, whereas feedback projections selectively modulate alpha/low-beta (8 to 15 Hz) oscillations. Furthermore, the model reproduces a functional hierarchy based on frequency-dependent Granger causality analysis of interareal signaling, as reported in recent monkey and human experiments, and suggests a mechanism for the observed context-dependent hierarchy dynamics. Together, this work highlights the necessity of multiscale approaches and provides a modeling platform for studies of large-scale brain circuit dynamics and functions.

Feedforward and feedback frequency-dependent interactions in a large-scale laminar network of the primate cortex

PubMed Central

Mejias, Jorge F.; Murray, John D.; Kennedy, Henry; Wang, Xiao-Jing

2016-01-01

Interactions between top-down and bottom-up processes in the cerebral cortex hold the key to understanding attentional processes, predictive coding, executive control, and a gamut of other brain functions. However, the underlying circuit mechanism remains poorly understood and represents a major challenge in neuroscience. We approached this problem using a large-scale computational model of the primate cortex constrained by new directed and weighted connectivity data. In our model, the interplay between feedforward and feedback signaling depends on the cortical laminar structure and involves complex dynamics across multiple (intralaminar, interlaminar, interareal, and whole cortex) scales. The model was tested by reproducing, as well as providing insights into, a wide range of neurophysiological findings about frequency-dependent interactions between visual cortical areas, including the observation that feedforward pathways are associated with enhanced gamma (30 to 70 Hz) oscillations, whereas feedback projections selectively modulate alpha/low-beta (8 to 15 Hz) oscillations. Furthermore, the model reproduces a functional hierarchy based on frequency-dependent Granger causality analysis of interareal signaling, as reported in recent monkey and human experiments, and suggests a mechanism for the observed context-dependent hierarchy dynamics. Together, this work highlights the necessity of multiscale approaches and provides a modeling platform for studies of large-scale brain circuit dynamics and functions. PMID:28138530

Review of Aerosol–Cloud Interactions: Mechanisms, Significance, and Challenges

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

Fan, Jiwen; Wang, Yuan; Rosenfeld, Daniel

2016-11-01

Over the past decade, the number of studies that investigate aerosol-cloud interactions has increased considerably. Although tremendous progress has been made to improve our understanding of basic physical mechanisms of aerosol-cloud interactions and reduce their uncertainties in climate forcing, we are still in poor understanding of (1) some of the mechanisms that interact with each other over multiple spatial and temporal scales, (2) the feedback between microphysical and dynamical processes and between local-scale processes and large-scale circulations, and (3) the significance of cloud-aerosol interactions on weather systems as well as regional and global climate. This review focuses on recent theoreticalmore » studies and important mechanisms on aerosol-cloud interactions, and discusses the significances of aerosol impacts on raditative forcing and precipitation extremes associated with different cloud systems. Despite significant understanding has been gained about aerosol impacts on the main cloud types, there are still many unknowns especially associated with various deep convective systems. Therefore, large efforts are needed to escalate our understanding. Future directions should focus on obtaining concurrent measurements of aerosol properties, cloud microphysical and dynamic properties over a range of temporal and spatial scales collected over typical climate regimes and closure studies, as well as improving understanding and parameterizations of cloud microphysics such as ice nucleation, mixed-phase properties, and hydrometeor size and fall speed« less

Anomalous glassy dynamics in simple models of dense biological tissue

NASA Astrophysics Data System (ADS)

Sussman, Daniel M.; Paoluzzi, M.; Marchetti, M. Cristina; Manning, M. Lisa

2018-02-01

In order to understand the mechanisms for glassy dynamics in biological tissues and shed light on those in non-biological materials, we study the low-temperature disordered phase of 2D vertex-like models. Recently it has been noted that vertex models have quite unusual behavior in the zero-temperature limit, with rigidity transitions that are controlled by residual stresses and therefore exhibit very different scaling and phenomenology compared to particulate systems. Here we investigate the finite-temperature phase of two-dimensional Voronoi and Vertex models, and show that they have highly unusual, sub-Arrhenius scaling of dynamics with temperature. We connect the anomalous glassy dynamics to features of the potential energy landscape associated with zero-temperature inherent states.

On unravelling mechanism of interplay between cloud and large scale circulation: a grey area in climate science

NASA Astrophysics Data System (ADS)

De, S.; Agarwal, N. K.; Hazra, Anupam; Chaudhari, Hemantkumar S.; Sahai, A. K.

2018-04-01

The interaction between cloud and large scale circulation is much less explored area in climate science. Unfolding the mechanism of coupling between these two parameters is imperative for improved simulation of Indian summer monsoon (ISM) and to reduce imprecision in climate sensitivity of global climate model. This work has made an effort to explore this mechanism with CFSv2 climate model experiments whose cloud has been modified by changing the critical relative humidity (CRH) profile of model during ISM. Study reveals that the variable CRH in CFSv2 has improved the nonlinear interactions between high and low frequency oscillations in wind field (revealed as internal dynamics of monsoon) and modulates realistically the spatial distribution of interactions over Indian landmass during the contrasting monsoon season compared to the existing CRH profile of CFSv2. The lower tropospheric wind error energy in the variable CRH simulation of CFSv2 appears to be minimum due to the reduced nonlinear convergence of error to the planetary scale range from long and synoptic scales (another facet of internal dynamics) compared to as observed from other CRH experiments in normal and deficient monsoons. Hence, the interplay between cloud and large scale circulation through CRH may be manifested as a change in internal dynamics of ISM revealed from scale interactive quasi-linear and nonlinear kinetic energy exchanges in frequency as well as in wavenumber domain during the monsoon period that eventually modify the internal variance of CFSv2 model. Conversely, the reduced wind bias and proper modulation of spatial distribution of scale interaction between the synoptic and low frequency oscillations improve the eastward and northward extent of water vapour flux over Indian landmass that in turn give feedback to the realistic simulation of cloud condensates attributing improved ISM rainfall in CFSv2.

The atomic-scale nucleation mechanism of NiTi metallic glasses upon isothermal annealing studied via molecular dynamics simulations.

PubMed

Li, Yang; Li, JiaHao; Liu, BaiXin

2015-10-28

Nucleation is one of the most essential transformation paths in phase transition and exerts a significant influence on the crystallization process. Molecular dynamics simulations were performed to investigate the atomic-scale nucleation mechanisms of NiTi metallic glasses upon devitrification at various temperatures (700 K, 750 K, 800 K, and 850 K). Our simulations reveal that at 700 K and 750 K, nucleation is polynuclear with high nucleation density, while at 800 K it is mononuclear. The underlying nucleation mechanisms have been clarified, manifesting that nucleation can be induced either by the initial ordered clusters (IOCs) or by the other precursors of nuclei evolved directly from the supercooled liquid. IOCs and other precursors stem from the thermal fluctuations of bond orientational order in supercooled liquids during the quenching process and during the annealing process, respectively. The simulation results not only elucidate the underlying nucleation mechanisms varied with temperature, but also unveil the origin of nucleation. These discoveries offer new insights into the devitrification mechanism of metallic glasses.

A Multi-Scale, Integrated Approach to Representing Watershed Systems

NASA Astrophysics Data System (ADS)

Ivanov, Valeriy; Kim, Jongho; Fatichi, Simone; Katopodes, Nikolaos

2014-05-01

Understanding and predicting process dynamics across a range of scales are fundamental challenges for basic hydrologic research and practical applications. This is particularly true when larger-spatial-scale processes, such as surface-subsurface flow and precipitation, need to be translated to fine space-time scale dynamics of processes, such as channel hydraulics and sediment transport, that are often of primary interest. Inferring characteristics of fine-scale processes from uncertain coarse-scale climate projection information poses additional challenges. We have developed an integrated model simulating hydrological processes, flow dynamics, erosion, and sediment transport, tRIBS+VEGGIE-FEaST. The model targets to take the advantage of the current generation of wealth of data representing watershed topography, vegetation, soil, and landuse, as well as to explore the hydrological effects of physical factors and their feedback mechanisms over a range of scales. We illustrate how the modeling system connects precipitation-hydrologic runoff partition process to the dynamics of flow, erosion, and sedimentation, and how the soil's substrate condition can impact the latter processes, resulting in a non-unique response. We further illustrate an approach to using downscaled climate change information with a process-based model to infer the moments of hydrologic variables in future climate conditions and explore the impact of climate information uncertainty.

Healing efficiency and dynamic mechanical properties of self-healing epoxy systems

NASA Astrophysics Data System (ADS)

Guadagno, Liberata; Raimondo, Marialuigia; Naddeo, Carlo; Longo, Pasquale; Mariconda, Annaluisa; Binder, Wolfgang H.

2014-03-01

Several systems to develop self-repairing epoxy resins have recently been formulated. In this paper the effect of matrix nature and curing cycle on the healing efficiency and dynamic mechanical properties of self-healing epoxy resins were investigated. We discuss several aspects by transferring self-healing systems from the laboratory scale to real applications in the aeronautic field, such as the possibility to choose systems with increased glass transition temperature, high storage modulus and high values in the healing functionality under real working conditions.

Phoretic self-propulsion: a mesoscopic description of reaction dynamics that powers motion.

PubMed

de Buyl, Pierre; Kapral, Raymond

2013-02-21

The fabrication of synthetic self-propelled particles and the experimental investigations of their dynamics have stimulated interest in self-generated phoretic effects that propel nano- and micron-scale objects. Theoretical modeling of these phenomena is often based on a continuum description of the solvent for different phoretic propulsion mechanisms, including, self-electrophoresis, self-diffusiophoresis and self-thermophoresis. The work in this paper considers various types of catalytic chemical reaction at the motor surface and in the bulk fluid that come into play in mesoscopic descriptions of the dynamics. The formulation is illustrated by developing the mesoscopic reaction dynamics for exothermic and dissociation reactions that are used to power motor motion. The results of simulations of the self-propelled dynamics of composite Janus particles by these mechanisms are presented.

Functional connectivity dynamically evolves on multiple time-scales over a static structural connectome: Models and mechanisms.

PubMed

Cabral, Joana; Kringelbach, Morten L; Deco, Gustavo

2017-10-15

Over the last decade, we have observed a revolution in brain structural and functional Connectomics. On one hand, we have an ever-more detailed characterization of the brain's white matter structural connectome. On the other, we have a repertoire of consistent functional networks that form and dissipate over time during rest. Despite the evident spatial similarities between structural and functional connectivity, understanding how different time-evolving functional networks spontaneously emerge from a single structural network requires analyzing the problem from the perspective of complex network dynamics and dynamical system's theory. In that direction, bottom-up computational models are useful tools to test theoretical scenarios and depict the mechanisms at the genesis of resting-state activity. Here, we provide an overview of the different mechanistic scenarios proposed over the last decade via computational models. Importantly, we highlight the need of incorporating additional model constraints considering the properties observed at finer temporal scales with MEG and the dynamical properties of FC in order to refresh the list of candidate scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

Spin-Mechanical Inertia in Antiferromagnet

NASA Astrophysics Data System (ADS)

Cheng, Ran; Wu, Xiaochuan; Xiao, Di

Interplay between spin dynamics and mechanical motions is responsible for numerous striking phenomena, which has shaped a rapidly expanding field known as spin-mechanics. The guiding principle of this field has been the conservation of angular momentum that involves both quantum spins and classical mechanical rotations. However, in an antiferromagnet, the macroscopic magnetization vanishes while the order parameter (Néel order) does not carry an angular momentum. It is therefore not clear whether the order parameter dynamics has any mechanical consequence as its ferromagnetic counterparts. Here we demonstrate that the Néel order dynamics affects the mechanical motion of a rigid body by modifying its inertia tensor in the presence of strong magnetocrystalline anisotropy. This effect depends on temperature when magnon excitations are considered. Such a spin-mechanical inertia can produce measurable consequences at nanometer scales. Our discovery establishes spin-mechanical inertia as an essential ingredient to properly describe spin-mechanical effects in AFs, which supplements the known governing physics from angular momentum conservation. This work was supported by the DOE, Basic Energy Sciences, Grant No. DE-SC0012509. D.X. also acknowledges support from a Research Corporation for Science Advancement Cottrell Scholar Award.

Spatio-temporal correlations in models of collective motion ruled by different dynamical laws.

PubMed

Cavagna, Andrea; Conti, Daniele; Giardina, Irene; Grigera, Tomas S; Melillo, Stefania; Viale, Massimiliano

2016-11-15

Information transfer is an essential factor in determining the robustness of biological systems with distributed control. The most direct way to study the mechanisms ruling information transfer is to experimentally observe the propagation across the system of a signal triggered by some perturbation. However, this method may be inefficient for experiments in the field, as the possibilities to perturb the system are limited and empirical observations must rely on natural events. An alternative approach is to use spatio-temporal correlations to probe the information transfer mechanism directly from the spontaneous fluctuations of the system, without the need to have an actual propagating signal on record. Here we test this method on models of collective behaviour in their deeply ordered phase by using ground truth data provided by numerical simulations in three dimensions. We compare two models characterized by very different dynamical equations and information transfer mechanisms: the classic Vicsek model, describing an overdamped noninertial dynamics and the inertial spin model, characterized by an underdamped inertial dynamics. By using dynamic finite-size scaling, we show that spatio-temporal correlations are able to distinguish unambiguously the diffusive information transfer mechanism of the Vicsek model from the linear mechanism of the inertial spin model.

Phase transitions triggered by quantum fluctuations in the inflationary universe

NASA Technical Reports Server (NTRS)

Nagasawa, Michiyasu; Yokoyama, Junichi

1991-01-01

The dynamics of a second-order phase transition during inflation, which is induced by time-variation of spacetime curvature, is studied as a natural mechanism to produce topological defects of typical grand unification scales such as cosmic strings or global textures. It is shown that their distribution is almost scale-invariant with small- and large-scale cutoffs. Also discussed is how these cutoffs are given.

Experimental Trapped-ion Quantum Simulation of the Kibble-Zurek dynamics in momentum space

PubMed Central

Cui, Jin-Ming; Huang, Yun-Feng; Wang, Zhao; Cao, Dong-Yang; Wang, Jian; Lv, Wei-Min; Luo, Le; del Campo, Adolfo; Han, Yong-Jian; Li, Chuan-Feng; Guo, Guang-Can

2016-01-01

The Kibble-Zurek mechanism is the paradigm to account for the nonadiabatic dynamics of a system across a continuous phase transition. Its study in the quantum regime is hindered by the requisite of ground state cooling. We report the experimental quantum simulation of critical dynamics in the transverse-field Ising model by a set of Landau-Zener crossings in pseudo-momentum space, that can be probed with high accuracy using a single trapped ion. We test the Kibble-Zurek mechanism in the quantum regime in the momentum space and find the measured scaling of excitations is in accordance with the theoretical prediction. PMID:27633087

Consequences of Molecular-Scale Non-Equilibrium Activity on the Dynamics and Mechanics of Self-Assembled Actin-Based Structures and Materials

NASA Astrophysics Data System (ADS)

Marshall Mccall, Patrick

Living cells are hierarchically self-organized forms of active soft matter: molecules on the nanometer scale form functional structures and organelles on the micron scale, which then compose cells on the scale of 10s of microns. While the biological functions of intracellular organelles are defined by the composition and properties of the structures themselves, how those bulk properties emerge from the properties and interactions of individual molecules remains poorly understood. Actin, a globular protein which self-assembles into dynamic semi-flexible polymers, is the basic structural material of cells and the major component of many functional organelles. In this thesis, I have used purified actin as a model system to explore the interplay between molecular-scale dynamics and organelle-scale functionality, with particular focus on the role of molecular-scale non-equilibrium activity. One of the most canonical forms of molecular-scale non-equilibrium activity is that of mechanoenzymes, also called motor proteins. These proteins utilized the free energy liberated by hydrolysis of ATP to perform mechanical work, thereby introducing non-equilibrium "active" stresses on the molecular scale. Combining experiments with mathematical modeling, we demonstrate in this thesis that non-equilibrium motor activity is sufficient to drive self-organization and pattern formation of the multimeric actin-binding motor protein Myosin II on 1D reconstituted actomyosin bundles. Like myosin, actin is itself an ATPase. However, nono-equilibrium ATP hydrolysis on actin is known to regulate the stability and assembly kinetics of actin filaments rather than generate active stresses per se. At the level of single actin filaments, the inhomogeneous nucleotide composition generated along the filament length by hydrolysis directs binding of regulatory proteins like cofilin, which mediate filament disassembly and thereby accelerate actin filament turnover. The concequences of this non-equilibrium turnover on the steady-state properties of collections of filaments remained unclear. Here, I reconstituted tunable, non-equilibrium actin turnover dynamics in entangled solutions of actin filaments as a model of the actin cortex of living cells. We found that this non-equilibrium turnover decouples solution mechanics from microstructure, enabling structurally indistinguishable materials to behave effectively as either viscous fluids or elastic gels. Additionally, we employed computer simulations to identify the dynamical regime in which actin turnover controls the effective viscosity of 2D cross-linked actin networks in the presence of motors. Additionally, I examine in this thesis the localization and self-assembly of actin filaments in condensed liquid phases called polyelectrolyte coacervates as a model membrane-less organelle. We find that concentration of actin through spontaneous partitioning preferentially to the coacervate phase accelerates the assembly of filaments. These filaments then localize to the coacervate-bulk interface, generating particles with visco-elastic shells surrounding liquid cores. In this case, the properties of the condensed phase enable regulation of actin assembly dynamics.

Nonlinear and Stochastic Dynamics in the Heart

PubMed Central

Qu, Zhilin; Hu, Gang; Garfinkel, Alan; Weiss, James N.

2014-01-01

In a normal human life span, the heart beats about 2 to 3 billion times. Under diseased conditions, a heart may lose its normal rhythm and degenerate suddenly into much faster and irregular rhythms, called arrhythmias, which may lead to sudden death. The transition from a normal rhythm to an arrhythmia is a transition from regular electrical wave conduction to irregular or turbulent wave conduction in the heart, and thus this medical problem is also a problem of physics and mathematics. In the last century, clinical, experimental, and theoretical studies have shown that dynamical theories play fundamental roles in understanding the mechanisms of the genesis of the normal heart rhythm as well as lethal arrhythmias. In this article, we summarize in detail the nonlinear and stochastic dynamics occurring in the heart and their links to normal cardiac functions and arrhythmias, providing a holistic view through integrating dynamics from the molecular (microscopic) scale, to the organelle (mesoscopic) scale, to the cellular, tissue, and organ (macroscopic) scales. We discuss what existing problems and challenges are waiting to be solved and how multi-scale mathematical modeling and nonlinear dynamics may be helpful for solving these problems. PMID:25267872

Developing, mechanizing and testing of a digital active flutter suppression system for a modified B-52 wind-tunnel model

NASA Technical Reports Server (NTRS)

Matthew, J. R.

1980-01-01

A digital flutter suppression system was developed and mechanized for a significantly modified version of the 1/30-scale B-52E aeroelastic wind tunnel model. A model configuration was identified that produced symmetric and antisymmetric flutter modes that occur at 2873N/sq m (60 psf) dynamic pressure with violent onset. The flutter suppression system, using one trailing edge control surface and the accelerometers on each wing, extended the flutter dynamic pressure of the model beyond the design limit of 4788N/sq m (100 psf). The hardware and software required to implement the flutter suppression system were designed and mechanized using digital computers in a fail-operate configuration. The model equipped with the system was tested in the Transonic Dynamics Tunnel at NASA Langley Research Center and results showed the flutter dynamic pressure of the model was extended beyond 4884N/sq m (102 psf).

The mechanisms of plastic strain accommodation and post critical behavior of heterogeneous reactive composites subject to dynamic loading

NASA Astrophysics Data System (ADS)

Olney, Karl L.

The dynamic behavior of granular/porous and laminate reactive materials is of interest due to their practical applications; reactive structural components, reactive fragments, etc. The mesostructural properties control meso- and macro-scale dynamic behavior of these heterogeneous composites including the behavior during the post-critical stage of deformation. They heavily influence mechanisms of fragment generation and the in situ development of local hot spots, which act as sites of ignition in these materials. This dissertation concentrates on understanding the mechanisms of plastic strain accommodation in two representative reactive material systems with different heterogeneous mesostructrues: Aluminum-Tungsten granular/porous and Nickel-Aluminum laminate composites. The main focus is on the interpretation of results of the following dynamic experiments conducted at different strain and strain rates: drop weight tests, explosively expanded ring experiments, and explosively collapsed thick walled cylinder experiments. Due to the natural limitations in the evaluation of the mesoscale behavior of these materials experimentally and the large variation in the size scales between the mesostructural level and the sample, it is extremely difficult, if not impossible, to examine the mesoscale behavior in situ. Therefore, numerical simulations of the corresponding experiments are used as the main tool to explore material behavior at the mesoscale. Numerical models were developed to elucidate the mechanisms of plastic strain accommodation and post critical behavior in these heterogeneous composites subjected to dynamic loading. These simulations were able to reproduce the qualitative and quantitative features that were observable in the experiments and provided insight into the evolution of the mechanisms of plastic strain accommodation and post critical behavior in these materials with complex mesotructure. Additionally, these simulations provided a framework to examine the influence of various mesoscale properties such as the bonding of interfaces, the role of material properties, and the influence of mesoscale geometry. The results of this research are helpful in the design of material mesotructures conducive to the desirable behavior under dynamic loading.

Atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

NASA Astrophysics Data System (ADS)

Pabst, Stefan

2013-04-01

Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in recent years made it possible to generate ultrashort pulses, which can be used to trigger, to watch, and to control atomic and molecular motion. This tutorial focuses on experimental and theoretical advances which are used to study the dynamics of electrons and molecules in the presence of ultrashort pulses. In the first part, the rotational dynamics of molecules, which happens on picosecond and femtosecond time scales, is reviewed. Well-aligned molecules are particularly suitable for angle-dependent investigations like x-ray diffraction or strong-field ionization experiments. In the second part, the ionization dynamics of atoms is studied. The characteristic time scale lies, here, in the attosecond to few-femtosecond regime. Although a one-particle picture has been successfully applied to many processes, many-body effects do constantly occur. After a broad overview of the main mechanisms and the most common tools in attosecond physics, examples of many-body dynamics in the attosecond world (e.g., in high-harmonic generation and attosecond transient absorption spectroscopy) are discussed.

A bifractal nature of reticular patterns induced by oxygen plasma on polymer films

NASA Astrophysics Data System (ADS)

Bae, Junwan; Lee, I. J.

2015-05-01

Plasma etching was demonstrated to be a promising tool for generating self-organized nano-patterns on various commercial films. Unfortunately, dynamic scaling approach toward fundamental understanding of the formation and growth of the plasma-induced nano-structure has not always been straightforward. The temporal evolution of self-aligned nano-patterns may often evolve with an additional scale-invariance, which leads to breakdown of the well-established dynamic scaling law. The concept of a bifractal interface is successfully applied to reticular patterns induced by oxygen plasma on the surface of polymer films. The reticular pattern, composed of nano-size self-aligned protuberances and underlying structure, develops two types of anomalous dynamic scaling characterized by super-roughening and intrinsic anomalous scaling, respectively. The diffusion and aggregation of short-cleaved chains under the plasma environment are responsible for the regular distribution of the nano-size protuberances. Remarkably, it is uncovered that the dynamic roughening of the underlying structure is governed by a relaxation mechanism described by the Edwards-Wilkinson universality class with a conservative noise. The evidence for the basic phase, characterized by the negative roughness and growth exponents, has been elusive since its first theoretical consideration more than two decades ago.

Constraint methods that accelerate free-energy simulations of biomolecules.

PubMed

Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A

2015-12-28

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

Emergent mechanics of biological structures

PubMed Central

Dumont, Sophie; Prakash, Manu

2014-01-01

Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework “emergent mechanics.” Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead. PMID:25368421

Atomic scale dynamics of a solid state chemical reaction directly determined by annular dark-field electron microscopy.

PubMed

Pennycook, Timothy J; Jones, Lewys; Pettersson, Henrik; Coelho, João; Canavan, Megan; Mendoza-Sanchez, Beatriz; Nicolosi, Valeria; Nellist, Peter D

2014-12-22

Dynamic processes, such as solid-state chemical reactions and phase changes, are ubiquitous in materials science, and developing a capability to observe the mechanisms of such processes on the atomic scale can offer new insights across a wide range of materials systems. Aberration correction in scanning transmission electron microscopy (STEM) has enabled atomic resolution imaging at significantly reduced beam energies and electron doses. It has also made possible the quantitative determination of the composition and occupancy of atomic columns using the atomic number (Z)-contrast annular dark-field (ADF) imaging available in STEM. Here we combine these benefits to record the motions and quantitative changes in the occupancy of individual atomic columns during a solid-state chemical reaction in manganese oxides. These oxides are of great interest for energy-storage applications such as for electrode materials in pseudocapacitors. We employ rapid scanning in STEM to both drive and directly observe the atomic scale dynamics behind the transformation of Mn3O4 into MnO. The results demonstrate we now have the experimental capability to understand the complex atomic mechanisms involved in phase changes and solid state chemical reactions.

High-speed nanoscale characterization of dewetting via dynamic transmission electron microscopy

NASA Astrophysics Data System (ADS)

Hihath, Sahar; Santala, Melissa K.; Campbell, Geoffrey; van Benthem, Klaus

2016-08-01

The dewetting of thin films can occur in either the solid or the liquid state for which different mass transport mechanisms are expected to control morphological changes. Traditionally, dewetting dynamics have been examined on time scales between several seconds to hours, and length scales ranging between nanometers and millimeters. The determination of mass transport mechanisms on the nanoscale, however, requires nanoscale spatial resolution and much shorter time scales. This study reports the high-speed observation of dewetting phenomena for kinetically constrained Ni thin films on crystalline SrTiO3 substrates. Movie-mode Dynamic Transmission Electron Microscopy (DTEM) was used for high-speed image acquisition during thin film dewetting at different temperatures. DTEM imaging confirmed that the initial stages of film agglomeration include edge retraction, hole formation, and growth. Finite element modeling was used to simulate temperature distributions within the DTEM samples after laser irradiation with different energies. For pulsed laser irradiation at 18 μJ, experimentally observed hole growth suggests that Marangoni flow dominates hole formation in the liquid nickel film. After irradiation with 13.8 μJ, however, the observations suggest that dewetting was initiated by nucleation of voids followed by hole growth through solid-state surface diffusion.

Droplets and the three-phase contact line at the nano-scale. Statics and dynamics

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Sibley, David; Savva, Nikos; Kalliadasis, Serafim

2014-11-01

Understanding the behaviour of the solid-liquid-vapour contact line at the scale of several tens of molecular diameters is important in wetting hydrodynamics with applications in micro- and nano-fluidics, including the design of lab-on-a-chip devices and surfaces with specific wetting properties. Due to the fluid inhomogeneity at the nano-scale, the application of continuum-mechanical approaches is limited, and a natural way to remedy this is to seek descriptions accounting for the non-local molecular-level interactions. Density Functional Theory (DFT) for fluids offers a statistical-mechanical framework based on expressing the free energy of the fluid-solid pair as a functional of the spatially varying fluid density. DFT allows us to investigate small drops deposited on planar substrates whilst keeping track of the microscopic structural details of the fluid. Starting from a model of intermolecular forces, we systematically obtain interfaces, surface tensions, and the microscopic contact angle. Using a dynamic extension of equilibrium DFT, we investigate the diffusion-driven evolution of the three-phase contact line to gain insight into the dynamic behaviour of the microscopic contact angle, which is still under debate.

Molecular dynamics study of the isotropic-nematic quench.

PubMed

Bradac, Z; Kralj, S; Zumer, S

2002-02-01

Effects of cylindrical and spherical confinement on the kinetics of the isotropic-nematic quench is studied numerically. The nematic liquid crystal structure was modeled by a modified induced-dipole--induced-dipole interaction. Molecules were allowed to wander around points of a hexagonal lattice. Brownian molecular dynamics was used in order to access macroscopic time scales. In the bulk we distinguish between the early, domain, and late stage regime. The early regime is characterized by the exponential growth of the nematic uniaxial order parameter. In the domain regime domains are clearly visible and the average nematic domain size xi(d) obeys the dynamical scaling law xi(d)-t(gamma). The late stage evolution is dominated by dynamics of individual defects. In a confined system the qualitative change of the scaling behavior appears when xi(d) becomes comparable to a typical linear dimension R of the confinement. In the confining regime (xi(d)>or=R) the scaling coefficient gamma depends on the details of the confinement and also the final equilibrium nematic structure. The domain growth is well described with the Kibble-Zurek mechanism.

Cluster growth mechanisms in Lennard-Jones fluids: A comparison between molecular dynamics and Brownian dynamics simulations

NASA Astrophysics Data System (ADS)

Jung, Jiyun; Lee, Jumin; Kim, Jun Soo

2015-03-01

We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.

Hierarchical organization as a diagnostic approach to volcano mechanics: Validation on Piton de la Fournaise

NASA Astrophysics Data System (ADS)

Grasso, J. R.; Bachèlery, P.

Self-organized systems are often used to describe natural phenomena where power laws and scale invariant geometry are observed. The Piton de la Fournaise volcano shows power-law behavior in many aspects. These include the temporal distribution of eruptions, the frequency-size distributions of induced earthquakes, dikes, fissures, lava flows and interflow periods, all evidence of self-similarity over a finite scale range. We show that the bounds to scale-invariance can be used to derive geomechanical constraints on both the volcano structure and the volcano mechanics. We ascertain that the present magma bodies are multi-lens reservoirs in a quasi-eruptive condition, i.e. a marginally critical state. The scaling organization of dynamic fluid-induced observables on the volcano, such as fluid induced earthquakes, dikes and surface fissures, appears to be controlled by underlying static hierarchical structure (geology) similar to that proposed for fluid circulations in human physiology. The emergence of saturation lengths for the scalable volcanic observable argues for the finite scalability of complex naturally self-organized critical systems, including volcano dynamics.

Comparison of three different scales techniques for the dynamic mechanical characterization of two polymers (PDMS and SU8)

NASA Astrophysics Data System (ADS)

Le Rouzic, J.; Delobelle, P.; Vairac, P.; Cretin, B.

2009-10-01

In this article the dynamic mechanical characterization of PDMS and SU8 resin using dynamic mechanical analysis, nanoindentation and the scanning microdeformation microscope have been presented. The methods are hereby explained, extended for viscoelastic behaviours, and their compatibility underlined. The storage and loss moduli of these polymers over a wide range of frequencies (from 0.01 Hz to somekHz) have been measured. These techniques are shown fairly matching and the two different viscoelastic behaviours of these two polymers have been exhibited. Indeed, PDMS shows moduli which still increase at 5kHz whereas SU8 ones decrease much sooner. From a material point of view, the Havriliak and Negami model to estimate instantaneous, relaxed moduli and time constant of these materials has been identified.

Addressing spatial scales and new mechanisms in climate impact ecosystem modeling

NASA Astrophysics Data System (ADS)

Poulter, B.; Joetzjer, E.; Renwick, K.; Ogunkoya, G.; Emmett, K.

2015-12-01

Climate change impacts on vegetation distributions are typically addressed using either an empirical approach, such as a species distribution model (SDM), or with process-based methods, for example, dynamic global vegetation models (DGVMs). Each approach has its own benefits and disadvantages. For example, an SDM is constrained by data and few parameters, but does not include adaptation or acclimation processes or other ecosystem feedbacks that may act to mitigate or enhance climate effects. Alternatively, a DGVM model includes many mechanisms relating plant growth and disturbance to climate, but simulations are costly to perform at high-spatial resolution and there remains large uncertainty on a variety of fundamental physical processes. To address these issues, here, we present two DGVM-based case studies where i) high-resolution (1 km) simulations are being performed for vegetation in the Greater Yellowstone Ecosystem using a biogeochemical, forest gap model, LPJ-GUESS, and ii) where new mechanisms for simulating tropical tree-mortality are being introduced. High-resolution DGVM model simulations require not only computing and reorganizing code but also a consideration of scaling issues on vegetation dynamics and stochasticity and also on disturbance and migration. New mechanisms for simulating forest mortality must consider hydraulic limitations and carbon reserves and their interactions on source-sink dynamics and in controlling water potentials. Improving DGVM approaches by addressing spatial scale challenges and integrating new approaches for estimating forest mortality will provide new insights more relevant for land management and possibly reduce uncertainty by physical processes more directly comparable to experimental and observational evidence.

A large-scale circuit mechanism for hierarchical dynamical processing in the primate cortex

PubMed Central

Chaudhuri, Rishidev; Knoblauch, Kenneth; Gariel, Marie-Alice; Kennedy, Henry; Wang, Xiao-Jing

2015-01-01

We developed a large-scale dynamical model of the macaque neocortex, which is based on recently acquired directed- and weighted-connectivity data from tract-tracing experiments, and which incorporates heterogeneity across areas. A hierarchy of timescales naturally emerges from this system: sensory areas show brief, transient responses to input (appropriate for sensory processing), whereas association areas integrate inputs over time and exhibit persistent activity (suitable for decision-making and working memory). The model displays multiple temporal hierarchies, as evidenced by contrasting responses to visual versus somatosensory stimulation. Moreover, slower prefrontal and temporal areas have a disproportionate impact on global brain dynamics. These findings establish a circuit mechanism for “temporal receptive windows” that are progressively enlarged along the cortical hierarchy, suggest an extension of time integration in decision-making from local to large circuits, and should prompt a re-evaluation of the analysis of functional connectivity (measured by fMRI or EEG/MEG) by taking into account inter-areal heterogeneity. PMID:26439530

Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes

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

Wehrens, Martijn; Rein ten Wolde, Pieter; Mugler, Andrew, E-mail: amugler@purdue.edu

2014-11-28

Clustering of molecules on biological membranes is a widely observed phenomenon. A key example is the clustering of the oncoprotein Ras, which is known to be important for signal transduction in mammalian cells. Yet, the mechanism by which Ras clusters form and are maintained remains unclear. Recently, it has been discovered that activated Ras promotes further Ras activation. Here we show using particle-based simulation that this positive feedback is sufficient to produce persistent clusters of active Ras molecules at the nanometer scale via a dynamic nucleation mechanism. Furthermore, we find that our cluster statistics are consistent with experimental observations ofmore » the Ras system. Interestingly, we show that our model does not support a Turing regime of macroscopic reaction-diffusion patterning, and therefore that the clustering we observe is a purely stochastic effect, arising from the coupling of positive feedback with the discrete nature of individual molecules. These results underscore the importance of stochastic and dynamic properties of reaction diffusion systems for biological behavior.« less

Fast Atomic-Scale Chemical Imaging of Crystalline Materials and Dynamic Phase Transformations.

PubMed

Lu, Ping; Yuan, Ren Liang; Ihlefeld, Jon F; Spoerke, Erik David; Pan, Wei; Zuo, Jian Min

2016-04-13

Atomic-scale phenomena fundamentally influence materials form and function that makes the ability to locally probe and study these processes critical to advancing our understanding and development of materials. Atomic-scale chemical imaging by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) is a powerful approach to investigate solid crystal structures. Inefficient X-ray emission and collection, however, require long acquisition times (typically hundreds of seconds), making the technique incompatible with electron-beam sensitive materials and study of dynamic material phenomena. Here we describe an atomic-scale STEM-EDS chemical imaging technique that decreases the acquisition time to as little as one second, a reduction of more than 100 times. We demonstrate this new approach using LaAlO3 single crystal and study dynamic phase transformation in beam-sensitive Li[Li0.2Ni0.2Mn0.6]O2 (LNMO) lithium ion battery cathode material. By capturing a series of time-lapsed chemical maps, we show for the first time clear atomic-scale evidence of preferred Ni-mobility in LNMO transformation, revealing new kinetic mechanisms. These examples highlight the potential of this approach toward temporal, atomic-scale mapping of crystal structure and chemistry for investigating dynamic material phenomena.

Fluctuations of global energy release and crackling in nominally brittle heterogeneous fracture.

PubMed

Barés, J; Hattali, M L; Dalmas, D; Bonamy, D

2014-12-31

The temporal evolution of mechanical energy and spatially averaged crack speed are both monitored in slowly fracturing artificial rocks. Both signals display an irregular burstlike dynamics, with power-law distributed fluctuations spanning a broad range of scales. Yet, the elastic power released at each time step is proportional to the global velocity all along the process, which enables defining a material-constant fracture energy. We characterize the intermittent dynamics by computing the burst statistics. This latter displays the scale-free features signature of crackling dynamics, in qualitative but not quantitative agreement with the depinning interface models derived for fracture problems. The possible sources of discrepancies are pointed out and discussed.

Dynamic information routing in complex networks

PubMed Central

Kirst, Christoph; Timme, Marc; Battaglia, Demian

2016-01-01

Flexible information routing fundamentally underlies the function of many biological and artificial networks. Yet, how such systems may specifically communicate and dynamically route information is not well understood. Here we identify a generic mechanism to route information on top of collective dynamical reference states in complex networks. Switching between collective dynamics induces flexible reorganization of information sharing and routing patterns, as quantified by delayed mutual information and transfer entropy measures between activities of a network's units. We demonstrate the power of this mechanism specifically for oscillatory dynamics and analyse how individual unit properties, the network topology and external inputs co-act to systematically organize information routing. For multi-scale, modular architectures, we resolve routing patterns at all levels. Interestingly, local interventions within one sub-network may remotely determine nonlocal network-wide communication. These results help understanding and designing information routing patterns across systems where collective dynamics co-occurs with a communication function. PMID:27067257

Synaptic Scaling Enables Dynamically Distinct Short- and Long-Term Memory Formation

PubMed Central

Tetzlaff, Christian; Kolodziejski, Christoph; Timme, Marc; Tsodyks, Misha; Wörgötter, Florentin

2013-01-01

Memory storage in the brain relies on mechanisms acting on time scales from minutes, for long-term synaptic potentiation, to days, for memory consolidation. During such processes, neural circuits distinguish synapses relevant for forming a long-term storage, which are consolidated, from synapses of short-term storage, which fade. How time scale integration and synaptic differentiation is simultaneously achieved remains unclear. Here we show that synaptic scaling – a slow process usually associated with the maintenance of activity homeostasis – combined with synaptic plasticity may simultaneously achieve both, thereby providing a natural separation of short- from long-term storage. The interaction between plasticity and scaling provides also an explanation for an established paradox where memory consolidation critically depends on the exact order of learning and recall. These results indicate that scaling may be fundamental for stabilizing memories, providing a dynamic link between early and late memory formation processes. PMID:24204240

Synaptic scaling enables dynamically distinct short- and long-term memory formation.

PubMed

Tetzlaff, Christian; Kolodziejski, Christoph; Timme, Marc; Tsodyks, Misha; Wörgötter, Florentin

2013-10-01

Memory storage in the brain relies on mechanisms acting on time scales from minutes, for long-term synaptic potentiation, to days, for memory consolidation. During such processes, neural circuits distinguish synapses relevant for forming a long-term storage, which are consolidated, from synapses of short-term storage, which fade. How time scale integration and synaptic differentiation is simultaneously achieved remains unclear. Here we show that synaptic scaling - a slow process usually associated with the maintenance of activity homeostasis - combined with synaptic plasticity may simultaneously achieve both, thereby providing a natural separation of short- from long-term storage. The interaction between plasticity and scaling provides also an explanation for an established paradox where memory consolidation critically depends on the exact order of learning and recall. These results indicate that scaling may be fundamental for stabilizing memories, providing a dynamic link between early and late memory formation processes.

Metal-coordination: Using one of nature’s tricks to control soft material mechanics

PubMed Central

Holten-Andersen, Niels; Jaishankar, Aditya; Harrington, Matthew; Fullenkamp, Dominic E.; DiMarco, Genevieve; He, Lihong; McKinley, Gareth H.; Messersmith, Phillip B.; Lee, Ka Yee C.

2015-01-01

Growing evidence supports a critical role of dynamic metal-coordination crosslinking in soft biological material properties such as self-healing and underwater adhesion1. Using bio-inspired metal-coordinating polymers, initial efforts to mimic these properties have shown promise2. Here we demonstrate how bio-inspired aqueous polymer network mechanics can be easily controlled via metal-coordination crosslink dynamics; metal ion-based crosslink stability control allows aqueous polymer network relaxation times to be finely tuned over several orders of magnitude. In addition to further biological material insights, our demonstration of this compositional scaling mechanism should provide inspiration for new polymer material property-control designs. PMID:26413297

PREFACE: Scales of understanding in biological development Scales of understanding in biological development

NASA Astrophysics Data System (ADS)

Newman, Timothy

2011-08-01

The development of an adult organism from a fertilized egg remains one of the deep mysteries of biology. Great strides have been made in the past three decades, primarily through ever more sophisticated genetic analyses and the advent of live-cell imaging, yet the underlying principles governing development are elusive. Recently, a new generation of biological physicists has entered the field, attracted by the hallmarks of development— coordinated dynamics and pattern formation arising from cell-cell interactions—which reflect tantalizing analogs with many-body systems in condensed matter physics and related fields. There have been corresponding influxes of researchers from other quantitative disciplines. With new workers come new questions and foci at different scales in space, time and complexity. The reductionist philosophy of developmental genetics has become increasingly complemented by a search for effective mechanisms at higher scales, a strategy which has a proven track record of success in the study of complex systems in physics. Are there new and universal mechanisms of development, supra-genetic in nature, waiting to be discovered by focusing on higher scales, or is development fundamentally the intricately scripted unfolding of complex genetic instructions? In this special focus issue of Physical Biology, we present cutting-edge research into embryo development from a broad spectrum of groups representing cell and developmental biology, biological physics, bioengineering and biomathematics. We are provided with a sense of how this multidisciplinary community views the fundamental issue of scale in development and are given some excellent examples of how we can bridge these scales through interdisciplinary collaboration, in order to create new levels of understanding. We start with two reviews which will provide newcomers with a guide to some of the outstanding questions in the field. Winklbauer and Müller use the phenomenon of mesoderm spreading as a platform to discuss the fascinating challenge of connecting cell-level behaviours to tissue-scale dynamics, thereby putting meat on the bones of traditional physical metaphors of 'the embryonic tissue as a material'. A fresh look at natural variation in embryonic phenotypes through the lens of physics, especially mechanics, is provided by von Dassow and Davidson. They stress the importance of environmental scales in providing both physical challenges and an evolutionary backdrop for robust development. The next two papers are concerned with the crucial role of signalling in morphogenesis. Zartman et al study in detail a stage of oogenesis in Drosophila, and show how quantitative experimental determination of pattern formation can be used as a stringent test of proposed underlying molecular mechanisms; in turn, they show how such selected mechanisms can thereafter be tested by newly designed experiments. Streichan et al consider collective cell motion in the zebrafish embryo. They propose an elegant theoretical mechanism to explain how directed collective cell motion can be generated in a uniform signalling landscape through a non-linear chemotactic feedback loop, and propose experimental tests of this idea. The next two papers describe state-of-the-art spatio-temporal quantification of whole embryo dynamics with cell-level resolution. Fernandez-Gonzalez and Zallen study the fascinating phenomenon of cell surface oscillations during axis elongation in Drosophila. They use a newly designed computer algorithm to measure spatio-temporal statistics of the oscillations and connect this information to intracellular actomyosin dynamics. Szabó et al study extracellular matrix (ECM) dynamics during primitive streak extension in the avian embryo. Using computer tracking and analysis they are able to measure spatial and temporal correlations of the ECM during development and use this data to inform the crucial, yet poorly understood, role of cell-ECM interactions. The last two papers are companion articles by Sandersius et al. The first paper describes the integration of active subcellular dynamics into an existing multicellular simulation algorithm. The resulting algorithm, which is parameterized at length and time scales of microns and seconds, is capable of reproducing various experimentally observed phenotypes at significantly higher scales, namely large-strain cell stretching, effective viscosity of embryonic epithelia and streaming patterns of collective cell motion within tissues. The second paper uses this new algorithm to quantitatively test the hypothesis that a dipolar arrangement of chemotactic sources is capable of driving primitive streak formation in amniotes. The hypothesis is found to be consistent with experimental data on cell movement patterns and quantitative estimates are given for the robustness of the chemotaxis mechanism. Is the simplest model of an embryo an embryo? Alternatively, are there higher scales of understanding that will provide predictive and powerful new insights into development? We hope this special focus issue of Physical Biology will provide a snapshot of how quantitative and interdisciplinary approaches are helping to answer these fundamental questions.

Mechanical Properties of Materials with Nanometer Scale Microstructures

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

William D. Nix

2004-10-31

We have been engaged in research on the mechanical properties of materials with nanometer-scale microstructural dimensions. Our attention has been focused on studying the mechanical properties of thin films and interfaces and very small volumes of material. Because the dimensions of thin film samples are small (typically 1 mm in thickness, or less), specialized mechanical testing techniques based on nanoindentation, microbeam bending and dynamic vibration of micromachined structures have been developed and used. Here we report briefly on some of the results we have obtained over the past three years. We also give a summary of all of the dissertations,more » talks and publications completed on this grant during the past 15 years.« less

Ontogenetic scaling of hydrostatic skeletons: geometric, static stress and dynamic stress scaling of the earthworm lumbricus terrestris

PubMed

Quillin

1998-05-21

Soft-bodied organisms with hydrostatic skeletons range enormously in body size, both during the growth of individuals and in the comparison of species. Therefore, body size is an important consideration in an examination of the mechanical function of hydrostatic skeletons. The scaling of hydrostatic skeletons cannot be inferred from existing studies of the lever-like skeletons of vertebrates and arthropods because the two skeleton types function by different mechanisms. Hydrostats are constructed of an extensible body wall in tension surrounding a fluid or deformable tissue under compression. It is the pressurized internal fluid (rather than the rigid levers of vertebrates and arthropods) that enables the maintenance of posture, antagonism of muscles and transfer of muscle forces to the environment. The objectives of the present study were (1) to define the geometric, static stress and dynamic stress similarity scaling hypotheses for hydrostatic skeletons on the basis of their generalized form and function, and (2) to apply these similarity hypotheses in a study of the ontogenetic scaling of earthworms, Lumbricus terrestris, to determine which parameters of skeletal function are conserved or changed as a function of body mass during growth (from 0.01 to 8 g). Morphometric measurements on anesthetized earthworms revealed that the earthworms grew isometrically; the external proportions and number of segments were constant as a function of body size. Calculations of static stresses (forces per cross-sectional area in the body wall) during rest and dynamic stresses during peristaltic crawling (calculated from measurements of internal pressure and body wall geometry) revealed that the earthworms also maintained static and dynamic stress similarity, despite a slight increase in body wall thickness in segment 50 (but not in segment 15). In summary, the hydrostatic skeletons of earthworms differ fundamentally from the rigid, lever-like skeletons of their terrestrial counterparts in their ability to grow isometrically while maintaining similarity in both static and dynamic stresses.

Scaling law and enhancement of lift generation of an insect-size hovering flexible wing

PubMed Central

Kang, Chang-kwon; Shyy, Wei

2013-01-01

We report a comprehensive scaling law and novel lift generation mechanisms relevant to the aerodynamic functions of structural flexibility in insect flight. Using a Navier–Stokes equation solver, fully coupled to a structural dynamics solver, we consider the hovering motion of a wing of insect size, in which the dynamics of fluid–structure interaction leads to passive wing rotation. Lift generated on the flexible wing scales with the relative shape deformation parameter, whereas the optimal lift is obtained when the wing deformation synchronizes with the imposed translation, consistent with previously reported observations for fruit flies and honeybees. Systematic comparisons with rigid wings illustrate that the nonlinear response in wing motion results in a greater peak angle compared with a simple harmonic motion, yielding higher lift. Moreover, the compliant wing streamlines its shape via camber deformation to mitigate the nonlinear lift-degrading wing–wake interaction to further enhance lift. These bioinspired aeroelastic mechanisms can be used in the development of flapping wing micro-robots. PMID:23760300

Ranges of Applicability for the Continuum-beam Model in the Constitutive Analysis of Carbon Nanotubes: Nanotubes or Nano-beams?

NASA Technical Reports Server (NTRS)

Harik, Vasyl Michael; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

Ranges of validity for the continuum-beam model, the length-scale effects and continuum assumptions are analyzed in the framework of scaling analysis of NT structure. Two coupled criteria for the applicability of the continuum model are presented. Scaling analysis of NT buckling and geometric parameters (e.g., diameter and length) is carried out to determine the key non-dimensional parameters that control the buckling strains and modes of NT buckling. A model applicability map, which represents two classes of NTs, is constructed in the space of non-dimensional parameters. In an analogy with continuum mechanics, a mechanical law of geometric similitude is presented for two classes of beam-like NTs having different geometries. Expressions for the critical buckling loads and strains are tailored for the distinct groups of NTs and compared with the data provided by the molecular dynamics simulations. Implications for molecular dynamics simulations and the NT-based scanning probes are discussed.

Mapping hydration dynamics and coupled water-protein fluctuations around a protein surface

NASA Astrophysics Data System (ADS)

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2009-03-01

Elucidation of the molecular mechanism of water-protein interactions is critical to understanding many fundamental aspects of protein science, such as protein folding and misfolding and enzyme catalysis. We recently carried out a global mapping of protein-surface hydration dynamics around a globular α-helical protein apomyoglobin. The intrinsic optical probe tryptophan was employed to scan the protein surface one at a time by site-specific mutagenesis. With femtosecond resolution, we mapped out the dynamics of water-protein interactions with more than 20 mutants and for two states, native and molten globular. A robust bimodal distribution of time scales was observed, representing two types of water motions: local relaxation and protein-coupled fluctuations. The time scales show a strong correlation with the local protein structural rigidity and chemical identity. We also resolved two distinct contributions to the overall Stokes-shifts from the two time scales. These results are significant to understanding the role of hydration water on protein structural stability, dynamics and function.

Aeroelasticity and mechanical stability report, 0.27 Mach scale model of the YAH-64 advanced attack helicopter

NASA Technical Reports Server (NTRS)

Straub, F. K.; Johnston, R. A.

1987-01-01

A 27% dynamically scaled model of the YAH-64 Advanced Attack Helicopter main rotor and hub has been designed and fabricated. The model will be tested in the NASA Langley Research Center V/STOL wind tunnel using the General Rotor Model System (GRMS). This report documents the studies performed to ensure dynamic similarity of the model with its full scale parent. It also contains a preliminary aeroelastic and aeromechanical substantiation for the rotor installation in the wind tunnel. From the limited studies performed no aeroelastic stability or load problems are projected. To alleviate a projected ground resonance problem, a modification of the roll characteristics of the GRMS is recommended.

A dynamical weak scale from inflation

NASA Astrophysics Data System (ADS)

You, Tevong

2017-09-01

Dynamical scanning of the Higgs mass by an axion-like particle during inflation may provide a cosmological component to explaining part of the hierarchy problem. We propose a novel interplay of this cosmological relaxation mechanism with inflation, whereby the backreaction of the Higgs vacuum expectation value near the weak scale causes inflation to end. As Hubble drops, the relaxion's dissipative friction increases relative to Hubble and slows it down enough to be trapped by the barriers of its periodic potential. Such a scenario raises the natural cut-off of the theory up to ~ 1010 GeV, while maintaining a minimal relaxion sector without having to introduce additional scanning scalars or new physics coincidentally close to the weak scale.

Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface.

PubMed

Li, Hongzhi; Yang, Wei

2007-03-21

An approach is developed in the replica exchange framework to enhance conformational sampling for the quantum mechanical (QM) potential based molecular dynamics simulations. Importantly, with our enhanced sampling treatment, a decent convergence for electronic structure self-consistent-field calculation is robustly guaranteed, which is made possible in our replica exchange design by avoiding direct structure exchanges between the QM-related replicas and the activated (scaled by low scaling parameters or treated with high "effective temperatures") molecular mechanical (MM) replicas. Although the present approach represents one of the early efforts in the enhanced sampling developments specifically for quantum mechanical potentials, the QM-based simulations treated with the present technique can possess the similar sampling efficiency to the MM based simulations treated with the Hamiltonian replica exchange method (HREM). In the present paper, by combining this sampling method with one of our recent developments (the dual-topology alchemical HREM approach), we also introduce a method for the sampling enhanced QM-based free energy calculations.

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

Majda, Andrew J.; Xing, Yulong; Mohammadian, Majid

Determining the finite-amplitude preconditioned states in the hurricane embryo, which lead to tropical cyclogenesis, is a central issue in contemporary meteorology. In the embryo there is competition between different preconditioning mechanisms involving hydrodynamics and moist thermodynamics, which can lead to cyclogenesis. Here systematic asymptotic methods from applied mathematics are utilized to develop new simplified moist multi-scale models starting from the moist anelastic equations. Three interesting multi-scale models emerge in the analysis. The balanced mesoscale vortex (BMV) dynamics and the microscale balanced hot tower (BHT) dynamics involve simplified balanced equations without gravity waves for vertical vorticity amplification due to moist heatmore » sources and incorporate nonlinear advective fluxes across scales. The BMV model is the central one for tropical cyclogenesis in the embryo. The moist mesoscale wave (MMW) dynamics involves simplified equations for mesoscale moisture fluctuations, as well as linear hydrostatic waves driven by heat sources from moisture and eddy flux divergences. A simplified cloud physics model for deep convection is introduced here and used to study moist axisymmetric plumes in the BHT model. A simple application in periodic geometry involving the effects of mesoscale vertical shear and moist microscale hot towers on vortex amplification is developed here to illustrate features of the coupled multi-scale models. These results illustrate the use of these models in isolating key mechanisms in the embryo in a simplified content.« less

Computational Nanotechnology of Materials, Devices, and Machines: Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Kwak, Dolhan (Technical Monitor)

2000-01-01

The mechanics and chemistry of carbon nanotubes have relevance for their numerous electronic applications. Mechanical deformations such as bending and twisting affect the nanotube's conductive properties, and at the same time they possess high strength and elasticity. Two principal techniques were utilized including the analysis of large scale classical molecular dynamics on a shared memory architecture machine and a quantum molecular dynamics methodology. In carbon based electronics, nanotubes are used as molecular wires with topological defects which are mediated through various means. Nanotubes can be connected to form junctions.

Fluid mechanics and mass transfer in melt crystal growth: Analysis of the floating zone and vertical Bridgman processes

NASA Technical Reports Server (NTRS)

Brown, R. A.

1986-01-01

This research program focuses on analysis of the transport mechanisms in solidification processes, especially one of interest to the Microgravity Sciences and Applications Program of NASA. Research during the last year has focused on analysis of the dynamics of the floating zone process for growth of small-scale crystals, on studies of the effect of applied magnetic fields on convection and solute segregation in directional solidification, and on the dynamics of microscopic cell formation in two-dimensional solidification of binary alloys. Significant findings are given.

Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations

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

Nguyen, Trung D; Carrillo, Jan-Michael Y; Brown, W Michael

2014-01-01

The ability of liquid crystal (LC) molecules to respond to changes in their environment makes them an interesting candidate for thin film applications, particularly in bio-sensing, bio-mimicking devices, and optics. Yet the understanding of the (in)stability of this family of thin films has been limited by the inherent challenges encountered by experiment and continuum models. Using unprecedented largescale molecular dynamics (MD) simulations, we address the rupture origin of LC thin films wetting a solid substrate at length scales similar to those in experiment. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top ofmore » thermal nucleation, and importantly, for the first time, evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. We further demonstrate that the primary driving force for rupture is closely related to the tendency of the LC mesogens to recover their local environment in the bulk state. Our study not only provides new insights into the rupture mechanism of liquid crystal films, but also sets the stage for future investigations of thin film systems using peta-scale molecular dynamics simulations.« less

Nanoscale movements of cellulose microfibrils in primary cell walls.

PubMed

Zhang, Tian; Vavylonis, Dimitrios; Durachko, Daniel M; Cosgrove, Daniel J

2017-04-28

The growing plant cell wall is commonly considered to be a fibre-reinforced structure whose strength, extensibility and anisotropy depend on the orientation of crystalline cellulose microfibrils, their bonding to the polysaccharide matrix and matrix viscoelasticity 1-4 . Structural reinforcement of the wall by stiff cellulose microfibrils is central to contemporary models of plant growth, mechanics and meristem dynamics 4-12 . Although passive microfibril reorientation during wall extension has been inferred from theory and from bulk measurements 13-15 , nanometre-scale movements of individual microfibrils have not been directly observed. Here we combined nanometre-scale imaging of wet cell walls by atomic force microscopy (AFM) with a stretching device and endoglucanase treatment that induces wall stress relaxation and creep, mimicking wall behaviours during cell growth. Microfibril movements during forced mechanical extensions differ from those during creep of the enzymatically loosened wall. In addition to passive angular reorientation, we observed a diverse repertoire of microfibril movements that reveal the spatial scale of molecular connections between microfibrils. Our results show that wall loosening alters microfibril connectivity, enabling microfibril dynamics not seen during mechanical stretch. These insights into microfibril movements and connectivities need to be incorporated into refined models of plant cell wall structure, growth and morphogenesis.

Multiscale System for Environmentally-Driven Infectious Disease with Threshold Control Strategy

NASA Astrophysics Data System (ADS)

Sun, Xiaodan; Xiao, Yanni

A multiscale system for environmentally-driven infectious disease is proposed, in which control measures at three different scales are implemented when the number of infected hosts exceeds a certain threshold. Our coupled model successfully describes the feedback mechanisms of between-host dynamics on within-host dynamics by employing one-scale variable guided enhancement of interventions on other scales. The modeling approach provides a novel idea of how to link the large-scale dynamics to small-scale dynamics. The dynamic behaviors of the multiscale system on two time-scales, i.e. fast system and slow system, are investigated. The slow system is further simplified to a two-dimensional Filippov system. For the Filippov system, we study the dynamics of its two subsystems (i.e. free-system and control-system), the sliding mode dynamics, the boundary equilibrium bifurcations, as well as the global behaviors. We prove that both subsystems may undergo backward bifurcations and the sliding domain exists. Meanwhile, it is possible that the pseudo-equilibrium exists and is globally stable, or the pseudo-equilibrium, the disease-free equilibrium and the real equilibrium are tri-stable, or the pseudo-equilibrium and the real equilibrium are bi-stable, or the pseudo-equilibrium and disease-free equilibrium are bi-stable, which depends on the threshold value and other parameter values. The global stability of the pseudo-equilibrium reveals that we may maintain the number of infected hosts at a previously given value. Moreover, the bi-stability and tri-stability indicate that whether the number of infected individuals tends to zero or a previously given value or other positive values depends on the parameter values and the initial states of the system. These results highlight the challenges in the control of environmentally-driven infectious disease.

Cellular dynamics of bovine aortic smooth muscle cells measured using MEMS force sensors

NASA Astrophysics Data System (ADS)

Tsukagoshi, Takuya; Nguyen, Thanh-Vinh; Hirayama Shoji, Kayoko; Takahashi, Hidetoshi; Matsumoto, Kiyoshi; Shimoyama, Isao

2018-04-01

Adhesive cells perceive the mechanical properties of the substrates to which they adhere, adjusting their cellular mechanical forces according to their biological characteristics. This mechanical interaction subsequently affects the growth, locomotion, and differentiation of the cell. However, little is known about the detailed mechanism that underlies this interaction between adherent cells and substrates because dynamically measuring mechanical phenomena is difficult. Here, we utilize microelectromechamical systems force sensors that can measure cellular traction forces with high temporal resolution (~2.5 µs) over long periods (~3 h). We found that the cellular dynamics reflected physical phenomena with time scales from milliseconds to hours, which contradicts the idea that cellular motion is slow. A single focal adhesion (FA) generates an average force of 7 nN, which disappears in ms via the action of trypsin-ethylenediaminetetraacetic acid. The force-changing rate obtained from our measurements suggests that the time required for an FA to decompose was nearly proportional to the force acting on the FA.

Investigating lithium-ion battery materials during overcharge-induced thermal runaway: an operando and multi-scale X-ray CT study.

PubMed

Finegan, Donal P; Scheel, Mario; Robinson, James B; Tjaden, Bernhard; Di Michiel, Marco; Hinds, Gareth; Brett, Dan J L; Shearing, Paul R

2016-11-16

Catastrophic failure of lithium-ion batteries occurs across multiple length scales and over very short time periods. A combination of high-speed operando tomography, thermal imaging and electrochemical measurements is used to probe the degradation mechanisms leading up to overcharge-induced thermal runaway of a LiCoO 2 pouch cell, through its interrelated dynamic structural, thermal and electrical responses. Failure mechanisms across multiple length scales are explored using a post-mortem multi-scale tomography approach, revealing significant morphological and phase changes in the LiCoO 2 electrode microstructure and location dependent degradation. This combined operando and multi-scale X-ray computed tomography (CT) technique is demonstrated as a comprehensive approach to understanding battery degradation and failure.

Solving the flatness problem with an anisotropic instanton in Hořava-Lifshitz gravity

NASA Astrophysics Data System (ADS)

Bramberger, Sebastian F.; Coates, Andrew; Magueijo, João; Mukohyama, Shinji; Namba, Ryo; Watanabe, Yota

2018-02-01

In Hořava-Lifshitz gravity a scaling isotropic in space but anisotropic in spacetime, often called "anisotropic scaling," with the dynamical critical exponent z =3 , lies at the base of its renormalizability. This scaling also leads to a novel mechanism of generating scale-invariant cosmological perturbations, solving the horizon problem without inflation. In this paper we propose a possible solution to the flatness problem, in which we assume that the initial condition of the Universe is set by a small instanton respecting the same scaling. We argue that the mechanism may be more general than the concrete model presented here. We rely simply on the deformed dispersion relations of the theory, and on equipartition of the various forms of energy at the starting point.

Non-local damage rheology and size effect

NASA Astrophysics Data System (ADS)

Lyakhovsky, V.

2011-12-01

We study scaling relations controlling the onset of transiently-accelerating fracturing and transition to dynamic rupture propagation in a non-local damage rheology model. The size effect is caused principally by growth of a fracture process zone, involving stress redistribution and energy release associated with a large fracture. This implies that rupture nucleation and transition to dynamic propagation are inherently scale-dependent processes. Linear elastic fracture mechanics (LEFM) and local damage mechanics are formulated in terms of dimensionless strain components and thus do not allow introducing any space scaling, except linear relations between fracture length and displacements. Generalization of Weibull theory provides scaling relations between stress and crack length at the onset of failure. A powerful extension of the LEFM formulation is the displacement-weakening model which postulates that yielding is complete when the crack wall displacement exceeds some critical value or slip-weakening distance Dc at which a transition to kinetic friction is complete. Scaling relations controlling the transition to dynamic rupture propagation in slip-weakening formulation are widely accepted in earthquake physics. Strong micro-crack interaction in a process zone may be accounted for by adopting either integral or gradient type non-local damage models. We formulate a gradient-type model with free energy depending on the scalar damage parameter and its spatial derivative. The damage-gradient term leads to structural stresses in the constitutive stress-strain relations and a damage diffusion term in the kinetic equation for damage evolution. The damage diffusion eliminates the singular localization predicted by local models. The finite width of the localization zone provides a fundamental length scale that allows numerical simulations with the model to achieve the continuum limit. A diffusive term in the damage evolution gives rise to additional damage diffusive time scale associated with the structural length scale. The ratio between two time scales associated with damage accumulation and diffusion, the damage diffusivity ratio, reflects the role of the diffusion-controlled delocalization. We demonstrate that localized fracturing occurs at the damage diffusivity ratio below certain critical value leading to a linear scaling between stress and crack length compatible with size effect for failures at crack initiation. A subseuqent quasi-static fracture growth is self-similar with increasing size of the process zone proportional to the fracture length. At a certain stage, controlled by dynamic weakening, the self-similarity breaks down and crack velocity significantly deviates from that predicted by the quasi-static regime, the size of the process zone decreases, and the rate of crack growth ceases to be controlled by the rate of damage increase. Furthermore, the crack speed approaches that predicted by the elasto-dynamic equation. The non-local damage rheology model predicts that the nucleation size of the dynamic fracture scales with fault zone thickness distance of the stress interraction.

Noise Response Data Reveal Novel Controllability Gramian for Nonlinear Network Dynamics

PubMed Central

Kashima, Kenji

2016-01-01

Control of nonlinear large-scale dynamical networks, e.g., collective behavior of agents interacting via a scale-free connection topology, is a central problem in many scientific and engineering fields. For the linear version of this problem, the so-called controllability Gramian has played an important role to quantify how effectively the dynamical states are reachable by a suitable driving input. In this paper, we first extend the notion of the controllability Gramian to nonlinear dynamics in terms of the Gibbs distribution. Next, we show that, when the networks are open to environmental noise, the newly defined Gramian is equal to the covariance matrix associated with randomly excited, but uncontrolled, dynamical state trajectories. This fact theoretically justifies a simple Monte Carlo simulation that can extract effectively controllable subdynamics in nonlinear complex networks. In addition, the result provides a novel insight into the relationship between controllability and statistical mechanics. PMID:27264780

STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

NASA Astrophysics Data System (ADS)

Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; Lehoux, Jean-Guy; Lavigne, Pierre

2016-06-01

START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6.

Statistical mechanics of neocortical interactions: Path-integral evolution of short-term memory

NASA Astrophysics Data System (ADS)

Ingber, Lester

1994-05-01

Previous papers in this series of statistical mechanics of neocortical interactions (SMNI) have detailed a development from the relatively microscopic scales of neurons up to the macroscopic scales as recorded by electroencephalography (EEG), requiring an intermediate mesocolumnar scale to be developed at the scale of minicolumns (~=102 neurons) and macrocolumns (~=105 neurons). Opportunity was taken to view SMNI as sets of statistical constraints, not necessarily describing specific synaptic or neuronal mechanisms, on neuronal interactions, on some aspects of short-term memory (STM), e.g., its capacity, stability, and duration. A recently developed c-language code, pathint, provides a non-Monte Carlo technique for calculating the dynamic evolution of arbitrary-dimension (subject to computer resources) nonlinear Lagrangians, such as derived for the two-variable SMNI problem. Here, pathint is used to explicitly detail the evolution of the SMNI constraints on STM.

Self-organization in leaky threshold systems: The influence of near-mean field dynamics and its implications for earthquakes, neurobiology, and forecasting

PubMed Central

Rundle, J. B.; Tiampo, K. F.; Klein, W.; Sá Martins, J. S.

2002-01-01

Threshold systems are known to be some of the most important nonlinear self-organizing systems in nature, including networks of earthquake faults, neural networks, superconductors and semiconductors, and the World Wide Web, as well as political, social, and ecological systems. All of these systems have dynamics that are strongly correlated in space and time, and all typically display a multiplicity of spatial and temporal scales. Here we discuss the physics of self-organization in earthquake threshold systems at two distinct scales: (i) The “microscopic” laboratory scale, in which consideration of results from simulations leads to dynamical equations that can be used to derive the results obtained from sliding friction experiments, and (ii) the “macroscopic” earthquake fault-system scale, in which the physics of strongly correlated earthquake fault systems can be understood by using time-dependent state vectors defined in a Hilbert space of eigenstates, similar in many respects to the mathematics of quantum mechanics. In all of these systems, long-range interactions induce the existence of locally ergodic dynamics. The existence of dissipative effects leads to the appearance of a “leaky threshold” dynamics, equivalent to a new scaling field that controls the size of nucleation events relative to the size of background fluctuations. At the macroscopic earthquake fault-system scale, these ideas show considerable promise as a means of forecasting future earthquake activity. PMID:11875204

Mechanical impact of dynamic phenomena in Francis turbines at off design conditions

NASA Astrophysics Data System (ADS)

Duparchy, F.; Brammer, J.; Thibaud, M.; Favrel, A.; Lowys, P. Y.; Avellan, F.

2017-04-01

At partial load and overload conditions, Francis turbines are subjected to hydraulic instabilities that can potentially result in high dynamic solicitations of the turbine components and significantly reduce their lifetime. This study presents both experimental data and numerical simulations that were used as complementary approaches to study these dynamic solicitations. Measurements performed on a reduced scale physical model, including a special runner instrumented with on-board strain gauges and pressure sensors, were used to investigate the dynamic phenomena experienced by the runner. They were also taken as reference to validate the numerical simulation results. After validation, advantage was taken from the numerical simulations to highlight the mechanical response of the structure to the unsteady hydraulic phenomena, as well as their impact on the fatigue damage of the runner.

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

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

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

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

Multi-Scale Low-Entropy Method for Optimizing the Processing Parameters during Automated Fiber Placement

PubMed Central

Han, Zhenyu; Sun, Shouzheng; Fu, Hongya; Fu, Yunzhong

2017-01-01

Automated fiber placement (AFP) process includes a variety of energy forms and multi-scale effects. This contribution proposes a novel multi-scale low-entropy method aiming at optimizing processing parameters in an AFP process, where multi-scale effect, energy consumption, energy utilization efficiency and mechanical properties of micro-system could be taken into account synthetically. Taking a carbon fiber/epoxy prepreg as an example, mechanical properties of macro–meso–scale are obtained by Finite Element Method (FEM). A multi-scale energy transfer model is then established to input the macroscopic results into the microscopic system as its boundary condition, which can communicate with different scales. Furthermore, microscopic characteristics, mainly micro-scale adsorption energy, diffusion coefficient entropy–enthalpy values, are calculated under different processing parameters based on molecular dynamics method. Low-entropy region is then obtained in terms of the interrelation among entropy–enthalpy values, microscopic mechanical properties (interface adsorbability and matrix fluidity) and processing parameters to guarantee better fluidity, stronger adsorption, lower energy consumption and higher energy quality collaboratively. Finally, nine groups of experiments are carried out to verify the validity of the simulation results. The results show that the low-entropy optimization method can reduce void content effectively, and further improve the mechanical properties of laminates. PMID:28869520

Multi-Scale Low-Entropy Method for Optimizing the Processing Parameters during Automated Fiber Placement.

PubMed

Han, Zhenyu; Sun, Shouzheng; Fu, Hongya; Fu, Yunzhong

2017-09-03

Automated fiber placement (AFP) process includes a variety of energy forms and multi-scale effects. This contribution proposes a novel multi-scale low-entropy method aiming at optimizing processing parameters in an AFP process, where multi-scale effect, energy consumption, energy utilization efficiency and mechanical properties of micro-system could be taken into account synthetically. Taking a carbon fiber/epoxy prepreg as an example, mechanical properties of macro-meso-scale are obtained by Finite Element Method (FEM). A multi-scale energy transfer model is then established to input the macroscopic results into the microscopic system as its boundary condition, which can communicate with different scales. Furthermore, microscopic characteristics, mainly micro-scale adsorption energy, diffusion coefficient entropy-enthalpy values, are calculated under different processing parameters based on molecular dynamics method. Low-entropy region is then obtained in terms of the interrelation among entropy-enthalpy values, microscopic mechanical properties (interface adsorbability and matrix fluidity) and processing parameters to guarantee better fluidity, stronger adsorption, lower energy consumption and higher energy quality collaboratively. Finally, nine groups of experiments are carried out to verify the validity of the simulation results. The results show that the low-entropy optimization method can reduce void content effectively, and further improve the mechanical properties of laminates.

Examination of turbulent entrainment-mixing mechanisms using a combined approach

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

Lu, C.; Liu, Y.; Niu, S.

2011-10-01

Turbulent entrainment-mixing mechanisms are investigated by applying a combined approach to the aircraft measurements of three drizzling and two nondrizzling stratocumulus clouds collected over the U.S. Department of Energy's Atmospheric Radiation Measurement Southern Great Plains site during the March 2000 cloud Intensive Observation Period. Microphysical analysis shows that the inhomogeneous entrainment-mixing process occurs much more frequently than the homogeneous counterpart, and most cases of the inhomogeneous entrainment-mixing process are close to the extreme scenario, having drastically varying cloud droplet concentration but roughly constant volume-mean radius. It is also found that the inhomogeneous entrainment-mixing process can occur both near the cloudmore » top and in the middle level of a cloud, and in both the nondrizzling clouds and nondrizzling legs in the drizzling clouds. A new dimensionless number, the scale number, is introduced as a dynamical measure for different entrainment-mixing processes, with a larger scale number corresponding to a higher degree of homogeneous entrainment mixing. Further empirical analysis shows that the scale number that separates the homogeneous from the inhomogeneous entrainment-mixing process is around 50, and most legs have smaller scale numbers. Thermodynamic analysis shows that sampling average of filament structures finer than the instrumental spatial resolution also contributes to the dominance of inhomogeneous entrainment-mixing mechanism. The combined microphysical-dynamical-thermodynamic analysis sheds new light on developing parameterization of entrainment-mixing processes and their microphysical and radiative effects in large-scale models.« less

Floquet–Magnus theory and generic transient dynamics in periodically driven many-body quantum systems

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

Kuwahara, Tomotaka, E-mail: tomotaka.phys@gmail.com; WPI, Advanced Institute for Materials Research, Tohoku University, Sendai 980-8577; Mori, Takashi

2016-04-15

This work explores a fundamental dynamical structure for a wide range of many-body quantum systems under periodic driving. Generically, in the thermodynamic limit, such systems are known to heat up to infinite temperature states in the long-time limit irrespective of dynamical details, which kills all the specific properties of the system. In the present study, instead of considering infinitely long-time scale, we aim to provide a general framework to understand the long but finite time behavior, namely the transient dynamics. In our analysis, we focus on the Floquet–Magnus (FM) expansion that gives a formal expression of the effective Hamiltonian onmore » the system. Although in general the full series expansion is not convergent in the thermodynamics limit, we give a clear relationship between the FM expansion and the transient dynamics. More precisely, we rigorously show that a truncated version of the FM expansion accurately describes the exact dynamics for a certain time-scale. Our theory reveals an experimental time-scale for which non-trivial dynamical phenomena can be reliably observed. We discuss several dynamical phenomena, such as the effect of small integrability breaking, efficient numerical simulation of periodically driven systems, dynamical localization and thermalization. Especially on thermalization, we discuss a generic scenario on the prethermalization phenomenon in periodically driven systems. -- Highlights: •A general framework to describe transient dynamics for periodically driven systems. •The theory is applicable to generic quantum many-body systems including long-range interacting systems. •Physical meaning of the truncation of the Floquet–Magnus expansion is rigorously established. •New mechanism of the prethermalization is proposed. •Revealing an experimental time-scale for which non-trivial dynamical phenomena can be reliably observed.« less

The Virtual Brain Integrates Computational Modeling and Multimodal Neuroimaging

PubMed Central

Schirner, Michael; McIntosh, Anthony R.; Jirsa, Viktor K.

2013-01-01

Abstract Brain function is thought to emerge from the interactions among neuronal populations. Apart from traditional efforts to reproduce brain dynamics from the micro- to macroscopic scales, complementary approaches develop phenomenological models of lower complexity. Such macroscopic models typically generate only a few selected—ideally functionally relevant—aspects of the brain dynamics. Importantly, they often allow an understanding of the underlying mechanisms beyond computational reproduction. Adding detail to these models will widen their ability to reproduce a broader range of dynamic features of the brain. For instance, such models allow for the exploration of consequences of focal and distributed pathological changes in the system, enabling us to identify and develop approaches to counteract those unfavorable processes. Toward this end, The Virtual Brain (TVB) (www.thevirtualbrain.org), a neuroinformatics platform with a brain simulator that incorporates a range of neuronal models and dynamics at its core, has been developed. This integrated framework allows the model-based simulation, analysis, and inference of neurophysiological mechanisms over several brain scales that underlie the generation of macroscopic neuroimaging signals. In this article, we describe how TVB works, and we present the first proof of concept. PMID:23442172

Quantum Kibble-Zurek Mechanism in a Spin-1 Bose-Einstein Condensate

NASA Astrophysics Data System (ADS)

Anquez, M.; Robbins, B. A.; Bharath, H. M.; Boguslawski, M.; Hoang, T. M.; Chapman, M. S.

2016-04-01

The dynamics of a quantum phase transition are explored using slow quenches from the polar to the broken-axisymmetry phases in a small spin-1 ferromagnetic Bose-Einstein condensate. Measurements of the evolution of the spin populations reveal a power-law scaling of the temporal onset of excitations versus quench speed as predicted from quantum extensions of the Kibble-Zurek mechanism. The satisfactory agreement of the measured scaling exponent with the analytical theory and numerical simulations provides experimental confirmation of the quantum Kibble-Zurek model.

Multiscale Aspects of Modeling Gas-Phase Nanoparticle Synthesis

PubMed Central

Buesser, B.; Gröhn, A.J.

2013-01-01

Aerosol reactors are utilized to manufacture nanoparticles in industrially relevant quantities. The development, understanding and scale-up of aerosol reactors can be facilitated with models and computer simulations. This review aims to provide an overview of recent developments of models and simulations and discuss their interconnection in a multiscale approach. A short introduction of the various aerosol reactor types and gas-phase particle dynamics is presented as a background for the later discussion of the models and simulations. Models are presented with decreasing time and length scales in sections on continuum, mesoscale, molecular dynamics and quantum mechanics models. PMID:23729992

A continuum dislocation dynamics framework for plasticity of polycrystalline materials

NASA Astrophysics Data System (ADS)

Askari, Hesam Aldin

The objective of this research is to investigate the mechanical response of polycrystals in different settings to identify the mechanisms that give rise to specific response observed in the deformation process. Particularly the large deformation of magnesium alloys and yield properties of copper in small scales are investigated. We develop a continuum dislocation dynamics framework based on dislocation mechanisms and interaction laws and implement this formulation in a viscoplastic self-consistent scheme to obtain the mechanical response in a polycrystalline system. The versatility of this method allows various applications in the study of problems involving large deformation, study of microstructure and its evolution, superplasticity, study of size effect in polycrystals and stochastic plasticity. The findings from the numerical solution are compared to the experimental results to validate the simulation results. We apply this framework to study the deformation mechanisms in magnesium alloys at moderate to fast strain rates and room temperature to 450 °C. Experiments for the same range of strain rates and temperatures were carried out to obtain the mechanical and material properties, and to compare with the numerical results. The numerical approach for magnesium is divided into four main steps; 1) room temperature unidirectional loading 2) high temperature deformation without grain boundary sliding 3) high temperature with grain boundary sliding mechanism 4) room temperature cyclic loading. We demonstrate the capability of our modeling approach in prediction of mechanical properties and texture evolution and discuss the improvement obtained by using the continuum dislocation dynamics method. The framework was also applied to nano-sized copper polycrystals to study the yield properties at small scales and address the observed yield scatter. By combining our developed method with a Monte Carlo simulation approach, the stochastic plasticity at small length scales was studied and the sources of the uncertainty in the polycrystalline structure are discussed. Our results suggest that the stochastic response is mainly because of a) stochastic plasticity due to dislocation substructure inside crystals and b) the microstructure of the polycrystalline material. The extent of the uncertainty is correlated to the "effective cell length" in the sampling procedure whether using simulations and experimental approach.

Molecular-dynamics simulations of crosslinking and confinement effects on structure, segmental mobility and mechanics of filled elastomers

NASA Astrophysics Data System (ADS)

Davris, Theodoros; Lyulin, Alexey V.

2016-05-01

The significant drop of the storage modulus under uniaxial deformation (Payne effect) restrains the performance of the elastomer-based composites and the development of possible new applications. In this paper molecular-dynamics (MD) computer simulations using LAMMPS MD package have been performed to study the mechanical properties of a coarse-grained model of this family of nanocomposite materials. Our goal is to provide simulational insights into the viscoelastic properties of filled elastomers, and try to connect the macroscopic mechanics with composite microstructure, the strength of the polymer-filler interactions and the polymer mobility at different scales. To this end we simulate random copolymer films capped between two infinite solid (filler aggregate) walls. We systematically vary the strength of the polymer-substrate adhesion interactions, degree of polymer confinement (film thickness), polymer crosslinking density, and study their influence on the equilibrium and non-equilibrium structure, segmental dynamics, and the mechanical properties of the simulated systems. The glass-transition temperature increases once the mesh size became smaller than the chain radius of gyration; otherwise it remained invariant to mesh-size variations. This increase in the glass-transition temperature was accompanied by a monotonic slowing-down of segmental dynamics on all studied length scales. This observation is attributed to the correspondingly decreased width of the bulk density layer that was obtained in films whose thickness was larger than the end-to-end distance of the bulk polymer chains. To test this hypothesis additional simulations were performed in which the crystalline walls were replaced with amorphous or rough walls.

Discovering mechanisms relevant for radiation damage evolution

DOE PAGES

Uberuaga, Blas Pedro; Martinez, Enrique Saez; Perez, Danny; ...

2018-02-22

he response of a material to irradiation is a consequence of the kinetic evolution of defects produced during energetic damage events. Thus, accurate predictions of radiation damage evolution require knowing the atomic scale mechanisms associated with those defects. Atomistic simulations are a key tool in providing insight into the types of mechanisms possible. Further, by extending the time scale beyond what is achievable with conventional molecular dynamics, even greater insight can be obtained. Here, we provide examples in which such simulations have revealed new kinetic mechanisms that were not obvious before performing the simulations. We also demonstrate, through the couplingmore » with higher level models, how those mechanisms impact experimental observables in irradiated materials. Lastly, we discuss the importance of these types of simulations in the context of predicting material behavior.« less

Multi-scale mechanics from molecules to morphogenesis

PubMed Central

Davidson, Lance; von Dassow, Michelangelo; Zhou, Jian

2009-01-01

Dynamic mechanical processes shape the embryo and organs during development. Little is understood about the basic physics of these processes, what forces are generated, or how tissues resist or guide those forces during morphogenesis. This review offers an outline of some of the basic principles of biomechanics, provides working examples of biomechanical analyses of developing embryos, and reviews the role of structural proteins in establishing and maintaining the mechanical properties of embryonic tissues. Drawing on examples we highlight the importance of investigating mechanics at multiple scales from milliseconds to hours and from individual molecules to whole embryos. Lastly, we pose a series of questions that will need to be addressed if we are to understand the larger integration of molecular and physical mechanical processes during morphogenesis and organogenesis. PMID:19394436

Discovering mechanisms relevant for radiation damage evolution

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

Uberuaga, Blas Pedro; Martinez, Enrique Saez; Perez, Danny

he response of a material to irradiation is a consequence of the kinetic evolution of defects produced during energetic damage events. Thus, accurate predictions of radiation damage evolution require knowing the atomic scale mechanisms associated with those defects. Atomistic simulations are a key tool in providing insight into the types of mechanisms possible. Further, by extending the time scale beyond what is achievable with conventional molecular dynamics, even greater insight can be obtained. Here, we provide examples in which such simulations have revealed new kinetic mechanisms that were not obvious before performing the simulations. We also demonstrate, through the couplingmore » with higher level models, how those mechanisms impact experimental observables in irradiated materials. Lastly, we discuss the importance of these types of simulations in the context of predicting material behavior.« less

Shock Wave Propagation in Cementitious Materials at Micro/Meso Scales

NASA Astrophysics Data System (ADS)

Rajendran, Arunachalam

2015-06-01

The mechanical and constitutive response of materials like cement, and bio materials like fish scale and abalone shell is very complex due to heterogeneities that are inherently present in the nano and microstructures. The intrinsic constitutive behaviors are driven by the chemical composition and the molecular, micro, and meso structures. Therefore, it becomes important to identify the material genome as the building block for the material. For instance, in cementitious materials, the genome of C-S-H phase (the glue or the paste) that holds the various clinkers, such as the dicalcium silicate, tricalcium silicate, calcium ferroaluminates, and others is extremely complex. Often mechanical behaviors of C-S-H type materials are influenced by the chemistry and the structures at all nano to micro length scales. By explicitly modeling the molecular structures using appropriate potentials, it is then possible to compute the elastic tensor from molecular dynamics simulations using all atom method. The elastic tensors for the C-S-H gel and other clinkers are determined using the software suite ``Accelrys Materials Studio.'' A strain rate dependent, fracture mechanics based tensile damage model has been incorporated into ABAQUS finite element code to model spall evolution in the heterogeneous cementitious material with all constituents explicitly modeled through one micron element resolution. This paper presents results from nano/micro/meso scale analyses of shock wave propagation in a heterogeneous cementitious material using both molecular dynamic and finite element codes.

Entraining the topology and the dynamics of a network of phase oscillators

NASA Astrophysics Data System (ADS)

Sendiña-Nadal, I.; Leyva, I.; Buldú, J. M.; Almendral, J. A.; Boccaletti, S.

2009-04-01

We show that the topology and dynamics of a network of unsynchronized Kuramoto oscillators can be simultaneously controlled by means of a forcing mechanism which yields a phase locking of the oscillators to that of an external pacemaker in connection with the reshaping of the network’s degree distribution. The entrainment mechanism is based on the addition, at regular time intervals, of unidirectional links from oscillators that follow the dynamics of a pacemaker to oscillators in the pristine graph whose phases hold a prescribed phase relationship. Such a dynamically based rule in the attachment process leads to the emergence of a power-law shape in the final degree distribution of the graph whenever the network is entrained to the dynamics of the pacemaker. We show that the arousal of a scale-free distribution in connection with the success of the entrainment process is a robust feature, characterizing different networks’ initial configurations and parameters.

Markov State Models Provide Insights into Dynamic Modulation of Protein Function

PubMed Central

2015-01-01

Conspectus Protein function is inextricably linked to protein dynamics. As we move from a static structural picture to a dynamic ensemble view of protein structure and function, novel computational paradigms are required for observing and understanding conformational dynamics of proteins and its functional implications. In principle, molecular dynamics simulations can provide the time evolution of atomistic models of proteins, but the long time scales associated with functional dynamics make it difficult to observe rare dynamical transitions. The issue of extracting essential functional components of protein dynamics from noisy simulation data presents another set of challenges in obtaining an unbiased understanding of protein motions. Therefore, a methodology that provides a statistical framework for efficient sampling and a human-readable view of the key aspects of functional dynamics from data analysis is required. The Markov state model (MSM), which has recently become popular worldwide for studying protein dynamics, is an example of such a framework. In this Account, we review the use of Markov state models for efficient sampling of the hierarchy of time scales associated with protein dynamics, automatic identification of key conformational states, and the degrees of freedom associated with slow dynamical processes. Applications of MSMs for studying long time scale phenomena such as activation mechanisms of cellular signaling proteins has yielded novel insights into protein function. In particular, from MSMs built using large-scale simulations of GPCRs and kinases, we have shown that complex conformational changes in proteins can be described in terms of structural changes in key structural motifs or “molecular switches” within the protein, the transitions between functionally active and inactive states of proteins proceed via multiple pathways, and ligand or substrate binding modulates the flux through these pathways. Finally, MSMs also provide a theoretical toolbox for studying the effect of nonequilibrium perturbations on conformational dynamics. Considering that protein dynamics in vivo occur under nonequilibrium conditions, MSMs coupled with nonequilibrium statistical mechanics provide a way to connect cellular components to their functional environments. Nonequilibrium perturbations of protein folding MSMs reveal the presence of dynamically frozen glass-like states in their conformational landscape. These frozen states are also observed to be rich in β-sheets, which indicates their possible role in the nucleation of β-sheet rich aggregates such as those observed in amyloid-fibril formation. Finally, we describe how MSMs have been used to understand the dynamical behavior of intrinsically disordered proteins such as amyloid-β, human islet amyloid polypeptide, and p53. While certainly not a panacea for studying functional dynamics, MSMs provide a rigorous theoretical foundation for understanding complex entropically dominated processes and a convenient lens for viewing protein motions. PMID:25625937

Manipulating Si(100) at 5 K using qPlus frequency modulated atomic force microscopy: Role of defects and dynamics in the mechanical switching of atoms

NASA Astrophysics Data System (ADS)

Sweetman, A.; Jarvis, S.; Danza, R.; Bamidele, J.; Kantorovich, L.; Moriarty, P.

2011-08-01

We use small-amplitude qPlus frequency modulated atomic force microscopy (FM-AFM), at 5 K, to investigate the atomic-scale mechanical stability of the Si(100) surface. By operating at zero applied bias the effect of tunneling electrons is eliminated, demonstrating that surface manipulation can be performed by solely mechanical means. Striking differences in surface response are observed between different regions of the surface, most likely due to variations in strain associated with the presence of surface defects. We investigate the variation in local energy surface by ab initio simulation, and comment on the dynamics observed during force spectroscopy.

High-speed nanoscale characterization of dewetting via dynamic transmission electron microscopy

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

Hihath, Sahar; Department of Physics, University of California, Davis, 1 Shields Ave., Davis, California 95616; Santala, Melissa K.

The dewetting of thin films can occur in either the solid or the liquid state for which different mass transport mechanisms are expected to control morphological changes. Traditionally, dewetting dynamics have been examined on time scales between several seconds to hours, and length scales ranging between nanometers and millimeters. The determination of mass transport mechanisms on the nanoscale, however, requires nanoscale spatial resolution and much shorter time scales. This study reports the high-speed observation of dewetting phenomena for kinetically constrained Ni thin films on crystalline SrTiO{sub 3} substrates. Movie-mode Dynamic Transmission Electron Microscopy (DTEM) was used for high-speed image acquisitionmore » during thin film dewetting at different temperatures. DTEM imaging confirmed that the initial stages of film agglomeration include edge retraction, hole formation, and growth. Finite element modeling was used to simulate temperature distributions within the DTEM samples after laser irradiation with different energies. For pulsed laser irradiation at 18 μJ, experimentally observed hole growth suggests that Marangoni flow dominates hole formation in the liquid nickel film. After irradiation with 13.8 μJ, however, the observations suggest that dewetting was initiated by nucleation of voids followed by hole growth through solid-state surface diffusion.« less

Quantum Many-Body Dynamics with Driven Bose Condensates: Kibble-Zurek Mechanism and Bose Fireworks

NASA Astrophysics Data System (ADS)

Clark, Logan William

In recent years there has been an explosion of interest in the field of quantum many-body physics. Understanding the complex and often unintuitive behavior of systems containing interacting quantum constituents is not only fascinating but also crucial for developing the next generation of quantum technology, including better materials, sensors, and computers. Yet understanding such systems remains a challenge, particularly when considering the dynamics which occur when they are excited far from equilibrium. Ultracold atomic gases provide an ideal system with which to study dynamics by enabling clean, well-controlled experiments at length- and time-scales which allow us to observe the dynamics directly. This thesis describes experiments on the many-body dynamics of ultracold, bosonic cesium atoms. Our apparatus epitomizes the versatility of ultracold atoms by providing extensive control over the quantum gas. In particular, we will discuss our use of a digital micromirror device to project arbitrary, dynamic external potentials onto the gas; our development of a powerful new scheme for optically controlling Feshbach resonances to enable spatiotemporal control of the interactions between atoms; and our use of near-resonant shaking lattices to modify the kinetic energy of atoms. Taking advantage of this flexible apparatus, we have been able to test a longstanding conjecture based on the Kibble-Zurek mechanism, which says that the dynamics of a system crossing a quantum phase transition should obey a universal scaling symmetry of space and time. After accounting for this scaling symmetry, critical dynamics would be essentially independent of the rate at which a system crossed a phase transition. We tested the universal scaling of critical dynamics by using near-resonant shaking to drive Bose-Einstein condensates across an effectively ferromagnetic quantum phase transition. After crossing the phase transition, condensates divide themselves spatially into domains with finite quasimomentum. We measured the growth of these domains over time and the correlation functions describing their spatial distribution by directly reconstructing the quasimomentum distribution. We observed the expected scaling laws across more than an order of magnitude in the crossing rate, aside from which the observed critical dynamics were indeed independent of the crossing rate. These experiments provide strong support for the universal scaling symmetry of space and time and the extension of the Kibble-Zurek mechanism to quantum phase transitions. We also present the first observation of Bose Fireworks: the sudden emission of many bright, narrow jets of atoms from condensates with oscillating interaction strength. Even though the underlying inelastic s-wave collisions induced by oscillating interactions are isotropic, the collective nature of collisions in the condensate causes the outgoing bosonic atoms to bunch into narrow jets in the horizontal plane. This bunching results from runaway stimulated collisions, which we find can only occur above a threshold oscillation amplitude. The observed atom number in the jets suggests that they are seeded by quantum fluctuations. Moreover, in azimuthal correlation functions we observe forward correlations consistent with theory, which saturate the limit from the uncertainty principle. We also observe partial correlation between counterpropagating jets. Bose Fireworks provide a well-controlled platform for understanding the diverse class of systems in which a coherent source rapidly emits pairs of counterpropagating bosons.

Presentation of an approach for the analysis of the mechanical response of propellant under a large spectrum of loadings: numerical and mechanical issues

NASA Astrophysics Data System (ADS)

Fanget, Alain

2009-06-01

Many authors claim that to understand the response of a propellant, specifically under quasi static and dynamic loading, the mesostructural morphology and the mechanical behaviour of each of its components have to be known. However the scale of the mechanical description of the behaviour of a propellant is relative to its heterogeneities and the wavelength of loading. The shorter it is, the more important the topological description of the material is. In our problems, involving the safety of energetic materials, the propellant can be subjected to a large spectrum of loadings. This presentation is divided into five parts. The first part describes the processes used to extract the information about the morphology of the meso-structure of the material and presents some results. The results, the difficulties and the perspectives for this part will be recalled. The second part determines the physical processes involved at this scale from experimental results. Taking into account the knowledge of the morphology, two ways have been chosen to describe the response of the material. One concerns the quasi static loading, the object of the third part, in which we show how we use the mesoscopic scale as a base of development to build constitutive models. The fourth part presents for low but dynamic loading the comparison between numerical analysis and experiments.

Introduction to the Special Issue: Across the horizon: scale effects in global change research.

PubMed

Gornish, Elise S; Leuzinger, Sebastian

2015-01-01

As a result of the increasing speed and magnitude in which habitats worldwide are experiencing environmental change, making accurate predictions of the effects of global change on ecosystems and the organisms that inhabit them have become an important goal for ecologists. Experimental and modelling approaches aimed at understanding the linkages between factors of global change and biotic responses have become numerous and increasingly complex in order to adequately capture the multifarious dynamics associated with these relationships. However, constrained by resources, experiments are often conducted at small spatiotemporal scales (e.g. looking at a plot of a few square metres over a few years) and at low organizational levels (looking at organisms rather than ecosystems) in spite of both theoretical and experimental work that suggests ecological dynamics across scales can be dissimilar. This phenomenon has been hypothesized to occur because the mechanisms that drive dynamics across scales differ. A good example is the effect of elevated CO2 on transpiration. While at the leaf level, transpiration can be reduced, at the stand level, transpiration can increase because leaf area per unit ground area increases. The reported net effect is then highly dependent on the spatiotemporal scale. This special issue considers the biological relevancy inherent in the patterns associated with the magnitude and type of response to changing environmental conditions, across scales. This collection of papers attempts to provide a comprehensive treatment of this phenomenon in order to help develop an understanding of the extent of, and mechanisms involved with, ecological response to global change. Published by Oxford University Press on behalf of the Annals of Botany Company.

A dynamical weak scale from inflation

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

You, Tevong, E-mail: tty20@cam.ac.uk

Dynamical scanning of the Higgs mass by an axion-like particle during inflation may provide a cosmological component to explaining part of the hierarchy problem. We propose a novel interplay of this cosmological relaxation mechanism with inflation, whereby the backreaction of the Higgs vacuum expectation value near the weak scale causes inflation to end. As Hubble drops, the relaxion's dissipative friction increases relative to Hubble and slows it down enough to be trapped by the barriers of its periodic potential. Such a scenario raises the natural cut-off of the theory up to ∼ 10{sup 10} GeV, while maintaining a minimal relaxionmore » sector without having to introduce additional scanning scalars or new physics coincidentally close to the weak scale.« less

A novel land surface-hydrologic-sediment dynamics model for stream corridor conservation assessment and its first application

NASA Astrophysics Data System (ADS)

Smithgall, K.; Shen, C.; Langendoen, E. J.; Johnson, P. A.

2015-12-01

Nationally and in the Chesapeake Bay (CB), Stream Corridor restoration costs unsustainable amount of public resources, but decisions are often made with inadequate knowledge of regional-scale system behavior. Bank erosion is a significant issue relevant to sediment and nutrient pollution, aquatic and riparian habitat and stream health. Existing modeling effort either focuses only on reach-scale responses or overly simplifies the descriptions for bank failure mechanics. In this work we present a novel regional-scale processes model integrating hydrology, vegetation dynamics, hydraulics, bank mechanics and sediment transport, based on a coupling between Community Land Model, Process-based Adaptive Watershed Simulator and CONservational Channel Evolution and Pollutant Transport System (CLM + PAWS + CONCEPTS, CPC). We illustrate the feasibility of this modeling platform in a Valley and Ridge basin in Pennsylvania, USA, with channel geometry data collected in 2004 and 2014. The simulations are able to reproduce essential pattern of the observed trends. We study the causes of the noticeable evolution of a relocated channel and the hydrologic controls. Bridging processes on multiple scales, the CPC model creates a new, integrated system that may serve as a confluence point for inter-disciplinary research.

Grain scale observations of stick-slip dynamics in fluid saturated granular fault gouge

NASA Astrophysics Data System (ADS)

Johnson, P. A.; Dorostkar, O.; Guyer, R. A.; Marone, C.; Carmeliet, J.

2017-12-01

We are studying granular mechanics during slip. In the present work, we conduct coupled computational fluid dynamics (CFD) and discrete element method (DEM) simulations to study grain scale characteristics of slip instabilities in fluid saturated granular fault gouge. The granular sample is confined with constant normal load (10 MPa), and sheared with constant velocity (0.6 mm/s). This loading configuration is chosen to promote stick-slip dynamics, based on a phase-space study. Fluid is introduced in the beginning of stick phase and characteristics of slip events i.e. macroscopic friction coefficient, kinetic energy and layer thickness are monitored. At the grain scale, we monitor particle coordination number, fluid-particle interaction forces as well as particle and fluid kinetic energy. Our observations show that presence of fluids in a drained granular fault gouge stabilizes the layer in the stick phase and increases the recurrence time. In saturated model, we observe that average particle coordination number reaches higher values compared to dry granular gouge. Upon slip, we observe that a larger portion of the granular sample is mobilized in saturated gouge compared to dry system. We also observe that regions with high particle kinetic energy are correlated with zones of high fluid motion. Our observations highlight that spatiotemporal profile of fluid dynamic pressure affects the characteristics of slip instabilities, increasing macroscopic friction coefficient drop, kinetic energy release and granular layer compaction. We show that numerical simulations help characterize the micromechanics of fault mechanics.

A Multi-Scale Approach to Airway Hyperresponsiveness: From Molecule to Organ

PubMed Central

Lauzon, Anne-Marie; Bates, Jason H. T.; Donovan, Graham; Tawhai, Merryn; Sneyd, James; Sanderson, Michael J.

2012-01-01

Airway hyperresponsiveness (AHR), a characteristic of asthma that involves an excessive reduction in airway caliber, is a complex mechanism reflecting multiple processes that manifest over a large range of length and time scales. At one extreme, molecular interactions determine the force generated by airway smooth muscle (ASM). At the other, the spatially distributed constriction of the branching airways leads to breathing difficulties. Similarly, asthma therapies act at the molecular scale while clinical outcomes are determined by lung function. These extremes are linked by events operating over intermediate scales of length and time. Thus, AHR is an emergent phenomenon that limits our understanding of asthma and confounds the interpretation of studies that address physiological mechanisms over a limited range of scales. A solution is a modular computational model that integrates experimental and mathematical data from multiple scales. This includes, at the molecular scale, kinetics, and force production of actin-myosin contractile proteins during cross-bridge and latch-state cycling; at the cellular scale, Ca2+ signaling mechanisms that regulate ASM force production; at the tissue scale, forces acting between contracting ASM and opposing viscoelastic tissue that determine airway narrowing; at the organ scale, the topographic distribution of ASM contraction dynamics that determine mechanical impedance of the lung. At each scale, models are constructed with iterations between theory and experimentation to identify the parameters that link adjacent scales. This modular model establishes algorithms for modeling over a wide range of scales and provides a framework for the inclusion of other responses such as inflammation or therapeutic regimes. The goal is to develop this lung model so that it can make predictions about bronchoconstriction and identify the pathophysiologic mechanisms having the greatest impact on AHR and its therapy. PMID:22701430

Structural versus dynamical origins of mean-field behavior in a self-organized critical model of neuronal avalanches

NASA Astrophysics Data System (ADS)

Moosavi, S. Amin; Montakhab, Afshin

2015-11-01

Critical dynamics of cortical neurons have been intensively studied over the past decade. Neuronal avalanches provide the main experimental as well as theoretical tools to consider criticality in such systems. Experimental studies show that critical neuronal avalanches show mean-field behavior. There are structural as well as recently proposed [Phys. Rev. E 89, 052139 (2014), 10.1103/PhysRevE.89.052139] dynamical mechanisms that can lead to mean-field behavior. In this work we consider a simple model of neuronal dynamics based on threshold self-organized critical models with synaptic noise. We investigate the role of high-average connectivity, random long-range connections, as well as synaptic noise in achieving mean-field behavior. We employ finite-size scaling in order to extract critical exponents with good accuracy. We conclude that relevant structural mechanisms responsible for mean-field behavior cannot be justified in realistic models of the cortex. However, strong dynamical noise, which can have realistic justifications, always leads to mean-field behavior regardless of the underlying structure. Our work provides a different (dynamical) origin than the conventionally accepted (structural) mechanisms for mean-field behavior in neuronal avalanches.

Symmetry aspects in emergent quantum mechanics

NASA Astrophysics Data System (ADS)

Elze, Hans-Thomas

2009-06-01

We discuss an explicit realization of the dissipative dynamics anticipated in the proof of 't Hooft's existence theorem, which states that 'For any quantum system there exists at least one deterministic model that reproduces all its dynamics after prequantization'. - There is an energy-parity symmetry hidden in the Liouville equation, which mimics the Kaplan-Sundrum protective symmetry for the cosmological constant. This symmetry may be broken by the coarse-graining inherent in physics at scales much larger than the Planck length. We correspondingly modify classical ensemble theory by incorporating dissipative fluctuations (information loss) - which are caused by discrete spacetime continually 'measuring' matter. In this way, aspects of quantum mechanics, such as the von Neumann equation, including a Lindblad term, arise dynamically and expectations of observables agree with the Born rule. However, the resulting quantum coherence is accompanied by an intrinsic decoherence and continuous localization mechanism. Our proposal leads towards a theory that is linear and local at the quantum mechanical level, but the relation to the underlying classical degrees of freedom is nonlocal.

Dynamics and universal scaling law in geometrically-controlled sessile drop evaporation

PubMed Central

Sáenz, P. J.; Wray, A. W.; Che, Z.; Matar, O. K.; Valluri, P.; Kim, J.; Sefiane, K.

2017-01-01

The evaporation of a liquid drop on a solid substrate is a remarkably common phenomenon. Yet, the complexity of the underlying mechanisms has constrained previous studies to spherically symmetric configurations. Here we investigate well-defined, non-spherical evaporating drops of pure liquids and binary mixtures. We deduce a universal scaling law for the evaporation rate valid for any shape and demonstrate that more curved regions lead to preferential localized depositions in particle-laden drops. Furthermore, geometry induces well-defined flow structures within the drop that change according to the driving mechanism. In the case of binary mixtures, geometry dictates the spatial segregation of the more volatile component as it is depleted. Our results suggest that the drop geometry can be exploited to prescribe the particle deposition and evaporative dynamics of pure drops and the mixing characteristics of multicomponent drops, which may be of interest to a wide range of industrial and scientific applications. PMID:28294114

Multi-scale modeling of irradiation effects in spallation neutron source materials

NASA Astrophysics Data System (ADS)

Yoshiie, T.; Ito, T.; Iwase, H.; Kaneko, Y.; Kawai, M.; Kishida, I.; Kunieda, S.; Sato, K.; Shimakawa, S.; Shimizu, F.; Hashimoto, S.; Hashimoto, N.; Fukahori, T.; Watanabe, Y.; Xu, Q.; Ishino, S.

2011-07-01

Changes in mechanical property of Ni under irradiation by 3 GeV protons were estimated by multi-scale modeling. The code consisted of four parts. The first part was based on the Particle and Heavy-Ion Transport code System (PHITS) code for nuclear reactions, and modeled the interactions between high energy protons and nuclei in the target. The second part covered atomic collisions by particles without nuclear reactions. Because the energy of the particles was high, subcascade analysis was employed. The direct formation of clusters and the number of mobile defects were estimated using molecular dynamics (MD) and kinetic Monte-Carlo (kMC) methods in each subcascade. The third part considered damage structural evolutions estimated by reaction kinetic analysis. The fourth part involved the estimation of mechanical property change using three-dimensional discrete dislocation dynamics (DDD). Using the above four part code, stress-strain curves for high energy proton irradiated Ni were obtained.

Dynamics and universal scaling law in geometrically-controlled sessile drop evaporation.

PubMed

Sáenz, P J; Wray, A W; Che, Z; Matar, O K; Valluri, P; Kim, J; Sefiane, K

2017-03-15

The evaporation of a liquid drop on a solid substrate is a remarkably common phenomenon. Yet, the complexity of the underlying mechanisms has constrained previous studies to spherically symmetric configurations. Here we investigate well-defined, non-spherical evaporating drops of pure liquids and binary mixtures. We deduce a universal scaling law for the evaporation rate valid for any shape and demonstrate that more curved regions lead to preferential localized depositions in particle-laden drops. Furthermore, geometry induces well-defined flow structures within the drop that change according to the driving mechanism. In the case of binary mixtures, geometry dictates the spatial segregation of the more volatile component as it is depleted. Our results suggest that the drop geometry can be exploited to prescribe the particle deposition and evaporative dynamics of pure drops and the mixing characteristics of multicomponent drops, which may be of interest to a wide range of industrial and scientific applications.

Pore configuration landscape of granular crystallization.

PubMed

Saadatfar, M; Takeuchi, H; Robins, V; Francois, N; Hiraoka, Y

2017-05-12

Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics.

Pore configuration landscape of granular crystallization

PubMed Central

Saadatfar, M.; Takeuchi, H.; Robins, V.; Francois, N.; Hiraoka, Y.

2017-01-01

Uncovering grain-scale mechanisms that underlie the disorder–order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics. PMID:28497794

Pore configuration landscape of granular crystallization

NASA Astrophysics Data System (ADS)

Saadatfar, M.; Takeuchi, H.; Robins, V.; Francois, N.; Hiraoka, Y.

2017-05-01

Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics.

Active Vertex Model for cell-resolution description of epithelial tissue mechanics

PubMed Central

Barton, Daniel L.; Henkes, Silke

2017-01-01

We introduce an Active Vertex Model (AVM) for cell-resolution studies of the mechanics of confluent epithelial tissues consisting of tens of thousands of cells, with a level of detail inaccessible to similar methods. The AVM combines the Vertex Model for confluent epithelial tissues with active matter dynamics. This introduces a natural description of the cell motion and accounts for motion patterns observed on multiple scales. Furthermore, cell contacts are generated dynamically from positions of cell centres. This not only enables efficient numerical implementation, but provides a natural description of the T1 transition events responsible for local tissue rearrangements. The AVM also includes cell alignment, cell-specific mechanical properties, cell growth, division and apoptosis. In addition, the AVM introduces a flexible, dynamically changing boundary of the epithelial sheet allowing for studies of phenomena such as the fingering instability or wound healing. We illustrate these capabilities with a number of case studies. PMID:28665934

Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

NASA Astrophysics Data System (ADS)

Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.; Volkov, Sergey N.; Solov'yov, Andrey V.

2016-01-01

The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey V. Solov'yov, Nigel Mason, Gustavo Garcia and Eugene Surdutovich.

Active Vertex Model for cell-resolution description of epithelial tissue mechanics.

PubMed

Barton, Daniel L; Henkes, Silke; Weijer, Cornelis J; Sknepnek, Rastko

2017-06-01

We introduce an Active Vertex Model (AVM) for cell-resolution studies of the mechanics of confluent epithelial tissues consisting of tens of thousands of cells, with a level of detail inaccessible to similar methods. The AVM combines the Vertex Model for confluent epithelial tissues with active matter dynamics. This introduces a natural description of the cell motion and accounts for motion patterns observed on multiple scales. Furthermore, cell contacts are generated dynamically from positions of cell centres. This not only enables efficient numerical implementation, but provides a natural description of the T1 transition events responsible for local tissue rearrangements. The AVM also includes cell alignment, cell-specific mechanical properties, cell growth, division and apoptosis. In addition, the AVM introduces a flexible, dynamically changing boundary of the epithelial sheet allowing for studies of phenomena such as the fingering instability or wound healing. We illustrate these capabilities with a number of case studies.

Engineering science and mechanics; Proceedings of the International Symposium, Tainan, Republic of China, December 29-31, 1981. Parts 1 & 2

NASA Astrophysics Data System (ADS)

Hsia, H.-M.; Chou, Y.-L.; Longman, R. W.

1983-07-01

The topics considered are related to measurements and controls in physical systems, the control of large scale and distributed parameter systems, chemical engineering systems, aerospace science and technology, thermodynamics and fluid mechanics, and computer applications. Subjects in structural dynamics are discussed, taking into account finite element approximations in transient analysis, buckling finite element analysis of flat plates, dynamic analysis of viscoelastic structures, the transient analysis of large frame structures by simple models, large amplitude vibration of an initially stressed thick plate, nonlinear aeroelasticity, a sensitivity analysis of a combined beam-spring-mass structure, and the optimal design and aeroelastic investigation of segmented windmill rotor blades. Attention is also given to dynamics and control of mechanical and civil engineering systems, composites, and topics in materials. For individual items see A83-44002 to A83-44061

Dynamic Contact Angle at the Nanoscale: A Unified View.

PubMed

Lukyanov, Alex V; Likhtman, Alexei E

2016-06-28

Generation of a dynamic contact angle in the course of wetting is a fundamental phenomenon of nature. Dynamic wetting processes have a direct impact on flows at the nanoscale, and therefore, understanding them is exceptionally important to emerging technologies. Here, we reveal the microscopic mechanism of dynamic contact angle generation. It has been demonstrated using large-scale molecular dynamics simulations of bead-spring model fluids that the main cause of local contact angle variations is the distribution of microscopic force acting at the contact line region. We were able to retrieve this elusive force with high accuracy. It has been directly established that the force distribution can be solely predicted on the basis of a general friction law for liquid flow at solid surfaces by Thompson and Troian. The relationship with the friction law provides both an explanation of the phenomenon of dynamic contact angle and a methodology for future predictions. The mechanism is intrinsically microscopic, universal, and irreducible and is applicable to a wide range of problems associated with wetting phenomena.

Scaling of rotational inertia of primate mandibles.

PubMed

Ross, Callum F; Iriarte-Diaz, Jose; Platts, Ellen; Walsh, Treva; Heins, Liam; Gerstner, Geoffrey E; Taylor, Andrea B

2017-05-01

The relative importance of pendulum mechanics and muscle mechanics in chewing dynamics has implications for understanding the optimality criteria driving the evolution of primate feeding systems. The Spring Model (Ross et al., 2009b), which modeled the primate chewing system as a forced mass-spring system, predicted that chew cycle time would increase faster than was actually observed. We hypothesized that if mandibular momentum plays an important role in chewing dynamics, more accurate estimates of the rotational inertia of the mandible would improve the accuracy with which the Spring Model predicts the scaling of primate chew cycle period. However, if mass-related momentum effects are of negligible importance in the scaling of primate chew cycle period, this hypothesis would be falsified. We also predicted that greater "robusticity" of anthropoid mandibles compared with prosimians would be associated with higher moments of inertia. From computed tomography scans, we estimated the scaling of the moment of inertia (I j ) of the mandibles of thirty-one species of primates, including 22 anthropoid and nine prosimian species, separating I j into the moment about a transverse axis through the center of mass (I xx ) and the moment of the center of mass about plausible axes of rotation. We found that across primates I j increases with positive allometry relative to jaw length, primarily due to positive allometry of jaw mass and I xx , and that anthropoid mandibles have greater rotational inertia compared with prosimian mandibles of similar length. Positive allometry of I j of primate mandibles actually lowers the predictive ability of the Spring Model, suggesting that scaling of primate chew cycle period, and chewing dynamics in general, are more strongly influenced by factors other than scaling of inertial properties of the mandible, such as the dynamic properties of the jaw muscles and neural control. Differences in cycle period scaling between chewing and locomotion systems reinforce the suggestion that displacement and force control are more important in the design of feeding systems than energetics and speed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mechanical Evolution and Dynamics of Decollement Slip in Contractional Systems: Correlating Macro- and Micro-Scale Processes in Particle Dynamics Simulation

NASA Astrophysics Data System (ADS)

Morgan, J. K.

2014-12-01

Particle-based numerical simulations allow detailed investigations of small-scale processes and mechanisms associated with fault initiation and slip, which emerge naturally in such models. This study investigates the evolving mechanical conditions and associated micro-mechanisms during transient slip on a weak decollement propagating beneath a growing contractional wedge (e.g., accretionary prism, fold and thrust belt). The models serve as analogs of the seismic cycle, although lacking full earthquake dynamics. Nonetheless, the mechanical evolution of both decollement and upper plate can be monitored, and correlated with the particle-scale physical and contact properties, providing insights into changes that accompany such stick-slip behavior. In this study, particle assemblages consolidated under gravity and bonded to impart cohesion, are pushed at a constant velocity above a weak, unbonded decollement surface. Forward propagation of decollement slip occurs in discrete pulses, modulated by heterogeneous stress conditions (e.g., roughness, contact bridging) along the fault. Passage of decollement slip resets the stress along this horizon, producing distinct patterns: shear stress is enhanced in front of the slipped decollement due to local contact bridging and fault locking; shear stress minima occur immediately above the tip, denoting local stress release and contact reorganization following slip; more mature portions of the fault exhibit intermediate shear stress, reflecting more stable contact force distributions and magnitudes. This pattern of shear stress pre-conditions the decollement for future slip events, which must overcome the high stresses at the fault tip. Long-term slip along the basal decollement induces upper plate contraction. When upper plate stresses reach critical strength conditions, new thrust faults break through the upper plate, relieving stresses and accommodating horizontal shortening. Decollement activity retreats back to the newly formed thrust fault. The cessation of upper plate fault slip causes gradual increases in upper plate stresses, rebuilding shear stresses along the decollement and enabling renewed pulses of decollement slip. Thus, upper plate deformation occurs out of phase with decollement propagation.

The dynamics of droplets in moist Rayleigh-Benard turbulence

NASA Astrophysics Data System (ADS)

Chandrakar, Kamal Kant; van der Voort, Dennis; Kinney, Greg; Cantrell, Will; Shaw, Raymond

2017-11-01

Clouds are an intricate part of the climate, and strongly influence atmospheric dynamics and radiative balances. While properties such as cloud albedo and precipitation rate are large scale effects, these properties are determined by dynamics on the microscale, such droplet sizes, liquid water content, etc. The growth of droplets from condensation is dependent on a multitude of parameters, such as aerosol concentration (nucleation sites) and turbulence (scalar fluctuations and coalescence). However, the precise mechanism behind droplet growth and clustering in a cloud environment is still unclear. In this investigation we use a facility called the Pi Chamber to generate a (miniature) cloud in a laboratory setting with known boundary conditions, such as aerosol concentration, temperature, and humidity. Through the use of particle imaging velocimetry (PIV) on the droplets generated in the cloud, we can investigate the dynamics of these cloud droplets in the convective (Rayleigh-Benard) turbulence generated through an induced temperature gradient. We show the influence of the temperature gradient and Froude number (gravity forces) on the changing turbulence anisotropy, large scale circulation, and small-scale dissipation rates. This work was supported by National Science Foundation Grant AGS-1623429.

Meso-scopic Densification in Brittle Granular Materials

NASA Astrophysics Data System (ADS)

Neal, William; Appleby-Thomas, Gareth; Collins, Gareth

2013-06-01

Particulate materials are ideally suited to shock absorbing applications due to the large amounts of energy required to deform their inherently complex meso-structure. Significant effort is being made to improve macro-scale material models to represent these atypical materials. On the long road towards achieving this capability, an important milestone would be to understand how particle densification mechanisms are affected by loading rate. In brittle particulate materials, the majority of densification is caused by particle fracture. Macro-scale quasi-static and dynamic compaction curves have been measured that show good qualitative agreement. There are, however, some differences that appear to be dependent on the loading rate that require further investigation. This study aims to investigate the difference in grain-fracture behavior between the quasi-static and shock loading response of brittle glass microsphere beds using a combination of quasi-static and dynamic loading techniques. Results from pressure-density measurements, sample recovery, and meso-scale hydrocode models (iSALE, an in-house simulation package) are discussed to explain the differences in particle densification mechanisms between the two loading rate regimes. Gratefully funded by AWE.plc.

A review of major progresses in mesoscale dynamic research in China since 1999

NASA Astrophysics Data System (ADS)

Zhou, Xiaoping; Lu, Hancheng; Ni, Yunqi; Tan, Zhemin

2004-06-01

Mesoscale research conducted by Chinese meteorologists during the past four years is reviewed. Advances in theoretical studies include (a) mesoscale quasi-balanced and semi-balanced dynamics, derived through scale analysis and the perturbation method which are suitable for describing mesoscale vortices; (b) subcritical instability and vortex-sheet instability; (c) frontal adjustment mechanism and the effect of topography on frontgenesis; and (d) slantwise vorticity development theories, the slantwise vortex equation, and moist potential vorticity (MPV) anomalies with precipitation-related heat and mass sinks and MPV impermeability theorem. From the MPV conservation viewpoint, the transformation mechanism between different scale weather systems is analyzed. Based on the data analysis, a new dew-point front near the periphery of the West Pacific subtropical high is identified. In the light of MPV theory and Q-vector theory, some events associated with torrential rain systems and severe storms are analyzed and diagnosed. Progress in mesoscale numerical simulation has been made in the development of meso-α, meso-β vortices, meso-γ-scale downbursts and precipitation produced by deep convective systems with MM5 and other mesoscale models.

Dislocation dynamics simulations of plasticity at small scales

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

Zhou, Caizhi

2010-01-01

As metallic structures and devices are being created on a dimension comparable to the length scales of the underlying dislocation microstructures, the mechanical properties of them change drastically. Since such small structures are increasingly common in modern technologies, there is an emergent need to understand the critical roles of elasticity, plasticity, and fracture in small structures. Dislocation dynamics (DD) simulations, in which the dislocations are the simulated entities, offer a way to extend length scales beyond those of atomistic simulations and the results from DD simulations can be directly compared with the micromechanical tests. The primary objective of this researchmore » is to use 3-D DD simulations to study the plastic deformation of nano- and micro-scale materials and understand the correlation between dislocation motion, interactions and the mechanical response. Specifically, to identify what critical events (i.e., dislocation multiplication, cross-slip, storage, nucleation, junction and dipole formation, pinning etc.) determine the deformation response and how these change from bulk behavior as the system decreases in size and correlate and improve our current knowledge of bulk plasticity with the knowledge gained from the direct observations of small-scale plasticity. Our simulation results on single crystal micropillars and polycrystalline thin films can march the experiment results well and capture the essential features in small-scale plasticity. Furthermore, several simple and accurate models have been developed following our simulation results and can reasonably predict the plastic behavior of small scale materials.« less

Scaling laws and deformation mechanisms of nanoporous copper under adiabatic uniaxial strain compression

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

Yuan, Fuping, E-mail: fpyuan@lnm.imech.ac.cn; Wu, Xiaolei, E-mail: xlwu@imech.ac.cn

2014-12-15

A series of large-scale molecular dynamics simulations were conducted to investigate the scaling laws and the related atomistic deformation mechanisms of Cu monocrystal samples containing randomly placed nanovoids under adiabatic uniaxial strain compression. At onset of yielding, plastic deformation is accommodated by dislocations emitted from void surfaces as shear loops. The collapse of voids are observed by continuous emissions of dislocations from void surfaces and their interactions with further plastic deformation. The simulation results also suggest that the effect modulus, the yield stress and the energy aborption density of samples under uniaxial strain are linearly proportional to the relative densitymore » ρ. Moreover, the yield stress, the average flow stress and the energy aborption density of samples with the same relative density show a strong dependence on the void diameter d, expressed by exponential relations with decay coefficients much higher than -1/2. The corresponding atomistic mechanisms for scaling laws of the relative density and the void diameter were also presented. The present results should provide insights for understanding deformation mechanisms of nanoporous metals under extreme conditions.« less

Underlying dynamics of typical fluctuations of an emerging market price index: The Heston model from minutes to months

NASA Astrophysics Data System (ADS)

Vicente, Renato; de Toledo, Charles M.; Leite, Vitor B. P.; Caticha, Nestor

2006-02-01

We investigate the Heston model with stochastic volatility and exponential tails as a model for the typical price fluctuations of the Brazilian São Paulo Stock Exchange Index (IBOVESPA). Raw prices are first corrected for inflation and a period spanning 15 years characterized by memoryless returns is chosen for the analysis. Model parameters are estimated by observing volatility scaling and correlation properties. We show that the Heston model with at least two time scales for the volatility mean reverting dynamics satisfactorily describes price fluctuations ranging from time scales larger than 20 min to 160 days. At time scales shorter than 20 min we observe autocorrelated returns and power law tails incompatible with the Heston model. Despite major regulatory changes, hyperinflation and currency crises experienced by the Brazilian market in the period studied, the general success of the description provided may be regarded as an evidence for a general underlying dynamics of price fluctuations at intermediate mesoeconomic time scales well approximated by the Heston model. We also notice that the connection between the Heston model and Ehrenfest urn models could be exploited for bringing new insights into the microeconomic market mechanics.

Dispersion of response times reveals cognitive dynamics.

PubMed

Holden, John G; Van Orden, Guy C; Turvey, Michael T

2009-04-01

Trial-to-trial variation in word-pronunciation times exhibits 1/f scaling. One explanation is that human performances are consequent on multiplicative interactions among interdependent processes-interaction dominant dynamics. This article describes simulated distributions of pronunciation times in a further test for multiplicative interactions and interdependence. Individual participant distributions of approximately 1,100 word-pronunciation times were successfully mimicked for each participant in combinations of lognormal and power-law behavior. Successful hazard function simulations generalized these results to establish interaction dominant dynamics, in contrast with component dominant dynamics, as a likely mechanism for cognitive activity. (c) 2009 APA, all rights reserved

Dispersion of Response Times Reveals Cognitive Dynamics

PubMed Central

Holden, John G.; Van Orden, Guy C.; Turvey, Michael T.

2013-01-01

Trial to trial variation in word pronunciation times exhibits 1/f scaling. One explanation is that human performances are consequent on multiplicative interactions among interdependent processes – interaction dominant dynamics. This article describes simulated distributions of pronunciation times in a further test for multiplicative interactions and interdependence. Individual participant distributions of ≈1100 word pronunciation times are successfully mimicked for each participant in combinations of lognormal and power law behavior. Successful hazard function simulations generalize these results to establish interaction dominant dynamics, in contrast with component dominant dynamics, as a likely mechanism for cognitive activity. PMID:19348544

Cytoskeletal mechanics: Structure and Dynamics

NASA Astrophysics Data System (ADS)

Bausch, Andreas

2008-03-01

The actin cytoskeleton, a dynamic network of semiflexible filaments and associated regulatory proteins, is responsible for the extraordinary viscoelastic properties of cells. Especially for cellular motility the controlled self assembly to defined structures and the dynamic reorganization on different time scales are of outstanding importance. A prominent example for the controlled self assembly are actin bundles: in many cytoskeletal processes cells rely on the tight control of the structural and mechanical properties of the actin bundles. Using an in vitro model system we show that size control relies on a mismatch between the helical structure of individual actin filaments and the packing symmetry within bundles. While such self assembled structure may evoke the picture of a static network the contrary is the case: the cytoskeleton is highly dynamic and a constant remodeling takes place in vivo. Such dynamic reorganization of the cytoskeleton relies on the non-static nature of single actin/ABP bonds. Here, we study the thermal and forced unbinding events of individual ABP in such in vitro networks. The binding kinetics of the transient crosslinkers determines the mechanical response of such networks -- in the linear as well in the non-linear regime. These effects are important prerequisites for the high adaptability of cells and at the same time might be the molecular mechanism employed by them for mechanosensing.

RISK ASSESSMENT OF MANUFACTURED NANOMATERIAL: MORE THAN JUST SIZE

EPA Science Inventory

Nanotechnology is a dynamic and enabling technology capable of producing nano-scale materials with unique electrical, catalytic, thermal, mechanical, or imaging properties for a variety of applications. Nanomaterials may display unique toxicological properties and routes of expos...

Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model

PubMed Central

Gigante, Guido; Deco, Gustavo; Marom, Shimon; Del Giudice, Paolo

2015-01-01

Cortical networks, in-vitro as well as in-vivo, can spontaneously generate a variety of collective dynamical events such as network spikes, UP and DOWN states, global oscillations, and avalanches. Though each of them has been variously recognized in previous works as expression of the excitability of the cortical tissue and the associated nonlinear dynamics, a unified picture of the determinant factors (dynamical and architectural) is desirable and not yet available. Progress has also been partially hindered by the use of a variety of statistical measures to define the network events of interest. We propose here a common probabilistic definition of network events that, applied to the firing activity of cultured neural networks, highlights the co-occurrence of network spikes, power-law distributed avalanches, and exponentially distributed ‘quasi-orbits’, which offer a third type of collective behavior. A rate model, including synaptic excitation and inhibition with no imposed topology, synaptic short-term depression, and finite-size noise, accounts for all these different, coexisting phenomena. We find that their emergence is largely regulated by the proximity to an oscillatory instability of the dynamics, where the non-linear excitable behavior leads to a self-amplification of activity fluctuations over a wide range of scales in space and time. In this sense, the cultured network dynamics is compatible with an excitation-inhibition balance corresponding to a slightly sub-critical regime. Finally, we propose and test a method to infer the characteristic time of the fatigue process, from the observed time course of the network’s firing rate. Unlike the model, possessing a single fatigue mechanism, the cultured network appears to show multiple time scales, signalling the possible coexistence of different fatigue mechanisms. PMID:26558616

Viscoelastic characterization of soft biological materials

NASA Astrophysics Data System (ADS)

Nayar, Vinod Timothy

Progressive and irreversible retinal diseases are among the primary causes of blindness in the United States, attacking the cells in the eye that transform environmental light into neural signals for the optic pathway. Medical implants designed to restore visual function to afflicted patients can cause mechanical stress and ultimately damage to the host tissues. Research shows that an accurate understanding of the mechanical properties of the biological tissues can reduce damage and lead to designs with improved safety and efficacy. Prior studies on the mechanical properties of biological tissues show characterization of these materials can be affected by environmental, length-scale, time, mounting, stiffness, size, viscoelastic, and methodological conditions. Using porcine sclera tissue, the effects of environmental, time, and mounting conditions are evaluated when using nanoindentation. Quasi-static tests are used to measure reduced modulus during extended exposure to phosphate-buffered saline (PBS), as well as the chemical and mechanical analysis of mounting the sample to a solid substrate using cyanoacrylate. The less destructive nature of nanoindentation tests allows for variance of tests within a single sample to be compared to the variance between samples. The results indicate that the environmental, time, and mounting conditions can be controlled for using modified nanoindentation procedures for biological samples and are in line with averages modulus values from previous studies but with increased precision. By using the quasi-static and dynamic characterization capabilities of the nanoindentation setup, the additional stiffness and viscoelastic variables are measured. Different quasi-static control methods were evaluated along with maximum load parameters and produced no significant difference in reported reduced modulus values. Dynamic characterization tests varied frequency and quasi-static load, showing that the agar could be modeled as a linearly elastic material. The effects of sample stiffness were evaluated by testing both the quasi-static and dynamic mechanical properties of different concentration agar samples, ranging from 0.5% to 5.0%. The dynamic nanoindentation protocol showed some sensitivity to sample stiffness, but characterization remained consistently applicable to soft biological materials. Comparative experiments were performed on both 0.5% and 5.0% agar as well as porcine eye tissue samples using published dynamic macrocompression standards. By comparing these new tests to those obtained with nanoindentation, the effects due to length-scale, stiffness, size, viscoelastic, and methodological conditions are evaluated. Both testing methodologies can be adapted for the environmental and mounting conditions, but the limitations of standardized macro-scale tests are explored. The factors affecting mechanical characterization of soft and thin viscoelastic biological materials are researched and a comprehensive protocol is presented. This work produces material mechanical properties for use in improving future medical implant designs on a wide variety of biological tissue and materials.

Seeing the Song: Left Auditory Structures May Track Auditory-Visual Dynamic Alignment

PubMed Central

Mossbridge, Julia A.; Grabowecky, Marcia; Suzuki, Satoru

2013-01-01

Auditory and visual signals generated by a single source tend to be temporally correlated, such as the synchronous sounds of footsteps and the limb movements of a walker. Continuous tracking and comparison of the dynamics of auditory-visual streams is thus useful for the perceptual binding of information arising from a common source. Although language-related mechanisms have been implicated in the tracking of speech-related auditory-visual signals (e.g., speech sounds and lip movements), it is not well known what sensory mechanisms generally track ongoing auditory-visual synchrony for non-speech signals in a complex auditory-visual environment. To begin to address this question, we used music and visual displays that varied in the dynamics of multiple features (e.g., auditory loudness and pitch; visual luminance, color, size, motion, and organization) across multiple time scales. Auditory activity (monitored using auditory steady-state responses, ASSR) was selectively reduced in the left hemisphere when the music and dynamic visual displays were temporally misaligned. Importantly, ASSR was not affected when attentional engagement with the music was reduced, or when visual displays presented dynamics clearly dissimilar to the music. These results appear to suggest that left-lateralized auditory mechanisms are sensitive to auditory-visual temporal alignment, but perhaps only when the dynamics of auditory and visual streams are similar. These mechanisms may contribute to correct auditory-visual binding in a busy sensory environment. PMID:24194873

Modeling Impact-induced Failure of Polysilicon MEMS: A Multi-scale Approach.

PubMed

Mariani, Stefano; Ghisi, Aldo; Corigliano, Alberto; Zerbini, Sarah

2009-01-01

Failure of packaged polysilicon micro-electro-mechanical systems (MEMS) subjected to impacts involves phenomena occurring at several length-scales. In this paper we present a multi-scale finite element approach to properly allow for: (i) the propagation of stress waves inside the package; (ii) the dynamics of the whole MEMS; (iii) the spreading of micro-cracking in the failing part(s) of the sensor. Through Monte Carlo simulations, some effects of polysilicon micro-structure on the failure mode are elucidated.

Molecular dynamics simulations of graphoepitaxy of organic semiconductors, sexithiophene, and pentacene: Molecular-scale mechanisms of organic graphoepitaxy

NASA Astrophysics Data System (ADS)

Ikeda, Susumu

2018-03-01

Molecular dynamics (MD) simulations of the organic semiconductors α-sexithiophene (6T) and pentacene were carried out to clarify the mechanism of organic graphoepitaxy at the molecular level. First, the models of the grooved substrates were made and the surfaces of the inside of the grooves were modified with -OH or -OSi(CH3)3, making the surfaces hydrophilic or hydrophobic. By the MD simulations of 6T, it was found that three stable azimuthal directions exist (0, ˜45, and 90° the angle that the c-axis makes with the groove), being consistent with experimental results. MD simulations of deposition processes of 6T and pentacene were also carried out, and pentacene molecules showed the spontaneous formation of herringbone packing during deposition. Some pentacene molecules stood on the surface and formed a cluster whose a-axis was parallel to the groove. It is expected that a deep understanding of the molecular-scale mechanisms will lead graphoepitaxy to practical applications, improving the performance of organic devices.

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.

PubMed

Pasi, Marco; Lavery, Richard; Ceres, Nicoletta

2013-01-08

We present a coarse-grain protein model PaLaCe (Pasi-Lavery-Ceres) that has been developed principally to allow fast computational studies of protein mechanics and to clarify the links between mechanics and function. PaLaCe uses a two-tier protein representation with one to three pseudoatoms representing each amino acid for the main nonbonded interactions, combined with atomic-scale peptide groups and some side chain atoms to allow the explicit representation of backbone hydrogen bonds and to simplify the treatment of bonded interactions. The PaLaCe force field is composed of physics-based terms, parametrized using Boltzmann inversion of conformational probability distributions derived from a protein structure data set, and iteratively refined to reproduce the experimental distributions. PaLaCe has been implemented in the MMTK simulation package and can be used for energy minimization, normal mode calculations, and molecular or stochastic dynamics. We present simulations with PaLaCe that test its ability to maintain stable structures for folded proteins, reproduce their dynamic fluctuations, and correctly model large-scale, force-induced conformational changes.

Controlling shockwave dynamics using architecture in periodic porous materials

DOE PAGES

Branch, Brittany; Ionita, Axinte; Clements, Bradford E.; ...

2017-04-07

Additive manufacturing (AM) is an attractive approach for the design and fabrication of structures capable of achieving controlled mechanical response of the underlying deformation mechanisms. While there are numerous examples illustrating how the quasi-static mechanical responses of polymer foams have been tailored by additive manufacturing, there is limited understanding of the response of these materials under shockwave compression. Dynamic compression experiments coupled with time-resolved X-ray imaging were performed to obtain insights into the in situ evolution of shockwave coupling to porous, periodic polymer foams. We further demonstrate shock wave modulation or “spatially graded-flow” in shock-driven experiments via the spatial controlmore » of layer symmetries afforded by additive manufacturing techniques at the micron scale.« less

Statistical physics approach to earthquake occurrence and forecasting

NASA Astrophysics Data System (ADS)

de Arcangelis, Lucilla; Godano, Cataldo; Grasso, Jean Robert; Lippiello, Eugenio

2016-04-01

There is striking evidence that the dynamics of the Earth crust is controlled by a wide variety of mutually dependent mechanisms acting at different spatial and temporal scales. The interplay of these mechanisms produces instabilities in the stress field, leading to abrupt energy releases, i.e., earthquakes. As a consequence, the evolution towards instability before a single event is very difficult to monitor. On the other hand, collective behavior in stress transfer and relaxation within the Earth crust leads to emergent properties described by stable phenomenological laws for a population of many earthquakes in size, time and space domains. This observation has stimulated a statistical mechanics approach to earthquake occurrence, applying ideas and methods as scaling laws, universality, fractal dimension, renormalization group, to characterize the physics of earthquakes. In this review we first present a description of the phenomenological laws of earthquake occurrence which represent the frame of reference for a variety of statistical mechanical models, ranging from the spring-block to more complex fault models. Next, we discuss the problem of seismic forecasting in the general framework of stochastic processes, where seismic occurrence can be described as a branching process implementing space-time-energy correlations between earthquakes. In this context we show how correlations originate from dynamical scaling relations between time and energy, able to account for universality and provide a unifying description for the phenomenological power laws. Then we discuss how branching models can be implemented to forecast the temporal evolution of the earthquake occurrence probability and allow to discriminate among different physical mechanisms responsible for earthquake triggering. In particular, the forecasting problem will be presented in a rigorous mathematical framework, discussing the relevance of the processes acting at different temporal scales for different levels of prediction. In this review we also briefly discuss how the statistical mechanics approach can be applied to non-tectonic earthquakes and to other natural stochastic processes, such as volcanic eruptions and solar flares.

Identifying time scales for violation/preservation of Stokes-Einstein relation in supercooled water

PubMed Central

Kawasaki, Takeshi; Kim, Kang

2017-01-01

The violation of the Stokes-Einstein (SE) relation D ~ (η/T)−1 between the shear viscosity η and the translational diffusion constant D at temperature T is of great importance for characterizing anomalous dynamics of supercooled water. Determining which time scales play key roles in the SE violation remains elusive without the measurement of η. We provide comprehensive simulation results of the dynamic properties involving η and D in the TIP4P/2005 supercooled water. This enabled the thorough identification of the appropriate time scales for the SE relation Dη/T. In particular, it is demonstrated that the temperature dependence of various time scales associated with structural relaxation, hydrogen bond breakage, stress relaxation, and dynamic heterogeneities can be definitely classified into only two classes. That is, we propose the generalized SE relations that exhibit “violation” or “preservation.” The classification depends on the examined time scales that are coupled or decoupled with the diffusion. On the basis of the classification, we explain the physical origins of the violation in terms of the increase in the plateau modulus and the nonexponentiality of stress relaxation. This implies that the mechanism of SE violation is attributed to the attained solidity upon supercooling, which is in accord with the growth of non-Gaussianity and spatially heterogeneous dynamics. PMID:28835918

Dynamic and impact contact mechanics of geologic materials: Grain-scale experiments and modeling

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

Cole, David M.; Hopkins, Mark A.; Ketcham, Stephen A.

2013-06-18

High fidelity treatments of the generation and propagation of seismic waves in naturally occurring granular materials is becoming more practical given recent advancements in our ability to model complex particle shapes and their mechanical interaction. Of particular interest are the grain-scale processes that are activated by impact events and the characteristics of force transmission through grain contacts. To address this issue, we have developed a physics based approach that involves laboratory experiments to quantify the dynamic contact and impact behavior of granular materials and incorporation of the observed behavior indiscrete element models. The dynamic experiments do not involve particle damagemore » and emphasis is placed on measured values of contact stiffness and frictional loss. The normal stiffness observed in dynamic contact experiments at low frequencies (e.g., 10 Hz) are shown to be in good agreement with quasistatic experiments on quartz sand. The results of impact experiments - which involve moderate to extensive levels of particle damage - are presented for several types of naturally occurring granular materials (several quartz sands, magnesite and calcium carbonate ooids). Implementation of the experimental findings in discrete element models is discussed and the results of impact simulations involving up to 5 Multiplication-Sign 105 grains are presented.« less

Dissociable effects of local inhibitory and excitatory theta-burst stimulation on large-scale brain dynamics

PubMed Central

Sale, Martin V.; Lord, Anton; Zalesky, Andrew; Breakspear, Michael; Mattingley, Jason B.

2015-01-01

Normal brain function depends on a dynamic balance between local specialization and large-scale integration. It remains unclear, however, how local changes in functionally specialized areas can influence integrated activity across larger brain networks. By combining transcranial magnetic stimulation with resting-state functional magnetic resonance imaging, we tested for changes in large-scale integration following the application of excitatory or inhibitory stimulation on the human motor cortex. After local inhibitory stimulation, regions encompassing the sensorimotor module concurrently increased their internal integration and decreased their communication with other modules of the brain. There were no such changes in modular dynamics following excitatory stimulation of the same area of motor cortex nor were there changes in the configuration and interactions between core brain hubs after excitatory or inhibitory stimulation of the same area. These results suggest the existence of selective mechanisms that integrate local changes in neural activity, while preserving ongoing communication between brain hubs. PMID:25717162

Elastic Multi-scale Mechanisms: Computation and Biological Evolution.

PubMed

Diaz Ochoa, Juan G

2018-01-01

Explanations based on low-level interacting elements are valuable and powerful since they contribute to identify the key mechanisms of biological functions. However, many dynamic systems based on low-level interacting elements with unambiguous, finite, and complete information of initial states generate future states that cannot be predicted, implying an increase of complexity and open-ended evolution. Such systems are like Turing machines, that overlap with dynamical systems that cannot halt. We argue that organisms find halting conditions by distorting these mechanisms, creating conditions for a constant creativity that drives evolution. We introduce a modulus of elasticity to measure the changes in these mechanisms in response to changes in the computed environment. We test this concept in a population of predators and predated cells with chemotactic mechanisms and demonstrate how the selection of a given mechanism depends on the entire population. We finally explore this concept in different frameworks and postulate that the identification of predictive mechanisms is only successful with small elasticity modulus.

Surfing on Protein Waves: Proteophoresis as a Mechanism for Bacterial Genome Partitioning

NASA Astrophysics Data System (ADS)

Walter, J.-C.; Dorignac, J.; Lorman, V.; Rech, J.; Bouet, J.-Y.; Nollmann, M.; Palmeri, J.; Parmeggiani, A.; Geniet, F.

2017-07-01

Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component machinery, fueled by adenosine triphosphate, called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or "volumetric" chemophoresis, force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation, and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a nonlinear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and traveling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry.

Dynamically consistent parameterization of mesoscale eddies. Part III: Deterministic approach

NASA Astrophysics Data System (ADS)

Berloff, Pavel

2018-07-01

This work continues development of dynamically consistent parameterizations for representing mesoscale eddy effects in non-eddy-resolving and eddy-permitting ocean circulation models and focuses on the classical double-gyre problem, in which the main dynamic eddy effects maintain eastward jet extension of the western boundary currents and its adjacent recirculation zones via eddy backscatter mechanism. Despite its fundamental importance, this mechanism remains poorly understood, and in this paper we, first, study it and, then, propose and test its novel parameterization. We start by decomposing the reference eddy-resolving flow solution into the large-scale and eddy components defined by spatial filtering, rather than by the Reynolds decomposition. Next, we find that the eastward jet and its recirculations are robustly present not only in the large-scale flow itself, but also in the rectified time-mean eddies, and in the transient rectified eddy component, which consists of highly anisotropic ribbons of the opposite-sign potential vorticity anomalies straddling the instantaneous eastward jet core and being responsible for its continuous amplification. The transient rectified component is separated from the flow by a novel remapping method. We hypothesize that the above three components of the eastward jet are ultimately driven by the small-scale transient eddy forcing via the eddy backscatter mechanism, rather than by the mean eddy forcing and large-scale nonlinearities. We verify this hypothesis by progressively turning down the backscatter and observing the induced flow anomalies. The backscatter analysis leads us to formulating the key eddy parameterization hypothesis: in an eddy-permitting model at least partially resolved eddy backscatter can be significantly amplified to improve the flow solution. Such amplification is a simple and novel eddy parameterization framework implemented here in terms of local, deterministic flow roughening controlled by single parameter. We test the parameterization skills in an hierarchy of non-eddy-resolving and eddy-permitting modifications of the original model and demonstrate, that indeed it can be highly efficient for restoring the eastward jet extension and its adjacent recirculation zones. The new deterministic parameterization framework not only combines remarkable simplicity with good performance but also is dynamically transparent, therefore, it provides a powerful alternative to the common eddy diffusion and emerging stochastic parameterizations.

3D Realistic Modeling of the Interaction of Quiet-Sun Magnetic Fields with the Chromosphere

NASA Technical Reports Server (NTRS)

Kitiashvili, I. N.; Kosovichev, A. G.; Mansour, N. N.; Wray, A. A.

2017-01-01

High-resolution observations and 3D simulations suggest that a local dynamo operates near the surface and produces ubiquitous small-scale magnetic elements, thus contributing to the magnetic carpet in the photosphere and to the magnetic structure and dynamics of the solar atmosphere. It appears that the traditional mechanisms of chromospheric energy and mass transport by acoustic waves and shocks are likely to play a secondary role; instead, the primary drivers in the energetics and dynamics of the chromosphere and transition region are small-scale, previously unresolved, quiet-Sun magnetic fields. These fields appear as ubiquitous, rapidly changing (on the scale of a few seconds), tiny magnetic loops and magnetized vortex tubes. Questions then arise about their origin and dynamics in the chromosphere, their links to magnetic fields in the photosphere, and their role in the energy storage and exchange between subsurface layers and the chromosphere. In the talk we will present results of 3D radiative MHD simulations obtained with the StellarBox code and discuss the energetics and dynamical interlinks between the subphotospheric layers and low chromosphere, their effects on the structure of the chromosphere, and signatures of the fine-scale magnetic features in high-resolution spectro-polarimetric observations.

Forecasting of magnitude and duration of currency crises based on the analysis of distortions of fractal scaling in exchange rate fluctuations

NASA Astrophysics Data System (ADS)

Uritskaya, Olga Y.

2005-05-01

Results of fractal stability analysis of daily exchange rate fluctuations of more than 30 floating currencies for a 10-year period are presented. It is shown for the first time that small- and large-scale dynamical instabilities of national monetary systems correlate with deviations of the detrended fluctuation analysis (DFA) exponent from the value 1.5 predicted by the efficient market hypothesis. The observed dependence is used for classification of long-term stability of floating exchange rates as well as for revealing various forms of distortion of stable currency dynamics prior to large-scale crises. A normal range of DFA exponents consistent with crisis-free long-term exchange rate fluctuations is determined, and several typical scenarios of unstable currency dynamics with DFA exponents fluctuating beyond the normal range are identified. It is shown that monetary crashes are usually preceded by prolonged periods of abnormal (decreased or increased) DFA exponent, with the after-crash exponent tending to the value 1.5 indicating a more reliable exchange rate dynamics. Statistically significant regression relations (R=0.99, p<0.01) between duration and magnitude of currency crises and the degree of distortion of monofractal patterns of exchange rate dynamics are found. It is demonstrated that the parameters of these relations characterizing small- and large-scale crises are nearly equal, which implies a common instability mechanism underlying these events. The obtained dependences have been used as a basic ingredient of a forecasting technique which provided correct in-sample predictions of monetary crisis magnitude and duration over various time scales. The developed technique can be recommended for real-time monitoring of dynamical stability of floating exchange rate systems and creating advanced early-warning-system models for currency crisis prevention.

High-frequency microrheology reveals cytoskeleton dynamics in living cells

NASA Astrophysics Data System (ADS)

Rigato, Annafrancesca; Miyagi, Atsushi; Scheuring, Simon; Rico, Felix

2017-08-01

Living cells are viscoelastic materials, dominated by an elastic response on timescales longer than a millisecond. On shorter timescales, the dynamics of individual cytoskeleton filaments are expected to emerge, but active microrheology measurements on cells accessing this regime are scarce. Here, we develop high-frequency microrheology experiments to probe the viscoelastic response of living cells from 1 Hz to 100 kHz. We report the viscoelasticity of different cell types under cytoskeletal drug treatments. On previously inaccessible short timescales, cells exhibit rich viscoelastic responses that depend on the state of the cytoskeleton. Benign and malignant cancer cells revealed remarkably different scaling laws at high frequencies, providing a unique mechanical fingerprint. Microrheology over a wide dynamic range--up to the frequency characterizing the molecular components--provides a mechanistic understanding of cell mechanics.

Geometrical influence of a deposited particle on the performance of bridged carbon nanotube-based mass detectors

NASA Astrophysics Data System (ADS)

Ali-Akbari, H. R.; Ceballes, S.; Abdelkefi, A.

2017-10-01

A nonlocal continuum-based model is derived to simulate the dynamic behavior of bridged carbon nanotube-based nano-scale mass detectors. The carbon nanotube (CNT) is modeled as an elastic Euler-Bernoulli beam considering von-Kármán type geometric nonlinearity. In order to achieve better accuracy in characterization of the CNTs, the geometrical properties of an attached nano-scale particle are introduced into the model by its moment of inertia with respect to the central axis of the beam. The inter-atomic long-range interactions within the structure of the CNT are incorporated into the model using Eringen's nonlocal elastic field theory. In this model, the mass can be deposited along an arbitrary length of the CNT. After deriving the full nonlinear equations of motion, the natural frequencies and corresponding mode shapes are extracted based on a linear eigenvalue problem analysis. The results show that the geometry of the attached particle has a significant impact on the dynamic behavior of the CNT-based mechanical resonator, especially, for those with small aspect ratios. The developed model and analysis are beneficial for nano-scale mass identification when a CNT-based mechanical resonator is utilized as a small-scale bio-mass sensor and the deposited particles are those, such as proteins, enzymes, cancer cells, DNA and other nano-scale biological objects with different and complex shapes.

Rapid Neocortical Dynamics: Cellular and Network Mechanisms

PubMed Central

Haider, Bilal; McCormick, David A.

2011-01-01

The highly interconnected local and large-scale networks of the neocortical sheet rapidly and dynamically modulate their functional connectivity according to behavioral demands. This basic operating principle of the neocortex is mediated by the continuously changing flow of excitatory and inhibitory synaptic barrages that not only control participation of neurons in networks but also define the networks themselves. The rapid control of neuronal responsiveness via synaptic bombardment is a fundamental property of cortical dynamics that may provide the basis of diverse behaviors, including sensory perception, motor integration, working memory, and attention. PMID:19409263

Substructured multibody molecular dynamics.

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

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Dynamic heterogeneity in crossover spin facilitated model of supercooled liquid and fractional Stokes-Einstein relation

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

Choi, Seo-Woo; Kim, Soree; Jung, YounJoon, E-mail: yjjung@snu.ac.kr

Kinetically constrained models have gained much interest as models that assign the origins of interesting dynamic properties of supercooled liquids to dynamical facilitation mechanisms that have been revealed in many experiments and numerical simulations. In this work, we investigate the dynamic heterogeneity in the fragile-to-strong liquid via Monte Carlo method using the model that linearly interpolates between the strong liquid-like behavior and the fragile liquid-like behavior by an asymmetry parameter b. When the asymmetry parameter is sufficiently small, smooth fragile-to-strong transition is observed both in the relaxation time and the diffusion constant. Using these physical quantities, we investigate fractional Stokes-Einsteinmore » relations observed in this model. When b is fixed, the system shows constant power law exponent under the temperature change, and the exponent has the value between that of the Frederickson-Andersen model and the East model. Furthermore, we investigate the dynamic length scale of our systems and also find the crossover relation between the relaxation time. We ascribe the competition between energetically favored symmetric relaxation mechanism and entropically favored asymmetric relaxation mechanism to the fragile-to-strong crossover behavior.« less

Synaptic Scaling in Combination with Many Generic Plasticity Mechanisms Stabilizes Circuit Connectivity

PubMed Central

Tetzlaff, Christian; Kolodziejski, Christoph; Timme, Marc; Wörgötter, Florentin

2011-01-01

Synaptic scaling is a slow process that modifies synapses, keeping the firing rate of neural circuits in specific regimes. Together with other processes, such as conventional synaptic plasticity in the form of long term depression and potentiation, synaptic scaling changes the synaptic patterns in a network, ensuring diverse, functionally relevant, stable, and input-dependent connectivity. How synaptic patterns are generated and stabilized, however, is largely unknown. Here we formally describe and analyze synaptic scaling based on results from experimental studies and demonstrate that the combination of different conventional plasticity mechanisms and synaptic scaling provides a powerful general framework for regulating network connectivity. In addition, we design several simple models that reproduce experimentally observed synaptic distributions as well as the observed synaptic modifications during sustained activity changes. These models predict that the combination of plasticity with scaling generates globally stable, input-controlled synaptic patterns, also in recurrent networks. Thus, in combination with other forms of plasticity, synaptic scaling can robustly yield neuronal circuits with high synaptic diversity, which potentially enables robust dynamic storage of complex activation patterns. This mechanism is even more pronounced when considering networks with a realistic degree of inhibition. Synaptic scaling combined with plasticity could thus be the basis for learning structured behavior even in initially random networks. PMID:22203799

A combined molecular dynamics/micromechanics/finite element approach for multiscale constitutive modeling of nanocomposites with interface effects

NASA Astrophysics Data System (ADS)

Yang, B. J.; Shin, H.; Lee, H. K.; Kim, H.

2013-12-01

We introduce a multiscale framework based on molecular dynamic (MD) simulation, micromechanics, and finite element method (FEM). A micromechanical model, which considers influences of the interface properties, nanoparticle (NP) size, and microcracks, is developed. Then, we perform MD simulations to characterize the mechanical properties of the nanocomposite system (silica/nylon 6) with varying volume fraction and size of NPs. By comparing the MD with micromechanics results, intrinsic physical properties at interfacial region are derived. Finally, we implement the developed model in the FEM code with the derived interfacial parameters, and predict the mechanical behavior of the nanocomposite at the macroscopic scale.

A comparison of some static and dynamic mechanical properties of 18 x 5.5 and 49 x 17 type 7 aircraft tires as measured by three test facilities

NASA Technical Reports Server (NTRS)

Dodge, R. N.; Clark, S. K.

1981-01-01

The properties were measured during static, slow rolling, and high-speed tests, and comparisons were made between data as acquired on indoor drum dynamometers and on an outdoor test track. In addition, mechanical properties were also obtained from scale model tires and compared with corresponding properties from full-size tires. While the tests covered a wide range of tire properties, results seem to indicate that speed effects are not large, scale models may be used for obtaining some but not all tire properties, and that predictive equations developed in NASA TR R-64 are still useful in estimating most mechanical properties.

Transport Phenomena in Fluid Dynamics: Matrix Heat Exchangers and Their Applications in Energy Systems

DTIC Science & Technology

2009-07-01

presented a summary of recent research on boiling in microchannels . He addressed the topics of macro scale versus micro scale heat transfer , two phase...flow regime, flow boiling 14 heat transfer results for microchannels , heat transfer mechanisms in microchannels , and flow boiling models for... Heat Transfer Boiling In Minichannel And Microchannel Flow Passages Of Compact Evaporators, Keynote Lecture Presented at the Engineering Foundation

Exploring Entrainment Patterns of Human Emotion in Social Media

PubMed Central

Luo, Chuan; Zhang, Zhu

2016-01-01

Emotion entrainment, which is generally defined as the synchronous convergence of human emotions, performs many important social functions. However, what the specific mechanisms of emotion entrainment are beyond in-person interactions, and how human emotions evolve under different entrainment patterns in large-scale social communities, are still unknown. In this paper, we aim to examine the massive emotion entrainment patterns and understand the underlying mechanisms in the context of social media. As modeling emotion dynamics on a large scale is often challenging, we elaborate a pragmatic framework to characterize and quantify the entrainment phenomenon. By applying this framework on the datasets from two large-scale social media platforms, we find that the emotions of online users entrain through social networks. We further uncover that online users often form their relations via dual entrainment, while maintain it through single entrainment. Remarkably, the emotions of online users are more convergent in nonreciprocal entrainment. Building on these findings, we develop an entrainment augmented model for emotion prediction. Experimental results suggest that entrainment patterns inform emotion proximity in dyads, and encoding their associations promotes emotion prediction. This work can further help us to understand the underlying dynamic process of large-scale online interactions and make more reasonable decisions regarding emergency situations, epidemic diseases, and political campaigns in cyberspace. PMID:26953692

Exploring Entrainment Patterns of Human Emotion in Social Media.

PubMed

He, Saike; Zheng, Xiaolong; Zeng, Daniel; Luo, Chuan; Zhang, Zhu

2016-01-01

Emotion entrainment, which is generally defined as the synchronous convergence of human emotions, performs many important social functions. However, what the specific mechanisms of emotion entrainment are beyond in-person interactions, and how human emotions evolve under different entrainment patterns in large-scale social communities, are still unknown. In this paper, we aim to examine the massive emotion entrainment patterns and understand the underlying mechanisms in the context of social media. As modeling emotion dynamics on a large scale is often challenging, we elaborate a pragmatic framework to characterize and quantify the entrainment phenomenon. By applying this framework on the datasets from two large-scale social media platforms, we find that the emotions of online users entrain through social networks. We further uncover that online users often form their relations via dual entrainment, while maintain it through single entrainment. Remarkably, the emotions of online users are more convergent in nonreciprocal entrainment. Building on these findings, we develop an entrainment augmented model for emotion prediction. Experimental results suggest that entrainment patterns inform emotion proximity in dyads, and encoding their associations promotes emotion prediction. This work can further help us to understand the underlying dynamic process of large-scale online interactions and make more reasonable decisions regarding emergency situations, epidemic diseases, and political campaigns in cyberspace.

Ordering of the nanoscale step morphology as a mechanism for droplet self-propulsion.

PubMed

Hilner, Emelie; Zakharov, Alexei A; Schulte, Karina; Kratzer, Peter; Andersen, Jesper N; Lundgren, Edvin; Mikkelsen, Anders

2009-07-01

We establish a new mechanism for self-propelled motion of droplets, in which ordering of the nanoscale step morphology by sublimation beneath the droplets themselves acts to drive them perpendicular and up the surface steps. The mechanism is demonstrated and explored for Ga droplets on GaP(111)B, using several experimental techniques allowing studies of the structure and dynamics from micrometers to the atomic scale. We argue that the simple assumptions underlying the propulsion mechanism make it relevant for a wide variety of materials systems.

Microtubule Dynamics Scale with Cell Size to Set Spindle Length and Assembly Timing.

PubMed

Lacroix, Benjamin; Letort, Gaëlle; Pitayu, Laras; Sallé, Jérémy; Stefanutti, Marine; Maton, Gilliane; Ladouceur, Anne-Marie; Canman, Julie C; Maddox, Paul S; Maddox, Amy S; Minc, Nicolas; Nédélec, François; Dumont, Julien

2018-05-21

Successive cell divisions during embryonic cleavage create increasingly smaller cells, so intracellular structures must adapt accordingly. Mitotic spindle size correlates with cell size, but the mechanisms for this scaling remain unclear. Using live cell imaging, we analyzed spindle scaling during embryo cleavage in the nematode Caenorhabditis elegans and sea urchin Paracentrotus lividus. We reveal a common scaling mechanism, where the growth rate of spindle microtubules scales with cell volume, which explains spindle shortening. Spindle assembly timing is, however, constant throughout successive divisions. Analyses in silico suggest that controlling the microtubule growth rate is sufficient to scale spindle length and maintain a constant assembly timing. We tested our in silico predictions to demonstrate that modulating cell volume or microtubule growth rate in vivo induces a proportional spindle size change. Our results suggest that scalability of the microtubule growth rate when cell size varies adapts spindle length to cell volume. Copyright © 2018 Elsevier Inc. All rights reserved.

Shock wave energy dissipation behavior (SWED) in Network forming ionic liquids (NILs): A Molecular dynamics study

NASA Astrophysics Data System (ADS)

Guda Vishnu, Karthik; Strachan, Alejandro

2017-06-01

SWED materials play a crucial role in protecting both personnel and structures in close proximity to blasts or ballistic impact. Exposure to shock waves with intensities as low as 1 MPa can cause brain injury in personnel and, hence, it is extremely important to understand the mechanisms operating in SWED materials and help design improved formulations. Recent experimental studies show that NILs containing di-ammonium cations and citrate anions with glass transition temperatures (Tg) below room temperature exhibit shockwave absorption characteristics that outperform polyurea (PU), a benchmark SWED assessment material. The experimentalists further hypothesized that the increased SWED ability in NILs with longer side chains (in di-ammonium cation) is due to a permanent structural ordering and nano-scale segregation. We use molecular dynamics simulations with the Dreiding force field to study shock propagation mechanisms in NILs. Shock propagation mechanisms in these materials are explored by performing both Hugoniostat and large scale non-equilibrium molecular dynamics (NEMD) simulations at 300 K. The simulation results show that the NIL 5-6 (5 C atoms (back bone) and 6 C atoms (side chain)) attenuates shocks better than NIL 5-3 (3 C atoms (side chain) and higher Tg) and PMMA in agreement with experimental observation. The simulations show that under shock loading the structures lose long range order; we find no evidence of nano-segregation nor or permanent structural changes.

Metabolic dynamics in skeletal muscle during acute reduction in blood flow and oxygen supply to mitochondria: in-silico studies using a multi-scale, top-down integrated model.

PubMed

Dash, Ranjan K; Li, Yanjun; Kim, Jaeyeon; Beard, Daniel A; Saidel, Gerald M; Cabrera, Marco E

2008-09-09

Control mechanisms of cellular metabolism and energetics in skeletal muscle that may become evident in response to physiological stresses such as reduction in blood flow and oxygen supply to mitochondria can be quantitatively understood using a multi-scale computational model. The analysis of dynamic responses from such a model can provide insights into mechanisms of metabolic regulation that may not be evident from experimental studies. For the purpose, a physiologically-based, multi-scale computational model of skeletal muscle cellular metabolism and energetics was developed to describe dynamic responses of key chemical species and reaction fluxes to muscle ischemia. The model, which incorporates key transport and metabolic processes and subcellular compartmentalization, is based on dynamic mass balances of 30 chemical species in both capillary blood and tissue cells (cytosol and mitochondria) domains. The reaction fluxes in cytosol and mitochondria are expressed in terms of a general phenomenological Michaelis-Menten equation involving the compartmentalized energy controller ratios ATP/ADP and NADH/NAD(+). The unknown transport and reaction parameters in the model are estimated simultaneously by minimizing the differences between available in vivo experimental data on muscle ischemia and corresponding model outputs in coupled with the resting linear flux balance constraints using a robust, nonlinear, constrained-based, reduced gradient optimization algorithm. With the optimal parameter values, the model is able to simulate dynamic responses to reduced blood flow and oxygen supply to mitochondria associated with muscle ischemia of several key metabolite concentrations and metabolic fluxes in the subcellular cytosolic and mitochondrial compartments, some that can be measured and others that can not be measured with the current experimental techniques. The model can be applied to test complex hypotheses involving dynamic regulation of cellular metabolism and energetics in skeletal muscle during physiological stresses such as ischemia, hypoxia, and exercise.

Statistical mechanical approach to secondary processes and structural relaxation in glasses and glass formers: a leading model to describe the onset of Johari-Goldstein processes and their relationship with fully cooperative processes.

PubMed

Crisanti, A; Leuzzi, L; Paoluzzi, M

2011-09-01

The interrelation of dynamic processes active on separated time-scales in glasses and viscous liquids is investigated using a model displaying two time-scale bifurcations both between fast and secondary relaxation and between secondary and structural relaxation. The study of the dynamics allows for predictions on the system relaxation above the temperature of dynamic arrest in the mean-field approximation, that are compared with the outcomes of the equations of motion directly derived within the Mode Coupling Theory (MCT) for under-cooled viscous liquids. By varying the external thermodynamic parameters, a wide range of phenomenology can be represented, from a very clear separation of structural and secondary peak in the susceptibility loss to excess wing structures.

Dynamical Nuclear Magnetic Resonance Imaging of Micron-scale Liquids

NASA Astrophysics Data System (ADS)

Sixta, Aimee; Choate, Alexandra; Maeker, Jake; Bogat, Sophia; Tennant, Daniel; Mozaffari, Shirin; Markert, John

We report our efforts in the development of Nuclear Magnetic Resonance Force Microscopy (NMRFM) for dynamical imaging of liquid media at the micron scale. Our probe contains microfluidic samples sealed in thin-walled (µm) quartz tubes, with a micro-oscillator sensor nearby in vacuum to maintain its high mechanical resonance quality factor. Using 10 µm spherical permalloy magnets at the oscillator tips, a 3D T1-resolved image of spin density can be obtained by reconstruction from our magnetostatics-modelled resonance slices; as part of this effort, we are exploring single-shot T1 measurements for faster dynamical imaging. We aim to further enhance imaging by using a 2 ω technique to eliminate artifact signals during the cyclic inversion of nuclear spins. The ultimate intent of these efforts is to perform magnetic resonance imaging of individual biological cells.

A Summary of the Naval Postgraduate School Research Program.

DTIC Science & Technology

1979-09-30

Research (M. G. Sovereign) 116 Review of COMWTH II Model (M. G. Sovereign and J. K. Arima ) 117 Optimization of Combat Dynamics (J. G. Taylor) 118...Studies (R. L. Elsberry) 291 4 Numerical Models of Ocean Circulation and Climate Interaction--A Review (R. L. Haney) 292 Numerical Studies of the Dynamics... climatic numerical models to investigate the various mechan- isms pertinent to the large-scale interaction between tropi- cal atmosphere and oceans. Among

Vibrational energy transfer between carbon nanotubes and nonaqueous solvents: a molecular dynamics study.

PubMed

Nelson, Tammie R; Chaban, Vitaly V; Prezhdo, Victor V; Prezhdo, Oleg V

2011-05-12

We report molecular dynamics (MD) simulation of energy exchange between single-walled carbon nanotubes (CNTs) and two aprotic solvents, acetonitrile and cyclohexane. Following our earlier study of hydrated CNTs, we find that the time scales and molecular mechanisms of the energy transfer are largely independent of the nature of the surrounding medium, and therefore, should hold for other media including polymer matrices and DNA. The vibrational energy exchange between CNT and solvents exhibits two time-scales. Over half of the energy is transferred in less than one picosecond, indicating that the dominant exchange mechanism is inertial relaxation. It occurs by collisions of solvent molecules with CNT walls, facilitated by the short-range Lennard-Jones interaction. Additional several picoseconds are required for the remainder of the vibrational energy exchange, corresponding to the diffusive relaxation mechanism and involving collective molecular motions. The faster stage of the CNT-solvent energy exchange occurs on the same time-scale, and therefore, competes with the vibrational energy relaxation inside CNTs. The energy exchange time-scales are significantly influenced by the arrangement of solvent molecules inside CNTs. Generally, the effects of confinement on the dynamics can be rationalized by analysis of the solvent structure. For the same CNT diameter, the extent of the confinement effect strongly depends on the size of the solvent molecules. Icelike properties in water seen in small CNTs disappear in CNTs with intermediate diameters. In acetonitrile and cyclohexane, medium size CNTs still show strong confinement effects. Rotational motions of acetonitrile molecules are inhibited, and the cyclohexane density is dramatically decreased. The disbalance between the local temperatures of the inside and outside regions of the solvent equilibrates through a tube-mediated interaction, rather than by a direct coupling between the two solvent subsystems. In all cases, the CNT-solvent energy transfer is mediated by slow motions in the frequency range of CNT radial breathing modes.

Casting Control of Floating-films into Ribbon-shape Structure by modified Dynamic FTM

NASA Astrophysics Data System (ADS)

Tripathi, A.; Pandey, M.; Nagamatsu, S.; Pandey, S. S.; Hayase, S.; Takashima, W.

2017-11-01

We have developed a new method to obtain Ribbon-shaped floating films via dynamic casting of floating-film and transfer method (dynamic-FTM). Dynamic-FTM is a unique method to prepare oriented thin-film of conjugated polymers (CPs) which is quick and easy. This method has several advantages as compared to the other conventional casting procedure to prepare oriented CP films. In the conventional dynamic FTM appearance of large scale circular orientation poses difficulty not only for practical applications but also hinders the detailed analysis of the orientation mechanism. In this present work, pros and cons of this newly proposed ribbon-shaped floating-film have been discussed in detail from those of the conventional floating-film prepared by dynamic-FTM.

EDITORIAL: Fracture: from the atomic to the geophysical scale Fracture: from the atomic to the geophysical scale

NASA Astrophysics Data System (ADS)

Bouchaud, Elisabeth; Soukiassian, Patrick

2009-11-01

Although fracture is a very common experience in every day life, it still harbours many unanswered questions. New avenues of investigation arise concerning the basic mechanisms leading to deformation and failure in heterogeneous materials, particularly in non-metals. The processes involved are even more complex when plasticity, thermal fluctuations or chemical interactions between the material and its environment introduce a specific time scale. Sub-critical failure, which may be reached at unexpectedly low loads, is particularly important for silicate glasses. Another source of complications originates from dynamic fracture, when loading rates become so high that the acoustic waves produced by the crack interact with the material heterogeneities, in turn producing new waves that modify the propagation. Recent progress in experimental techniques, allowing one to test and probe materials at sufficiently small length or time scales or in three dimensions, has led to a quantitative understanding of the physical processes involved. In parallel, simulations have also progressed, by extending the time and length scales they are able to reach, and thus attaining experimentally accessible conditions. However, one central question remains the inclusion of these basic mechanisms into a statistical description. This is not an easy task, mostly because of the strong stress gradients present at the tip of a crack, and because the averaging of fracture properties over a heterogeneous material, containing more or less brittle phases, requires rare event statistics. Substantial progress has been made in models and simulations based on accurate experiments. From these models, scaling laws have been derived, linking the behaviour at a micro- or even nano-scale to the macroscopic and even to geophysical scales. The reviews in this Cluster Issue of Journal of Physics D: Applied Physics cover several of these important topics, including the physical processes in fracture mechanisms, the sub-critical failure issue, the dynamical fracture propagation, and the scaling laws from the micro- to the geophysical scales. Achievements and progress are reported, and the many open questions are discussed, which should provide a sound basis for present and future prospects.

Memory Dynamics in Cross-linked Actin Networks

NASA Astrophysics Data System (ADS)

Scheff, Danielle; Majumdar, Sayantan; Gardel, Margaret

Cells demonstrate the remarkable ability to adapt to mechanical stimuli through rearrangement of the actin cytoskeleton, a cross-linked network of actin filaments. In addition to its importance in cell biology, understanding this mechanical response provides strategies for creation of novel materials. A recent study has demonstrated that applied stress can encode mechanical memory in these networks through changes in network geometry, which gives rise to anisotropic shear response. Under later shear, the network is stiffer in the direction of the previously applied stress. However, the dynamics behind the encoding of this memory are unknown. To address this question, we explore the effect of varying either the rigidity of the cross-linkers or the length of actin filament on the time scales required for both memory encoding and over which it later decays. While previous experiments saw only a long-lived memory, initial results suggest another mechanism where memories relax relatively quickly. Overall, our study is crucial for understanding the process by which an external stress can impact network arrangement and thus the dynamics of memory formation.

Scale effects in crystal plasticity

NASA Astrophysics Data System (ADS)

Padubidri Janardhanachar, Guruprasad

The goal of this research work is to further the understanding of crystal plasticity, particularly at reduced structural and material length scales. Fundamental understanding of plasticity is central to various challenges facing design and manufacturing of materials for structural and electronic device applications. The development of microstructurally tailored advanced metallic materials with enhanced mechanical properties that can withstand extremes in stress, strain, and temperature, will aid in increasing the efficiency of power generating systems by allowing them to work at higher temperatures and pressures. High specific strength materials can lead to low fuel consumption in transport vehicles. Experiments have shown that enhanced mechanical properties can be obtained in materials by constraining their size, microstructure (e.g. grain size), or both for various applications. For the successful design of these materials, it is necessary to have a thorough understanding of the influence of different length scales and evolving microstructure on the overall behavior. In this study, distinction is made between the effect of structural and material length scale on the mechanical behavior of materials. A length scale associated with an underlying physical mechanism influencing the mechanical behavior can overlap with either structural length scales or material length scales. If it overlaps with structural length scales, then the material is said to be dimensionally constrained. On the other hand, if it overlaps with material length scales, for example grain size, then the material is said to be microstructurally constrained. The objectives of this research work are: (1) to investigate scale and size effects due to dimensional constraints; (2) to investigate size effects due to microstructural constraints; and (3) to develop a size dependent hardening model through coarse graining of dislocation dynamics. A discrete dislocation dynamics (DDD) framework where the scale of analysis is intermediate between a fully discretized (e.g. atomistic) and fully continuum is used for this study. This mesoscale tool allows to address all the stated objectives of this study within a single framework. Within this framework, the effect of structural and the material length scales are naturally accounted for in the simulations and need not be specified in an ad hoc manner, as in some continuum models. It holds the promise of connecting the evolution of the defect microstructure to the effective response of the crystal. Further, it provides useful information to develop physically motivated continuum models to model size effects in materials. The contributions of this study are: (a) provides a new interpretation of mechanical size effect due to only dimensional constraint using DDD; (b) a development of an experimentally validated DDD simulation methodology to model Cu micropillars; (c) a coarse graining technique using DDD to develop a phenomenological model to capture size effect on strain hardening; and (d) a development of a DDD framework for polycrystals to investigate grain size effect on yield strength and strain hardening.

Mechanical Overstimulation of Hair Bundles: Suppression and Recovery of Active Motility

PubMed Central

Kao, Albert; Meenderink, Sebastiaan W. F.; Bozovic, Dolores

2013-01-01

We explore the effects of high-amplitude mechanical stimuli on hair bundles of the bullfrog sacculus. Under in vitro conditions, these bundles exhibit spontaneous limit cycle oscillations. Prolonged deflection exerted two effects. First, it induced an offset in the position of the bundle. Recovery to the original position displayed two distinct time scales, suggesting the existence of two adaptive mechanisms. Second, the stimulus suppressed spontaneous oscillations, indicating a change in the hair bundle’s dynamic state. After cessation of the stimulus, active bundle motility recovered with time. Both effects were dependent on the duration of the imposed stimulus. External calcium concentration also affected the recovery to the oscillatory state. Our results indicate that both offset in the bundle position and calcium concentration control the dynamic state of the bundle. PMID:23505461

Inverse and Direct Energy Cascades in Three-Dimensional Magnetohydrodynamic Turbulence at Low Magnetic Reynolds Number

NASA Astrophysics Data System (ADS)

Baker, Nathaniel T.; Pothérat, Alban; Davoust, Laurent; Debray, François

2018-06-01

This experimental study analyzes the relationship between the dimensionality of turbulence and the upscale or downscale nature of its energy transfers. We do so by forcing low-R m magnetohydrodynamic turbulence in a confined channel, while precisely controlling its dimensionality by means of an externally applied magnetic field. We first identify a specific length scale l^⊥ c that separates smaller 3D structures from larger quasi-2D ones. We then show that an inverse energy cascade of horizontal kinetic energy along horizontal scales is always observable at large scales, and that it extends well into the region of 3D structures. At the same time, a direct energy cascade confined to the smallest and strongly 3D scales is observed. These dynamics therefore appear not to be simply determined by the dimensionality of individual scales, nor by the forcing scale, unlike in other studies. In fact, our findings suggest that the relationship between kinematics and dynamics is not universal and may strongly depend on the forcing and dissipating mechanisms at play.

Moon-based Earth Observation for Large Scale Geoscience Phenomena

NASA Astrophysics Data System (ADS)

Guo, Huadong; Liu, Guang; Ding, Yixing

2016-07-01

The capability of Earth observation for large-global-scale natural phenomena needs to be improved and new observing platform are expected. We have studied the concept of Moon as an Earth observation in these years. Comparing with manmade satellite platform, Moon-based Earth observation can obtain multi-spherical, full-band, active and passive information,which is of following advantages: large observation range, variable view angle, long-term continuous observation, extra-long life cycle, with the characteristics of longevity ,consistency, integrity, stability and uniqueness. Moon-based Earth observation is suitable for monitoring the large scale geoscience phenomena including large scale atmosphere change, large scale ocean change,large scale land surface dynamic change,solid earth dynamic change,etc. For the purpose of establishing a Moon-based Earth observation platform, we already have a plan to study the five aspects as follows: mechanism and models of moon-based observing earth sciences macroscopic phenomena; sensors' parameters optimization and methods of moon-based Earth observation; site selection and environment of moon-based Earth observation; Moon-based Earth observation platform; and Moon-based Earth observation fundamental scientific framework.

Charge carrier recombination dynamics in perovskite and polymer solar cells

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

Paulke, Andreas; Kniepert, Juliane; Kurpiers, Jona

2016-03-14

Time-delayed collection field experiments are applied to planar organometal halide perovskite (CH{sub 3}NH{sub 3}PbI{sub 3}) based solar cells to investigate charge carrier recombination in a fully working solar cell at the nanosecond to microsecond time scale. Recombination of mobile (extractable) charges is shown to follow second-order recombination dynamics for all fluences and time scales tested. Most importantly, the bimolecular recombination coefficient is found to be time-dependent, with an initial value of ca. 10{sup −9} cm{sup 3}/s and a progressive reduction within the first tens of nanoseconds. Comparison to the prototypical organic bulk heterojunction device PTB7:PC{sub 71}BM yields important differences with regardmore » to the mechanism and time scale of free carrier recombination.« less

A mathematical model for active contraction in healthy and failing myocytes and left ventricles.

PubMed

Cai, Li; Wang, Yongheng; Gao, Hao; Li, Yiqiang; Luo, Xiaoyu

2017-01-01

Cardiovascular disease is one of the leading causes of death worldwide, in particular myocardial dysfunction, which may lead to heart failure eventually. Understanding the electro-mechanics of the heart will help in developing more effective clinical treatments. In this paper, we present a multi-scale electro-mechanics model of the left ventricle (LV). The Holzapfel-Ogden constitutive law was used to describe the passive myocardial response in tissue level, a modified Grandi-Pasqualini-Bers model was adopted to model calcium dynamics in individual myocytes, and the active tension was described using the Niederer-Hunter-Smith myofilament model. We first studied the electro-mechanics coupling in a single myocyte in the healthy and diseased left ventricle, and then the single cell model was embedded in a dynamic LV model to investigate the compensation mechanism of LV pump function due to myocardial dysfunction caused by abnormality in cellular calcium dynamics. The multi-scale LV model was solved using an in-house developed hybrid immersed boundary method with finite element extension. The predictions of the healthy LV model agreed well with the clinical measurements and other studies, and likewise, the results in the failing states were also consistent with clinical observations. In particular, we found that a low level of intracellular Ca2+ transient in myocytes can result in LV pump function failure even with increased myocardial contractility, decreased systolic blood pressure, and increased diastolic filling pressure, even though they will increase LV stroke volume. Our work suggested that treatments targeted at increased contractility and lowering the systolic blood pressure alone are not sufficient in preventing LV pump dysfunction, restoring a balanced physiological Ca2+ handling mechanism is necessary.

Scaled boundary finite element simulation and modeling of the mechanical behavior of cracked nanographene sheets

NASA Astrophysics Data System (ADS)

Honarmand, M.; Moradi, M.

2018-06-01

In this paper, by using scaled boundary finite element method (SBFM), a perfect nanographene sheet or cracked ones were simulated for the first time. In this analysis, the atomic carbon bonds were modeled by simple bar elements with circular cross-sections. Despite of molecular dynamics (MD), the results obtained from SBFM analysis are quite acceptable for zero degree cracks. For all angles except zero, Griffith criterion can be applied for the relation between critical stress and crack length. Finally, despite the simplifications used in nanographene analysis, obtained results can simulate the mechanical behavior with high accuracy compared with experimental and MD ones.

Finite Element Simulation of the Shear Effect of Ultrasonic on Heat Exchanger Descaling

NASA Astrophysics Data System (ADS)

Lu, Shaolv; Wang, Zhihua; Wang, Hehui

2018-03-01

The shear effect on the interface of metal plate and its attached scale is an important mechanism of ultrasonic descaling, which is caused by the different propagation speed of ultrasonic wave in two different mediums. The propagating of ultrasonic wave on the shell is simulated based on the ANSYS/LS-DYNA explicit dynamic analysis. The distribution of shear stress in different paths under ultrasonic vibration is obtained through the finite element analysis and it reveals the main descaling mechanism of shear effect. The simulation result is helpful and enlightening to the reasonable design and the application of the ultrasonic scaling technology on heat exchanger.

Light induced kickoff of magnetic domain walls in Ising chains

NASA Astrophysics Data System (ADS)

Bogani, Lapo

2012-02-01

Controlling the speed at which systems evolve is a challenge shared by all disciplines, and otherwise unrelated areas use common theoretical frameworks towards this goal. A particularly widespread model is Glauber dynamics, which describes the time evolution of the Ising model and can be applied to any binary system. Here we show, using molecular nanowires under irradiation, that Glauber dynamics can be controlled by a novel domain-wall kickoff mechanism. Contrary to known processes, the kickoff has unambiguous fingerprints, slowing down the spin-flip attempt rate by several orders of magnitude, and following a scaling law. The required irradiation power is very low, a substantial improvement over present methods of magnetooptical switching: in our experimental demonstration we switched molecular nanowires with light, using powers thousands of times lower than in previous optical switching methods. This manipulation of stochastic dynamic processes is extremely clean, leading to fingerprint signatures and scaling laws. These observations can be used, in material science, to better study domain-wall displacements and solitons in discrete lattices. These results provide a new way to control and study stochastic dynamic processes. Being general for Glauber dynamics, they can be extended to different kinds of magnetic nanowires and to a myriad of fields, ranging from social evolution to neural networks and chemical reactivity. For nanoelectronics and molecular spintronics the kickoff affords external control of molecular spin-valves and a magnetic fingerprint in single molecule measurements. It can also be applied to the dynamics of mechanical switches and the related study of phasons and order-disorder transitions.

Structure and Dynamics of Polymer/Polymer grafted nanoparticle composite

NASA Astrophysics Data System (ADS)

Archer, Lynden

Addition of nanoparticles to polymers is a well-practiced methodology for augmenting various properties of the polymer host, including mechanical strength, thermal stability, barrier properties, dimensional stability and wear resistance. Many of these property changes are known to arise from nanoparticle-induced modification of polymer structure and chain dynamics, which are strong functions of the dispersion state of the nanoparticles' and on their relative size (D) to polymer chain dimensions (e.g. Random coil radius Rg or entanglement mesh size a) . This talk will discuss polymer nanocomposites (PNCs) comprised of Polyethylene Glycol (PEG) tethered silica nanoparticles (SiO2-PEG) dispersed in polymers as model systems for investigating phase stability and dynamics of PNCs. On the basis of small-angle X-ray Scattering, it will be shown that favorable enthalpic interactions between particle-tethered chains and a polymer host provides an important mechanism for creating PNCs in which particle aggregation is avoided. The talk will report on polymer and particle scale dynamics in these materials and will show that grafted nanoparticles well dispersed in a polymer host strongly influence the host polymer relaxation dynamics on all timescales and the polymers in turn produce dramatic changes in the nature (from diffusive to hyperdiffusive) and speed of nano particle decorrelation dynamics at the polymer entanglement threshold. A local viscosity model capable of explaining these observations is discussed and the results compared with scaling theories for NP motions in polymers This material is based on work supported by the National Science Foundation Award Nos. DMR-1609125 and CBET-1512297.

Polymer chain dynamics under nanoscopic confinements.

PubMed

Kimmich, Rainer; Fatkullin, Nail; Mattea, Carlos; Fischer, Elmar

2005-02-01

It is shown that the confinement of polymer melts in nanopores leads to chain dynamics dramatically different from bulk behavior. This so-called corset effect occurs both above and below the critical molecular mass and induces the dynamic features predicted for reptation. A spinodal demixing technique was employed for the preparation of linear poly(ethylene oxide) (PEO) confined to nanoscopic strands that are in turn embedded in a quasi-solid and impenetrable methacrylate matrix. Both the molecular weight of the PEO and the mean diameter of the strands were varied to a certain degree. The chain dynamics of the PEO in the molten state was examined with the aid of field-gradient NMR diffusometry (time scale, 10(-2)-10(0) s) and field-cycling NMR relaxometry (time scale, 10(-9)-10(-4) s). The dominating mechanism for translational displacements probed in the nanoscopic strands by either technique is shown to be reptation. On the time scale of spin-lattice relaxation time measurements, the frequency dependence signature of reptation (i.e., T1 approximately nu(3/4)) showed up in all samples. A "tube" diameter of only 0.6 nm was concluded to be effective on this time scale even when the strand diameter was larger than the radius of gyration of the PEO random coils. This corset effect is traced back to the lack of the local fluctuation capacity of the free volume in nanoscopic confinements. The confinement dimension is estimated at which the crossover from confined to bulk chain dynamics is expected.

Accelerating Calculations of Reaction Dissipative Particle Dynamics in LAMMPS

DTIC Science & Technology

2017-05-17

order reaction mechanism, the best acceleration was 6.1 times. For a larger, more chemically detailed mechanism, the best acceleration exceeded 60 times...simulations at previously inaccessible scales. A principle feature of DPD-RX is its ability to model chemical reactions within each CG particle. The...change in composition due to chemical reactions is described by a system of ordinary differential equations (ODEs) that are evaluated at each DPD time

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

Bernardin, John D; Baca, Allen G

This paper presents the mechanical design, fabrication and dynamic testing of an electrostatic analyzer spacecraft instrument. The functional and environmental requirements combined with limited spacecraft accommodations, resulted in complex component geometries, unique material selections, and difficult fabrication processes. The challenging aspects of the mechanical design and several of the more difficult production processes are discussed. In addition, the successes, failures, and lessons learned from acoustic and random vibration testing of a full-scale prototype instrument are presented.

Fluid dynamic mechanisms and interactions within separated flows and their effects on missile aerodynamics

NASA Astrophysics Data System (ADS)

Addy, A. L.; Chow, W. L.; Korst, H. H.; White, R. A.

1983-05-01

Significant data and detailed results of a joint research effort investigating the fluid dynamic mechanisms and interactions within separated flows are presented. The results were obtained through analytical, experimental, and computational investigations of base flow related configurations. The research objectives focus on understanding the component mechanisms and interactions which establish and maintain separated flow regions. Flow models and theoretical analyses were developed to describe the base flowfield. The research approach has been to conduct extensive small-scale experiments on base flow configurations and to analyze these flows by component models and finite-difference techniques. The modeling of base flows of missiles (both powered and unpowered) for transonic and supersonic freestreams has been successful by component models. Research on plume effects and plume modeling indicated the need to match initial plume slope and plume surface curvature for valid wind tunnel simulation of an actual rocket plume. The assembly and development of a state-of-the-art laser Doppler velocimeter (LDV) system for experiments with two-dimensional small-scale models has been completed and detailed velocity and turbulence measurements are underway. The LDV experiments include the entire range of base flowfield mechanisms - shear layer development, recompression/reattachment, shock-induced separation, and plume-induced separation.

Effect of small scale transport processes on phytoplankton distribution in coastal seas.

PubMed

Hernández-Carrasco, Ismael; Orfila, Alejandro; Rossi, Vincent; Garçon, Veronique

2018-06-05

Coastal ocean ecosystems are major contributors to the global biogeochemical cycles and biological productivity. Physical factors induced by the turbulent flow play a crucial role in regulating marine ecosystems. However, while large-scale open-ocean dynamics is well described by geostrophy, the role of multiscale transport processes in coastal regions is still poorly understood due to the lack of continuous high-resolution observations. Here, the influence of small-scale dynamics (O(3.5-25) km, i.e. spanning upper submesoscale and mesoscale processes) on surface phytoplankton derived from satellite chlorophyll-a (Chl-a) is studied using Lagrangian metrics computed from High-Frequency Radar currents. The combination of complementary Lagrangian diagnostics, including the Lagrangian divergence along fluid trajectories, provides an improved description of the 3D flow geometry which facilitates the interpretation of two non-exclusive physical mechanisms affecting phytoplankton dynamics and patchiness. Attracting small-scale fronts, unveiled by backwards Lagrangian Coherent Structures, are associated to negative divergence where particles and Chl-a standing stocks cluster. Filaments of positive divergence, representing large accumulated upward vertical velocities and suggesting accrued injection of subsurface nutrients, match areas with large Chl-a concentrations. Our findings demonstrate that an accurate characterization of small-scale transport processes is necessary to comprehend bio-physical interactions in coastal seas.

Anisotropic polyvinyl alcohol hydrogel phantom for shear wave elastography in fibrous biological soft tissue: a multimodality characterization

NASA Astrophysics Data System (ADS)

Chatelin, Simon; Bernal, Miguel; Deffieux, Thomas; Papadacci, Clément; Flaud, Patrice; Nahas, Amir; Boccara, Claude; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

2014-11-01

Shear wave elastography imaging techniques provide quantitative measurement of soft tissues elastic properties. Tendons, muscles and cerebral tissues are composed of fibers, which induce a strong anisotropic effect on the mechanical behavior. Currently, these tissues cannot be accurately represented by existing elastography phantoms. Recently, a novel approach for orthotropic hydrogel mimicking soft tissues has been developed (Millon et al 2006 J. Biomed. Mater. Res. B 305-11). The mechanical anisotropy is induced in a polyvinyl alcohol (PVA) cryogel by stretching the physical crosslinks of the polymeric chains while undergoing freeze/thaw cycles. In the present study we propose an original multimodality imaging characterization of this new transverse isotropic (TI) PVA hydrogel. Multiple properties were investigated using a large variety of techniques at different scales compared with an isotropic PVA hydrogel undergoing similar imaging and rheology protocols. The anisotropic mechanical (dynamic and static) properties were studied using supersonic shear wave imaging technique, full-field optical coherence tomography (FFOCT) strain imaging and classical linear rheometry using dynamic mechanical analysis. The anisotropic optical and ultrasonic spatial coherence properties were measured by FFOCT volumetric imaging and backscatter tensor imaging, respectively. Correlation of mechanical and optical properties demonstrates the complementarity of these techniques for the study of anisotropy on a multi-scale range as well as the potential of this TI phantom as fibrous tissue-mimicking phantom for shear wave elastographic applications.

Scaling of avian bipedal locomotion reveals independent effects of body mass and leg posture on gait.

PubMed

Daley, Monica A; Birn-Jeffery, Aleksandra

2018-05-22

Birds provide an interesting opportunity to study the relationships between body size, limb morphology and bipedal locomotor function. Birds are ecologically diverse and span a large range of body size and limb proportions, yet all use their hindlimbs for bipedal terrestrial locomotion, for at least some part of their life history. Here, we review the scaling of avian striding bipedal gaits to explore how body mass and leg morphology influence walking and running. We collate literature data from 21 species, spanning a 2500× range in body mass from painted quail to ostriches. Using dynamic similarity theory to interpret scaling trends, we find evidence for independent effects of body mass, leg length and leg posture on gait. We find no evidence for scaling of duty factor with body size, suggesting that vertical forces scale with dynamic similarity. However, at dynamically similar speeds, large birds use relatively shorter stride lengths and higher stride frequencies compared with small birds. We also find that birds with long legs for their mass, such as the white stork and red-legged seriema, use longer strides and lower swing frequencies, consistent with the influence of high limb inertia on gait. We discuss the observed scaling of avian bipedal gait in relation to mechanical demands for force, work and power relative to muscle actuator capacity, muscle activation costs related to leg cycling frequency, and considerations of stability and agility. Many opportunities remain for future work to investigate how morphology influences gait dynamics among birds specialized for different habitats and locomotor behaviors. © 2018. Published by The Company of Biologists Ltd.

Controlled flight of a biologically inspired, insect-scale robot.

PubMed

Ma, Kevin Y; Chirarattananon, Pakpong; Fuller, Sawyer B; Wood, Robert J

2013-05-03

Flies are among the most agile flying creatures on Earth. To mimic this aerial prowess in a similarly sized robot requires tiny, high-efficiency mechanical components that pose miniaturization challenges governed by force-scaling laws, suggesting unconventional solutions for propulsion, actuation, and manufacturing. To this end, we developed high-power-density piezoelectric flight muscles and a manufacturing methodology capable of rapidly prototyping articulated, flexure-based sub-millimeter mechanisms. We built an 80-milligram, insect-scale, flapping-wing robot modeled loosely on the morphology of flies. Using a modular approach to flight control that relies on limited information about the robot's dynamics, we demonstrated tethered but unconstrained stable hovering and basic controlled flight maneuvers. The result validates a sufficient suite of innovations for achieving artificial, insect-like flight.

Circadian clock and cardiac vulnerability: A time stamp on multi-scale neuroautonomic regulation

NASA Astrophysics Data System (ADS)

Ivanov, Plamen Ch.

2005-03-01

Cardiovascular vulnerability displays a 24-hour pattern with a peak between 9AM and 11AM. This daily pattern in cardiac risk is traditionally attributed to external factors including activity levels and sleep-wake cycles. However,influences from the endogenous circadian pacemaker independent from behaviors may also affect cardiac control. We investigate heartbeat dynamics in healthy subjects recorded throughout a 10-day protocol wherein the sleep/wake and behavior cycles are desynchronized from the endogenous circadian cycle,enabling assessment of circadian factors while controlling for behavior-related factors. We demonstrate that the scaling exponent characterizing temporal correlations in heartbeat dynamics over multiple time scales does exhibit a significant circadian rhythm with a sharp peak at the circadian phase corresponding to the period 9-11AM, and that this rhythm is independent from scheduled behaviors and mean heart rate. Our findings of strong circadian rhythms in the multi-scale heartbeat dynamics of healthy young subjects indicate that the underlying mechanism of cardiac regulation is strongly influenced by the endogenous circadian pacemaker. A similar circadian effect in vulnerable individuals with underlying cardiovascular disease would contribute to the morning peak of adverse cardiac events observed in epidemiological studies.

Dielectric relaxation dynamics and AC conductivity scaling of metal-organic framework (MOF-5) based polymer electrolyte nanocomposites incorporated with ionic liquid

NASA Astrophysics Data System (ADS)

Dutta, Rituraj; Kumar, A.

2017-10-01

Dielectric relaxation dynamics and AC conductivity scaling of a metal-organic framework (MOF-5) based poly (vinylidene fluoride-co-hexafluoropropylene) (PVdf-HFP) incorporated with 1-Butyl-3-methylimidazolium hexafluorophosphate have been studied over a frequency range of 40 Hz-5 MHz and in the temperature range of 300 K-380 K. High values of dielectric permittivity (~{{\\varepsilon }\\prime} ) having strong dispersion are obtained at low frequency because of interfacial polarization. The real part of the dielectric modulus spectra (M‧) shows no prominent peak, whereas the imaginary part (M″) shows certain peaks, with a reduction in relaxation time (τ) that can be attributed to a non-Debye relaxation mechanism. The spectra also depict both concentration- and temperature-independent scaling behavior. The power law dependent variation of AC conductivity follows the jump relaxation model and reveals activated ion hopping over diffusion barriers. The value of the frequency exponent is observed to decrease with increasing concentration of ionic liquid, indicating the forward hopping of ions in the relaxation process. The AC conductivity scaling curves at different temperatures also depict the temperature-independent relaxation dynamics.

Invisible axionlike dark matter from the electroweak bosonic seesaw mechanism

NASA Astrophysics Data System (ADS)

Ishida, Hiroyuki; Matsuzaki, Shinya; Yamaguchi, Yuya

2016-11-01

We explore a model based on the classically scale-invariant standard model (SM) with a strongly coupled vectorlike dynamics, which is called hypercolor (HC). The scale symmetry is dynamically broken by the vectorlike condensation at the TeV scale, so that the SM Higgs acquires the negative mass squared by the bosonic seesaw mechanism to realize the electroweak symmetry breaking. An elementary pseudoscalar S is introduced to give masses for the composite Nambu-Goldstone bosons (HC pions): The HC pion can be a good target to explore through a diphoton channel at the LHC. As a consequence of the bosonic seesaw, the fluctuating mode of S , which we call s , develops tiny couplings to the SM particles and is predicted to be very light. The s predominantly decays to a diphoton and can behave as invisible axionlike dark matter. The mass of the s dark matter is constrained by currently available cosmological and astrophysical limits to be 10-4 eV ≲ms≲1 eV . We find that a sufficient amount of relic abundance for the s dark matter can be accumulated via the coherent oscillation. The detection potential in microwave cavity experiments is also addressed.

Surface heterogeneity impacts on boundary layer dynamics via energy balance partitioning

USDA-ARS?s Scientific Manuscript database

The role of land-atmosphere interactions under heterogeneous surface conditions is investigated in order to identify mechanisms responsible for altering surface heat and moisture fluxes. Twelve coupled land surface – large eddy simulation scenarios with four different length scales of surface variab...

Mesoscale mechanics of twisting carbon nanotube yarns.

PubMed

Mirzaeifar, Reza; Qin, Zhao; Buehler, Markus J

2015-03-12

Fabricating continuous macroscopic carbon nanotube (CNT) yarns with mechanical properties close to individual CNTs remains a major challenge. Spinning CNT fibers and ribbons for enhancing the weak interactions between the nanotubes is a simple and efficient method for fabricating high-strength and tough continuous yarns. Here we investigate the mesoscale mechanics of twisting CNT yarns using full atomistic and coarse grained molecular dynamics simulations, considering concurrent mechanisms at multiple length-scales. To investigate the mechanical response of such a complex structure without losing insights into the molecular mechanism, we applied a multiscale strategy. The full atomistic results are used for training a coarse grained model for studying larger systems consisting of several CNTs. The mesoscopic model parameters are updated as a function of the twist angle, based on the full atomistic results, in order to incorporate the atomistic scale deformation mechanisms in larger scale simulations. By bridging across two length scales, our model is capable of accurately predicting the mechanical behavior of twisted yarns while the atomistic level deformations in individual nanotubes are integrated into the model by updating the parameters. Our results focused on studying a bundle of close packed nanotubes provide novel mechanistic insights into the spinning of CNTs. Our simulations reveal how twisting a bundle of CNTs improves the shear interaction between the nanotubes up to a certain level due to increasing the interaction surface. Furthermore, twisting the bundle weakens the intertube interactions due to excessive deformation in the cross sections of individual CNTs in the bundle.

A multi-machine scaling of halo current rotation

NASA Astrophysics Data System (ADS)

Myers, C. E.; Eidietis, N. W.; Gerasimov, S. N.; Gerhardt, S. P.; Granetz, R. S.; Hender, T. C.; Pautasso, G.; Contributors, JET

2018-01-01

Halo currents generated during unmitigated tokamak disruptions are known to develop rotating asymmetric features that are of great concern to ITER because they can dynamically amplify the mechanical stresses on the machine. This paper presents a multi-machine analysis of these phenomena. More specifically, data from C-Mod, NSTX, ASDEX Upgrade, DIII-D, and JET are used to develop empirical scalings of three key quantities: (1) the machine-specific minimum current quench time, \

A multi-machine scaling of halo current rotation

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

Myers, C. E.; Eidietis, N. W.; Gerasimov, S. N.

Halo currents generated during unmitigated tokamak disruptions are known to develop rotating asymmetric features that are of great concern to ITER because they can dynamically amplify the mechanical stresses on the machine. This paper presents a multi-machine analysis of these phenomena. More specifically, data from C-Mod, NSTX, ASDEX Upgrade, DIII-D, and JET are used to develop empirical scalings of three key quantities: the machine-specific minimum current quench time,more » $$ \

A multi-machine scaling of halo current rotation

DOE PAGES

Myers, C. E.; Eidietis, N. W.; Gerasimov, S. N.; ...

2017-12-12

Halo currents generated during unmitigated tokamak disruptions are known to develop rotating asymmetric features that are of great concern to ITER because they can dynamically amplify the mechanical stresses on the machine. This paper presents a multi-machine analysis of these phenomena. More specifically, data from C-Mod, NSTX, ASDEX Upgrade, DIII-D, and JET are used to develop empirical scalings of three key quantities: the machine-specific minimum current quench time,more » $$ \

All-electrical detection of spin dynamics in magnetic antidot lattices by the inverse spin Hall effect

DOE PAGES

Jungfleisch, Matthias B.; Zhang, Wei; Ding, Junjia; ...

2016-02-03

The understanding of spin dynamics in laterally confined structures on sub-micron length scales has become a significant aspect of the development of novel magnetic storage technologies. Numerous ferromagnetic resonance measurements, optical characterization by Kerr microscopy and Brillouin light scattering spectroscopy and x-ray studies were carried out to detect the dynamics in patterned magnetic antidot lattices. Here, we investigate Oersted-field driven spin dynamics in rectangular Ni80Fe20/Pt antidot lattices with different lattice parameters by electrical means. When the system is driven to resonance, a dc voltage across the length of the sample is detected that changes its sign upon field reversal, whichmore » is in agreement with a rectification mechanism based on the inverse spin Hall effect. Furthermore, we show that the voltage output scales linearly with the applied microwave drive in the investigated range of powers. Lastly, our findings have direct implications on the development of engineered magnonics applications and devices.« less

Formation and organization of protein domains in the immunological synapse

NASA Astrophysics Data System (ADS)

Carlson, Andreas; Mahadevan, L.

2014-11-01

The cellular basis for the adaptive immune response during antigen recognition relies on a specialized protein interface known as the immunological synapse. Here, we propose a minimal mathematical model for the dynamics of the IS that encompass membrane mechanics, hydrodynamics and protein kinetics. Simple scaling laws describe the dynamics of protein clusters as a function of membrane stiffness, rigidity of the adhesive proteins, and fluid flow in the synaptic cleft. Numerical simulations complement the scaling laws by quantifying the nucleation, growth and stabilization of proteins domains on the size of the cell. Direct comparison with experiment suggests that passive dynamics suffices to describe the short-time formation and organization of protein clusters, while the stabilization and long time dynamics of the synapse is likely determined by active cytoskeleton processes triggered by receptor binding. Our study reveals that the fluid flow generated by the interplay between membrane deformation and protein binding kinetics can assist immune cells in regulating protein sorting.

Integrating macro and micro scale approaches in the agent-based modeling of residential dynamics

NASA Astrophysics Data System (ADS)

Saeedi, Sara

2018-06-01

With the advancement of computational modeling and simulation (M&S) methods as well as data collection technologies, urban dynamics modeling substantially improved over the last several decades. The complex urban dynamics processes are most effectively modeled not at the macro-scale, but following a bottom-up approach, by simulating the decisions of individual entities, or residents. Agent-based modeling (ABM) provides the key to a dynamic M&S framework that is able to integrate socioeconomic with environmental models, and to operate at both micro and macro geographical scales. In this study, a multi-agent system is proposed to simulate residential dynamics by considering spatiotemporal land use changes. In the proposed ABM, macro-scale land use change prediction is modeled by Artificial Neural Network (ANN) and deployed as the agent environment and micro-scale residential dynamics behaviors autonomously implemented by household agents. These two levels of simulation interacted and jointly promoted urbanization process in an urban area of Tehran city in Iran. The model simulates the behavior of individual households in finding ideal locations to dwell. The household agents are divided into three main groups based on their income rank and they are further classified into different categories based on a number of attributes. These attributes determine the households' preferences for finding new dwellings and change with time. The ABM environment is represented by a land-use map in which the properties of the land parcels change dynamically over the simulation time. The outputs of this model are a set of maps showing the pattern of different groups of households in the city. These patterns can be used by city planners to find optimum locations for building new residential units or adding new services to the city. The simulation results show that combining macro- and micro-level simulation can give full play to the potential of the ABM to understand the driving mechanism of urbanization and provide decision-making support for urban management.

Generating scale-invariant perturbations from rapidly-evolving equation of state

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

Khoury, Justin; Steinhardt, Paul J.

2011-06-15

Recently, we introduced an ekpyrotic model based on a single, canonical scalar field that generates nearly scale-invariant curvature fluctuations through a purely ''adiabatic mechanism'' in which the background evolution is a dynamical attractor. Despite the starkly different physical mechanism for generating fluctuations, the two-point function is identical to inflation. In this paper, we further explore this concept, focusing in particular on issues of non-Gaussianity and quantum corrections. We find that the degeneracy with inflation is broken at three-point level: for the simplest case of an exponential potential, the three-point amplitude is strongly scale dependent, resulting in a breakdown of perturbationmore » theory on small scales. However, we show that the perturbative breakdown can be circumvented--and all issues raised in Linde et al. (arXiv:0912.0944) can be addressed--by altering the potential such that power is suppressed on small scales. The resulting range of nearly scale-invariant, Gaussian modes can be as much as 12 e-folds, enough to span the scales probed by microwave background and large-scale structure observations. On smaller scales, the spectrum is not scale invariant but is observationally acceptable.« less

Large Scale Water Vapor Sources Relative to the October 2000 Piedmont Flood

NASA Technical Reports Server (NTRS)

Turato, Barbara; Reale, Oreste; Siccardi, Franco

2003-01-01

Very intense mesoscale or synoptic-scale rainfall events can occasionally be observed in the Mediterranean region without any deep cyclone developing over the areas affected by precipitation. In these perplexing cases the synoptic situation can superficially look similar to cases in which very little precipitation occurs. These situations could possibly baffle the operational weather forecasters. In this article, the major precipitation event that affected Piedmont (Italy) between 13 and 16 October 2000 is investigated. This is one of the cases in which no intense cyclone was observed within the Mediterranean region at any time, only a moderate system was present, and yet exceptional rainfall and flooding occurred. The emphasis of this study is on the moisture origin and transport. Moisture and energy balances are computed on different space- and time-scales, revealing that precipitation exceeds evaporation over an area inclusive of Piedmont and the northwestern Mediterranean region, on a time-scale encompassing the event and about two weeks preceding it. This is suggestive of an important moisture contribution originating from outside the region. A synoptic and dynamic analysis is then performed to outline the potential mechanisms that could have contributed to the large-scale moisture transport. The central part of the work uses a quasi-isentropic water-vapor back trajectory technique. The moisture sources obtained by this technique are compared with the results of the balances and with the synoptic situation, to unveil possible dynamic mechanisms and physical processes involved. It is found that moisture sources on a variety of atmospheric scales contribute to this event. First, an important contribution is caused by the extratropical remnants of former tropical storm Leslie. The large-scale environment related to this system allows a significant amount of moisture to be carried towards Europe. This happens on a time- scale of about 5-15 days preceding the Piedmont event. Second, water-vapor intrusions from the African Inter-Tropical Convergence Zone and evaporation from the eastern Atlantic contribute on the 2-5 day time-scale. The large-scale moist dynamics appears therefore to be one important factor enabling a moderate Mediterranean cyclone to produce heavy precipitation. Finally, local evaporation from the Mediterranean, water-vapor recycling, and orographically-induced low-level convergence enhance and concentrate the moisture over the area where heavy precipitation occurs. This happens on a 12-72 hour time-scale.

Neural Computations in a Dynamical System with Multiple Time Scales.

PubMed

Mi, Yuanyuan; Lin, Xiaohan; Wu, Si

2016-01-01

Neural systems display rich short-term dynamics at various levels, e.g., spike-frequency adaptation (SFA) at the single-neuron level, and short-term facilitation (STF) and depression (STD) at the synapse level. These dynamical features typically cover a broad range of time scales and exhibit large diversity in different brain regions. It remains unclear what is the computational benefit for the brain to have such variability in short-term dynamics. In this study, we propose that the brain can exploit such dynamical features to implement multiple seemingly contradictory computations in a single neural circuit. To demonstrate this idea, we use continuous attractor neural network (CANN) as a working model and include STF, SFA and STD with increasing time constants in its dynamics. Three computational tasks are considered, which are persistent activity, adaptation, and anticipative tracking. These tasks require conflicting neural mechanisms, and hence cannot be implemented by a single dynamical feature or any combination with similar time constants. However, with properly coordinated STF, SFA and STD, we show that the network is able to implement the three computational tasks concurrently. We hope this study will shed light on the understanding of how the brain orchestrates its rich dynamics at various levels to realize diverse cognitive functions.

On the relationship between the dynamic behavior and nanoscale staggered structure of the bone

NASA Astrophysics Data System (ADS)

Qwamizadeh, Mahan; Zhang, Zuoqi; Zhou, Kun; Zhang, Yong Wei

2015-05-01

Bone, a typical load-bearing biological material, composed of ordinary base materials such as organic protein and inorganic mineral arranged in a hierarchical architecture, exhibits extraordinary mechanical properties. Up to now, most of previous studies focused on its mechanical properties under static loading. However, failure of the bone occurs often under dynamic loading. An interesting question is: Are the structural sizes and layouts of the bone related or even adapted to the functionalities demanded by its dynamic performance? In the present work, systematic finite element analysis was performed on the dynamic response of nanoscale bone structures under dynamic loading. It was found that for a fixed mineral volume fraction and unit cell area, there exists a nanoscale staggered structure at some specific feature size and layout which exhibits the fastest attenuation of stress waves. Remarkably, these specific feature sizes and layouts are in excellent agreement with those experimentally observed in the bone at the same scale, indicating that the structural size and layout of the bone at the nanoscale are evolutionarily adapted to its dynamic behavior. The present work points out the importance of dynamic effect on the biological evolution of load-bearing biological materials.

Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

PubMed

van der Vaart, Arjan

2015-05-01

Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

Investigations into the mechanism of material removal and surface modification at atomic scale on stainless steel using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Ranjan, Prabhat; Balasubramaniam, R.; Jain, V. K.

2018-06-01

A molecular dynamics simulation (MDS) has been carried out to investigate the material removal phenomenon of chemo-mechanical magnetorheological finishing (CMMRF) process. To understand the role of chemical assisted mechanical abrasion in CMMRF process, material removal phenomenon is subdivided into three different stages. In the first stage, new atomic bonds viz. Fe-O-Si is created on the surface of the workpiece (stainless steel). The second stage deals with the rupture of parent bonds like Fe-Fe on the workpiece. In the final stage, removal of material from the surface in the form of dislodged debris (cluster of atoms) takes place. Effects of process parameters like abrasive particles, depth of penetration and initial surface condition on finishing force, potential energy (towards secondary phenomenon such as chemical instability of the finished surface) and material removal at atomic scale have been investigated. It was observed that the type of abrasive particle is one of the important parameters to produce atomically smooth surface. Experiments were also conducted as per the MDS to generate defect-free and sub-nanometre-level finished surface (Ra value better than 0.2 nm). The experimental results reasonably agree well with the simulation results.

CO2 studies remain key to understanding a future world.

PubMed

Becklin, Katie M; Walker, S Michael; Way, Danielle A; Ward, Joy K

2017-04-01

Contents 34 I. 34 II. 36 III. 37 IV. 37 V. 38 38 References 38 SUMMARY: Characterizing plant responses to past, present and future changes in atmospheric carbon dioxide concentration ([CO 2 ]) is critical for understanding and predicting the consequences of global change over evolutionary and ecological timescales. Previous CO 2 studies have provided great insights into the effects of rising [CO 2 ] on leaf-level gas exchange, carbohydrate dynamics and plant growth. However, scaling CO 2 effects across biological levels, especially in field settings, has proved challenging. Moreover, many questions remain about the fundamental molecular mechanisms driving plant responses to [CO 2 ] and other global change factors. Here we discuss three examples of topics in which significant questions in CO 2 research remain unresolved: (1) mechanisms of CO 2 effects on plant developmental transitions; (2) implications of rising [CO 2 ] for integrated plant-water dynamics and drought tolerance; and (3) CO 2 effects on symbiotic interactions and eco-evolutionary feedbacks. Addressing these and other key questions in CO 2 research will require collaborations across scientific disciplines and new approaches that link molecular mechanisms to complex physiological and ecological interactions across spatiotemporal scales. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Reliable binary cell-fate decisions based on oscillations

NASA Astrophysics Data System (ADS)

Pfeuty, B.; Kaneko, K.

2014-02-01

Biological systems have often to perform binary decisions under highly dynamic and noisy environments, such as during cell-fate determination. These decisions can be implemented by two main bifurcation mechanisms based on the transitions from either monostability or oscillation to bistability. We compare these two mechanisms by using stochastic models with time-varying fields and by establishing asymptotic formulas for the choice probabilities. Different scaling laws for decision sensitivity with respect to noise strength and signal timescale are obtained, supporting a role for oscillatory dynamics in performing noise-robust and temporally tunable binary decision-making. This result provides a rationale for recent experimental evidences showing that oscillatory expression of proteins often precedes binary cell-fate decisions.

Inferring multi-scale neural mechanisms with brain network modelling

PubMed Central

Schirner, Michael; McIntosh, Anthony Randal; Jirsa, Viktor; Deco, Gustavo

2018-01-01

The neurophysiological processes underlying non-invasive brain activity measurements are incompletely understood. Here, we developed a connectome-based brain network model that integrates individual structural and functional data with neural population dynamics to support multi-scale neurophysiological inference. Simulated populations were linked by structural connectivity and, as a novelty, driven by electroencephalography (EEG) source activity. Simulations not only predicted subjects' individual resting-state functional magnetic resonance imaging (fMRI) time series and spatial network topologies over 20 minutes of activity, but more importantly, they also revealed precise neurophysiological mechanisms that underlie and link six empirical observations from different scales and modalities: (1) resting-state fMRI oscillations, (2) functional connectivity networks, (3) excitation-inhibition balance, (4, 5) inverse relationships between α-rhythms, spike-firing and fMRI on short and long time scales, and (6) fMRI power-law scaling. These findings underscore the potential of this new modelling framework for general inference and integration of neurophysiological knowledge to complement empirical studies. PMID:29308767

Interaural Level Difference Dependent Gain Control and Synaptic Scaling Underlying Binaural Computation

PubMed Central

Xiong, Xiaorui R.; Liang, Feixue; Li, Haifu; Mesik, Lukas; Zhang, Ke K.; Polley, Daniel B.; Tao, Huizhong W.; Xiao, Zhongju; Zhang, Li I.

2013-01-01

Binaural integration in the central nucleus of inferior colliculus (ICC) plays a critical role in sound localization. However, its arithmetic nature and underlying synaptic mechanisms remain unclear. Here, we showed in mouse ICC neurons that the contralateral dominance is created by a “push-pull”-like mechanism, with contralaterally dominant excitation and more bilaterally balanced inhibition. Importantly, binaural spiking response is generated apparently from an ipsilaterally-mediated scaling of contralateral response, leaving frequency tuning unchanged. This scaling effect is attributed to a divisive attenuation of contralaterally-evoked synaptic excitation onto ICC neurons with their inhibition largely unaffected. Thus, a gain control mediates the linear transformation from monaural to binaural spike responses. The gain value is modulated by interaural level difference (ILD) primarily through scaling excitation to different levels. The ILD-dependent synaptic scaling and gain adjustment allow ICC neurons to dynamically encode interaural sound localization cues while maintaining an invariant representation of other independent sound attributes. PMID:23972599

Fluid dynamic and thermodynamic analysis of a model pertaining to cryogenic fluid management in low gravity environments for a system with dynamically induced settling

NASA Technical Reports Server (NTRS)

Rios, J.

1982-01-01

The settling behavior of the liquid and gaseous phases of a fluid in a propellant and in a zero-g environment, when such settling is induced through the use of a dynamic device, in this particular case, a helical screw was studied. Particular emphasis was given to: (1) the description of a fluid mechanics model which seems applicable to the system under consideration, (2) a First Law of Thermodynamics analysis of the system, and (3) a discussion of applicable scaling rules.

Relaxation Dynamics in the Merging of N Independent Condensates

NASA Astrophysics Data System (ADS)

Aidelsburger, M.; Ville, J. L.; Saint-Jalm, R.; Nascimbène, S.; Dalibard, J.; Beugnon, J.

2017-11-01

Controlled quantum systems such as ultracold atoms can provide powerful platforms to study nonequilibrium dynamics of closed many-body quantum systems, especially since a complete theoretical description is generally challenging. In this Letter, we present a detailed study of the rich out-of-equilibrium dynamics of an adjustable number N of uncorrelated condensates after connecting them in a ring-shaped optical trap. We observe the formation of long-lived supercurrents and confirm the scaling of their winding number with N in agreement with the geodesic rule. Moreover, we provide insight into the microscopic mechanism that underlies the smoothening of the phase profile.

Effect of smoothing on robust chaos.

PubMed

Deshpande, Amogh; Chen, Qingfei; Wang, Yan; Lai, Ying-Cheng; Do, Younghae

2010-08-01

In piecewise-smooth dynamical systems, situations can arise where the asymptotic attractors of the system in an open parameter interval are all chaotic (e.g., no periodic windows). This is the phenomenon of robust chaos. Previous works have established that robust chaos can occur through the mechanism of border-collision bifurcation, where border is the phase-space region where discontinuities in the derivatives of the dynamical equations occur. We investigate the effect of smoothing on robust chaos and find that periodic windows can arise when a small amount of smoothness is present. We introduce a parameter of smoothing and find that the measure of the periodic windows in the parameter space scales linearly with the parameter, regardless of the details of the smoothing function. Numerical support and a heuristic theory are provided to establish the scaling relation. Experimental evidence of periodic windows in a supposedly piecewise linear dynamical system, which has been implemented as an electronic circuit, is also provided.

Mesoscale magnetism

DOE PAGES

Hoffmann, Axel; Schultheiß, Helmut

2014-12-17

Magnetic interactions give rise to a surprising amount of complexity due to the fact that both static and dynamic magnetic properties are governed by competing short-range exchange interactions and long-range dipolar coupling. Even though the underlying dynamical equations are well established, the connection of magnetization dynamics to other degrees of freedom, such as optical excitations, charge and heat flow, or mechanical motion, make magnetism a mesoscale research problem that is still wide open for exploration. Synthesizing magnetic materials and heterostructures with tailored properties will allow to take advantage of magnetic interactions spanning many length-scales, which can be probed with advancedmore » spectroscopy and microscopy and modeled with multi-scale simulations. Finally, this paper highlights some of the current basic research topics in mesoscale magnetism, which beyond their fundamental science impact are also expected to influence applications ranging from information technologies to magnetism based energy conversion.« less

The effect of nanoclay on the rheology and dynamics of polychlorinated biphenyl.

PubMed

Roy, D; Casalini, R; Roland, C M

2015-12-28

The thermal, rheological, and mechanical and dielectric relaxation properties of exfoliated dispersions of montmorillonite clay in a molecular liquid, polychlorobiphenyl (PCB), were studied. The viscosity enhancement at low concentrations of clay (≤5%) exceeded by a factor of 50 the increase obtainable with conventional fillers. However, the effect of the nanoclay on the local dynamics, including the glass transition temperature, was quite small. All materials herein conformed to density-scaling of the reorientation relaxation time of the PCB for a common value of the scaling exponent. A new relaxation process was observed in the mixtures, associated with PCB molecules in proximity to the clay surface. This process has an anomalously high dielectric strength, suggesting a means to exploit nanoparticles to achieve large electrical energy absorption. This lower frequency dispersion has a weaker dependence on pressure and density, consistent with dynamics constrained by interactions with the particle surface.

Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

DOE PAGES

Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; ...

2015-10-22

Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholinemore » catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.« less

Analysis and design of a capsule landing system and surface vehicle control system for Mars exploration

NASA Technical Reports Server (NTRS)

Frederick, D. K.; Lashmet, P. K.; Moyer, W. R.; Sandor, G. N.; Shen, C. N.; Smith, E. J.; Yerazunis, S. W.

1973-01-01

The following tasks related to the design, construction, and evaluation of a mobile planetary vehicle for unmanned exploration of Mars are discussed: (1) design and construction of a 0.5 scale dynamic vehicle; (2) mathematical modeling of vehicle dynamics; (3) experimental 0.4 scale vehicle dynamics measurements and interpretation; (4) vehicle electro-mechanical control systems; (5) remote control systems; (6) collapsibility and deployment concepts and hardware; (7) design, construction and evaluation of a wheel with increased lateral stiffness, (8) system design optimization; (9) design of an on-board computer; (10) design and construction of a laser range finder; (11) measurement of reflectivity of terrain surfaces; (12) obstacle perception by edge detection; (13) terrain modeling based on gradients; (14) laser scan systems; (15) path selection system simulation and evaluation; (16) gas chromatograph system concepts; (17) experimental chromatograph separation measurements and chromatograph model improvement and evaluation.

Towards the computation of time-periodic inertial range dynamics

NASA Astrophysics Data System (ADS)

van Veen, L.; Vela-Martín, A.; Kawahara, G.

2018-04-01

We explore the possibility of computing simple invariant solutions, like travelling waves or periodic orbits, in Large Eddy Simulation (LES) on a periodic domain with constant external forcing. The absence of material boundaries and the simple forcing mechanism make this system a comparatively simple target for the study of turbulent dynamics through invariant solutions. We show, that in spite of the application of eddy viscosity the computations are still rather challenging and must be performed on GPU cards rather than conventional coupled CPUs. We investigate the onset of turbulence in this system by means of bifurcation analysis, and present a long-period, large-amplitude unstable periodic orbit that is filtered from a turbulent time series. Although this orbit is computed on a coarse grid, with only a small separation between the integral scale and the LES filter length, the periodic dynamics seem to capture a regeneration process of the large-scale vortices.

Final Report on DOE Project entitled Dynamic Optimized Advanced Scheduling of Bandwidth Demands for Large-Scale Science Applications

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

Ramamurthy, Byravamurthy

2014-05-05

In this project, developed scheduling frameworks for dynamic bandwidth demands for large-scale science applications. In particular, we developed scheduling algorithms for dynamic bandwidth demands in this project. Apart from theoretical approaches such as Integer Linear Programming, Tabu Search and Genetic Algorithm heuristics, we have utilized practical data from ESnet OSCARS project (from our DOE lab partners) to conduct realistic simulations of our approaches. We have disseminated our work through conference paper presentations and journal papers and a book chapter. In this project we addressed the problem of scheduling of lightpaths over optical wavelength division multiplexed (WDM) networks. We published severalmore » conference papers and journal papers on this topic. We also addressed the problems of joint allocation of computing, storage and networking resources in Grid/Cloud networks and proposed energy-efficient mechanisms for operatin optical WDM networks.« less

Mechanical integrity of a carbon nanotube/copper-based through-silicon via for 3D integrated circuits: a multi-scale modeling approach.

PubMed

Awad, Ibrahim; Ladani, Leila

2015-12-04

Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions.

Simulation Studies of Mechanical Properties of Novel Silica Nano-structures

NASA Astrophysics Data System (ADS)

Muralidharan, Krishna; Torras Costa, Joan; Trickey, Samuel B.

2006-03-01

Advances in nanotechnology and the importance of silica as a technological material continue to stimulate computational study of the properties of possible novel silica nanostructures. Thus we have done classical molecular dynamics (MD) and multi-scale quantum mechanical (QM/MD) simulation studies of the mechanical properties of single-wall and multi-wall silica nano-rods of varying dimensions. Such nano-rods have been predicted by Mallik et al. to be unusually strong in tensile failure. Here we compare failure mechanisms of such nano-rods under tension, compression, and bending. The concurrent multi-scale QM/MD studies use the general PUPIL system (Torras et al.). In this case, PUPIL provides automated interoperation of the MNDO Transfer Hamiltonian QM code (Taylor et al.) and a locally written MD code. Embedding of the QM-forces domain is via the scheme of Mallik et al. Work supported by NSF ITR award DMR-0325553.

Spatial averaging of a dissipative particle dynamics model for active suspensions

NASA Astrophysics Data System (ADS)

Panchenko, Alexander; Hinz, Denis F.; Fried, Eliot

2018-03-01

Starting from a fine-scale dissipative particle dynamics (DPD) model of self-motile point particles, we derive meso-scale continuum equations by applying a spatial averaging version of the Irving-Kirkwood-Noll procedure. Since the method does not rely on kinetic theory, the derivation is valid for highly concentrated particle systems. Spatial averaging yields stochastic continuum equations similar to those of Toner and Tu. However, our theory also involves a constitutive equation for the average fluctuation force. According to this equation, both the strength and the probability distribution vary with time and position through the effective mass density. The statistics of the fluctuation force also depend on the fine scale dissipative force equation, the physical temperature, and two additional parameters which characterize fluctuation strengths. Although the self-propulsion force entering our DPD model contains no explicit mechanism for aligning the velocities of neighboring particles, our averaged coarse-scale equations include the commonly encountered cubically nonlinear (internal) body force density.

Liquidity crises on different time scales

NASA Astrophysics Data System (ADS)

Corradi, Francesco; Zaccaria, Andrea; Pietronero, Luciano

2015-12-01

We present an empirical analysis of the microstructure of financial markets and, in particular, of the static and dynamic properties of liquidity. We find that on relatively large time scales (15 min) large price fluctuations are connected to the failure of the subtle mechanism of compensation between the flows of market and limit orders: in other words, the missed revelation of the latent order book breaks the dynamical equilibrium between the flows, triggering the large price jumps. On smaller time scales (30 s), instead, the static depletion of the limit order book is an indicator of an intrinsic fragility of the system, which is related to a strongly nonlinear enhancement of the response. In order to quantify this phenomenon we introduce a measure of the liquidity imbalance present in the book and we show that it is correlated to both the sign and the magnitude of the next price movement. These findings provide a quantitative definition of the effective liquidity, which proves to be strongly dependent on the considered time scales.

Liquidity crises on different time scales.

PubMed

Corradi, Francesco; Zaccaria, Andrea; Pietronero, Luciano

2015-12-01

We present an empirical analysis of the microstructure of financial markets and, in particular, of the static and dynamic properties of liquidity. We find that on relatively large time scales (15 min) large price fluctuations are connected to the failure of the subtle mechanism of compensation between the flows of market and limit orders: in other words, the missed revelation of the latent order book breaks the dynamical equilibrium between the flows, triggering the large price jumps. On smaller time scales (30 s), instead, the static depletion of the limit order book is an indicator of an intrinsic fragility of the system, which is related to a strongly nonlinear enhancement of the response. In order to quantify this phenomenon we introduce a measure of the liquidity imbalance present in the book and we show that it is correlated to both the sign and the magnitude of the next price movement. These findings provide a quantitative definition of the effective liquidity, which proves to be strongly dependent on the considered time scales.

Probing slow dynamics of consolidated granular multicomposite materials by diffuse acoustic wave spectroscopy.

PubMed

Tremblay, Nicolas; Larose, Eric; Rossetto, Vincent

2010-03-01

The stiffness of a consolidated granular medium experiences a drop immediately after a moderate mechanical solicitation. Then the stiffness rises back toward its initial value, following a logarithmic time evolution called slow dynamics. In the literature, slow dynamics has been probed by macroscopic quantities averaged over the sample volume, for instance, by the resonant frequency of vibrational eigenmodes. This article presents a different approach based on diffuse acoustic wave spectroscopy, a technique that is directly sensitive to the details of the sample structure. The parameters of the dynamics are found to depend on the damage of the medium. Results confirm that slow dynamics is, at least in part, due to tiny structural rearrangements at the microscopic scale, such as inter-grain contacts.

Characterizing popularity dynamics of online videos

NASA Astrophysics Data System (ADS)

Ren, Zhuo-Ming; Shi, Yu-Qiang; Liao, Hao

2016-07-01

Online popularity has a major impact on videos, music, news and other contexts in online systems. Characterizing online popularity dynamics is nature to explain the observed properties in terms of the already acquired popularity of each individual. In this paper, we provide a quantitative, large scale, temporal analysis of the popularity dynamics in two online video-provided websites, namely MovieLens and Netflix. The two collected data sets contain over 100 million records and even span a decade. We characterize that the popularity dynamics of online videos evolve over time, and find that the dynamics of the online video popularity can be characterized by the burst behaviors, typically occurring in the early life span of a video, and later restricting to the classic preferential popularity increase mechanism.

Airborne Subscale Transport Aircraft Research Testbed: Aircraft Model Development

NASA Technical Reports Server (NTRS)

Jordan, Thomas L.; Langford, William M.; Hill, Jeffrey S.

2005-01-01

The Airborne Subscale Transport Aircraft Research (AirSTAR) testbed being developed at NASA Langley Research Center is an experimental flight test capability for research experiments pertaining to dynamics modeling and control beyond the normal flight envelope. An integral part of that testbed is a 5.5% dynamically scaled, generic transport aircraft. This remotely piloted vehicle (RPV) is powered by twin turbine engines and includes a collection of sensors, actuators, navigation, and telemetry systems. The downlink for the plane includes over 70 data channels, plus video, at rates up to 250 Hz. Uplink commands for aircraft control include over 30 data channels. The dynamic scaling requirement, which includes dimensional, weight, inertial, actuator, and data rate scaling, presents distinctive challenges in both the mechanical and electrical design of the aircraft. Discussion of these requirements and their implications on the development of the aircraft along with risk mitigation strategies and training exercises are included here. Also described are the first training (non-research) flights of the airframe. Additional papers address the development of a mobile operations station and an emulation and integration laboratory.

Scale invariance in Newton–Cartan and Hořava–Lifshitz gravity

NASA Astrophysics Data System (ADS)

Olgu Devecioğlu, Deniz; Özdemir, Neşe; Ozkan, Mehmet; Zorba, Utku

2018-06-01

We present a detailed analysis of the construction of z  =  2 and scale invariant Hořava–Lifshitz gravity. The construction procedure is based on the realization of Hořava–Lifshitz gravity as the dynamical Newton–Cartan geometry as well as a non-relativistic tensor calculus in the presence of the scale symmetry. An important consequence of this method is that it provides us with the necessary mechanism to distinguish the local scale invariance from the local Schrödinger invariance. Based on this result we discuss the z  =  2 scale invariant Hořava–Lifshitz gravity and the symmetry enhancement to the full Schrödinger group.

In silico strategies toward enzyme function and dynamics.

PubMed

Estácio, Sílvia G

2012-01-01

Enzymes are outstanding biocatalysts involved in a plethora of chemical reactions occurring in the cell. Despite their incommensurable importance, a comprehensive understanding of enzyme catalysis is still missing. This task becomes more laborious given the unavoidability of including the inherent dynamic nature of enzymes into that description. As such, it is essential to ascertain the nature and contribution of enzyme conformational changes to catalysis and to evaluate the adequacy of the proposal associating protein internal motions to the rate enhancement achieved. Dynamic events in enzymes span a wide range of time- and length-scales which have led to a surge in multiscale methodologies targeting enzyme function and dynamics. Computational strategies assume a preponderant role in such studies by allowing the atomic detail investigation of the fundamental mechanisms of enzyme catalysis thus surpassing what is achievable through experiments. While high-accuracy quantum mechanical methods are indicated to uncover the details of the chemical reaction occurring at the active site, molecular mechanical force fields and molecular dynamics approaches provide powerful means to access the conformational energy landscape accessible to enzymes. This review outlines some of the most important in silico methodologies in this area, highlighting examples of problems tackled and the insights obtained. Copyright © 2012 Elsevier Inc. All rights reserved.

Diffusive, Displacive Deformations and Local Phase Transformation Govern the Mechanics of Layered Crystals: The Case Study of Tobermorite.

PubMed

Tao, Lei; Shahsavari, Rouzbeh

2017-07-19

Understanding the deformation mechanisms underlying the mechanical behavior of materials is the key to fundamental and engineering advances in materials' performance. Herein, we focus on crystalline calcium-silicate-hydrates (C-S-H) as a model system with applications in cementitious materials, bone-tissue engineering, drug delivery and refractory materials, and use molecular dynamics simulation to investigate its loading geometry dependent mechanical properties. By comparing various conventional (e.g. shear, compression and tension) and nano-indentation loading geometries, our findings demonstrate that the former loading leads to size-independent mechanical properties while the latter results in size-dependent mechanical properties at the nanometer scales. We found three key mechanisms govern the deformation and thus mechanics of the layered C-S-H: diffusive-controlled and displacive-controlled deformation mechanisms, and strain gradient with local phase transformations. Together, these elaborately classified mechanisms provide deep fundamental understanding and new insights on the relationship between the macro-scale mechanical properties and underlying molecular deformations, providing new opportunities to control and tune the mechanics of layered crystals and other complex materials such as glassy C-S-H, natural composite structures, and manmade laminated structures.

Local Structures of High-Entropy Alloys (HEAs) on Atomic Scales: An Overview

DOE PAGES

Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; ...

2015-08-29

The high-entropy alloys (HEAs), containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on atomic level are essential to understand the mechanical behaviors and related mechanisms. In this paper, the local structure and stress on the atomic level are reviewed by the pair-distribution function (PDF) of neutron-diffraction data, ab-initio-molecular-dynamics (AIMD) simulations, and atomic-probe microscopy (APT).

A challenge to chaotic itinerancy from brain dynamics

NASA Astrophysics Data System (ADS)

Kay, Leslie M.

2003-09-01

Brain hermeneutics and chaotic itinerancy proposed by Tsuda are attractive characterizations of perceptual dynamics in the mammalian olfactory system. This theory proposes that perception occurs at the interface between itinerant neural representation and interaction with the environment. Quantifiable application of these dynamics has been hampered by the lack of definable history and action processes which characterize the changes induced by behavioral state, attention, and learning. Local field potentials measured from several brain areas were used to characterize dynamic activity patterns for their use as representations of history and action processes. The signals were recorded from olfactory areas (olfactory bulb, OB, and pyriform cortex) and hippocampal areas (entorhinal cortex and dentate gyrus, DG) in the brains of rats. During odor-guided behavior the system shows dynamics at three temporal scales. Short time-scale changes are system-wide and can occur in the space of a single sniff. They are predictable, associated with learned shifts in behavioral state and occur periodically on the scale of the intertrial interval. These changes occupy the theta (2-12 Hz), beta (15-30 Hz), and gamma (40-100 Hz) frequency bands within and between all areas. Medium time-scale changes occur relatively unpredictably, manifesting in these data as alterations in connection strength between the OB and DG. These changes are strongly correlated with performance in associated trial blocks (5-10 min) and may be due to fluctuations in attention, mood, or amount of reward received. Long time-scale changes are likely related to learning or decline due to aging or disease. These may be modeled as slow monotonic processes that occur within or across days or even weeks or years. The folding of different time scales is proposed as a mechanism for chaotic itinerancy, represented by dynamic processes instead of static connection strengths. Thus, the individual maintains continuity of experience within the stability of fast periodic and slow monotonic processes, while medium scale events alter experience and performance dramatically but temporarily. These processes together with as yet to be determined action effects from motor system feedback are proposed as an instantiation of brain hermeneutics and chaotic itinerancy.

Steps Towards Understanding Large-scale Deformation of Gas Hydrate-bearing Sediments

NASA Astrophysics Data System (ADS)

Gupta, S.; Deusner, C.; Haeckel, M.; Kossel, E.

2016-12-01

Marine sediments bearing gas hydrates are typically characterized by heterogeneity in the gas hydrate distribution and anisotropy in the sediment-gas hydrate fabric properties. Gas hydrates also contribute to the strength and stiffness of the marine sediment, and any disturbance in the thermodynamic stability of the gas hydrates is likely to affect the geomechanical stability of the sediment. Understanding mechanisms and triggers of large-strain deformation and failure of marine gas hydrate-bearing sediments is an area of extensive research, particularly in the context of marine slope-stability and industrial gas production. The ultimate objective is to predict severe deformation events such as regional-scale slope failure or excessive sand production by using numerical simulation tools. The development of such tools essentially requires a careful analysis of thermo-hydro-chemo-mechanical behavior of gas hydrate-bearing sediments at lab-scale, and its stepwise integration into reservoir-scale simulators through definition of effective variables, use of suitable constitutive relations, and application of scaling laws. One of the focus areas of our research is to understand the bulk coupled behavior of marine gas hydrate systems with contributions from micro-scale characteristics, transport-reaction dynamics, and structural heterogeneity through experimental flow-through studies using high-pressure triaxial test systems and advanced tomographical tools (CT, ERT, MRI). We combine these studies to develop mathematical model and numerical simulation tools which could be used to predict the coupled hydro-geomechanical behavior of marine gas hydrate reservoirs in a large-strain framework. Here we will present some of our recent results from closely co-ordinated experimental and numerical simulation studies with an objective to capture the large-deformation behavior relevant to different gas production scenarios. We will also report on a variety of mechanically relevant test scenarios focusing on effects of dynamic changes in gas hydrate saturation, highly uneven gas hydrate distributions, focused fluid migration and gas hydrate production through depressurization and CO2 injection.

Evaluation of the scale dependent dynamic SGS model in the open source code caffa3d.MBRi in wall-bounded flows

NASA Astrophysics Data System (ADS)

Draper, Martin; Usera, Gabriel

2015-04-01

The Scale Dependent Dynamic Model (SDDM) has been widely validated in large-eddy simulations using pseudo-spectral codes [1][2][3]. The scale dependency, particularly the potential law, has been proved also in a priori studies [4][5]. To the authors' knowledge there have been only few attempts to use the SDDM in finite difference (FD) and finite volume (FV) codes [6][7], finding some improvements with the dynamic procedures (scale independent or scale dependent approach), but not showing the behavior of the scale-dependence parameter when using the SDDM. The aim of the present paper is to evaluate the SDDM in the open source code caffa3d.MBRi, an updated version of the code presented in [8]. caffa3d.MBRi is a FV code, second-order accurate, parallelized with MPI, in which the domain is divided in unstructured blocks of structured grids. To accomplish this, 2 cases are considered: flow between flat plates and flow over a rough surface with the presence of a model wind turbine, taking for this case the experimental data presented in [9]. In both cases the standard Smagorinsky Model (SM), the Scale Independent Dynamic Model (SIDM) and the SDDM are tested. As presented in [6][7] slight improvements are obtained with the SDDM. Nevertheless, the behavior of the scale-dependence parameter supports the generalization of the dynamic procedure proposed in the SDDM, particularly taking into account that no explicit filter is used (the implicit filter is unknown). [1] F. Porté-Agel, C. Meneveau, M.B. Parlange. "A scale-dependent dynamic model for large-eddy simulation: application to a neutral atmospheric boundary layer". Journal of Fluid Mechanics, 2000, 415, 261-284. [2] E. Bou-Zeid, C. Meneveau, M. Parlante. "A scale-dependent Lagrangian dynamic model for large eddy simulation of complex turbulent flows". Physics of Fluids, 2005, 17, 025105 (18p). [3] R. Stoll, F. Porté-Agel. "Dynamic subgrid-scale models for momentum and scalar fluxes in large-eddy simulations of neutrally stratified atmospheric boundary layers over heterogeneous terrain". Water Resources Research, 2006, 42, WO1409 (18 p). [4] J. Keissl, M. Parlange, C. Meneveau. "Field experimental study of dynamic Smagorinsky models in the atmospheric surface layer". Journal of the Atmospheric Science, 2004, 61, 2296-2307. [5] E. Bou-Zeid, N. Vercauteren, M.B. Parlange, C. Meneveau. "Scale dependence of subgrid-scale model coefficients: An a priori study". Physics of Fluids, 2008, 20, 115106. [6] G. Kirkil, J. Mirocha, E. Bou-Zeid, F.K. Chow, B. Kosovic, "Implementation and evaluation of dynamic subfilter - scale stress models for large - eddy simulation using WRF". Monthly Weather Review, 2012, 140, 266-284. [7] S. Radhakrishnan, U. Piomelli. "Large-eddy simulation of oscillating boundary layers: model comparison and validation". Journal of Geophysical Research, 2008, 113, C02022. [8] G. Usera, A. Vernet, J.A. Ferré. "A parallel block-structured finite volume method for flows in complex geometry with sliding interfaces". Flow, Turbulence and Combustion, 2008, 81, 471-495. [9] Y-T. Wu, F. Porté-Agel. "Large-eddy simulation of wind-turbine wakes: evaluation of turbine parametrisations". BoundaryLayerMeteorology, 2011, 138, 345-366.

Accurate detection of hierarchical communities in complex networks based on nonlinear dynamical evolution

NASA Astrophysics Data System (ADS)

Zhuo, Zhao; Cai, Shi-Min; Tang, Ming; Lai, Ying-Cheng

2018-04-01

One of the most challenging problems in network science is to accurately detect communities at distinct hierarchical scales. Most existing methods are based on structural analysis and manipulation, which are NP-hard. We articulate an alternative, dynamical evolution-based approach to the problem. The basic principle is to computationally implement a nonlinear dynamical process on all nodes in the network with a general coupling scheme, creating a networked dynamical system. Under a proper system setting and with an adjustable control parameter, the community structure of the network would "come out" or emerge naturally from the dynamical evolution of the system. As the control parameter is systematically varied, the community hierarchies at different scales can be revealed. As a concrete example of this general principle, we exploit clustered synchronization as a dynamical mechanism through which the hierarchical community structure can be uncovered. In particular, for quite arbitrary choices of the nonlinear nodal dynamics and coupling scheme, decreasing the coupling parameter from the global synchronization regime, in which the dynamical states of all nodes are perfectly synchronized, can lead to a weaker type of synchronization organized as clusters. We demonstrate the existence of optimal choices of the coupling parameter for which the synchronization clusters encode accurate information about the hierarchical community structure of the network. We test and validate our method using a standard class of benchmark modular networks with two distinct hierarchies of communities and a number of empirical networks arising from the real world. Our method is computationally extremely efficient, eliminating completely the NP-hard difficulty associated with previous methods. The basic principle of exploiting dynamical evolution to uncover hidden community organizations at different scales represents a "game-change" type of approach to addressing the problem of community detection in complex networks.

Young's moduli of carbon materials investigated by various classical molecular dynamics schemes

NASA Astrophysics Data System (ADS)

Gayk, Florian; Ehrens, Julian; Heitmann, Tjark; Vorndamme, Patrick; Mrugalla, Andreas; Schnack, Jürgen

2018-05-01

For many applications classical carbon potentials together with classical molecular dynamics are employed to calculate structures and physical properties of such carbon-based materials where quantum mechanical methods fail either due to the excessive size, irregular structure or long-time dynamics. Although such potentials, as for instance implemented in LAMMPS, yield reasonably accurate bond lengths and angles for several carbon materials such as graphene, it is not clear how accurate they are in terms of mechanical properties such as for instance Young's moduli. We performed large-scale classical molecular dynamics investigations of three carbon-based materials using the various potentials implemented in LAMMPS as well as the EDIP potential of Marks. We show how the Young's moduli vary with classical potentials and compare to experimental results. Since classical descriptions of carbon are bound to be approximations it is not astonishing that different realizations yield differing results. One should therefore carefully check for which observables a certain potential is suited. Our aim is to contribute to such a clarification.

Spatially explicit modelling of cholera epidemics

NASA Astrophysics Data System (ADS)

Finger, F.; Bertuzzo, E.; Mari, L.; Knox, A. C.; Gatto, M.; Rinaldo, A.

2013-12-01

Epidemiological models can provide crucial understanding about the dynamics of infectious diseases. Possible applications range from real-time forecasting and allocation of health care resources to testing alternative intervention mechanisms such as vaccines, antibiotics or the improvement of sanitary conditions. We apply a spatially explicit model to the cholera epidemic that struck Haiti in October 2010 and is still ongoing. The dynamics of susceptibles as well as symptomatic and asymptomatic infectives are modelled at the scale of local human communities. Dissemination of Vibrio cholerae through hydrological transport and human mobility along the road network is explicitly taken into account, as well as the effect of rainfall as a driver of increasing disease incidence. The model is calibrated using a dataset of reported cholera cases. We further model the long term impact of several types of interventions on the disease dynamics by varying parameters appropriately. Key epidemiological mechanisms and parameters which affect the efficiency of treatments such as antibiotics are identified. Our results lead to conclusions about the influence of different intervention strategies on the overall epidemiological dynamics.

A hierarchical dislocation-grain boundary interaction model based on 3D discrete dislocation dynamics and molecular dynamics

NASA Astrophysics Data System (ADS)

Gao, Yuan; Zhuang, Zhuo; You, XiaoChuan

2011-04-01

We develop a new hierarchical dislocation-grain boundary (GB) interaction model to predict the mechanical behavior of polycrystalline metals at micro and submicro scales by coupling 3D Discrete Dislocation Dynamics (DDD) simulation with the Molecular Dynamics (MD) simulation. At the microscales, the DDD simulations are responsible for capturing the evolution of dislocation structures; at the nanoscales, the MD simulations are responsible for obtaining the GB energy and ISF energy which are then transferred hierarchically to the DDD level. In the present model, four kinds of dislocation-GB interactions, i.e. transmission, absorption, re-emission and reflection, are all considered. By this methodology, the compression of a Cu micro-sized bi-crystal pillar is studied. We investigate the characteristic mechanical behavior of the bi-crystal compared with that of the single-crystal. Moreover, the comparison between the present penetrable model of GB and the conventional impenetrable model also shows the accuracy and efficiency of the present model.

Watching Individual Enzymes at Work

NASA Astrophysics Data System (ADS)

Blank, Kerstin; Rocha, Susana; De Cremer, Gert; Roeffaers, Maarten B. J.; Uji-i, Hiroshi; Hofkens, Johan

Single-molecule fluorescence experiments are a powerful tool to analyze reaction mechanisms of enzymes. Because of their unique potential to detect heterogeneities in space and time, they have provided unprecedented insights into the nature and mechanisms of conformational changes related to the catalytic reaction. The most important finding from experiments with single enzymes is the generally observed phenomenon that the catalytic rate constants fluctuate over time (dynamic disorder). These fluctuations originate from conformational changes occurring on time scales, which are similar to or slower than that of the catalytic reaction. Here, we summarize experiments with enzymes that show dynamic disorder and introduce new experimental strategies showing how single-molecule fluorescence experiments can be applied to address other open questions in medical and industrial enzymology, such as enzyme inactivation processes, reactant transfer in cascade reactions, and the mechanisms of interfacial catalysis.

Insufficiency of the Young’s modulus for illustrating the mechanical behavior of GaN nanowires

NASA Astrophysics Data System (ADS)

Zamani Kouhpanji, Mohammad Reza; Behzadirad, Mahmoud; Feezell, Daniel; Busani, Tito

2018-05-01

We use a non-classical modified couple stress theory including the acceleration gradients (MCST-AG), to precisely demonstrate the size dependency of the mechanical properties of gallium nitride (GaN) nanowires (NWs). The fundamental elastic constants, Young’s modulus and length scales of the GaN NWs were estimated both experimentally, using a novel experimental technique applied to atomic force microscopy, and theoretically, using atomic simulations. The Young’s modulus, static and the dynamic length scales, calculated with the MCST-AG, were found to be 323 GPa, 13 and 14.5 nm, respectively, for GaN NWs from a few nanometers radii to bulk radii. Analyzing the experimental data using the classical continuum theory shows an improvement in the experimental results by introducing smaller error. Using the length scales determined in MCST-AG, we explain the inconsistency of the Young’s moduli reported in recent literature, and we prove the insufficiency of the Young’s modulus for predicting the mechanical behavior of GaN NWs.

Cast aluminium single crystals cross the threshold from bulk to size-dependent stochastic plasticity

NASA Astrophysics Data System (ADS)

Krebs, J.; Rao, S. I.; Verheyden, S.; Miko, C.; Goodall, R.; Curtin, W. A.; Mortensen, A.

2017-07-01

Metals are known to exhibit mechanical behaviour at the nanoscale different to bulk samples. This transition typically initiates at the micrometre scale, yet existing techniques to produce micrometre-sized samples often introduce artefacts that can influence deformation mechanisms. Here, we demonstrate the casting of micrometre-scale aluminium single-crystal wires by infiltration of a salt mould. Samples have millimetre lengths, smooth surfaces, a range of crystallographic orientations, and a diameter D as small as 6 μm. The wires deform in bursts, at a stress that increases with decreasing D. Bursts greater than 200 nm account for roughly 50% of wire deformation and have exponentially distributed intensities. Dislocation dynamics simulations show that single-arm sources that produce large displacement bursts halted by stochastic cross-slip and lock formation explain microcast wire behaviour. This microcasting technique may be extended to several other metals or alloys and offers the possibility of exploring mechanical behaviour spanning the micrometre scale.

Generation of mesoscale magnetic fields and the dynamics of Cosmic Ray acceleration

NASA Astrophysics Data System (ADS)

Diamond, P. H.; Malkov, M. A.

The problem of the cosmic ray origin is discussed in connection with their acceleration in supernova remnant shocks. The diffusive shock acceleration mechanism is reviewed and its potential to accelerate particles to the maximum energy of (presumably) galactic cosmic rays (1018eV ) is considered. It is argued that to reach such energies, a strong magnetic field at scales larger than the particle gyroradius must be created as a result of the acceleration process, itself. One specific mechanism suggested here is based on the generation of Alfven wave at the gyroradius scale with a subsequent transfer to longer scales via interaction with strong acoustic turbulence in the shock precursor. The acoustic turbulence in turn, may be generated by Drury instability or by parametric instability of the Alfven waves. The generation mechanism is modulational instability of CR generated Alfven wave packets induced, in turn, by scattering off acoustic fluctuations in the shock precursor which are generated by Drury instability.

Insufficiency of the Young's modulus for illustrating the mechanical behavior of GaN nanowires.

PubMed

Kouhpanji, Mohammad Reza Zamani; Behzadirad, Mahmoud; Feezell, Daniel; Busani, Tito

2018-05-18

We use a non-classical modified couple stress theory including the acceleration gradients (MCST-AG), to precisely demonstrate the size dependency of the mechanical properties of gallium nitride (GaN) nanowires (NWs). The fundamental elastic constants, Young's modulus and length scales of the GaN NWs were estimated both experimentally, using a novel experimental technique applied to atomic force microscopy, and theoretically, using atomic simulations. The Young's modulus, static and the dynamic length scales, calculated with the MCST-AG, were found to be 323 GPa, 13 and 14.5 nm, respectively, for GaN NWs from a few nanometers radii to bulk radii. Analyzing the experimental data using the classical continuum theory shows an improvement in the experimental results by introducing smaller error. Using the length scales determined in MCST-AG, we explain the inconsistency of the Young's moduli reported in recent literature, and we prove the insufficiency of the Young's modulus for predicting the mechanical behavior of GaN NWs.

Characterizing and modeling the dynamics of online popularity.

PubMed

Ratkiewicz, Jacob; Fortunato, Santo; Flammini, Alessandro; Menczer, Filippo; Vespignani, Alessandro

2010-10-08

Online popularity has an enormous impact on opinions, culture, policy, and profits. We provide a quantitative, large scale, temporal analysis of the dynamics of online content popularity in two massive model systems: the Wikipedia and an entire country's Web space. We find that the dynamics of popularity are characterized by bursts, displaying characteristic features of critical systems such as fat-tailed distributions of magnitude and interevent time. We propose a minimal model combining the classic preferential popularity increase mechanism with the occurrence of random popularity shifts due to exogenous factors. The model recovers the critical features observed in the empirical analysis of the systems analyzed here, highlighting the key factors needed in the description of popularity dynamics.

A Comparative Study of [CaEDTA](2-) and [MgEDTA](2-): Structural and Dynamical Insights from Quantum Mechanical Charge Field Molecular Dynamics.

PubMed

Tirler, Andreas O; Hofer, Thomas S

2015-07-09

Structure and dynamics of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution have been investigated via quantum mechanical/molecular mechanical (QM/MM) simulations. While for the first a 6-fold octahedral complex has been observed, the presence of an additional coordinating water ligand has been observed in the latter case. Because of rapidly exchanging water molecules, this 7-fold coordination complex was found to form pentagonal bipyramidal as well as capped trigonal prismatic configurations along the simulation interchanging on the picosecond time scale. Also in the case of [MgEDTA](2-) a trigonal prismatic configuration has been observed for a very short time period of approximately 1 ps. This work reports for the first time the presence of trigonal prismatic structures observed in the coordination sphere of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution. In addition to the detailed characterization of structure and dynamics of the systems, the prediction of the associated infrared spectra indicates that the ion-water vibrational mode found at approximately 250 cm(-1) provides a distinctive measure to experimentally detect the presence of the coordinating water molecule via low-frequency IR setups.

Coexistence in streams: Do source-sink dynamics allow salamanders to persist with fish predators?

USGS Publications Warehouse

Sepulveda, A.J.; Lowe, W.H.

2011-01-01

Theory suggests that source-sink dynamics can allow coexistence of intraguild predators and prey, but empirical evidence for this coexistence mechanism is limited. We used capture-mark-recapture, genetic methods, and stable isotopes to test whether source-sink dynamics promote coexistence between stream fishes, the intraguild predator, and stream salamanders (Dicamptodon aterrimus), the intraguild prey. Salamander populations from upstream reaches without fish were predicted to maintain or supplement sink populations in downstream reaches with fish. We found instead that downstream reaches with fish were not sinks even though fish consumed salamander larvae-apparent survival, recruitment, and population growth rate did not differ between upstream and downstream reaches. There was also no difference between upstream and downstream reaches in net emigration. We did find that D. aterrimus moved frequently along streams, but believe that this is a response to seasonal habitat changes rather than intraguild predation. Our study provides empirical evidence that local-scale mechanisms are more important than dispersal dynamics to coexistence of streams salamanders and fish. More broadly, it shows the value of empirical data on dispersal and gene flow for distinguishing between local and spatial mechanisms of coexistence. ?? 2011 Springer-Verlag.

Non-equilibrium dynamics due to moving deflagration front at RDX/HTPB interface

NASA Astrophysics Data System (ADS)

Chaudhuri, Santanu; Joshi, Kaushik; Lacevic, Naida

Reactive dissipative particle dynamics (DPD-RX), a promising tool in characterizing the sensitivity and performance of heterogeneous solid propellants like polymer bonded explosives (PSXs), requires further testing for non-equilibrium dynamics. It is important to understand detailed atomistic chemistry for developing coarse grain reactive models needed for the DPD-RX. In order to obtain insights into combustion chemistry of RDX/HTPB binder, we used reactive molecular dynamics (RMD) to obtain energy up-pumping and reaction mechanisms at RDX/HTPB interface when exposed to a self-sustaining deflagration front. Hot spots are ignited near and away from the heterogeneous interface using the thermal pulse. The results show that the hot spot near interface significantly delays the transition from ignition to deflagration. We will present the mechanical response and the combustion chemistry of HTPB when the propagating deflagration front hits the polymer binder. We will discuss our efforts to incorporate this RMD based chemistry into the DPD-RX which will enable us to perform such non-equilibrium dynamics simulations on large-length scale with microstructural heterogeneities. Funding from DTRA Grant Number HDTRA1-15-1-0034 is acknowledged.

Dynamical nexus of water supply, hydropower and environment based on the modeling of multiple socio-natural processes: from socio-hydrological perspective

NASA Astrophysics Data System (ADS)

Liu, D.; Wei, X.; Li, H. Y.; Lin, M.; Tian, F.; Huang, Q.

2017-12-01

In the socio-hydrological system, the ecological functions and environmental services, which are chosen to maintain, are determined by the preference of the society, which is making the trade-off among the values of riparian vegetation, fish, river landscape, water supply, hydropower, navigation and so on. As the society develops, the preference of the value will change and the ecological functions and environmental services which are chosen to maintain will change. The aim of the study is to focus on revealing the feedback relationship of water supply, hydropower and environment and the dynamical feedback mechanism at macro-scale, and to establish socio-hydrological evolution model of the watershed based on the modeling of multiple socio-natural processes. The study will aim at the Han River in China, analyze the impact of the water supply and hydropower on the ecology, hydrology and other environment elements, and study the effect on the water supply and hydropower to ensure the ecological and environmental water of the different level. Water supply and ecology are usually competitive. In some reservoirs, hydropower and ecology are synergic relationship while they are competitive in some reservoirs. The study will analyze the multiple mechanisms to implement the dynamical feedbacks of environment to hydropower, set up the quantitative relationship description of the feedback mechanisms, recognize the dominant processes in the feedback relationships of hydropower and environment and then analyze the positive and negative feedbacks in the feedback networks. The socio-hydrological evolution model at the watershed scale will be built and applied to simulate the long-term evolution processes of the watershed of the current situation. Dynamical nexus of water supply, hydropower and environment will be investigated.

Constraints Imposed by the Membrane Selectively Guide the Alternating Access Dynamics of the Glutamate Transporter GltPh

PubMed Central

Lezon, Timothy R.; Bahar, Ivet

2012-01-01

Substrate transport in sodium-coupled amino acid symporters involves a large-scale conformational change that shifts the access to the substrate-binding site from one side of the membrane to the other. The structural change is particularly substantial and entails a unique piston-like quaternary rearrangement in glutamate transporters, as evidenced by the difference between the outward-facing and inward-facing structures resolved for the archaeal aspartate transporter GltPh. These structural changes occur over time and length scales that extend beyond the reach of current fully atomic models, but are regularly explored with the use of elastic network models (ENMs). Despite their success with other membrane proteins, ENM-based approaches for exploring the collective dynamics of GltPh have fallen short of providing a plausible mechanism. This deficiency is attributed here to the anisotropic constraints imposed by the membrane, which are not incorporated into conventional ENMs. Here we employ two novel (to our knowledge) ENMs to demonstrate that one can largely capture the experimentally observed structural change using only the few lowest-energy modes of motion that are intrinsically accessible to the transporter, provided that the surrounding lipid molecules are incorporated into the ENM. The presence of the membrane reduces the overall energy of the transition compared with conventional models, showing that the membrane not only guides the selected mechanism but also acts as a facilitator. Finally, we show that the dynamics of GltPh is biased toward transitions of individual subunits of the trimer rather than cooperative transitions of all three subunits simultaneously, suggesting a mechanism of transport that exploits the intrinsic dynamics of individual subunits. Our software is available online at http://www.membranm.csb.pitt.edu. PMID:22455916

Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh.

PubMed

Lezon, Timothy R; Bahar, Ivet

2012-03-21

Substrate transport in sodium-coupled amino acid symporters involves a large-scale conformational change that shifts the access to the substrate-binding site from one side of the membrane to the other. The structural change is particularly substantial and entails a unique piston-like quaternary rearrangement in glutamate transporters, as evidenced by the difference between the outward-facing and inward-facing structures resolved for the archaeal aspartate transporter Glt(Ph). These structural changes occur over time and length scales that extend beyond the reach of current fully atomic models, but are regularly explored with the use of elastic network models (ENMs). Despite their success with other membrane proteins, ENM-based approaches for exploring the collective dynamics of Glt(Ph) have fallen short of providing a plausible mechanism. This deficiency is attributed here to the anisotropic constraints imposed by the membrane, which are not incorporated into conventional ENMs. Here we employ two novel (to our knowledge) ENMs to demonstrate that one can largely capture the experimentally observed structural change using only the few lowest-energy modes of motion that are intrinsically accessible to the transporter, provided that the surrounding lipid molecules are incorporated into the ENM. The presence of the membrane reduces the overall energy of the transition compared with conventional models, showing that the membrane not only guides the selected mechanism but also acts as a facilitator. Finally, we show that the dynamics of Glt(Ph) is biased toward transitions of individual subunits of the trimer rather than cooperative transitions of all three subunits simultaneously, suggesting a mechanism of transport that exploits the intrinsic dynamics of individual subunits. Our software is available online at http://www.membranm.csb.pitt.edu. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

You can run, you can hide: The epidemiology and statistical mechanics of zombies

NASA Astrophysics Data System (ADS)

Alemi, Alexander A.; Bierbaum, Matthew; Myers, Christopher R.; Sethna, James P.

2015-11-01

We use a popular fictional disease, zombies, in order to introduce techniques used in modern epidemiology modeling, and ideas and techniques used in the numerical study of critical phenomena. We consider variants of zombie models, from fully connected continuous time dynamics to a full scale exact stochastic dynamic simulation of a zombie outbreak on the continental United States. Along the way, we offer a closed form analytical expression for the fully connected differential equation, and demonstrate that the single person per site two dimensional square lattice version of zombies lies in the percolation universality class. We end with a quantitative study of the full scale US outbreak, including the average susceptibility of different geographical regions.

Space and time renormalization in phase transition dynamics

DOE PAGES

Francuz, Anna; Dziarmaga, Jacek; Gardas, Bartłomiej; ...

2016-02-18

Here, when a system is driven across a quantum critical point at a constant rate, its evolution must become nonadiabatic as the relaxation time τ diverges at the critical point. According to the Kibble-Zurek mechanism (KZM), the emerging post-transition excited state is characterized by a finite correlation length ξˆ set at the time tˆ=τˆ when the critical slowing down makes it impossible for the system to relax to the equilibrium defined by changing parameters. This observation naturally suggests a dynamical scaling similar to renormalization familiar from the equilibrium critical phenomena. We provide evidence for such KZM-inspired spatiotemporal scaling by investigatingmore » an exact solution of the transverse field quantum Ising chain in the thermodynamic limit.« less

Computational Materials Research

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A. (Editor); Gates, Thomas S. (Editor)

1996-01-01

Computational Materials aims to model and predict thermodynamic, mechanical, and transport properties of polymer matrix composites. This workshop, the second coordinated by NASA Langley, reports progress in measurements and modeling at a number of length scales: atomic, molecular, nano, and continuum. Assembled here are presentations on quantum calculations for force field development, molecular mechanics of interfaces, molecular weight effects on mechanical properties, molecular dynamics applied to poling of polymers for electrets, Monte Carlo simulation of aromatic thermoplastics, thermal pressure coefficients of liquids, ultrasonic elastic constants, group additivity predictions, bulk constitutive models, and viscoplasticity characterization.

Multi scale modeling of ignition and combustion of micro and nano aluminum particles

NASA Astrophysics Data System (ADS)

Puri, Puneesh

With renewed interest in nano scale energetic materials like aluminum, many fundamental issues concerning the ignition and combustion characteristics at nano scales, remain to be clarified. The overall aim of the current study is the establishment of a unified theory accommodating the various processes and mechanisms involved in the combustion and ignition of aluminum particles at micro and nano scales. A comprehensive review on the ignition and combustion of aluminum particles at multi scales was first performed identifying various processes and mechanisms involved. Research focus was also placed on the establishment of a Molecular Dynamics (MD) simulation tool to investigate the characteristics of nano-particulate aluminum through three major studies. The general computational framework involved parallelized preprocessing, post-processing and main code with capability to simulate different ensembles using appropriate algorithms. Size dependence of melting temperature of pure aluminum particles was investigated in the first study. Phenomena like dynamic coexistence of solid and liquid phase and effect of surface charges on melting were explored. The second study involved the study of effect of defects in the form of voids on melting of bulk and particulate phase aluminum. The third MD study was used to analyze the thermo-mechanical behavior of nano-sized aluminum particles with total diameter of 5-10 nm and oxide thickness of 1-2.5 nm. The ensuing solid-solid and solid-liquid phase changes in the core and shell, stresses developed within the shell, and the diffusion of aluminum cations in the oxide layer, were explored in depth for amorphous and crystalline oxide layers. In the limiting case, the condition for pyrophoricity/explosivity of nano-particulate aluminum was analyzed and modified. The size dependence of thermodynamic properties at nano scales were considered and incorporated into the existing theories developed for micro and larger scales. Finally, a phenomenological theory for ignition and combustion of aluminum particles was proposed. The whole time history from ignition till particle burnout was divided into five stages. An attempt was made to explore different modes of ignition based on the effect of pressure, temperature, oxidizer, oxide thickness and particle diameter and was investigated using length and time scales involved during ignition and combustion.

Anaplasma marginale superinfection attributable to pathogen strains with distinct genomic backgrounds.

USDA-ARS?s Scientific Manuscript database

Microbial strain structure is dynamic over space and time; shifts in pathogen strain structure result in changing patterns of disease. The scale of change in space and time differs markedly among pathogens depending on multiple factors including pathogen-specific mechanisms of genetic change and the...

Particulate Meso-scale Mechanics Diagnostics: Magnetic Sensors for Dynamic State Orientation

DTIC Science & Technology

2013-12-01

Research Laboratory for giving this opportunity to work at the Eglin AFB, FL. REFERENCES 1. Brian D. Reding , “Development of Particulate Materials...Measurements," Sandia Report, 1984. 15. I.N. Tansel, B. Reding , W. L. Cooper, “Lagrangian Point State Estimation with Optimized, Redundant Induction Coil

Formation and field-driven dynamics of nematic spheroids.

PubMed

Fu, Fred; Abukhdeir, Nasser Mohieddin

2017-07-19

Unlike the canonical application of liquid crystals (LCs), LC displays, emerging technologies based on LC materials are increasingly leveraging the presence of nanoscale defects. The inherent nanoscale characteristics of LC defects present both significant opportunities as well as barriers for the application of this fascinating class of materials. Simulation-based approaches to the study of the effects of confinement and interface anchoring conditions on LC domains has resulted in significant progress over the past decade, where simulations are now able to access experimentally-relevant length scales while simultaneously capturing nanoscale defect structures. In this work, continuum simulations were performed in order to study the dynamics of micron-scale nematic LC spheroids of varying shape. Nematic spheroids are one of the simplest inherently defect-containing LC structures and are relevant to polymer-dispersed LC-based "smart" window technology. Simulation results include nematic phase formation and external field-switching dynamics of nematic spheroids ranging in shape from oblate to prolate. Results include both qualitative and quantitative insight into the complex coupling of nanoscale defect dynamics and structure transitions to micron-scale reorientation. Dynamic mechanisms are presented and related to structural transitions in LC defects present in the nematic domain. Domain-averaged metrics including order parameters and response times are determined for a range of experimentally-accessible electric field strengths. These results have both fundamental and technological relevance, in that increased understanding of LC dynamics in the presence of defects is a key barrier to continued advancement in the field.

Capture of fixation by rotational flow; a deterministic hypothesis regarding scaling and stochasticity in fixational eye movements

PubMed Central

Wilkinson, Nicholas M.; Metta, Giorgio

2014-01-01

Visual scan paths exhibit complex, stochastic dynamics. Even during visual fixation, the eye is in constant motion. Fixational drift and tremor are thought to reflect fluctuations in the persistent neural activity of neural integrators in the oculomotor brainstem, which integrate sequences of transient saccadic velocity signals into a short term memory of eye position. Despite intensive research and much progress, the precise mechanisms by which oculomotor posture is maintained remain elusive. Drift exhibits a stochastic statistical profile which has been modeled using random walk formalisms. Tremor is widely dismissed as noise. Here we focus on the dynamical profile of fixational tremor, and argue that tremor may be a signal which usefully reflects the workings of oculomotor postural control. We identify signatures reminiscent of a certain flavor of transient neurodynamics; toric traveling waves which rotate around a central phase singularity. Spiral waves play an organizational role in dynamical systems at many scales throughout nature, though their potential functional role in brain activity remains a matter of educated speculation. Spiral waves have a repertoire of functionally interesting dynamical properties, including persistence, which suggest that they could in theory contribute to persistent neural activity in the oculomotor postural control system. Whilst speculative, the singularity hypothesis of oculomotor postural control implies testable predictions, and could provide the beginnings of an integrated dynamical framework for eye movements across scales. PMID:24616670

Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales

NASA Astrophysics Data System (ADS)

Mukherjee, Biswaroop; Peter, Christine; Kremer, Kurt

2017-09-01

Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.

Ultra-fast relaxation, decoherence, and localization of photoexcited states in π-conjugated polymers

NASA Astrophysics Data System (ADS)

Mannouch, Jonathan R.; Barford, William; Al-Assam, Sarah

2018-01-01

The exciton relaxation dynamics of photoexcited electronic states in poly(p-phenylenevinylene) are theoretically investigated within a coarse-grained model, in which both the exciton and nuclear degrees of freedom are treated quantum mechanically. The Frenkel-Holstein Hamiltonian is used to describe the strong exciton-phonon coupling present in the system, while external damping of the internal nuclear degrees of freedom is accounted for by a Lindblad master equation. Numerically, the dynamics are computed using the time evolving block decimation and quantum jump trajectory techniques. The values of the model parameters physically relevant to polymer systems naturally lead to a separation of time scales, with the ultra-fast dynamics corresponding to energy transfer from the exciton to the internal phonon modes (i.e., the C-C bond oscillations), while the longer time dynamics correspond to damping of these phonon modes by the external dissipation. Associated with these time scales, we investigate the following processes that are indicative of the system relaxing onto the emissive chromophores of the polymer: (1) Exciton-polaron formation occurs on an ultra-fast time scale, with the associated exciton-phonon correlations present within half a vibrational time period of the C-C bond oscillations. (2) Exciton decoherence is driven by the decay in the vibrational overlaps associated with exciton-polaron formation, occurring on the same time scale. (3) Exciton density localization is driven by the external dissipation, arising from "wavefunction collapse" occurring as a result of the system-environment interactions. Finally, we show how fluorescence anisotropy measurements can be used to investigate the exciton decoherence process during the relaxation dynamics.

Novel fine-scale aerial mapping approach quantifies grassland weed cover dynamics and response to management.

PubMed

Malmstrom, Carolyn M; Butterfield, H Scott; Planck, Laura; Long, Christopher W; Eviner, Valerie T

2017-01-01

Invasive weeds threaten the biodiversity and forage productivity of grasslands worldwide. However, management of these weeds is constrained by the practical difficulty of detecting small-scale infestations across large landscapes and by limits in understanding of landscape-scale invasion dynamics, including mechanisms that enable patches to expand, contract, or remain stable. While high-end hyperspectral remote sensing systems can effectively map vegetation cover, these systems are currently too costly and limited in availability for most land managers. We demonstrate application of a more accessible and cost-effective remote sensing approach, based on simple aerial imagery, for quantifying weed cover dynamics over time. In California annual grasslands, the target communities of interest include invasive weedy grasses (Aegilops triuncialis and Elymus caput-medusae) and desirable forage grass species (primarily Avena spp. and Bromus spp.). Detecting invasion of annual grasses into an annual-dominated community is particularly challenging, but we were able to consistently characterize these two communities based on their phenological differences in peak growth and senescence using maximum likelihood supervised classification of imagery acquired twice per year (in mid- and end-of season). This approach permitted us to map weed-dominated cover at a 1-m scale (correctly detecting 93% of weed patches across the landscape) and to evaluate weed cover change over time. We found that weed cover was more pervasive and persistent in management units that had no significant grazing for several years than in those that were grazed, whereas forage cover was more abundant and stable in the grazed units. This application demonstrates the power of this method for assessing fine-scale vegetation transitions across heterogeneous landscapes. It thus provides means for small-scale early detection of invasive species and for testing fundamental questions about landscape dynamics.

Novel fine-scale aerial mapping approach quantifies grassland weed cover dynamics and response to management

PubMed Central

Butterfield, H. Scott; Planck, Laura; Long, Christopher W.; Eviner, Valerie T.

2017-01-01

Invasive weeds threaten the biodiversity and forage productivity of grasslands worldwide. However, management of these weeds is constrained by the practical difficulty of detecting small-scale infestations across large landscapes and by limits in understanding of landscape-scale invasion dynamics, including mechanisms that enable patches to expand, contract, or remain stable. While high-end hyperspectral remote sensing systems can effectively map vegetation cover, these systems are currently too costly and limited in availability for most land managers. We demonstrate application of a more accessible and cost-effective remote sensing approach, based on simple aerial imagery, for quantifying weed cover dynamics over time. In California annual grasslands, the target communities of interest include invasive weedy grasses (Aegilops triuncialis and Elymus caput-medusae) and desirable forage grass species (primarily Avena spp. and Bromus spp.). Detecting invasion of annual grasses into an annual-dominated community is particularly challenging, but we were able to consistently characterize these two communities based on their phenological differences in peak growth and senescence using maximum likelihood supervised classification of imagery acquired twice per year (in mid- and end-of season). This approach permitted us to map weed-dominated cover at a 1-m scale (correctly detecting 93% of weed patches across the landscape) and to evaluate weed cover change over time. We found that weed cover was more pervasive and persistent in management units that had no significant grazing for several years than in those that were grazed, whereas forage cover was more abundant and stable in the grazed units. This application demonstrates the power of this method for assessing fine-scale vegetation transitions across heterogeneous landscapes. It thus provides means for small-scale early detection of invasive species and for testing fundamental questions about landscape dynamics. PMID:29016604

Unveiling the molecular mechanism of self-healing in a telechelic, supramolecular polymer network

PubMed Central

Yan, Tingzi; Schröter, Klaus; Herbst, Florian; Binder, Wolfgang H.; Thurn-Albrecht, Thomas

2016-01-01

Reversible polymeric networks can show self-healing properties due to their ability to reassemble after application of stress and fracture, but typically the relation between equilibrium molecular dynamics and self-healing kinetics has been difficult to disentangle. Here we present a well-characterized, self-assembled bulk network based on supramolecular assemblies, that allows a clear distinction between chain dynamics and network relaxation. Small angle x-ray scattering and rheological measurements provide evidence for a structurally well-defined, dense network of interconnected aggregates giving mechanical strength to the material. Different from a covalent network, the dynamic character of the supramolecular bonds enables macroscopic flow on a longer time scale and the establishment of an equilibrium structure. A combination of linear and nonlinear rheological measurements clearly identifies the terminal relaxation process as being responsible for the process of self-healing. PMID:27581380

Unraveling the mechanisms underlying postural instability in Parkinson's disease using dynamic posturography.

PubMed

Nonnekes, Jorik; de Kam, Digna; Geurts, Alexander C H; Weerdesteyn, Vivian; Bloem, Bastiaan R

2013-12-01

Postural instability, one of the cardinal symptoms of Parkinson's disease (PD), has devastating consequences for affected patients. Better strategies to prevent falls are needed, but this calls for an improved understanding of the complex mechanisms underlying postural instability. We must also improve our ability to timely identify patients at risk of falling. Dynamic posturography is a promising avenue to achieve these goals. The latest moveable platforms can deliver 'real-life' balance perturbations, permitting study of everyday fall circumstances. Dynamic posturography studies have shown that PD patients have fundamental problems in scaling their postural responses in accordance with the need of the actual balance task at hand. On-going studies evaluate the predictive ability of impaired posturography performance for daily life falls. We also review recent work aimed at exploring balance correcting steps in PD, and the presumed interaction between startle pathways and postural responses.

Neural mechanisms of movement planning: motor cortex and beyond.

PubMed

Svoboda, Karel; Li, Nuo

2018-04-01

Neurons in motor cortex and connected brain regions fire in anticipation of specific movements, long before movement occurs. This neural activity reflects internal processes by which the brain plans and executes volitional movements. The study of motor planning offers an opportunity to understand how the structure and dynamics of neural circuits support persistent internal states and how these states influence behavior. Recent advances in large-scale neural recordings are beginning to decipher the relationship of the dynamics of populations of neurons during motor planning and movements. New behavioral tasks in rodents, together with quantified perturbations, link dynamics in specific nodes of neural circuits to behavior. These studies reveal a neural network distributed across multiple brain regions that collectively supports motor planning. We review recent advances and highlight areas where further work is needed to achieve a deeper understanding of the mechanisms underlying motor planning and related cognitive processes. Copyright © 2017. Published by Elsevier Ltd.

Ballistic aggregation in systems of inelastic particles: Cluster growth, structure, and aging

NASA Astrophysics Data System (ADS)

Paul, Subhajit; Das, Subir K.

2017-07-01

We study far-from-equilibrium dynamics in models of freely cooling granular gas and ballistically aggregating compact clusters. For both the cases, from event-driven molecular dynamics simulations, we have presented detailed results on structure and dynamics in space dimensions d =1 and 2. Via appropriate analyses it has been confirmed that the ballistic aggregation mechanism applies in d =1 granular gases as well. Aging phenomena for this mechanism, in both the dimensions, have been studied via the two-time density autocorrelation function. This quantity is demonstrated to exhibit scaling property similar to that in the standard phase transition kinetics. The corresponding functional forms have been quantified and the outcomes have been discussed in connection with the structural properties. Our results on aging establish a more complete equivalence between the granular gas and the ballistic aggregation models in d =1 .

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

From Fibrils to Toughness: Multi-Scale Mechanics of Fibrillating Interfaces in Stretchable Electronics

PubMed Central

van der Sluis, Olaf; Vossen, Bart; Geers, Marc

2018-01-01

Metal-elastomer interfacial systems, often encountered in stretchable electronics, demonstrate remarkably high interface fracture toughness values. Evidently, a large gap exists between the rather small adhesion energy levels at the microscopic scale (‘intrinsic adhesion’) and the large measured macroscopic work-of-separation. This energy gap is closed here by unravelling the underlying dissipative mechanisms through a systematic numerical/experimental multi-scale approach. This self-containing contribution collects and reviews previously published results and addresses the remaining open questions by providing new and independent results obtained from an alternative experimental set-up. In particular, the experimental studies on Cu-PDMS (Poly(dimethylsiloxane)) samples conclusively reveal the essential role of fibrillation mechanisms at the micro-meter scale during the metal-elastomer delamination process. The micro-scale numerical analyses on single and multiple fibrils show that the dynamic release of the stored elastic energy by multiple fibril fracture, including the interaction with the adjacent deforming bulk PDMS and its highly nonlinear behaviour, provide a mechanistic understanding of the high work-of-separation. An experimentally validated quantitative relation between the macroscopic work-of-separation and peel front height is established from the simulation results. Finally, it is shown that a micro-mechanically motivated shape of the traction-separation law in cohesive zone models is essential to describe the delamination process in fibrillating metal-elastomer systems in a physically meaningful way. PMID:29393908

Multiple Scales in Fluid Dynamics and Meteorology: The DFG Priority Programme 1276 MetStröm

NASA Astrophysics Data System (ADS)

von Larcher, Th; Klein, R.

2012-04-01

Geophysical fluid motions are characterized by a very wide range of length and time scales, and by a rich collection of varying physical phenomena. The mathematical description of these motions reflects this multitude of scales and mechanisms in that it involves strong non-linearities and various scale-dependent singular limit regimes. Considerable progress has been made in recent years in the mathematical modelling and numerical simulation of such flows in detailed process studies, numerical weather forecasting, and climate research. One task of outstanding importance in this context has been and will remain for the foreseeable future the subgrid scale parameterization of the net effects of non-resolved processes that take place on spacio-temporal scales not resolvable even by the largest most recent supercomputers. Since the advent of numerical weather forecasting some 60 years ago, one simple but efficient means to achieve improved forecasting skills has been increased spacio-temporal resolution. This seems quite consistent with the concept of convergence of numerical methods in Applied Mathematics and Computational Fluid Dynamics (CFD) at a first glance. Yet, the very notion of increased resolution in atmosphere-ocean science is very different from the one used in Applied Mathematics: For the mathematician, increased resolution provides the benefit of getting closer to the ideal of a converged solution of some given partial differential equations. On the other hand, the atmosphere-ocean scientist would naturally refine the computational grid and adjust his mathematical model, such that it better represents the relevant physical processes that occur at smaller scales. This conceptual contradiction remains largely irrelevant as long as geophysical flow models operate with fixed computational grids and time steps and with subgrid scale parameterizations being optimized accordingly. The picture changes fundamentally when modern techniques from CFD involving spacio-temporal grid adaptivity get invoked in order to further improve the net efficiency in exploiting the given computational resources. In the setting of geophysical flow simulation one must then employ subgrid scale parameterizations that dynamically adapt to the changing grid sizes and time steps, implement ways to judiciously control and steer the newly available flexibility of resolution, and invent novel ways of quantifying the remaining errors. The DFG priority program MetStröm covers the expertise of Meteorology, Fluid Dynamics, and Applied Mathematics to develop model- as well as grid-adaptive numerical simulation concepts in multidisciplinary projects. The goal of this priority programme is to provide simulation models which combine scale-dependent (mathematical) descriptions of key physical processes with adaptive flow discretization schemes. Deterministic continuous approaches and discrete and/or stochastic closures and their possible interplay are taken into consideration. Research focuses on the theory and methodology of multiscale meteorological-fluid mechanics modelling. Accompanying reference experiments support model validation.

Inferring infection hazard in wildlife populations by linking data across individual and population scales.

PubMed

Pepin, Kim M; Kay, Shannon L; Golas, Ben D; Shriner, Susan S; Gilbert, Amy T; Miller, Ryan S; Graham, Andrea L; Riley, Steven; Cross, Paul C; Samuel, Michael D; Hooten, Mevin B; Hoeting, Jennifer A; Lloyd-Smith, James O; Webb, Colleen T; Buhnerkempe, Michael G

2017-03-01

Our ability to infer unobservable disease-dynamic processes such as force of infection (infection hazard for susceptible hosts) has transformed our understanding of disease transmission mechanisms and capacity to predict disease dynamics. Conventional methods for inferring FOI estimate a time-averaged value and are based on population-level processes. Because many pathogens exhibit epidemic cycling and FOI is the result of processes acting across the scales of individuals and populations, a flexible framework that extends to epidemic dynamics and links within-host processes to FOI is needed. Specifically, within-host antibody kinetics in wildlife hosts can be short-lived and produce patterns that are repeatable across individuals, suggesting individual-level antibody concentrations could be used to infer time since infection and hence FOI. Using simulations and case studies (influenza A in lesser snow geese and Yersinia pestis in coyotes), we argue that with careful experimental and surveillance design, the population-level FOI signal can be recovered from individual-level antibody kinetics, despite substantial individual-level variation. In addition to improving inference, the cross-scale quantitative antibody approach we describe can reveal insights into drivers of individual-based variation in disease response, and the role of poorly understood processes such as secondary infections, in population-level dynamics of disease. © 2017 John Wiley & Sons Ltd/CNRS.

Inferring infection hazard in wildlife populations by linking data across individual and population scales

USGS Publications Warehouse

Pepin, Kim M.; Kay, Shannon L.; Golas, Ben D.; Shriner, Susan A.; Gilbert, Amy T.; Miller, Ryan S.; Graham, Andrea L.; Riley, Steven; Cross, Paul C.; Samuel, Michael D.; Hooten, Mevin B.; Hoeting, Jennifer A.; Lloyd-Smith, James O.; Webb, Colleen T.; Buhnerkempe, Michael G.

2017-01-01

Our ability to infer unobservable disease-dynamic processes such as force of infection (infection hazard for susceptible hosts) has transformed our understanding of disease transmission mechanisms and capacity to predict disease dynamics. Conventional methods for inferring FOI estimate a time-averaged value and are based on population-level processes. Because many pathogens exhibit epidemic cycling and FOI is the result of processes acting across the scales of individuals and populations, a flexible framework that extends to epidemic dynamics and links within-host processes to FOI is needed. Specifically, within-host antibody kinetics in wildlife hosts can be short-lived and produce patterns that are repeatable across individuals, suggesting individual-level antibody concentrations could be used to infer time since infection and hence FOI. Using simulations and case studies (influenza A in lesser snow geese and Yersinia pestis in coyotes), we argue that with careful experimental and surveillance design, the population-level FOI signal can be recovered from individual-level antibody kinetics, despite substantial individual-level variation. In addition to improving inference, the cross-scale quantitative antibody approach we describe can reveal insights into drivers of individual-based variation in disease response, and the role of poorly understood processes such as secondary infections, in population-level dynamics of disease.

Ultrafast dynamics of defect-assisted electron-hole recombination in monolayer MoS2.

PubMed

Wang, Haining; Zhang, Changjian; Rana, Farhan

2015-01-14

In this Letter, we present nondegenerate ultrafast optical pump-probe studies of the carrier recombination dynamics in MoS2 monolayers. By tuning the probe to wavelengths much longer than the exciton line, we make the probe transmission sensitive to the total population of photoexcited electrons and holes. Our measurement reveals two distinct time scales over which the photoexcited electrons and holes recombine; a fast time scale that lasts ∼ 2 ps and a slow time scale that lasts longer than ∼ 100 ps. The temperature and the pump fluence dependence of the observed carrier dynamics are consistent with defect-assisted recombination as being the dominant mechanism for electron-hole recombination in which the electrons and holes are captured by defects via Auger processes. Strong Coulomb interactions in two-dimensional atomic materials, together with strong electron and hole correlations in two-dimensional metal dichalcogenides, make Auger processes particularly effective for carrier capture by defects. We present a model for carrier recombination dynamics that quantitatively explains all features of our data for different temperatures and pump fluences. The theoretical estimates for the rate constants for Auger carrier capture are in good agreement with the experimentally determined values. Our results underscore the important role played by Auger processes in two-dimensional atomic materials.

A discrete dislocation dynamics model of creeping single crystals

NASA Astrophysics Data System (ADS)

Rajaguru, M.; Keralavarma, S. M.

2018-04-01

Failure by creep is a design limiting issue for metallic materials used in several high temperature applications. Current theoretical models of creep are phenomenological with little connection to the underlying microscopic mechanisms. In this paper, a bottom-up simulation framework based on the discrete dislocation dynamics method is presented for dislocation creep aided by the diffusion of vacancies, known to be the rate controlling mechanism at high temperature and stress levels. The time evolution of the creep strain and the dislocation microstructure in a periodic unit cell of a nominally infinite single crystal is simulated using the kinetic Monte Carlo method, together with approximate constitutive laws formulated for the rates of thermal activation of dislocations over local pinning obstacles. The deformation of the crystal due to dislocation glide between individual thermal activation events is simulated using a standard dislocation dynamics algorithm, extended to account for constant stress periodic boundary conditions. Steady state creep conditions are obtained in the simulations with the predicted creep rates as a function of stress and temperature in good agreement with experimentally reported values. Arrhenius scaling of the creep rates as a function of temperature and power-law scaling with the applied stress are also reproduced, with the values of the power-law exponents in the high stress regime in good agreement with experiments.

Dynamic wind-tunnel tests of an aeromechanical gust-alleviation system using several different combinations of control surfaces

NASA Technical Reports Server (NTRS)

Stewart, E. C.; Doggett, R. V., Jr.

1978-01-01

Some experimental results are presented from wind tunnel studies of a dynamic model equipped with an aeromechanical gust alleviation system for reducing the normal acceleration response of light airplanes. The gust alleviation system consists of two auxiliary aerodynamic surfaces that deflect the wing flaps through mechanical linkages when a gust is encountered to maintain nearly constant airplane lift. The gust alleviation system was implemented on a 1/6-scale, rod mounted, free flying model that is geometrically and dynamically representative of small, four place, high wing, single engine, light airplanes. The effects of flaps with different spans, two size of auxiliary aerodynamic surfaces, plain and double hinged flaps, and a flap elevator interconnection were studied. The model test results are presented in terms of predicted root mean square response of the full scale airplane to atmospheric turbulence. The results show that the gust alleviation system reduces the root mean square normal acceleration response by 30 percent in comparison with the response in the flaps locked condition. Small reductions in pitch-rate response were also obtained. It is believed that substantially larger reductions in normal acceleration can be achieved by reducing the rather high levels of mechanical friction which were extant in the alleviation system of the present model.

A general theory for the lifetimes of giant molecular clouds under the influence of galactic dynamics

NASA Astrophysics Data System (ADS)

Jeffreson, Sarah M. R.; Kruijssen, J. M. Diederik

2018-05-01

We propose a simple analytic theory for environmentally dependent molecular cloud lifetimes, based on the large-scale (galactic) dynamics of the interstellar medium. Within this theory, the cloud lifetime is set by the time-scales for gravitational collapse, galactic shear, spiral arm interactions, epicyclic perturbations, and cloud-cloud collisions. It is dependent on five observable quantities, accessible through measurements of the galactic rotation curve, the gas and stellar surface densities, and the gas and stellar velocity dispersions of the host galaxy. We determine how the relative importance of each dynamical mechanism varies throughout the space of observable galactic properties, and conclude that gravitational collapse and galactic shear play the greatest role in setting the cloud lifetime for the considered range of galaxy properties, while cloud-cloud collisions exert a much lesser influence. All five environmental mechanisms are nevertheless required to obtain a complete picture of cloud evolution. We apply our theory to the galaxies M31, M51, M83, and the Milky Way, and find a strong dependence of the cloud lifetime upon galactocentric radius in each case, with a typical cloud lifetime between 10 and 50 Myr. Our theory is ideally suited for systematic observational tests with the Atacama Large Millimetre/submillimetre array.

Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models.

PubMed

Qin, Zhao; Buehler, Markus J

2011-01-01

Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer and the tetramer, however, have remained elusive due to persistent experimental challenges owing to the large size and fibrillar geometry of this protein. We have recently reported an atomistic-level model of the human vimentin dimer and tetramer, obtained through a bottom-up approach based on structural optimization via molecular simulation based on an implicit solvent model (Qin et al. in PLoS ONE 2009 4(10):e7294, 9). Here we present extensive simulations and structural analyses of the model based on ultra large-scale atomistic-level simulations in an explicit solvent model, with system sizes exceeding 500,000 atoms and simulations carried out at 20 ns time-scales. We report a detailed comparison of the structural and dynamical behavior of this large biomolecular model with implicit and explicit solvent models. Our simulations confirm the stability of the molecular model and provide insight into the dynamical properties of the dimer and tetramer. Specifically, our simulations reveal a heterogeneous distribution of the bending stiffness along the molecular axis with the formation of rather soft and highly flexible hinge-like regions defined by non-alpha-helical linker domains. We report a comparison of Ramachandran maps and the solvent accessible surface area between implicit and explicit solvent models, and compute the persistence length of the dimer and tetramer structure of vimentin intermediate filaments for various subdomains of the protein. Our simulations provide detailed insight into the dynamical properties of the vimentin dimer and tetramer intermediate filament building blocks, which may guide the development of novel coarse-grained models of intermediate filaments, and could also help in understanding assembly mechanisms.

Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition.

PubMed

Schlundt, Andreas; Tants, Jan-Niklas; Sattler, Michael

2017-04-15

Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain arrangements and dynamics. Principles of protein-RNA recognition and current approaches are reviewed and illustrated with recent studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Genome organization in the nucleus: From dynamic measurements to a functional model.

PubMed

Vivante, Anat; Brozgol, Eugene; Bronshtein, Irena; Garini, Yuval

2017-07-01

A biological system is by definition a dynamic environment encompassing kinetic processes that occur at different length scales and time ranges. To explore this type of system, spatial information needs to be acquired at different time scales. This means overcoming significant hurdles, including the need for stable and precise labeling of the required probes and the use of state of the art optical methods. However, to interpret the acquired data, biophysical models that can account for these biological mechanisms need to be developed. The structure and function of a biological system are closely related to its dynamic properties, thus further emphasizing the importance of identifying the rules governing the dynamics that cannot be directly deduced from information on the structure itself. In eukaryotic cells, tens of thousands of genes are packed in the small volume of the nucleus. The genome itself is organized in chromosomes that occupy specific volumes referred to as chromosome territories. This organization is preserved throughout the cell cycle, even though there are no sub-compartments in the nucleus itself. This organization, which is still not fully understood, is crucial for a large number of cellular functions such as gene regulation, DNA breakage repair and error-free cell division. Various techniques are in use today, including imaging, live cell imaging and molecular methods such as chromosome conformation capture (3C) methods to better understand these mechanisms. Live cell imaging methods are becoming well established. These include methods such as Single Particle Tracking (SPT), Continuous Photobleaching (CP), Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS) that are currently used for studying proteins, RNA, DNA, gene loci and nuclear bodies. They provide crucial information on its mobility, reorganization, interactions and binding properties. Here we describe how these dynamic methods can be used to gather information on genome organization, its stabilization mechanisms and the proteins that take part in it. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

PubMed

Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

2009-05-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

PubMed Central

Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

2012-01-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

Hot spot formation and chemical reaction initiation in shocked HMX crystals with nanovoids: a large-scale reactive molecular dynamics study.

PubMed

Zhou, Tingting; Lou, Jianfeng; Zhang, Yangeng; Song, Huajie; Huang, Fenglei

2016-07-14

We report million-atom reactive molecular dynamic simulations of shock initiation of β-cyclotetramethylene tetranitramine (β-HMX) single crystals containing nanometer-scale spherical voids. Shock induced void collapse and subsequent hot spot formation as well as chemical reaction initiation are observed which depend on the void size and impact strength. For an impact velocity of 1 km s(-1) and a void radius of 4 nm, the void collapse process includes three stages; the dominant mechanism is the convergence of upstream molecules toward the centerline and the downstream surface of the void forming flowing molecules. Hot spot formation also undergoes three stages, and the principal mechanism is kinetic energy transforming to thermal energy due to the collision of flowing molecules on the downstream surface. The high temperature of the hot spot initiates a local chemical reaction, and the breakage of the N-NO2 bond plays the key role in the initial reaction mechanism. The impact strength and void size have noticeable effects on the shock dynamical process, resulting in a variation of the predominant mechanisms leading to void collapse and hot spot formation. Larger voids or stronger shocks result in more intense hot spots and, thus, more violent chemical reactions, promoting more reaction channels and generating more reaction products in a shorter duration. The reaction products are mainly concentrated in the developed hot spot, indicating that the chemical reactivity of the hmx crystal is greatly enhanced by void collapse. The detailed information derived from this study can aid a thorough understanding of the role of void collapse in hot spot formation and the chemical reaction initiation of explosives.

Dynamic near-field optical interaction between oscillating nanomechanical structures

DOE PAGES

Ahn, Phillip; Chen, Xiang; Zhang, Zhen; ...

2015-05-27

Near-field optical techniques exploit light-matter interactions at small length scales for mechanical sensing and actuation of nanomechanical structures. Here, we study the optical interaction between two mechanical oscillators—a plasmonic nanofocusing probe-tip supported by a low frequency cantilever, and a high frequency nanomechanical resonator—and leverage their interaction for local detection of mechanical vibrations. The plasmonic nanofocusing probe provides a confined optical source to enhance the interaction between the two oscillators. Dynamic perturbation of the optical cavity between the probe-tip and the resonator leads to nonlinear modulation of the scattered light intensity at the sum and difference of their frequencies. This double-frequencymore » demodulation scheme is explored to suppress unwanted background and to detect mechanical vibrations with a minimum detectable displacement sensitivity of 0.45pm/Hz 1/2, which is limited by shot noise and electrical noise. We explore the demodulation scheme for imaging the bending vibration mode shape of the resonator with a lateral spatial resolution of 20nm. We also demonstrate the time-resolved aspect of the local optical interaction by recording the ring-down vibrations of the resonator at frequencies of up to 129MHz. The near-field optical technique is promising for studying dynamic mechanical processes in individual nanostructures.« less

Toward a more efficient and scalable checkpoint/restart mechanism in the Community Atmosphere Model

NASA Astrophysics Data System (ADS)

Anantharaj, Valentine

2015-04-01

The number of cores (both CPU as well as accelerator) in large-scale systems has been increasing rapidly over the past several years. In 2008, there were only 5 systems in the Top500 list that had over 100,000 total cores (including accelerator cores) whereas the number of system with such capability has jumped to 31 in Nov 2014. This growth however has also increased the risk of hardware failure rates, necessitating the implementation of fault tolerance mechanism in applications. The checkpoint and restart (C/R) approach is commonly used to save the state of the application and restart at a later time either after failure or to continue execution of experiments. The implementation of an efficient C/R mechanism will make it more affordable to output the necessary C/R files more frequently. The availability of larger systems (more nodes, memory and cores) has also facilitated the scaling of applications. Nowadays, it is more common to conduct coupled global climate simulation experiments at 1 deg horizontal resolution (atmosphere), often requiring about 103 cores. At the same time, a few climate modeling teams that have access to a dedicated cluster and/or large scale systems are involved in modeling experiments at 0.25 deg horizontal resolution (atmosphere) and 0.1 deg resolution for the ocean. These ultrascale configurations require the order of 104 to 105 cores. It is not only necessary for the numerical algorithms to scale efficiently but the input/output (IO) mechanism must also scale accordingly. An ongoing series of ultrascale climate simulations, using the Titan supercomputer at the Oak Ridge Leadership Computing Facility (ORNL), is based on the spectral element dynamical core of the Community Atmosphere Model (CAM-SE), which is a component of the Community Earth System Model and the DOE Accelerated Climate Model for Energy (ACME). The CAM-SE dynamical core for a 0.25 deg configuration has been shown to scale efficiently across 100,000 cpu cores. At this scale, there is an increased risk that the simulation could be terminated due to hardware failures, resulting in a loss that could be as high as 105 - 106 titan core hours. Increasing the frequency of the output of C/R files could mitigate this loss but at the cost of additional C/R overhead. We are testing a more efficient C/R mechanism in CAM-SE. Our early implementation has demonstrated a nearly 3X performance improvement for a 1 deg CAM-SE (with CAM5 physics and MOZART chemistry) configuration using nearly 103 cores. We are in the process of scaling our implementation to 105 cores. This would allow us to run ultra scale simulations with more sophisticated physics and chemistry options while making better utilization of resources.

Kinetic Simulations of the Interruption of Large-Amplitude Shear-Alfvén Waves in a High- β Plasma

DOE PAGES

Squire, J.; Kunz, M. W.; Quataert, E.; ...

2017-10-12

Using two-dimensional hybrid-kinetic simulations, we explore the nonlinear “interruption” of standing and traveling shear-Alfvén waves in collisionless plasmas. Interruption involves a self-generated pressure anisotropy removing the restoring force of a linearly polarized Alfvénic perturbation, and occurs for wave amplitudes δB ⊥/B 0≳β –1/2 (where β is the ratio of thermal to magnetic pressure). We use highly elongated domains to obtain maximal scale separation between the wave and the ion gyroscale. For standing waves above the amplitude limit, we find that the large-scale magnetic field of the wave decays rapidly. The dynamics are strongly affected by the excitation of oblique firehosemore » modes, which transition into long-lived parallel fluctuations at the ion gyroscale and cause significant particle scattering. Traveling waves are damped more slowly, but are also influenced by small-scale parallel fluctuations created by the decay of firehose modes. Our results demonstrate that collisionless plasmas cannot support linearly polarized Alfvén waves above δB ⊥/B 0~β –1/2. Here, they also provide a vivid illustration of two key aspects of low-collisionality plasma dynamics: (i) the importance of velocity-space instabilities in regulating plasma dynamics at high β, and (ii) how nonlinear collisionless processes can transfer mechanical energy directly from the largest scales into thermal energy and microscale fluctuations, without the need for a scale-by-scale turbulent cascade.« less

Kinetic Simulations of the Interruption of Large-Amplitude Shear-Alfvén Waves in a High- β Plasma

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

Squire, J.; Kunz, M. W.; Quataert, E.

Using two-dimensional hybrid-kinetic simulations, we explore the nonlinear “interruption” of standing and traveling shear-Alfvén waves in collisionless plasmas. Interruption involves a self-generated pressure anisotropy removing the restoring force of a linearly polarized Alfvénic perturbation, and occurs for wave amplitudes δB ⊥/B 0≳β –1/2 (where β is the ratio of thermal to magnetic pressure). We use highly elongated domains to obtain maximal scale separation between the wave and the ion gyroscale. For standing waves above the amplitude limit, we find that the large-scale magnetic field of the wave decays rapidly. The dynamics are strongly affected by the excitation of oblique firehosemore » modes, which transition into long-lived parallel fluctuations at the ion gyroscale and cause significant particle scattering. Traveling waves are damped more slowly, but are also influenced by small-scale parallel fluctuations created by the decay of firehose modes. Our results demonstrate that collisionless plasmas cannot support linearly polarized Alfvén waves above δB ⊥/B 0~β –1/2. Here, they also provide a vivid illustration of two key aspects of low-collisionality plasma dynamics: (i) the importance of velocity-space instabilities in regulating plasma dynamics at high β, and (ii) how nonlinear collisionless processes can transfer mechanical energy directly from the largest scales into thermal energy and microscale fluctuations, without the need for a scale-by-scale turbulent cascade.« less

A hypothesis linking chrysophyte microfossils to lake carbon dynamics on ecological and evolutionary time scales

NASA Astrophysics Data System (ADS)

Wolfe, Alexander P.; Siver, Peter A.

2013-12-01

Chrysophyte algae are common in the plankton of oligotrophic lakes and produce a rich microfossil record of siliceous cysts and scales. Paleolimnological investigations and phytoplankton records suggest that chrysophyte populations are increasing in a wide range of boreal and arctic lakes, ultimately representing one component of the limnological response to contemporary global changes. However, the exact mechanisms responsible for widespread increases of chrysophyte populations remain elusive. We hypothesize that recent increases in chrysophytes are related to rising pCO2 in lakes, in part because these algae lack carbon concentrating mechanisms and therefore rely on diffusive entry of CO2 to Rubisco during photosynthesis. We assessed the abundance of modern sediment chrysophyte microfossils in relation to summer CO2 relative saturation in 46 New England (USA) lakes, revealing significant positive relationships for both cysts and scales. These observations imply that correlations between chrysophytes and limnological conditions including low pH, oligotrophy, and elevated dissolved organic matter are ultimately underscored by the high pCO2 associated with these conditions. In lakes where chrysophyte populations have expanded over recent decades, we infer that increasingly heterotrophic conditions with respect to CO2 have stimulated production by these organisms. This linkage is supported by the remarkable abundance and diversity of chrysophytes from middle Eocene lake sediments, deposited under atmospheric CO2 concentrations significantly higher than present. The Eocene assemblages suggest that any chrysophyte-CO2 connection borne out of results from modern and sub-recent sediments also operated on evolutionary time scales, and thus the absence of carbon concentrating mechanisms appears to be an ancient feature within the group. Chrysophyte microfossils may potentially provide important insights concerning the temporal dynamics of carbon cycling in aquatic ecosystems.

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

NASA Astrophysics Data System (ADS)

Plimpton, Steve

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

The pivotal role of angiogenesis in a multi-scale modeling of tumor growth exhibiting the avascular and vascular phases.

PubMed

Salavati, Hooman; Soltani, M; Amanpour, Saeid

2018-05-06

The mechanisms involved in tumor growth mainly occur at the microenvironment, where the interactions between the intracellular, intercellular and extracellular scales mediate the dynamics of tumor. In this work, we present a multi-scale model of solid tumor dynamics to simulate the avascular and vascular growth as well as tumor-induced angiogenesis. The extracellular and intercellular scales are modeled using partial differential equations and cellular Potts model, respectively. Also, few biochemical and biophysical rules control the dynamics of intracellular level. On the other hand, the growth of melanoma tumors is modeled in an animal in-vivo study to evaluate the simulation. The simulation shows that the model successfully reproduces a completed image of processes involved in tumor growth such as avascular and vascular growth as well as angiogenesis. The model incorporates the phenotypes of cancerous cells including proliferating, quiescent and necrotic cells, as well as endothelial cells during angiogenesis. The results clearly demonstrate the pivotal effect of angiogenesis on the progression of cancerous cells. Also, the model exhibits important events in tumor-induced angiogenesis like anastomosis. Moreover, the computational trend of tumor growth closely follows the observations in the experimental study. Copyright © 2018 Elsevier Inc. All rights reserved.

Monoatomic layer removal mechanism in chemical mechanical polishing process: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Si, Lina; Guo, Dan; Luo, Jianbin; Lu, Xinchun

2010-03-01

Molecular dynamics simulations of nanoscratching processes were used to study the atomic-scale removal mechanism of single crystalline silicon in chemical mechanical polishing (CMP) process and particular attention was paid to the effect of scratching depth. The simulation results under a scratching depth of 1 nm showed that a thick layer of silicon material was removed by chip formation and an amorphous layer was formed on the silicon surface after nanoscratching. By contrast, the simulation results with a depth of 0.1 nm indicated that just one monoatomic layer of workpiece was removed and a well ordered crystalline surface was obtained, which is quite consistent with previous CMP experimental results. Therefore, monoatomic layer removal mechanism was presented, by which it is considered that during CMP process the material was removed by one monoatomic layer after another, and the mechanism could provide a reasonable understanding on how the high precision surface was obtained. Also, the effects of the silica particle size and scratching velocity on the removal mechanism were investigated; the wear regimes and interatomic forces between silica particle and workpiece were studied to account for the different removal mechanisms with indentation depths of 0.1 and 1 nm.

Water surface assisted synthesis of large-scale carbon nanotube film for high-performance and stretchable supercapacitors.

PubMed

Yu, Minghao; Zhang, Yangfan; Zeng, Yinxiang; Balogun, Muhammad-Sadeeq; Mai, Kancheng; Zhang, Zishou; Lu, Xihong; Tong, Yexiang

2014-07-16

A kind of multiwalled carbon-nanotube (MWCNT)/polydimethylsiloxane (PDMS) film with excellent conductivity and mechanical properties is developed using a facile and large-scale water surface assisted synthesis method. The film can act as a conductive support for electrochemically active PANI nano fibers. A device based on these PANI/MWCNT/PDMS electrodes shows good and stable capacitive behavior, even under static and dynamic stretching conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-scale strain localization within orthogneiss during subduction and exhumation (Tenda unit, Alpine Corsica)

NASA Astrophysics Data System (ADS)

Beaudoin, Alexandre; Augier, Romain; Jolivet, Laurent; Raimbourg, Hugues; Jourdon, Anthony; Scaillet, Stéphane; Cardello, Giovanni Luca

2016-04-01

Strain localization depends upon scale-related factors resulting in a gap between small-scale studies of deformation mechanisms and large-scale numerical and tectonic models. The former often ignore the variations in composition and water content across tectonic units, while the latter oversimplify the role of the deformation mechanisms. This study aims to heal this gap, by considering microstructures and strain localization not only at a single shear zone-scale but across a 40km-wide tectonic unit and throughout its complex polyphased evolution. The Tenda unit (Alpine Corsica) is an external continental unit mainly composed of granites, bounded by the East Tenda Shear Zone (ETSZ) that separates it from the overlying oceanic-derived HP tectonic units. Previous studies substantially agreed on (1) the burial of the Tenda unit down to blueschist-facies conditions associated with top-to-the-west shearing (D1) and (2) subsequent exhumation accommodated by a localized top-to-the-east shear zone (D2). Reaction-softening is the main localizing mechanism proposed in the literature, being associated with the transformation of K-feldspar into white-mica. In this work, the Tenda unit is reviewed through (1) the construction of a new field-based strain map accompanied by cross-sections representing volumes of rock deformed at different grades related to large-scale factors of strain localization and (2) the structural study of hand-specimens and thin-sections coupled with EBSD analysis in order to target the deformation processes. We aim to find how softening and localization are in relation to the map-scale distribution of strain. The large-scale study shows that the whole Tenda unit is affected by the two successive stages of deformation. However, a more intense deformation is observed along the eastern margin, which originally led to the definition of the ETSZ, with a present-day anastomosed geometry of deformation. Strain localization is clearly linked to rheological/lithological contrasts as it concentrates either along preexisting intrusive and tectonic contacts. As K-feldspar-poor granites remain relatively undeformed, reaction-softening seems to be a major mechanism during D1. However, evidences suggest that this mechanism is in competition with dynamic recrystallization: at outcrop and hand-specimen scale, the correlation between localized structures such as C-planes and phengite-rich zones is not always observed. This same competition remains active during D2 where top-to-the-east C-planes are common in phengite-rich layers, but an overall grain-size reduction is also observed across the different strain grades, suggesting that dynamic recrystallization remains active during the whole story. Final localization is sometimes observed in phengite-poor aplitic ultramylonites characterized by a very fine quartz-albite matrix suggesting that grain-size sensitive flow would be the major mechanism involved in the final rheology of the ETSZ.

Dynamic Response of Monolithic and Laminate/Particulate Reactive Mixtures

NASA Astrophysics Data System (ADS)

Wei, Chung-Ting

Two dynamic compression methods were applied to a monolithic metal and reactive mixtures to investigate their responses: (a) Dynamic experiments using a split Hopkinson pressure bar were applied to reactive mixtures densified by explosive consolidation in order to establish their mechanical response and failure mechanisms. (b) Laser compression and release, which can impart high stresses, up to hundreds GPa, in times of nanoseconds and fractions thereof, was applied to establish the spalling strength of vanadium and the reaction threshold for Ni/Al laminates. The spallation and fragmentation exhibited by recovered mono- and poly-crystalline vanadium prove that the laser intensities and crystal structure play important roles in determining spall strength, fragmentation, and microstructural processes. Densified reactive mixtures with different microstructures (Ni, Mo, W, Nb and Ta with Al) were subjected to the quasi-static and dynamic strain rates. Two distinct failure mechanisms, axial splitting and shear failure, were observed in the recovered specimens. Axial splitting occurred when the bonding between the powders was poor; shear failure was primarily associated with extensive deformation of continuous Ta and Nb phases. Finite element simulations provided valuable information in interpreting the experimental results and predicting failure mechanisms akin to those observed. Ni/Al laminates were subjected to laser compression. The strain rates varied from 105 to 108 s-1, and the initial stress varied from 30 to ˜300 GPa. It is found the thickness of the lamellar and the interlaminar bonding strength are the two critical factors in determining mechanical failure. The intermetallic reaction leading to Ni3Al and NiAl were produced by the laser energies and laser pulse durations in direct laser shock experiments. Laser-driven compression was also applied to study the high temperature synthesis in nano-scale Ni/Al laminates with bilayer thickness 54 nm. Intermetallic phases, NiAl and NiAl 3, were found on the plasma stagnated laminates. However, the self-propagating high temperature synthesis (SHS) did not self-sustain in the micro-scale laminate because of the short duration of the pulse.

Effects of orography on planetary scale flow

NASA Technical Reports Server (NTRS)

Smith, R. B.

1986-01-01

The earth's orography is composed of a wide variety of scales, each contributing to the spectrum of atmospheric motions. A well studied subject (originating with Charney and Eliassen) is the direct forcing of planetary scale waves by the planetary scale orography: primarily the Tibetan plateau and the Rockies. However, because of the non-linear terms in the equations of dynamic meteorology, even the smallest scales of mountain induced flow can contribute to the planetary scale if the amplitude of the small scale disturbance is sufficintly large. Two possible mechanisms for this are illustrated. First, preferentially located lee cyclones can force planetary waves by their meridional transport of heat and momentum (Hansen and Chen). Recent theories are helping to explain the phenomena of lee cyclogenesis (e.g., Smith, 1984, J.A.S.). Second, mesoscale mountain wave and severe downslope wind phenomena produce such a large local drag, that planetary scale waves can be produced. The mechanism of upscale transfer is easy to understand in this case as the standing planetary scale wave has a wavelength which depends on the mean structure of the atmosphere, and not on the width of the mountain (just as in small scale lee wave theory). An example of a theoretical description of a severe wind flow with very large drag is shown.

Brain and Cognitive Reserve: Translation via Network Control Theory

PubMed Central

Medaglia, John Dominic; Pasqualetti, Fabio; Hamilton, Roy H.; Thompson-Schill, Sharon L.; Bassett, Danielle S.

2017-01-01

Traditional approaches to understanding the brain’s resilience to neuropathology have identified neurophysiological variables, often described as brain or cognitive “reserve,” associated with better outcomes. However, mechanisms of function and resilience in large-scale brain networks remain poorly understood. Dynamic network theory may provide a basis for substantive advances in understanding functional resilience in the human brain. In this perspective, we describe recent theoretical approaches from network control theory as a framework for investigating network level mechanisms underlying cognitive function and the dynamics of neuroplasticity in the human brain. We describe the theoretical opportunities offered by the application of network control theory at the level of the human connectome to understand cognitive resilience and inform translational intervention. PMID:28104411

Electron-phonon interaction within classical molecular dynamics

DOE PAGES

Tamm, A.; Samolyuk, G.; Correa, A. A.; ...

2016-07-14

Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less

Dilatancy induced ductile-brittle transition of shear band in metallic glasses.

PubMed

Zeng, F; Jiang, M Q; Dai, L H

2018-04-01

Dilatancy-generated structural disordering, an inherent feature of metallic glasses (MGs), has been widely accepted as the physical mechanism for the primary origin and structural evolution of shear banding, as well as the resultant shear failure. However, it remains a great challenge to determine, to what degree of dilatation, a shear banding will evolve into a runaway shear failure. In this work, using in situ acoustic emission monitoring, we probe the dilatancy evolution at the different stages of individual shear band in MGs that underwent severely plastic deformation by the controlled cutting technology. A scaling law is revealed that the dilatancy in a shear band is linearly related to its evolution degree. A transition from ductile-to-brittle shear bands is observed, where the formers dominate stable serrated flow, and the latter lead to a runaway instability (catastrophe failure) of serrated flow. To uncover the underlying mechanics, we develop a theoretical model of shear-band evolution dynamics taking into account an atomic-scale deformation process. Our theoretical results agree with the experimental observations, and demonstrate that the atomic-scale volume expansion arises from an intrinsic shear-band evolution dynamics. Importantly, the onset of the ductile-brittle transition of shear banding is controlled by a critical dilatation.

Dilatancy induced ductile-brittle transition of shear band in metallic glasses

NASA Astrophysics Data System (ADS)

Zeng, F.; Jiang, M. Q.; Dai, L. H.

2018-04-01

Dilatancy-generated structural disordering, an inherent feature of metallic glasses (MGs), has been widely accepted as the physical mechanism for the primary origin and structural evolution of shear banding, as well as the resultant shear failure. However, it remains a great challenge to determine, to what degree of dilatation, a shear banding will evolve into a runaway shear failure. In this work, using in situ acoustic emission monitoring, we probe the dilatancy evolution at the different stages of individual shear band in MGs that underwent severely plastic deformation by the controlled cutting technology. A scaling law is revealed that the dilatancy in a shear band is linearly related to its evolution degree. A transition from ductile-to-brittle shear bands is observed, where the formers dominate stable serrated flow, and the latter lead to a runaway instability (catastrophe failure) of serrated flow. To uncover the underlying mechanics, we develop a theoretical model of shear-band evolution dynamics taking into account an atomic-scale deformation process. Our theoretical results agree with the experimental observations, and demonstrate that the atomic-scale volume expansion arises from an intrinsic shear-band evolution dynamics. Importantly, the onset of the ductile-brittle transition of shear banding is controlled by a critical dilatation.

A hybrid approach to simulation of electron transfer in complex molecular systems

PubMed Central

Kubař, Tomáš; Elstner, Marcus

2013-01-01

Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors. PMID:23883952

Toward a Multi-scale Phase Transition Kinetics Methodology: From Non-Equilibrium Statistical Mechanics to Hydrodynamics

NASA Astrophysics Data System (ADS)

Belof, Jonathan; Orlikowski, Daniel; Wu, Christine; McLaughlin, Keith

2013-06-01

Shock and ramp compression experiments are allowing us to probe condensed matter under extreme conditions where phase transitions and other non-equilibrium aspects can now be directly observed, but first principles simulation of kinetics remains a challenge. A multi-scale approach is presented here, with non-equilibrium statistical mechanical quantities calculated by molecular dynamics (MD) and then leveraged to inform a classical nucleation and growth kinetics model at the hydrodynamic scale. Of central interest is the free energy barrier for the formation of a critical nucleus, with direct NEMD presenting the challenge of relatively long timescales necessary to resolve nucleation. Rather than attempt to resolve the time-dependent nucleation sequence directly, the methodology derived here is built upon the non-equilibrium work theorem in order to bias the formation of a critical nucleus and thus construct the nucleation and growth rates. Having determined these kinetic terms from MD, a hydrodynamics implementation of Kolmogorov-Johnson-Mehl-Avrami (KJMA) kinetics and metastabilty is applied to the dynamic compressive freezing of water and compared with recent ramp compression experiments [Dolan et al., Nature (2007)] Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344.

Competing mechanisms and scaling laws for carbon nanotube scission by ultrasonication.

PubMed

Pagani, Guido; Green, Micah J; Poulin, Philippe; Pasquali, Matteo

2012-07-17

Dispersion of carbon nanotubes (CNTs) into liquids typically requires ultrasonication to exfoliate individuals CNTs from bundles. Experiments show that CNT length drops with sonication time (or energy) as a power law t(-m). Yet the breakage mechanism is not well understood, and the experimentally reported power law exponent m ranges from approximately 0.2 to 0.5. Here we simulate the motion of CNTs around cavitating bubbles by coupling brownian dynamics with the Rayleigh-Plesset equation. We observe that, during bubble growth, CNTs align tangentially to the bubble surface. Surprisingly, we find two dynamical regimes during the collapse: shorter CNTs align radially, longer ones buckle. We compute the phase diagram for CNT collapse dynamics as a function of CNT length, stiffness, and initial distance from the bubble nuclei and determine the transition from aligning to buckling. We conclude that, depending on their length, CNTs can break due to either buckling or stretching. These two mechanisms yield different power laws for the length decay (0.25 and 0.5, respectively), reconciling the apparent discrepancy in the experimental data.

Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD–DNA complexes

PubMed Central

Carter, Ashley R.; Seaberg, Maasa H.; Fan, Hsiu-Fang; Sun, Gang; Wilds, Christopher J.; Li, Hung-Wen; Perkins, Thomas T.

2016-01-01

RecBCD is a multifunctional enzyme that possesses both helicase and nuclease activities. To gain insight into the mechanism of its helicase function, RecBCD unwinding at low adenosine triphosphate (ATP) (2–4 μM) was measured using an optical-trapping assay featuring 1 base-pair (bp) precision. Instead of uniformly sized steps, we observed forward motion convolved with rapid, large-scale (∼4 bp) variations in DNA length. We interpret this motion as conformational dynamics of the RecBCD–DNA complex in an unwinding-competent state, arising, in part, by an enzyme-induced, back-and-forth motion relative to the dsDNA that opens and closes the duplex. Five observations support this interpretation. First, these dynamics were present in the absence of ATP. Second, the onset of the dynamics was coupled to RecBCD entering into an unwinding-competent state that required a sufficiently long 5′ strand to engage the RecD helicase. Third, the dynamics were modulated by the GC-content of the dsDNA. Fourth, the dynamics were suppressed by an engineered interstrand cross-link in the dsDNA that prevented unwinding. Finally, these dynamics were suppressed by binding of a specific non-hydrolyzable ATP analog. Collectively, these observations show that during unwinding, RecBCD binds to DNA in a dynamic mode that is modulated by the nucleotide state of the ATP-binding pocket. PMID:27220465

Using simulation to interpret experimental data in terms of protein conformational ensembles.

PubMed

Allison, Jane R

2017-04-01

In their biological environment, proteins are dynamic molecules, necessitating an ensemble structural description. Molecular dynamics simulations and solution-state experiments provide complimentary information in the form of atomically detailed coordinates and averaged or distributions of structural properties or related quantities. Recently, increases in the temporal and spatial scale of conformational sampling and comparison of the more diverse conformational ensembles thus generated have revealed the importance of sampling rare events. Excitingly, new methods based on maximum entropy and Bayesian inference are promising to provide a statistically sound mechanism for combining experimental data with molecular dynamics simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

PubMed

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

2014-05-15

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

Testing of Composite Fan Vanes With Erosion-Resistant Coating Accelerated

NASA Technical Reports Server (NTRS)

Bowman, Cheryl L.; Sutter, James K.; Otten, Kim D.; Samorezov, Sergey; Perusek, Gail P.

2004-01-01

The high-cycle fatigue of composite stator vanes provided an accelerated life-state prior to insertion in a test stand engine. The accelerated testing was performed in the Structural Dynamics Laboratory at the NASA Glenn Research Center under the guidance of Structural Mechanics and Dynamics Branch personnel. Previous research on fixturing and test procedures developed at Glenn determined that engine vibratory conditions could be simulated for polymer matrix composite vanes by using the excitation of a combined slip table and electrodynamic shaker in Glenn's Structural Dynamics Laboratory. Bench-top testing gave researchers the confidence to test the coated vanes in a full-scale engine test.

Dynamic DNA Methylation Controls Glutamate Receptor Trafficking and Synaptic Scaling

PubMed Central

Sweatt, J. David

2016-01-01

Hebbian plasticity, including LTP and LTD, has long been regarded as important for local circuit refinement in the context of memory formation and stabilization. However, circuit development and stabilization additionally relies on non-Hebbian, homoeostatic, forms of plasticity such as synaptic scaling. Synaptic scaling is induced by chronic increases or decreases in neuronal activity. Synaptic scaling is associated with cell-wide adjustments in postsynaptic receptor density, and can occur in a multiplicative manner resulting in preservation of relative synaptic strengths across the entire neuron's population of synapses. Both active DNA methylation and de-methylation have been validated as crucial regulators of gene transcription during learning, and synaptic scaling is known to be transcriptionally dependent. However, it has been unclear whether homeostatic forms of plasticity such as synaptic scaling are regulated via epigenetic mechanisms. This review describes exciting recent work that has demonstrated a role for active changes in neuronal DNA methylation and demethylation as a controller of synaptic scaling and glutamate receptor trafficking. These findings bring together three major categories of memory-associated mechanisms that were previously largely considered separately: DNA methylation, homeostatic plasticity, and glutamate receptor trafficking. PMID:26849493

Computational Models for Nanoscale Fluid Dynamics and Transport Inspired by Nonequilibrium Thermodynamics1

PubMed Central

Radhakrishnan, Ravi; Yu, Hsiu-Yu; Eckmann, David M.; Ayyaswamy, Portonovo S.

2017-01-01

Traditionally, the numerical computation of particle motion in a fluid is resolved through computational fluid dynamics (CFD). However, resolving the motion of nanoparticles poses additional challenges due to the coupling between the Brownian and hydrodynamic forces. Here, we focus on the Brownian motion of a nanoparticle coupled to adhesive interactions and confining-wall-mediated hydrodynamic interactions. We discuss several techniques that are founded on the basis of combining CFD methods with the theory of nonequilibrium statistical mechanics in order to simultaneously conserve thermal equipartition and to show correct hydrodynamic correlations. These include the fluctuating hydrodynamics (FHD) method, the generalized Langevin method, the hybrid method, and the deterministic method. Through the examples discussed, we also show a top-down multiscale progression of temporal dynamics from the colloidal scales to the molecular scales, and the associated fluctuations, hydrodynamic correlations. While the motivation and the examples discussed here pertain to nanoscale fluid dynamics and mass transport, the methodologies presented are rather general and can be easily adopted to applications in convective heat transfer. PMID:28035168

Impact of environment on dynamics of exciton complexes in a WS2 monolayer

NASA Astrophysics Data System (ADS)

Jakubczyk, Tomasz; Nogajewski, Karol; Molas, Maciej R.; Bartos, Miroslav; Langbein, Wolfgang; Potemski, Marek; Kasprzak, Jacek

2018-07-01

Scientific curiosity to uncover original optical properties and functionalities of atomically thin semiconductors, stemming from unusual Coulomb interactions in the two-dimensional geometry and multi-valley band structure, drives the research on monolayers of transition metal dichalcogenides (TMDs). While recent works ascertained the exotic energetic schemes of exciton complexes in TMDs, we here infer their unusual coherent dynamics occurring on subpicosecond time scale. The dynamics is largely affected by the disorder landscape on the submicron scale, thus can be uncovered using four-wave mixing in the frequency domain, which enables microscopic investigations and imaging. Focusing on a WS2 monolayer, we observe that exciton coherence is lost primarily due to interaction with phonons and relaxation processes towards optically dark excitonic states. Notably, when temperature is low and disorder weak, excitons large coherence volume results in enhanced oscillator strength, allowing to reach the regime of radiatively limited dephasing. Additionally, we observe long valley coherence for the negatively charged exciton complex. We therefore elucidate the crucial role of exciton environment in the TMDs on its dynamics and show that revealed mechanisms are ubiquitous within this family.

Data collapse and critical dynamics in neuronal avalanche data

NASA Astrophysics Data System (ADS)

Butler, Thomas; Friedman, Nir; Dahmen, Karin; Beggs, John; Deville, Lee; Ito, Shinya

2012-02-01

The tasks of information processing, computation, and response to stimuli require neural computation to be remarkably flexible and diverse. To optimally satisfy the demands of neural computation, neuronal networks have been hypothesized to operate near a non-equilibrium critical point. In spite of their importance for neural dynamics, experimental evidence for critical dynamics has been primarily limited to power law statistics that can also emerge from non-critical mechanisms. By tracking the firing of large numbers of synaptically connected cortical neurons and comparing the resulting data to the predictions of critical phenomena, we show that cortical tissues in vitro can function near criticality. Among the most striking predictions of critical dynamics is that the mean temporal profiles of avalanches of widely varying durations are quantitatively described by a single universal scaling function (data collapse). We show for the first time that this prediction is confirmed in neuronal networks. We also show that the data have three additional features predicted by critical phenomena: approximate power law distributions of avalanche sizes and durations, samples in subcritical and supercritical phases, and scaling laws between anomalous exponents.

Thermodynamic scaling of dynamics in polymer melts: predictions from the generalized entropy theory.

PubMed

Xu, Wen-Sheng; Freed, Karl F

2013-06-21

Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of a unique scaling function of the ratio ρ(γ)∕T, where ρ is the density, T is the temperature, and γ is a material dependent constant. Interest in the scaling is also heightened because the exponent γ enters prominently into considerations of the relative contributions to the dynamics from pressure effects (e.g., activation barriers) vs. volume effects (e.g., free volume). Although this scaling is clearly of great practical use, a molecular understanding of the scaling remains elusive. Providing this molecular understanding would greatly enhance the utility of the empirically observed scaling in assisting the rational design of materials by describing how controllable molecular factors, such as monomer structures, interactions, flexibility, etc., influence the scaling exponent γ and, hence, the dynamics. Given the successes of the generalized entropy theory in elucidating the influence of molecular details on the universal properties of glass-forming polymers, this theory is extended here to investigate the thermodynamic scaling in polymer melts. The predictions of theory are in accord with the appearance of thermodynamic scaling for pressures not in excess of ~50 MPa. (The failure at higher pressures arises due to inherent limitations of a lattice model.) In line with arguments relating the magnitude of γ to the steepness of the repulsive part of the intermolecular potential, the abrupt, square-well nature of the lattice model interactions lead, as expected, to much larger values of the scaling exponent. Nevertheless, the theory is employed to study how individual molecular parameters affect the scaling exponent in order to extract a molecular understanding of the information content contained in the exponent. The chain rigidity, cohesive energy, chain length, and the side group length are all found to significantly affect the magnitude of the scaling exponent, and the computed trends agree well with available experiments. The variations of γ with these molecular parameters are explained by establishing a correlation between the computed molecular dependence of the scaling exponent and the fragility. Thus, the efficiency of packing the polymers is established as the universal physical mechanism determining both the fragility and the scaling exponent γ.

Mechanized scaling with ultrasonics: Perils and proactive measures

PubMed Central

Paramashivaiah, Rashmi; Prabhuji, M. L. V

2013-01-01

Mechanized scaling for plaque removal is a routine procedure in the practice of periodontics. Though it appears innocuous by itself, there are retinues of hazards associated with it on various organ systems in the body. Some of these unwanted effects and measures to avoid or ameliorate the same are elaborated here. Exposure to ultrasonic scaling is inevitable before any other treatment procedure. Aerosol contamination, vibrational hazards, thermal effects on the dental pulp, altered vascular dynamics, disruption in electromagnetic device, diminished hearing and dental unit waterline contamination are some of the probable off-shoots a patient has to bear. Uses of barrier devices, proper attention to usage of equipment, protection for ear and water treatment are few of solutions for the same. Though documented evidence for the existence of all effects is lacking, it is never the less significant for the overall safety of the patient. A conscientious clinician should therefore inculcate the available steps to overcome the hazards of ultrasonic scaling. PMID:24174718

A hysteretic model considering Stribeck effect for small-scale magnetorheological damper

NASA Astrophysics Data System (ADS)

Zhao, Yu-Liang; Xu, Zhao-Dong

2018-06-01

Magnetorheological (MR) damper is an ideal semi-active control device for vibration suppression. The mechanical properties of this type of devices show strong nonlinear characteristics, especially the performance of the small-scale dampers. Therefore, developing an ideal model that can accurately describe the nonlinearity of such device is crucial to control design. In this paper, the dynamic characteristics of a small-scale MR damper developed by our research group is tested, and the Stribeck effect is observed in the low velocity region. Then, an improved model based on sigmoid model is proposed to describe this Stribeck effect observed in the experiment. After that, the parameters of this model are identified by genetic algorithms, and the mathematical relationship between these parameters and the input current, excitation frequency and amplitude is regressed. Finally, the predicted forces of the proposed model are validated with the experimental data. The results show that this model can well predict the mechanical properties of the small-scale damper, especially the Stribeck effect in the low velocity region.

Optical spring effect in nanoelectromechanical systems

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

Tian, Feng; Zhou, Guangya, E-mail: mpezgy@nus.edu.sg; Du, Yu

2014-08-11

In this Letter, we report a hybrid system consisting of nano-optical and nano-mechanical springs, in which the optical spring effect works to adjust the mechanical frequency of a nanoelectromechanical systems resonator. Nano-scale folded beams are fabricated as the mechanical springs and double-coupled one-dimensional photonic crystal cavities are used to pump the “optical spring.” The dynamic characteristics of this hybrid system are measured and analyzed at both low and high input optical powers. This study leads the physical phenomenon of optomechanics in complex nano-opto-electro-mechanical systems (NOEMS) and could benefit the future applications of NOEMS in chip-level communication and sensing.

Environmentally induced amplitude death and firing provocation in large-scale networks of neuronal systems

NASA Astrophysics Data System (ADS)

Pankratova, Evgeniya V.; Kalyakulina, Alena I.

2016-12-01

We study the dynamics of multielement neuronal systems taking into account both the direct interaction between the cells via linear coupling and nondiffusive cell-to-cell communication via common environment. For the cells exhibiting individual bursting behavior, we have revealed the dependence of the network activity on its scale. Particularly, we show that small-scale networks demonstrate the inability to maintain complicated oscillations: for a small number of elements in an ensemble, the phenomenon of amplitude death is observed. The existence of threshold network scales and mechanisms causing firing in artificial and real multielement neural networks, as well as their significance for biological applications, are discussed.

A Multi-Scale Modeling and Experimental Program for the Dynamic Mechanical Response of Tissue

DTIC Science & Technology

2014-12-09

diseases ”. Speaker, Session Chair of Pathological Fibrils, American Crystallographic Association, Albuquerque NM, May 2014. Joseph Orgel (7...Nonlinear, Soft Matter Phys., vol. 73, no. 3, p. 031901, Mar. 2006. [4] S. Münster, L. M. Jawerth, B. a Leslie, J. I. Weitz, B. Fabry , and D. a Weitz

Growth Kinetics of Intracellular RNA/Protein Droplets: Signature of a Liquid-Liquid Phase Transition?

NASA Astrophysics Data System (ADS)

Berry, Joel; Weber, Stephanie C.; Vaidya, Nilesh; Zhu, Lian; Haataja, Mikko; Brangwynne, Clifford P.

2015-03-01

Nonmembrane-bound organelles are functional, dynamic assemblies of RNA and/or protein that can self-assemble and disassemble within the cytoplasm or nucleoplasm. The possibility that underlying intracellular phase transitions may drive and mediate the morphological evolution of some membrane-less organelles has been supported by several recent studies. In this talk, results from a collaborative experimental-theoretical study of the growth and dissolution kinetics of nucleoli and extranucleolar droplets (ENDs) in C. elegans embryos will be presented. We have employed Flory-Huggins solution theory, reaction-diffusion kinetics, and quantitative statistical dynamic scaling analysis to characterize the specific growth mechanisms at work. Our findings indicate that both in vivo and in vitro droplet scaling and growth kinetics are consistent with those resulting from an equilibrium liquid-liquid phase transition mediated by passive nonequilibrium growth mechanisms - simultaneous Brownian coalescence and Ostwald ripening. This supports a view in which cells can employ phase transitions to drive structural organization, while utilizing active processes, such as local transcriptional activity, to fine tune the kinetics of these phase transitions in response to given conditions.

Self-organization in multilayer network with adaptation mechanisms based on competition

NASA Astrophysics Data System (ADS)

Pitsik, Elena N.; Makarov, Vladimir V.; Nedaivozov, Vladimir O.; Kirsanov, Daniil V.; Goremyko, Mikhail V.

2018-04-01

The paper considers the phenomena of competition in multiplex network whose structure evolves corresponding to dynamics of it's elements, forming closed loop of self-learning with the aim to reach the optimal topology. Numerical analysis of proposed model shows that it is possible to obtain scale-invariant structures for corresponding parameters as well as the structures with homogeneous distribution of connections in the layers. Revealed phenomena emerges as the consequence of the self-organization processes related to structure-dynamical selflearning based on homeostasis and homophily, as well as the result of the competition between the network's layers for optimal topology. It was shown that in the mode of partial and cluster synchronization the network reaches scale-free topology of complex nature that is different from layer to layer. However, in the mode of global synchronization the homogeneous topologies on all layer of the network are observed. This phenomenon is tightly connected with the competitive processes that represent themselves as the natural mechanism of reaching the optimal topology of the links in variety of real-world systems.

Biomimetic Flow Control

NASA Technical Reports Server (NTRS)

Anders, John B.

2000-01-01

Biologic flight has undoubtedly intrigued man for thousands of years, yet it has been only the last 100 years or so that any serious challenge has been mounted to the pre-eminence of birds. Although present-day large-scale aircraft are now clearly able to fly higher, faster and farther than any bird or insect, it is obvious that these biological creatures have a mastery of low Reynolds number, unsteady flows that is unrivaled by man-made systems. This paper suggests that biological flight should be examined for mechanisms that may apply to engineered flight systems, especially in the emerging field of small-scale, uninhabited aerial vehicles (UAV). This paper discusses the kinematics and aerodynamics of bird and insect flight, including some aspects of unsteady aerodynamics. The dynamics of flapping wing flight is briefly examined, including gait selection, flapping frequency and amplitude selection, as well as wing planform and angle-of-attack dynamics. Unsteady aerodynamic mechanisms as practiced by small birds and insects are reviewed. Drag reduction morphologies of birds and marine animals are discussed and fruitful areas of research are suggested.

Integrated Modeling and Experiments to Characterize Coupled Thermo-hydro-geomechanical-chemical processes in Hydraulic Fracturing

NASA Astrophysics Data System (ADS)

Viswanathan, H. S.; Carey, J. W.; Karra, S.; Porter, M. L.; Rougier, E.; Kang, Q.; Makedonska, N.; Hyman, J.; Jimenez Martinez, J.; Frash, L.; Chen, L.

2015-12-01

Hydraulic fracturing phenomena involve fluid-solid interactions embedded within coupled thermo-hydro-mechanical-chemical (THMC) processes over scales from microns to tens of meters. Feedbacks between processes result in complex dynamics that must be unraveled if one is to predict and, in the case of unconventional resources, facilitate fracture propagation, fluid flow, and interfacial transport processes. The proposed work is part of a broader class of complex systems involving coupled fluid flow and fractures that are critical to subsurface energy issues, such as shale oil, geothermal, carbon sequestration, and nuclear waste disposal. We use unique LANL microfluidic and triaxial core flood experiments integrated with state-of-the-art numerical simulation to reveal the fundamental dynamics of fracture-fluid interactions to characterize the key coupled processes that impact hydrocarbon production. We are also comparing CO2-based fracturing and aqueous fluids to enhance production, greatly reduce waste water, while simultaneously sequestering CO2. We will show pore, core and reservoir scale simulations/experiments that investigate the contolling mechanisms that control hydrocarbon production.

Multistage reaction pathways in detonating high explosives

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; CACS Collaboration; ALCF Team

2015-06-01

Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N2 and H2O within 10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct uni-molecular and intermolecular reaction pathways, respectively, for the rapid N2 and H2O productions. This work was supported by the Office of Naval Research Grant No. N000014-12-1-0555 and the Basic Research Program of Defense Threat Reduction Agency (DTRA) Grant No. HDTRA1-08-1-0036. All the simulations were performed at USC and Argonne LCF.

Uncoupled poroelastic and intrinsic viscoelastic dissipation in cartilage.

PubMed

Han, Guebum; Hess, Cole; Eriten, Melih; Henak, Corinne R

2018-04-26

This paper studies uncoupled poroelastic (flow-dependent) and intrinsic viscoelastic (flow-independent) energy dissipation mechanisms via their dependence on characteristic lengths to understand the root of cartilage's broadband dissipation behavior. Phase shift and dynamic modulus were measured from dynamic microindentation tests conducted on hydrated cartilage at different contact radii, as well as on dehydrated cartilage. Cartilage weight and thickness were recorded during dehydration. Phase shifts revealed poroelastic- and viscoelastic-dominant dissipation regimes in hydrated cartilage. Specifically, phase shift at a relatively small radius was governed by poroviscoelasticity, while phase shift at a relatively large radius was dominantly governed by intrinsic viscoelasticity. The uncoupled dissipation mechanisms demonstrated that intrinsic viscoelastic dissipation provided sustained broadband dissipation for all length scales, and additional poroelastic dissipation increased total dissipation at small length scales. Dehydration decreased intrinsic viscoelastic dissipation of cartilage. The findings demonstrated a possibility to measure poroelastic and intrinsic viscoelastic properties of cartilage at similar microscale lengths. Also they encouraged development of broadband cartilage like-dampers and provided important design parameters to maximize their performance. Copyright © 2018 Elsevier Ltd. All rights reserved.

A flow separation study over a shortfin mako shark pectoral fin

NASA Astrophysics Data System (ADS)

Bradshaw, Michael; Lang, Amy; Wahidi, Redha; Smith, Drew; Motta, Philip

2011-11-01

Many animals possess performance enhancing mechanisms, such as the denticles found on the skin of the shortfin mako shark (Isurus oxyrinchus). The shortfin mako, one of the fastest sharks on the planet, is covered by small, tooth-like scales that vary in bristling capability. Previous biological findings have shown that the scales increase in flexibility from the leading to trailing edge over the pectoral fin. As this fin is a primary control surface, the scale bristling may provide a mechanism for separation control that leads to decreased drag and increased maneuverability. Such findings can potentially lead to the development of similar micro-scale mechanisms to improve the efficiency of aerospace design. A left pectoral fin (71 cm span) was tested in a water tunnel facility under static and dynamic conditions. Digital Particle Image Velocimetry (DPIV) was used to characterize the flow over the fin. Various angles of attack at two speeds were tested (Re of 44,500 and 68,000). Two chord-wise locations, approximately mid-span where three-dimensional effects were minimized, were viewed to analyze the flow. After the initial testing, the fin was painted to eliminate the effect of the scales and retested to observe flow separation. Supported by REU SITE EEC grant number 1062611.

Linking dynamic patterns of neural activity in orbitofrontal cortex with decision making.

PubMed

Rich, Erin L; Stoll, Frederic M; Rudebeck, Peter H

2018-04-01

Humans and animals demonstrate extraordinary flexibility in choice behavior, particularly when deciding based on subjective preferences. We evaluate options on different scales, deliberate, and often change our minds. Little is known about the neural mechanisms that underlie these dynamic aspects of decision-making, although neural activity in orbitofrontal cortex (OFC) likely plays a central role. Recent evidence from studies in macaques shows that attention modulates value responses in OFC, and that ensembles of OFC neurons dynamically signal different options during choices. When contexts change, these ensembles flexibly remap to encode the new task. Determining how these dynamic patterns emerge and relate to choices will inform models of decision-making and OFC function. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Kibble-Zurek mechanism in phase transitions of non-equilibrium systems

NASA Astrophysics Data System (ADS)

Cheung, Hil F. H.; Patil, Yogesh S.; Date, Aditya G.; Vengalattore, Mukund

2017-04-01

We experimentally realize a driven-dissipative phase transition using a mechanical parametric amplifier to demonstrate key signatures of a second order phase transition, including a point where the susceptibilities and relaxation time scales diverge, and where the system exhibits a spontaneous breaking of symmetry. Though reminiscent of conventional equilibrium phase transitions, it is unclear if such driven-dissipative phase transitions are amenable to the conventional Landau-Ginsburg-Wilson paradigm, which relies on concepts of scale invariance and universality, and recent work has shown that such phase transitions can indeed lie beyond such conventional universality classes. By quenching the system past the critical point, we investigate the dynamics of the emergent ordered phase and find that our measurements are in excellent agreement with the Kibble-Zurek mechanism. In addition to verifying the Kibble-Zurek hypothesis in driven-dissipative phase transitions for the first time, we also demonstrate that the measured critical exponents accurately reflect the interplay between intrinsic coherent dynamics and environmental correlations, showing a clear departure from mean field exponents in the case of non-Markovian system-bath interactions. We further discuss how reservoir engineering and the imposition of artificial environmental correlations can result in the stabilization of novel many-body quantum phases and aid in the creation of exotic non-equilibrium states of matter.

Computational approach on PEB process in EUV resist: multi-scale simulation

NASA Astrophysics Data System (ADS)

Kim, Muyoung; Moon, Junghwan; Choi, Joonmyung; Lee, Byunghoon; Jeong, Changyoung; Kim, Heebom; Cho, Maenghyo

2017-03-01

For decades, downsizing has been a key issue for high performance and low cost of semiconductor, and extreme ultraviolet lithography is one of the promising candidates to achieve the goal. As a predominant process in extreme ultraviolet lithography on determining resolution and sensitivity, post exposure bake has been mainly studied by experimental groups, but development of its photoresist is at the breaking point because of the lack of unveiled mechanism during the process. Herein, we provide theoretical approach to investigate underlying mechanism on the post exposure bake process in chemically amplified resist, and it covers three important reactions during the process: acid generation by photo-acid generator dissociation, acid diffusion, and deprotection. Density functional theory calculation (quantum mechanical simulation) was conducted to quantitatively predict activation energy and probability of the chemical reactions, and they were applied to molecular dynamics simulation for constructing reliable computational model. Then, overall chemical reactions were simulated in the molecular dynamics unit cell, and final configuration of the photoresist was used to predict the line edge roughness. The presented multiscale model unifies the phenomena of both quantum and atomic scales during the post exposure bake process, and it will be helpful to understand critical factors affecting the performance of the resulting photoresist and design the next-generation material.

Dynamic Control of Synaptic Adhesion and Organizing Molecules in Synaptic Plasticity

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

Rudenko, Gabby

Synapses play a critical role in establishing and maintaining neural circuits, permitting targeted information transfer throughout the brain. A large portfolio of synaptic adhesion/organizing molecules (SAMs) exists in the mammalian brain involved in synapse development and maintenance. SAMs bind protein partners, formingtrans-complexes spanning the synaptic cleft orcis-complexes attached to the same synaptic membrane. SAMs play key roles in cell adhesion and in organizing protein interaction networks; they can also provide mechanisms of recognition, generate scaffolds onto which partners can dock, and likely take part in signaling processes as well. SAMs are regulated through a portfolio of different mechanisms that affectmore » their protein levels, precise localization, stability, and the availability of their partners at synapses. Interaction of SAMs with their partners can further be strengthened or weakened through alternative splicing, competing protein partners, ectodomain shedding, or astrocytically secreted factors. Given that numerous SAMs appear altered by synaptic activity, in vivo, these molecules may be used to dynamically scale up or scale down synaptic communication. Many SAMs, including neurexins, neuroligins, cadherins, and contactins, are now implicated in neuropsychiatric and neurodevelopmental diseases, such as autism spectrum disorder, schizophrenia, and bipolar disorder and studying their molecular mechanisms holds promise for developing novel therapeutics.« less

Dynamic Control of Synaptic Adhesion and Organizing Molecules in Synaptic Plasticity

PubMed Central

2017-01-01

Synapses play a critical role in establishing and maintaining neural circuits, permitting targeted information transfer throughout the brain. A large portfolio of synaptic adhesion/organizing molecules (SAMs) exists in the mammalian brain involved in synapse development and maintenance. SAMs bind protein partners, forming trans-complexes spanning the synaptic cleft or cis-complexes attached to the same synaptic membrane. SAMs play key roles in cell adhesion and in organizing protein interaction networks; they can also provide mechanisms of recognition, generate scaffolds onto which partners can dock, and likely take part in signaling processes as well. SAMs are regulated through a portfolio of different mechanisms that affect their protein levels, precise localization, stability, and the availability of their partners at synapses. Interaction of SAMs with their partners can further be strengthened or weakened through alternative splicing, competing protein partners, ectodomain shedding, or astrocytically secreted factors. Given that numerous SAMs appear altered by synaptic activity, in vivo, these molecules may be used to dynamically scale up or scale down synaptic communication. Many SAMs, including neurexins, neuroligins, cadherins, and contactins, are now implicated in neuropsychiatric and neurodevelopmental diseases, such as autism spectrum disorder, schizophrenia, and bipolar disorder and studying their molecular mechanisms holds promise for developing novel therapeutics. PMID:28255461

Coronal Mass Ejections and their Implications for the Corona and Heliosphere

NASA Technical Reports Server (NTRS)

Antiochos, Spiro K.

2008-01-01

Coronal mass ejections (CMEs) are the largest and most energetic form of transients that connect the Sun to the heliosphere. They are critically important both for understanding the physical mechanisms of explosive solar activity and for predicting space weather. Furthermore they are an extreme example of how cross-scale coupling can play a critical role in determining the properties of a large-scale dynamical system. In this presentation CME theories are reviewed and the latest results from 3D numerical modeling of CME initiation propagation to the heliosphere are presented. In particular the focus is on the breakout model, but many of the results hold for the flux rope models as well. The implications of these results for understanding heliospheric structure and dynamics and for upcoming space missions will be discussed.

Isomer-dependent fragmentation dynamics of inner-shell photoionized difluoroiodobenzene

DOE PAGES

Ablikim, Utuq; Bomme, Cédric; Savelyev, Evgeny; ...

2017-05-11

The fragmentation dynamics of 2,6- and 3,5-difluoroiodobenzene after iodine 4d inner-shell photoionization with soft X-rays are studied using coincident electron and ion momentum imaging. By analyzing the momentum correlation between iodine and fluorine cations in three-fold ion coincidence events, we can distinguish the two isomers experimentally. Classical Coulomb explosion simulations are in overall agreement with the experimentally determined fragment ion kinetic energies and momentum correlations and point toward different fragmentation mechanisms and time scales. Finally, while most three-body fragmentation channels show clear evidence for sequential fragmentation on a time scale larger than the rotational period of the fragments, the breakupmore » into iodine and fluorine cations and a third charged co-fragment appears to occur within several hundred femtoseconds.« less

Modeling and Simulation of Nanoindentation

NASA Astrophysics Data System (ADS)

Huang, Sixie; Zhou, Caizhi

2017-11-01

Nanoindentation is a hardness test method applied to small volumes of material which can provide some unique effects and spark many related research activities. To fully understand the phenomena observed during nanoindentation tests, modeling and simulation methods have been developed to predict the mechanical response of materials during nanoindentation. However, challenges remain with those computational approaches, because of their length scale, predictive capability, and accuracy. This article reviews recent progress and challenges for modeling and simulation of nanoindentation, including an overview of molecular dynamics, the quasicontinuum method, discrete dislocation dynamics, and the crystal plasticity finite element method, and discusses how to integrate multiscale modeling approaches seamlessly with experimental studies to understand the length-scale effects and microstructure evolution during nanoindentation tests, creating a unique opportunity to establish new calibration procedures for the nanoindentation technique.

Spray sealing: A breakthrough in integral fuel tank sealing technology

NASA Astrophysics Data System (ADS)

Richardson, Martin D.; Zadarnowski, J. H.

1989-11-01

In a continuing effort to increase readiness, a new approach to sealing integral fuel tanks is being developed. The technique seals potential leak sources by spraying elastomeric materials inside the tank cavity. Laboratory evaluations project an increase in aircraft supportability and reliability, an improved maintainability, decreasing acquisition and life cycle costs. Increased usable fuel volume and lower weight than conventional bladders improve performance. Concept feasibility was demonstrated on sub-scale aircraft fuel tanks. Materials were selected by testing sprayable elastomers in a fuel tank environment. Chemical stability, mechanical properties, and dynamic durability of the elastomer are being evaluated at the laboratory level and in sub-scale and full scale aircraft component fatigue tests. The self sealing capability of sprayable materials is also under development. Ballistic tests show an improved aircraft survivability, due in part to the elastomer's mechanical properties and its ability to damp vibrations. New application equipment, system removal, and repair methods are being investigated.

Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations.

PubMed

Velazquez, Hector A; Hamelberg, Donald

2015-02-21

Cis-trans isomerization of peptidyl-prolyl bonds of the protein backbone plays an important role in numerous biological processes. Cis-trans isomerization can be the rate-limiting step due its extremely slow dynamics, compared to the millisecond time scale of many processes, and is catalyzed by a widely studied family of peptidyl-prolyl cis-trans isomerase enzymes. Also, mechanical forces along the peptide chain can speed up the rate of isomerization, resulting in "mechanical catalysis," and have been used to study peptidyl-prolyl cis-trans isomerization and other mechanical properties of proteins. Here, we use constant force molecular dynamics simulations to study the dynamical effects of phosphorylation on serine/threonine-proline protein motifs that are involved in the function of many proteins and have been implicated in many aberrant biological processes. We show that the rate of cis-trans isomerization is slowed down by phosphorylation, in excellent agreement with experiments. We use a well-grounded theory to describe the force dependent rate of isomerization. The calculated rates at zero force are also in excellent agreement with experimentally measured rates, providing additional validation of the models and force field parameters. Our results suggest that the slowdown in the rate upon phosphorylation is mainly due to an increase in the friction along the peptidyl-prolyl bond angle during isomerization. Our results provide a microscopic description of the dynamical effects of post-translational phosphorylation on cis-trans isomerization and insights into the properties of proteins under tension.

Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Velazquez, Hector A.; Hamelberg, Donald

2015-02-01

Cis-trans isomerization of peptidyl-prolyl bonds of the protein backbone plays an important role in numerous biological processes. Cis-trans isomerization can be the rate-limiting step due its extremely slow dynamics, compared to the millisecond time scale of many processes, and is catalyzed by a widely studied family of peptidyl-prolyl cis-trans isomerase enzymes. Also, mechanical forces along the peptide chain can speed up the rate of isomerization, resulting in "mechanical catalysis," and have been used to study peptidyl-prolyl cis-trans isomerization and other mechanical properties of proteins. Here, we use constant force molecular dynamics simulations to study the dynamical effects of phosphorylation on serine/threonine-proline protein motifs that are involved in the function of many proteins and have been implicated in many aberrant biological processes. We show that the rate of cis-trans isomerization is slowed down by phosphorylation, in excellent agreement with experiments. We use a well-grounded theory to describe the force dependent rate of isomerization. The calculated rates at zero force are also in excellent agreement with experimentally measured rates, providing additional validation of the models and force field parameters. Our results suggest that the slowdown in the rate upon phosphorylation is mainly due to an increase in the friction along the peptidyl-prolyl bond angle during isomerization. Our results provide a microscopic description of the dynamical effects of post-translational phosphorylation on cis-trans isomerization and insights into the properties of proteins under tension.

Can Horton hear the whos? The importance of scale in mosquito-borne disease.

PubMed

Lord, C C; Alto, B W; Anderson, S L; Connelly, C R; Day, J F; Richards, S L; Smartt, C T; Tabachnick, W J

2014-03-01

The epidemiology of vector-borne pathogens is determined by mechanisms and interactions at different scales of biological organization, from individual-level cellular processes to community interactions between species and with the environment. Most research, however, focuses on one scale or level with little integration between scales or levels within scales. Understanding the interactions between levels and how they influence our perception of vector-borne pathogens is critical. Here two examples of biological scales (pathogen transmission and mosquito mortality) are presented to illustrate some of the issues of scale and to explore how processes on different levels may interact to influence mosquito-borne pathogen transmission cycles. Individual variation in survival, vector competence, and other traits affect population abundance, transmission potential, and community structure. Community structure affects interactions between individuals such as competition and predation, and thus influences the individual-level dynamics and transmission potential. Modeling is a valuable tool to assess interactions between scales and how processes at different levels can affect transmission dynamics. We expand an existing model to illustrate the types of studies needed, showing that individual-level variation in viral dose acquired or needed for infection can influence the number of infectious vectors. It is critical that interactions within and among biological scales and levels of biological organization are understood for greater understanding of pathogen transmission with the ultimate goal of improving control of vector-borne pathogens.

Dynamic pore-scale network model (PNM) of water imbibition in porous media

NASA Astrophysics Data System (ADS)

Li, J.; McDougall, S. R.; Sorbie, K. S.

2017-09-01

A dynamic pore-scale network model is presented which simulates 2-phase oil/water displacement during water imbibition by explicitly modelling intra-pore dynamic bulk and film flows using a simple local model. A new dynamic switching parameter, λ, is proposed within this model which is able to simulate the competition between local capillary forces and viscous forces over a very wide range of flow conditions. This quantity (λ) determines the primary pore filling mechanism during imbibition; i.e. whether the dominant force is (i) piston-like displacement under viscous forces, (ii) film swelling/collapse and snap-off due to capillary forces, or (iii) some intermediate local combination of both mechanisms. A series of 2D dynamic pore network simulations is presented which shows that the λ-model can satisfactorily reproduce and explain different filling regimes of water imbibition over a wide range of capillary numbers (Ca) and viscosity ratios (M). These imbibition regimes are more complex than those presented under drainage by (Lenormand et al. (1983)), since they are determined by a wider group of control parameters. Our simulations show that there is a coupling between viscous and capillary forces that is much less important in drainage. The effects of viscosity ratio during imbibition are apparent even under conditions of very slow flow (low Ca)-displacements that would normally be expected to be completely capillary dominated. This occurs as a result of the wetting films having a much greater relative mobility in the higher M cases (e.g. M = 10) thus leading to a higher level of film swelling/snap-off, resulting in local oil cluster bypassing and trapping, and hence a poorer oil recovery. This deeper coupled viscous mechanism is the underlying reason why the microscopic displacement efficiency is lower for higher M cases in water imbibition processes. Additional results are presented from the dynamic model on the corresponding effluent fractional flows (fw) and global pressure drops (ΔP) as functions of capillary number and viscosity ratio. These results indicate that unsteady-state (USS) relatively permeabilities in imbibition should be inherently rate dependent.

Compensating for intersegmental dynamics across the shoulder, elbow, and wrist joints during feedforward and feedback control.

PubMed

Maeda, Rodrigo S; Cluff, Tyler; Gribble, Paul L; Pruszynski, J Andrew

2017-10-01

Moving the arm is complicated by mechanical interactions that arise between limb segments. Such intersegmental dynamics cause torques applied at one joint to produce movement at multiple joints, and in turn, the only way to create single joint movement is by applying torques at multiple joints. We investigated whether the nervous system accounts for intersegmental limb dynamics across the shoulder, elbow, and wrist joints during self-initiated planar reaching and when countering external mechanical perturbations. Our first experiment tested whether the timing and amplitude of shoulder muscle activity account for interaction torques produced during single-joint elbow movements from different elbow initial orientations and over a range of movement speeds. We found that shoulder muscle activity reliably preceded movement onset and elbow agonist activity, and was scaled to compensate for the magnitude of interaction torques arising because of forearm rotation. Our second experiment tested whether elbow muscles compensate for interaction torques introduced by single-joint wrist movements. We found that elbow muscle activity preceded movement onset and wrist agonist muscle activity, and thus the nervous system predicted interaction torques arising because of hand rotation. Our third and fourth experiments tested whether shoulder muscles compensate for interaction torques introduced by different hand orientations during self-initiated elbow movements and to counter mechanical perturbations that caused pure elbow motion. We found that the nervous system predicted the amplitude and direction of interaction torques, appropriately scaling the amplitude of shoulder muscle activity during self-initiated elbow movements and rapid feedback control. Taken together, our results demonstrate that the nervous system robustly accounts for intersegmental dynamics and that the process is similar across the proximal to distal musculature of the arm as well as between feedforward (i.e., self-initiated) and feedback (i.e., reflexive) control. NEW & NOTEWORTHY Intersegmental dynamics complicate the mapping between applied joint torques and the resulting joint motions. We provide evidence that the nervous system robustly predicts these intersegmental limb dynamics across the shoulder, elbow, and wrist joints during reaching and when countering external perturbations. Copyright © 2017 the American Physiological Society.

Computational modeling of intrinsic dissipation in nano-structure

NASA Astrophysics Data System (ADS)

Kunal, Kumar

In this work, using computational modeling, we study the different mechanisms of intrinsic dissipation in nano-electro mechanical systems (NEMS). We, first, use molecular dynamics (MD) simulation and gain an understanding of the underlying loss mechanisms. Using insights from the MD simulation, a multi-scale method to model intrinsic damping is developed. The high frequency vibration in NEMS have important applications. A few examples include the sensing of atomic mass, detection of biological molecules and observation of quantum effects in macroscopic objects. For all these potential applications, dissipation plays a limiting role. While a number of experimental and theoretical studies have been performed, the individual role of different mechanisms remains unclear. In this work, we attempt to isolate and understand the surface and size effect on some of the intrinsic mechanisms. We, first, consider the case of the Akhiezer damping. The Akhiezer dynamics is expected to play an important role in nano-resonators with frequencies in the GHz range. Using a judiciously devised MD set-up, we isolate Akhiezer dynamics. We show that the surfaces aid in reducing the dissipation rate through increasing the rate of thermalization of the phonons. We, next, study damping under the flexure mode of operation. A comparative analysis with the stretching mode shows that the flexure mode is less dissipative. A reduced order model is considered to understand this novel behavior. We, also, investigate the role of tension on the Q factor, a measure of the inverse of dissipation rate. From these studies, we conclude that Akhiezer dynamics plays a dominant role in nano-resonators. We, then, develop a quasi-harmonic based multi-scale method to model Akhiezer damping. A stress component, that characterizes the non-equilibrium phonon population, is derived. We obtain constitutive relation that governs the time evolution of the non-equilibrium stress. Different methods to parametrize the constitutive relation are discussed. Using the proposed formulation, we compute the dissipation rate for different cases. The results are compared with those obtained using MD. Next, we use the Boltzmann transport equation and investigate the Q factor due to the thermo-elastic dissipation (TED). The Q factor obtained shows deviations from the classical theory of TED. Correction to the classical formula, for the case of longitudinal modes, is provided. We, then, study damping is low dimensional structure. We first consider the case of two dimensional graphene sheet and under in-plane stretching. We show that the coupling between the in-plane and the out-of-plane motions plays an important role in the loss of mechanical energy. Further, a hysteresis behavior in the out-of-plane dynamics is observed. Next, we investigate the stretching motion of graphene nano-ribbon. A normal mode Langevin dynamics is devised to understand the results from the MD simulation.

Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers.

PubMed

Deng, Xiang; Zhironkina, Oxana A; Cherepanynets, Varvara D; Strelkova, Olga S; Kireev, Igor I; Belmont, Andrew S

2016-09-26

In higher eukaryotic interphase nuclei, the 100- to >1,000-fold linear compaction of chromatin is difficult to reconcile with its function as a template for transcription, replication, and repair. It is challenging to imagine how DNA and RNA polymerases with their associated molecular machinery would move along the DNA template without transient decondensation of observed large-scale chromatin "chromonema" fibers [1]. Transcription or "replication factory" models [2], in which polymerases remain fixed while DNA is reeled through, are similarly difficult to conceptualize without transient decondensation of these chromonema fibers. Here, we show how a dynamic plasticity of chromatin folding within large-scale chromatin fibers allows DNA replication to take place without significant changes in the global large-scale chromatin compaction or shape of these large-scale chromatin fibers. Time-lapse imaging of lac-operator-tagged chromosome regions shows no major change in the overall compaction of these chromosome regions during their DNA replication. Improved pulse-chase labeling of endogenous interphase chromosomes yields a model in which the global compaction and shape of large-Mbp chromatin domains remains largely invariant during DNA replication, with DNA within these domains undergoing significant movements and redistribution as they move into and then out of adjacent replication foci. In contrast to hierarchical folding models, this dynamic plasticity of large-scale chromatin organization explains how localized changes in DNA topology allow DNA replication to take place without an accompanying global unfolding of large-scale chromatin fibers while suggesting a possible mechanism for maintaining epigenetic programming of large-scale chromatin domains throughout DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.

Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study.

PubMed

Mondal, Padmabati; Granucci, Giovanni; Rastädter, Dominique; Persico, Maurizio; Burghardt, Irene

2018-05-28

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a β-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans -to- cis isomerization is slowed down to a time scale of ∼10-15 picoseconds, in contrast to 500 femtoseconds in vacuo , with a quantum yield reduced by a factor of two. By contrast, cis -to- trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis -azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

Mass generation, the cosmological constant problem, conformal symmetry, and the Higgs boson

NASA Astrophysics Data System (ADS)

Mannheim, Philip D.

2017-05-01

In 2013 the Nobel Prize in Physics was awarded to Francois Englert and Peter Higgs for their work in 1964 along with the late Robert Brout on the mass generation mechanism (the Higgs mechanism) in local gauge theories. This mechanism requires the existence of a massive scalar particle, the Higgs boson, and in 2012 the Higgs boson was finally discovered at the Large Hadron Collider after being sought for almost half a century. In this article we review the work that led to the discovery of the Higgs boson and discuss its implications. We approach the topic from the perspective of a dynamically generated Higgs boson that is a fermion-antifermion bound state rather than an elementary field that appears in an input Lagrangian. In particular, we emphasize the connection with the Bardeen-Cooper-Schrieffer theory of superconductivity. We identify the double-well Higgs potential not as a fundamental potential but as a mean-field effective Lagrangian with a dynamical Higgs boson being generated through a residual interaction that accompanies the mean-field Lagrangian. We discuss what we believe to be the key challenge raised by the discovery of the Higgs boson, namely determining whether it is elementary or composite, and through study of a conformal invariant field theory model as realized with critical scaling and anomalous dimensions, suggest that the width of the Higgs boson might serve as a suitable diagnostic for discriminating between an elementary Higgs boson and a composite one. We discuss the implications of Higgs boson mass generation for the cosmological constant problem, as the cosmological constant receives contributions from the very mechanism that generates the Higgs boson mass in the first place. We show that the contribution to the cosmological constant due to a composite Higgs boson is more tractable and under control than the contribution due to an elementary Higgs boson, and is potentially completely under control if there is an underlying conformal symmetry not just in a critical scaling matter sector (which there would have to be if all mass scales are to be dynamical), but equally in the gravity sector to which the matter sector couples.

Investigation of steady and fluctuating pressures associated with the transonic buffeting and wing rock of a one-seventh scale model of the F-5A aircraft

NASA Technical Reports Server (NTRS)

Hwang, C.; Pi, W. S.

1978-01-01

A wind tunnel test of a 1/7 scale F-5A model is described. The pressure, force, and dynamic response measurements during buffet and wing rock are evaluated. Effects of Mach number, angle of attack, sideslip angle, and control surface settings were investigated. The mean and fluctuating static pressure data are presented and correlated with some corresponding flight test data of a F-5A aircraft. Details of the instrumentation and the specially designed support system which allowed the model to oscillate in roll to simulate wing rock are also described. A limit cycle mechanism causing wing rock was identified from this study, and this mechanism is presented.

Elasticity and critical bending moment of model colloidal aggregates.

PubMed

Pantina, John P; Furst, Eric M

2005-04-08

The bending mechanics of singly bonded colloidal aggregates are measured using laser tweezers. We find that the colloidal bonds are capable of supporting significant torques, providing a direct measurement of the tangential interactions between particles. A critical bending moment marks the limit of linear bending elasticity, past which small-scale rearrangements occur. These mechanical properties underlie the rheology and dynamics of colloidal gels formed by diffusion-limited cluster aggregation, and give critical insight into the contact interactions between Brownian particles.

Toggling Bistable Atoms via Mechanical Switching of Bond Angle

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Jarvis, Sam; Danza, Rosanna; Bamidele, Joseph; Gangopadhyay, Subhashis; Shaw, Gordon A.; Kantorovich, Lev; Moriarty, Philip

2011-04-01

We reversibly switch the state of a bistable atom by direct mechanical manipulation of bond angle using a dynamic force microscope. Individual buckled dimers at the Si(100) surface are flipped via the formation of a single covalent bond, actuating the smallest conceivable in-plane toggle switch (two atoms) via chemical force alone. The response of a given dimer to a flip event depends critically on both the local and nonlocal environment of the target atom—an important consideration for future atomic scale fabrication strategies.

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

Yoshii, Kazutomo; Llopis, Pablo; Zhang, Kaicheng

As CMOS scaling nears its end, parameter variations (process, temperature and voltage) are becoming a major concern. To overcome parameter variations and provide stability, modern processors are becoming dynamic, opportunistically adjusting voltage and frequency based on thermal and energy constraints, which negatively impacts traditional bulk-synchronous parallelism-minded hardware and software designs. As node-level architecture is growing in complexity, implementing variation control mechanisms only with hardware can be a challenging task. In this paper we investigate a software strategy to manage hardwareinduced variations, leveraging low-level monitoring/controlling mechanisms.

Fast Model Generalized Pseudopotential Theory Interatomic Potential Routine

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

2015-03-18

MGPT is an unclassified source code for the fast evaluation and application of quantum-based MGPT interatomic potentials for mrtals. The present version of MGPT has been developed entirely at LLNL, but is specifically designed for implementation in the open-source molecular0dynamics code LAMMPS maintained by Sandia National Laboratories. Using MGPT in LAMMPS, with separate input potential data, one can perform large-scale atomistic simulations of the structural, thermodynamic, defeat and mechanical properties of transition metals with quantum-mechanical realism.

Physically representative atomistic modeling of atomic-scale friction

NASA Astrophysics Data System (ADS)

Dong, Yalin

Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the interesting physical process is buried between the two contact interfaces, thus makes a direct measurement more difficult. Atomistic simulation is able to simulate the process with the dynamic information of each single atom, and therefore provides valuable interpretations for experiments. In this, we will systematically to apply Molecular Dynamics (MD) simulation to optimally model the Atomic Force Microscopy (AFM) measurement of atomic friction. Furthermore, we also employed molecular dynamics simulation to correlate the atomic dynamics with the friction behavior observed in experiments. For instance, ParRep dynamics (an accelerated molecular dynamic technique) is introduced to investigate velocity dependence of atomic friction; we also employ MD simulation to "see" how the reconstruction of gold surface modulates the friction, and the friction enhancement mechanism at a graphite step edge. Atomic stick-slip friction can be treated as a rate process. Instead of running a direction simulation of the process, we can apply transition state theory to predict its property. We will have a rigorous derivation of velocity and temperature dependence of friction based on the Prandtl-Tomlinson model as well as transition theory. A more accurate relation to prediction velocity and temperature dependence is obtained. Furthermore, we have included instrumental noise inherent in AFM measurement to interpret two discoveries in experiments, suppression of friction at low temperature and the attempt frequency discrepancy between AFM measurement and theoretical prediction. We also discuss the possibility to treat wear as a rate process.

Effects of habitat fragmentation on passerine birds breeding in Intermountain shrubsteppe

USGS Publications Warehouse

Knick, S.T.; Rotenberry, J.T.

2002-01-01

Habitat fragmentation and loss strongly influence the distribution and abundance of passerine birds breeding in Intermountain shrubsteppe. Wildfires, human activities, and change in vegetation communities often are synergistic in these systems and can result in radical conversion from shrubland to grasslands dominated by exotic annuals at large temporal and spatial scales from which recovery to native conditions is unlikely. As a result, populations of 5 of the 12 species in our review of Intermountain shrubsteppe birds are undergoing significant declines; 5 species are listed as at-risk or as candidates for protection in at least one state. The process by which fragmentation affects bird distributions in these habitats remains unknown because most research has emphasized the detection of population trends and patterns of habitat associations at relatively large spatial scales. Our research indicates that the distribution of shrubland-obligate species, such as Brewer's Sparrows (Spizella breweri), Sage Sparrows (Amphispiza belli), and Sage Thrashers (Oreoscoptes montanus), was highly sensitive to fragmentation of shrublands at spatial scales larger than individual home ranges. In contrast, the underlying mechanisms for both habitat change and bird population dynamics may operate independently of habitat boundaries. We propose alternative, but not necessarily exclusive, mechanisms to explain the relationship between habitat fragmentation and bird distribution and abundance. Fragmentation might influence productivity through differences in breeding density, nesting success, or predation. However, local and landscape variables were not significant determinants either of success, number fledged, or probability of predation or parasitism (although our tests had relatively low statistical power). Alternatively, relative absence of natal philopatry and redistribution by individuals among habitats following fledging or post-migration could account for the pattern of distribution and abundance. Thus, boundary dynamics may be important in determining the distribution of shrubland-obligate species but insignificant relative to the mechanisms causing the pattern of habitat and bird distribution. Because of the dichotomy in responses, Intermountain shrubsteppe systems present a unique challenge in understanding how landscape composition, configuration, and change influence bird population dynamics.

Implications of incorporating N cycling and N limitations on primary production in an individual-based dynamic vegetation model

NASA Astrophysics Data System (ADS)

Smith, B.; Wårlind, D.; Arneth, A.; Hickler, T.; Leadley, P.; Siltberg, J.; Zaehle, S.

2013-11-01

The LPJ-GUESS dynamic vegetation model uniquely combines an individual- and patch-based representation of vegetation dynamics with ecosystem biogeochemical cycling from regional to global scales. We present an updated version that includes plant and soil N dynamics, analysing the implications of accounting for C-N interactions on predictions and performance of the model. Stand structural dynamics and allometric scaling of tree growth suggested by global databases of forest stand structure and development were well-reproduced by the model in comparison to an earlier multi-model study. Accounting for N cycle dynamics improved the goodness-of-fit for broadleaved forests. N limitation associated with low N mineralisation rates reduces productivity of cold-climate and dry-climate ecosystems relative to mesic temperate and tropical ecosystems. In a model experiment emulating free-air CO2 enrichment (FACE) treatment for forests globally, N-limitation associated with low N mineralisation rates of colder soils reduces CO2-enhancement of NPP for boreal forests, while some temperate and tropical forests exhibit increased NPP enhancement. Under a business-as-usual future climate and emissions scenario, ecosystem C storage globally was projected to increase by c. 10%; additional N requirements to match this increasing ecosystem C were within the high N supply limit estimated on stoichiometric grounds in an earlier study. Our results highlight the importance of accounting for C-N interactions not only in studies of global terrestrial C cycling, but to understand underlying mechanisms on local scales and in different regional contexts.

Implications of incorporating N cycling and N limitations on primary production in an individual-based dynamic vegetation model

NASA Astrophysics Data System (ADS)

Smith, B.; Wårlind, D.; Arneth, A.; Hickler, T.; Leadley, P.; Siltberg, J.; Zaehle, S.

2014-04-01

The LPJ-GUESS dynamic vegetation model uniquely combines an individual- and patch-based representation of vegetation dynamics with ecosystem biogeochemical cycling from regional to global scales. We present an updated version that includes plant and soil N dynamics, analysing the implications of accounting for C-N interactions on predictions and performance of the model. Stand structural dynamics and allometric scaling of tree growth suggested by global databases of forest stand structure and development were well reproduced by the model in comparison to an earlier multi-model study. Accounting for N cycle dynamics improved the goodness of fit for broadleaved forests. N limitation associated with low N-mineralisation rates reduces productivity of cold-climate and dry-climate ecosystems relative to mesic temperate and tropical ecosystems. In a model experiment emulating free-air CO2 enrichment (FACE) treatment for forests globally, N limitation associated with low N-mineralisation rates of colder soils reduces CO2 enhancement of net primary production (NPP) for boreal forests, while some temperate and tropical forests exhibit increased NPP enhancement. Under a business-as-usual future climate and emissions scenario, ecosystem C storage globally was projected to increase by ca. 10%; additional N requirements to match this increasing ecosystem C were within the high N supply limit estimated on stoichiometric grounds in an earlier study. Our results highlight the importance of accounting for C-N interactions in studies of global terrestrial N cycling, and as a basis for understanding mechanisms on local scales and in different regional contexts.

Identifying psychotic defenses in a clinical interview.

PubMed

Berney, Sylvie; de Roten, Yves; Beretta, Véronique; Kramer, Ueli; Despland, Jean-Nicolas

2014-05-01

The Defense Mechanisms Rating Scales (DMRS), one of the most widely used and validated instruments in the study of defense mechanisms, does not include psychotic defenses. The Psychotic-DMRS (P-DMRS) has been developed to include 6 psychotic defense mechanisms: psychotic denial, autistic withdrawal, distortion, delusional projection, fragmentation, and concretization. We discuss psychotic defenses, including the difference between psychotic defenses and psychotic symptoms. Six clinical illustrations demonstrate how the 6 P-DMRS defenses can be identified in patients' narratives selected from the transcripts of dynamic interviews. Implications with respect to patient evaluation and treatment are discussed. © 2014 Wiley Periodicals, Inc.

A 3-D model of tumor progression based on complex automata driven by particle dynamics.

PubMed

Wcisło, Rafał; Dzwinel, Witold; Yuen, David A; Dudek, Arkadiusz Z

2009-12-01

The dynamics of a growing tumor involving mechanical remodeling of healthy tissue and vasculature is neglected in most of the existing tumor models. This is due to the lack of efficient computational framework allowing for simulation of mechanical interactions. Meanwhile, just these interactions trigger critical changes in tumor growth dynamics and are responsible for its volumetric and directional progression. We describe here a novel 3-D model of tumor growth, which combines particle dynamics with cellular automata concept. The particles represent both tissue cells and fragments of the vascular network. They interact with their closest neighbors via semi-harmonic central forces simulating mechanical resistance of the cell walls. The particle dynamics is governed by both the Newtonian laws of motion and the cellular automata rules. These rules can represent cell life-cycle and other biological interactions involving smaller spatio-temporal scales. We show that our complex automata, particle based model can reproduce realistic 3-D dynamics of the entire system consisting of the tumor, normal tissue cells, blood vessels and blood flow. It can explain phenomena such as the inward cell motion in avascular tumor, stabilization of tumor growth by the external pressure, tumor vascularization due to the process of angiogenesis, trapping of healthy cells by invading tumor, and influence of external (boundary) conditions on the direction of tumor progression. We conclude that the particle model can serve as a general framework for designing advanced multiscale models of tumor dynamics and it is very competitive to the modeling approaches presented before.

Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

NASA Astrophysics Data System (ADS)

Arfin, Najmul; Yadav, Avinash Chand; Bohidar, H. B.

2013-11-01

The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement ⟨R2⟩ exhibits a scaling with time as ⟨R2⟩ ˜ tα, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ˜ tβ/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

Hydrological versus biogeochemical controls on catchment nitrate export: a test of the flushing mechanism

NASA Astrophysics Data System (ADS)

Ocampo, Carlos J.; Oldham, Carolyn E.; Sivapalan, Murugesu; Turner, Jeffrey V.

2006-12-01

Deciphering the connection between streamflows and nitrate (NO-3) discharge requires identification of the various water flow pathways within a catchment, and the different time-scales at which hydrological and biogeochemical processes occur. Despite the complexity of the processes involved, many catchments around the world present a characteristic flushing response of NO-3 export. Yet the controls on the flushing response, and how they vary across space and time, are still not clearly understood. In this paper, the flushing response of NO-3 export from a rural catchment in Western Australia was investigated using isotopic (deuterium), chemical (chloride, NO-3), and hydrometric data across different antecedent conditions and time-scales. The catchment streamflow was at all time-scales dominated by a pre-event water source, and the NO-3 discharge was correlated with the magnitude of areas contributing to saturation overland flow. The NO-3 discharge also appeared related to the shallow groundwater dynamics. Thus, the antecedent moisture condition of the catchment at seasonal and interannual time-scales had a major impact on the NO-3 flushing response. In particular, the dynamics of the shallow ephemeral perched aquifer drove a shift from hydrological controls on NO-3 discharge during the early flushing stage to an apparent biogeochemical control on NO-3 discharge during the steady decline stage of the flushing response. This temporally variable control hypothesis provides a new and alternative description of the mechanisms behind the commonly seen flushing response. Copyright

Probing dynamics and pinning of single vortices in superconductors at nanometer scales.

PubMed

Embon, L; Anahory, Y; Suhov, A; Halbertal, D; Cuppens, J; Yakovenko, A; Uri, A; Myasoedov, Y; Rappaport, M L; Huber, M E; Gurevich, A; Zeldov, E

2015-01-07

The dynamics of quantized magnetic vortices and their pinning by materials defects determine electromagnetic properties of superconductors, particularly their ability to carry non-dissipative currents. Despite recent advances in the understanding of the complex physics of vortex matter, the behavior of vortices driven by current through a multi-scale potential of the actual materials defects is still not well understood, mostly due to the scarcity of appropriate experimental tools capable of tracing vortex trajectories on nanometer scales. Using a novel scanning superconducting quantum interference microscope we report here an investigation of controlled dynamics of vortices in lead films with sub-Angstrom spatial resolution and unprecedented sensitivity. We measured, for the first time, the fundamental dependence of the elementary pinning force of multiple defects on the vortex displacement, revealing a far more complex behavior than has previously been recognized, including striking spring softening and broken-spring depinning, as well as spontaneous hysteretic switching between cellular vortex trajectories. Our results indicate the importance of thermal fluctuations even at 4.2 K and of the vital role of ripples in the pinning potential, giving new insights into the mechanisms of magnetic relaxation and electromagnetic response of superconductors.

Probing dynamics and pinning of single vortices in superconductors at nanometer scales

NASA Astrophysics Data System (ADS)

Embon, L.; Anahory, Y.; Suhov, A.; Halbertal, D.; Cuppens, J.; Yakovenko, A.; Uri, A.; Myasoedov, Y.; Rappaport, M. L.; Huber, M. E.; Gurevich, A.; Zeldov, E.

2015-01-01

The dynamics of quantized magnetic vortices and their pinning by materials defects determine electromagnetic properties of superconductors, particularly their ability to carry non-dissipative currents. Despite recent advances in the understanding of the complex physics of vortex matter, the behavior of vortices driven by current through a multi-scale potential of the actual materials defects is still not well understood, mostly due to the scarcity of appropriate experimental tools capable of tracing vortex trajectories on nanometer scales. Using a novel scanning superconducting quantum interference microscope we report here an investigation of controlled dynamics of vortices in lead films with sub-Angstrom spatial resolution and unprecedented sensitivity. We measured, for the first time, the fundamental dependence of the elementary pinning force of multiple defects on the vortex displacement, revealing a far more complex behavior than has previously been recognized, including striking spring softening and broken-spring depinning, as well as spontaneous hysteretic switching between cellular vortex trajectories. Our results indicate the importance of thermal fluctuations even at 4.2 K and of the vital role of ripples in the pinning potential, giving new insights into the mechanisms of magnetic relaxation and electromagnetic response of superconductors.

Gait-force model and inertial measurement unit-based measurements: A new approach for gait analysis and balance monitoring.

PubMed

Li, Xinan; Xu, Hongyuan; Cheung, Jeffrey T

2016-12-01

This work describes a new approach for gait analysis and balance measurement. It uses an inertial measurement unit (IMU) that can either be embedded inside a dynamically unstable platform for balance measurement or mounted on the lower back of a human participant for gait analysis. The acceleration data along three Cartesian coordinates is analyzed by the gait-force model to extract bio-mechanics information in both the dynamic state as in the gait analyzer and the steady state as in the balance scale. For the gait analyzer, the simple, noninvasive and versatile approach makes it appealing to a broad range of applications in clinical diagnosis, rehabilitation monitoring, athletic training, sport-apparel design, and many other areas. For the balance scale, it provides a portable platform to measure the postural deviation and the balance index under visual or vestibular sensory input conditions. Despite its simple construction and operation, excellent agreement has been demonstrated between its performance and the high-cost commercial balance unit over a wide dynamic range. The portable balance scale is an ideal tool for routine monitoring of balance index, fall-risk assessment, and other balance-related health issues for both clinical and household use.

On the statistical mechanics of the 2D stochastic Euler equation

NASA Astrophysics Data System (ADS)

Bouchet, Freddy; Laurie, Jason; Zaboronski, Oleg

2011-12-01

The dynamics of vortices and large scale structures is qualitatively very different in two dimensional flows compared to its three dimensional counterparts, due to the presence of multiple integrals of motion. These are believed to be responsible for a variety of phenomena observed in Euler flow such as the formation of large scale coherent structures, the existence of meta-stable states and random abrupt changes in the topology of the flow. In this paper we study stochastic dynamics of the finite dimensional approximation of the 2D Euler flow based on Lie algebra su(N) which preserves all integrals of motion. In particular, we exploit rich algebraic structure responsible for the existence of Euler's conservation laws to calculate the invariant measures and explore their properties and also study the approach to equilibrium. Unexpectedly, we find deep connections between equilibrium measures of finite dimensional su(N) truncations of the stochastic Euler equations and random matrix models. Our work can be regarded as a preparation for addressing the questions of large scale structures, meta-stability and the dynamics of random transitions between different flow topologies in stochastic 2D Euler flows.

Testing the paradigms of the glass transition in colloids

NASA Astrophysics Data System (ADS)

Zia, Roseanna; Wang, Jialun; Peng, Xiaoguang; Li, Qi; McKenna, Gregory

2017-11-01

Many molecular liquids freeze upon fast enough cooling. This so-called glass state is path dependent and out of equilibrium, as measured by the Kovacs signature experiments, i.e. intrinsic isotherms, asymmetry of approach and memory effect. The reasons for this path- and time-dependence are not fully understood, due to fast molecular relaxations. Colloids provide a natural way to model such behavior, owing to disparity in colloidal versus solvent time scales that can slow dynamics. To shed light on the ambiguity of glass transition, we study via large-scale dynamic simulation of hard-sphere colloidal glass after volume-fraction jumps, where particle size increases at fixed system volume followed by protocols of the McKenna-Kovacs signature experiments. During and following each jump, the positions, velocities, and particle-phase stress are tracked and utilized to characterize relaxation time scales. The impact of both quench depth and quench rate on arrested dynamics and ``state'' variables is explored. In addition, we expand our view to various structural signatures, and rearrangement mechanism is proposed. The results provide insight into not only the existence of an ``ideal'' glass transition, but also the role of structure in such a dense amorphous system.

Compensatory dynamics stabilize aggregate community properties in response to multiple types of perturbations.

PubMed

Brown, Bryan L; Downing, Amy L; Leibold, Mathew A

2016-08-01

Compensatory dynamics are an important suite of mechanisms that can stabilize community and ecosystem attributes in systems subject to environmental fluctuations. However, few experimental investigations of compensatory dynamics have addressed these mechanisms in systems of real-world complexity, and existing evidence relies heavily on correlative analyses, retrospective examination, and experiments in simple systems. We investigated the potential for compensatory dynamics to stabilize plankton communities in plankton mesocosm systems of real-world complexity. We employed four types of perturbations including two types of nutrient pulses, shading, and acidification. To quantify how communities responded to these perturbations, we used a measure of community-wide synchrony combined with spectral analysis that allowed us to assess timescale-specific community dynamics, for example, whether dynamics were synchronous at some timescales but compensatory at others. The 150-d experiment produced 32-point time series of all zooplankton taxa in the mesocosms. We then used those time series to evaluate total zooplankton biomass as an aggregate property and to evaluate community dynamics. For three of our four perturbation types, total zooplankton biomass was significantly less variable in systems with environmental variation than in constant environments. For the same three perturbation types, community-wide synchrony was much lower in fluctuating environments than in the constant environment, particularly at longer timescales (periods ≈ 60 d). Additionally, there were strong negative correlations between population temporal variances and the level of community-wide synchrony. Taken together, these results strongly imply that compensatory interactions between species stabilized total biomass in response to perturbations. Diversity did not differ significantly across either treatments or perturbation types, thus ruling out several classes of mechanisms driven by changes in diversity. We also used several pieces of secondary evidence to evaluate the particular mechanism behind compensatory responses since a wide variety of mechanisms are hypothesized to produce compensatory dynamics. We concluded that fluctuation dependent endogenous cycles that occur as a consequence of consumer-resource interactions in competitive communities were the most likely explanation for the compensatory dynamics observed in our experiment. As with our previous work, scale-dependent dynamics were also a key to understanding compensatory dynamics in these experimental communities. © 2016 by the Ecological Society of America.

The Role of SST and Large-Scale Dynamical Motions on the Onset and Shutdown of the Super Greenhouse Effect

NASA Astrophysics Data System (ADS)

O'Brien, T. A.; Kashinath, K.; Collins, W.

2015-12-01

Over warm tropical oceans the increase in greenhouse trapping with increasing SST is faster than that of the surface emission, resulting in a decrease in outgoing longwave radiation at the top of the atmosphere (OLR) when SST increases, also known as the super greenhouse effect (SGE). If SGE is directly linked to SST changes, there are profound implications for positive climate feedbacks in the tropics. However, a number of studies in the last 20 years have provided compelling evidence that the OLR-SST relationship is coincidental rather than causal. These studies suggested that the onset of SGE is dominated by the large-scale dynamics, and that the apparent OLR-SST relationships disappear when individual large-scale regimes are considered. We show that these conclusions are contingent on the quality of the datasets used in the analysis, and that modern satellite observations and reanalyses support a strong relationship between SGE and SST. We find that the SGE occurs across all dynamical regimes, suggesting that this may be related primarily to SST rather than large-scale dynamics. We also find that the discontinuity in the relationship between OLR and SST at high SST (29.5 C), i.e. the shutdown of SGE, also occurs across almost all dynamical regimes, suggesting that this behavior may also be strongly linked to SST. Collectively, these results suggest that the SGE may actually be controlled by SST. Work is ongoing to understand the robustness of this new result to other datasets, to understand whether SST is truly the controlling variable, and to understand the mechanism by which OLR could decrease with increasing SST even under strongly subsiding conditions.

The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields

PubMed Central

Deco, Gustavo; Jirsa, Viktor K.; Robinson, Peter A.; Breakspear, Michael; Friston, Karl

2008-01-01

The cortex is a complex system, characterized by its dynamics and architecture, which underlie many functions such as action, perception, learning, language, and cognition. Its structural architecture has been studied for more than a hundred years; however, its dynamics have been addressed much less thoroughly. In this paper, we review and integrate, in a unifying framework, a variety of computational approaches that have been used to characterize the dynamics of the cortex, as evidenced at different levels of measurement. Computational models at different space–time scales help us understand the fundamental mechanisms that underpin neural processes and relate these processes to neuroscience data. Modeling at the single neuron level is necessary because this is the level at which information is exchanged between the computing elements of the brain; the neurons. Mesoscopic models tell us how neural elements interact to yield emergent behavior at the level of microcolumns and cortical columns. Macroscopic models can inform us about whole brain dynamics and interactions between large-scale neural systems such as cortical regions, the thalamus, and brain stem. Each level of description relates uniquely to neuroscience data, from single-unit recordings, through local field potentials to functional magnetic resonance imaging (fMRI), electroencephalogram (EEG), and magnetoencephalogram (MEG). Models of the cortex can establish which types of large-scale neuronal networks can perform computations and characterize their emergent properties. Mean-field and related formulations of dynamics also play an essential and complementary role as forward models that can be inverted given empirical data. This makes dynamic models critical in integrating theory and experiments. We argue that elaborating principled and informed models is a prerequisite for grounding empirical neuroscience in a cogent theoretical framework, commensurate with the achievements in the physical sciences. PMID:18769680

Fast "Feast/Famine" Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae.

PubMed

Suarez-Mendez, Camilo A; Sousa, Andre; Heijnen, Joseph J; Wahl, Aljoscha

2014-05-15

Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes in substrate availability in an aerobic glucose cultivation of Saccharomyces cerevisiae. After a few cycles, the feast/famine produced a stable and repetitive pattern with a reproducible metabolic response in time, thus providing a robust platform for studying the microorganism's physiology under dynamic conditions. We found that the biomass yield was slightly reduced (-5%) under the feast/famine regime, while the averaged substrate and oxygen consumption as well as the carbon dioxide production rates were comparable. The dynamic response of the intracellular metabolites showed specific differences in comparison to other dynamic experiments (especially stimulus-response experiments, SRE). Remarkably, the frequently reported ATP paradox observed in single pulse experiments was not present during the repetitive perturbations applied here. We found that intracellular dynamic accumulations led to an uncoupling of the substrate uptake rate (up to 9-fold change at 20 s.) Moreover, the dynamic profiles of the intracellular metabolites obtained with the feast/famine suggest the presence of regulatory mechanisms that resulted in a delayed response. With the feast famine setup many cellular states can be measured at high frequency given the feature of reproducible cycles. The feast/famine regime is thus a versatile platform for systems biology approaches, which can help us to identify and investigate metabolite regulations under realistic conditions (e.g., large-scale bioreactors or natural environments).

Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae

PubMed Central

Suarez-Mendez, Camilo A.; Sousa, Andre; Heijnen, Joseph J.; Wahl, Aljoscha

2014-01-01

Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes in substrate availability in an aerobic glucose cultivation of Saccharomyces cerevisiae. After a few cycles, the feast/famine produced a stable and repetitive pattern with a reproducible metabolic response in time, thus providing a robust platform for studying the microorganism’s physiology under dynamic conditions. We found that the biomass yield was slightly reduced (−5%) under the feast/famine regime, while the averaged substrate and oxygen consumption as well as the carbon dioxide production rates were comparable. The dynamic response of the intracellular metabolites showed specific differences in comparison to other dynamic experiments (especially stimulus-response experiments, SRE). Remarkably, the frequently reported ATP paradox observed in single pulse experiments was not present during the repetitive perturbations applied here. We found that intracellular dynamic accumulations led to an uncoupling of the substrate uptake rate (up to 9-fold change at 20 s.) Moreover, the dynamic profiles of the intracellular metabolites obtained with the feast/famine suggest the presence of regulatory mechanisms that resulted in a delayed response. With the feast famine setup many cellular states can be measured at high frequency given the feature of reproducible cycles. The feast/famine regime is thus a versatile platform for systems biology approaches, which can help us to identify and investigate metabolite regulations under realistic conditions (e.g., large-scale bioreactors or natural environments). PMID:24957030

Influences of roughness on the inertial mechanism of turbulent boundary-layer scale separation

NASA Astrophysics Data System (ADS)

Ebner, Rachel

Measurements and scaling analyses are conducted to clarify the combined effects of roughness and Reynolds number on momentum transport in the rough-wall zero pressure gradient turbulent boundary layer. A series of multi-sensor hot-wire experiments are presented that cover nearly a decade in Reynolds number and nearly three decades in the inner-normalized sand grain roughness. This dissertation utilizes the difference between two velocity-vorticity correlations to represent the turbulent inertia term in the statement of the mean dynamics for turbulent boundary layer flow. Analyses focus on the first term on the right hand side of the equation, because it is physically affiliated with change-of-scale effects (Tennekes and Lumley, 1972). Similarity analysis, streamwise correlations, and spectral methods are performed to elucidate the scaling behaviors of the turbulent inertia term relative to the mean dynamics. The present results reveal complex behaviors in the long-time statistics of the velocity-vorticity correlation that exhibit both Reynolds number and roughness dependencies. The results broadly support the combined roughness-Reynolds number description provided by Mehdi et al, (2013).

Transmission of chirality through space and across length scales

NASA Astrophysics Data System (ADS)

Morrow, Sarah M.; Bissette, Andrew J.; Fletcher, Stephen P.

2017-05-01

Chirality is a fundamental property and vital to chemistry, biology, physics and materials science. The ability to use asymmetry to operate molecular-level machines or macroscopically functional devices, or to give novel properties to materials, may address key challenges at the heart of the physical sciences. However, how chirality at one length scale can be translated to asymmetry at a different scale is largely not well understood. In this Review, we discuss systems where chiral information is translated across length scales and through space. A variety of synthetic systems involve the transmission of chiral information between the molecular-, meso- and macroscales. We show how fundamental stereochemical principles may be used to design and understand nanoscale chiral phenomena and highlight important recent advances relevant to nanotechnology. The survey reveals that while the study of stereochemistry on the nanoscale is a rich and dynamic area, our understanding of how to control and harness it and dial-up specific properties is still in its infancy. The long-term goal of controlling nanoscale chirality promises to be an exciting journey, revealing insight into biological mechanisms and providing new technologies based on dynamic physical properties.

The proximal-to-distal sequence in upper-limb motions on multiple levels and time scales.

PubMed

Serrien, Ben; Baeyens, Jean-Pierre

2017-10-01

The proximal-to-distal sequence is a phenomenon that can be observed in a large variety of motions of the upper limbs in both humans and other mammals. The mechanisms behind this sequence are not completely understood and motor control theories able to explain this phenomenon are currently incomplete. The aim of this narrative review is to take a theoretical constraints-led approach to the proximal-to-distal sequence and provide a broad multidisciplinary overview of relevant literature. This sequence exists at multiple levels (brain, spine, muscles, kinetics and kinematics) and on multiple time scales (motion, motor learning and development, growth and possibly even evolution). We hypothesize that the proximodistal spatiotemporal direction on each time scale and level provides part of the organismic constraints that guide the dynamics at the other levels and time scales. The constraint-led approach in this review may serve as a first onset towards integration of evidence and a framework for further experimentation to reveal the dynamics of the proximal-to-distal sequence. Copyright © 2017 Elsevier B.V. All rights reserved.

Modeling the heterogeneity of human dynamics based on the measurements of influential users in Sina Microblog

NASA Astrophysics Data System (ADS)

Wang, Chenxu; Guan, Xiaohong; Qin, Tao; Yang, Tao

2015-06-01

Online social network has become an indispensable communication tool in the information age. The development of microblog also provides us a great opportunity to study human dynamics that play a crucial role in the design of efficient communication systems. In this paper we study the characteristics of the tweeting behavior based on the data collected from Sina Microblog. The user activity level is measured to characterize how often a user posts a tweet. We find that the user activity level follows a bimodal distribution. That is, the microblog users tend to be either active or inactive. The inter-tweeting time distribution is then measured at both the aggregate and individual levels. We find that the inter-tweeting time follows a piecewise power law distribution of two tails. Furthermore, the exponents of the two tails have different correlations with the user activity level. These findings demonstrate that the dynamics of the tweeting behavior are heterogeneous in different time scales. We then develop a dynamic model co-driven by the memory and the interest mechanism to characterize the heterogeneity. The numerical simulations validate the model and verify that the short time interval tweeting behavior is driven by the memory mechanism while the long time interval behavior by the interest mechanism.

Aerodynamic generation of electric fields in turbulence laden with charged inertial particles.

PubMed

Di Renzo, M; Urzay, J

2018-04-26

Self-induced electricity, including lightning, is often observed in dusty atmospheres. However, the physical mechanisms leading to this phenomenon remain elusive as they are remarkably challenging to determine due to the high complexity of the multi-phase turbulent flows involved. Using a fast multi-pole method in direct numerical simulations of homogeneous turbulence laden with hundreds of millions of inertial particles, here we show that mesoscopic electric fields can be aerodynamically created in bi-disperse suspensions of oppositely charged particles. The generation mechanism is self-regulating and relies on turbulence preferentially concentrating particles of one sign in clouds while dispersing the others more uniformly. The resulting electric field varies over much larger length scales than both the mean inter-particle spacing and the size of the smallest eddies. Scaling analyses suggest that low ambient pressures, such as those prevailing in the atmosphere of Mars, increase the dynamical relevance of this aerodynamic mechanism for electrical breakdown.

Large scale structure from the Higgs fields of the supersymmetric standard model

NASA Astrophysics Data System (ADS)

Bastero-Gil, M.; di Clemente, V.; King, S. F.

2003-05-01

We propose an alternative implementation of the curvaton mechanism for generating the curvature perturbations which does not rely on a late decaying scalar decoupled from inflation dynamics. In our mechanism the supersymmetric Higgs scalars are coupled to the inflaton in a hybrid inflation model, and this allows the conversion of the isocurvature perturbations of the Higgs fields to the observed curvature perturbations responsible for large scale structure to take place during reheating. We discuss an explicit model which realizes this mechanism in which the μ term in the Higgs superpotential is generated after inflation by the vacuum expectation value of a singlet field. The main prediction of the model is that the spectral index should deviate significantly from unity, |n-1|˜0.1. We also expect relic isocurvature perturbations in neutralinos and baryons, but no significant departures from Gaussianity and no observable effects of gravity waves in the CMB spectrum.

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

PubMed

Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

2016-08-05

The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Spectral methods for study of the G-protein-coupled receptor rhodopsin. II. Magnetic resonance methods

NASA Astrophysics Data System (ADS)

Struts, A. V.; Barmasov, A. V.; Brown, M. F.

2016-02-01

This article continues our review of spectroscopic studies of G-protein-coupled receptors. Magnetic resonance methods including electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) provide specific structural and dynamical data for the protein in conjunction with optical methods (vibrational, electronic spectroscopy) as discussed in the accompanying article. An additional advantage is the opportunity to explore the receptor proteins in the natural membrane lipid environment. Solid-state 2H and 13C NMR methods yield information about both the local structure and dynamics of the cofactor bound to the protein and its light-induced changes. Complementary site-directed spin-labeling studies monitor the structural alterations over larger distances and correspondingly longer time scales. A multiscale reaction mechanism describes how local changes of the retinal cofactor unlock the receptor to initiate large-scale conformational changes of rhodopsin. Activation of the G-protein-coupled receptor involves an ensemble of conformational substates within the rhodopsin manifold that characterize the dynamically active receptor.

Multi-time scale dynamics in power electronics-dominated power systems

NASA Astrophysics Data System (ADS)

Yuan, Xiaoming; Hu, Jiabing; Cheng, Shijie

2017-09-01

Electric power infrastructure has recently undergone a comprehensive transformation from electromagnetics to semiconductors. Such a development is attributed to the rapid growth of power electronic converter applications in the load side to realize energy conservation and on the supply side for renewable generations and power transmissions using high voltage direct current transmission. This transformation has altered the fundamental mechanism of power system dynamics, which demands the establishment of a new theory for power system control and protection. This paper presents thoughts on a theoretical framework for the coming semiconducting power systems.

Dynamic fatigue of a machinable glass-ceramic

NASA Technical Reports Server (NTRS)

Smyth, K. K.; Magida, M. B.

1982-01-01

To assess the stress corrosion susceptibility of a machinable glass-ceramic, its dynamic fatigue behavior was investigated by measuring its strength as a function of stress rate. Fracture mechanics techniques were used to analyse the results for the purpose of making lifetime predictions for components of this material. This material was concluded to have only moderate resistance to stress in ambient conditions. The effects of specimen size on strength were assessed for the material used in this study: it was concluded that the Weibull edge-flaw scaling law adequately describes the observed strength-size relationship.

Dynamic interpretation of geoid anomalies

NASA Technical Reports Server (NTRS)

Hager, Bradford H.

1988-01-01

The NASA Geodynamics program has as two of its missions precise determination of spatial variations in earth's geopotential (or geoid) and highly accurate monitoring of polar motion, including changes in the length of day (LOD). For the past several years, data sets provided by NASA, along with data and models from other areas of geophysic were used to place fundamental contraints on the large scale dynamics of earth and her sister planet Venus. The main approach was using fluid mechanical models of mantle flow to predict the long-wavelength variations in the geoid.

Nonlinear dynamic theory for photorefractive phase hologram formation

NASA Technical Reports Server (NTRS)

Kim, D. M.; Shah, R. R.; Rabson, T. A.; Tittle, F. K.

1976-01-01

A nonlinear dynamic theory is developed for the formation of photorefractive volume phase holograms. A feedback mechanism existing between the photogenerated field and free-electron density, treated explicitly, yields the growth and saturation of the space-charge field in a time scale characterized by the coupling strength between them. The expression for the field reduces in the short-time limit to previous theories and approaches in the long-time limit the internal or photovoltaic field. Additionally, the phase of the space charge field is shown to be time-dependent.

Human dynamics scaling characteristics for aerial inbound logistics operation

NASA Astrophysics Data System (ADS)

Wang, Qing; Guo, Jin-Li

2010-05-01

In recent years, the study of power-law scaling characteristics of real-life networks has attracted much interest from scholars; it deviates from the Poisson process. In this paper, we take the whole process of aerial inbound operation in a logistics company as the empirical object. The main aim of this work is to study the statistical scaling characteristics of the task-restricted work patterns. We found that the statistical variables have the scaling characteristics of unimodal distribution with a power-law tail in five statistical distributions - that is to say, there obviously exists a peak in each distribution, the shape of the left part closes to a Poisson distribution, and the right part has a heavy-tailed scaling statistics. Furthermore, to our surprise, there is only one distribution where the right parts can be approximated by the power-law form with exponent α=1.50. Others are bigger than 1.50 (three of four are about 2.50, one of four is about 3.00). We then obtain two inferences based on these empirical results: first, the human behaviors probably both close to the Poisson statistics and power-law distributions on certain levels, and the human-computer interaction behaviors may be the most common in the logistics operational areas, even in the whole task-restricted work pattern areas. Second, the hypothesis in Vázquez et al. (2006) [A. Vázquez, J. G. Oliveira, Z. Dezsö, K.-I. Goh, I. Kondor, A.-L. Barabási. Modeling burst and heavy tails in human dynamics, Phys. Rev. E 73 (2006) 036127] is probably not sufficient; it claimed that human dynamics can be classified as two discrete university classes. There may be a new human dynamics mechanism that is different from the classical Barabási models.

Generation of skeletal mechanism by means of projected entropy participation indices

NASA Astrophysics Data System (ADS)

Paolucci, Samuel; Valorani, Mauro; Ciottoli, Pietro Paolo; Galassi, Riccardo Malpica

2017-11-01

When the dynamics of reactive systems develop very-slow and very-fast time scales separated by a range of active time scales, with gaps in the fast/active and slow/active time scales, then it is possible to achieve multi-scale adaptive model reduction along-with the integration of the ODEs using the G-Scheme. The scheme assumes that the dynamics is decomposed into active, slow, fast, and invariant subspaces. We derive expressions that establish a direct link between time scales and entropy production by using estimates provided by the G-Scheme. To calculate the contribution to entropy production, we resort to a standard model of a constant pressure, adiabatic, batch reactor, where the mixture temperature of the reactants is initially set above the auto-ignition temperature. Numerical experiments show that the contribution to entropy production of the fast subspace is of the same magnitude as the error threshold chosen for the identification of the decomposition of the tangent space, and the contribution of the slow subspace is generally much smaller than that of the active subspace. The information on entropy production associated with reactions within each subspace is used to define an entropy participation index that is subsequently utilized for model reduction.

Multiscale Cloud System Modeling

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo; Moncrieff, Mitchell W.

2009-01-01

The central theme of this paper is to describe how cloud system resolving models (CRMs) of grid spacing approximately 1 km have been applied to various important problems in atmospheric science across a wide range of spatial and temporal scales and how these applications relate to other modeling approaches. A long-standing problem concerns the representation of organized precipitating convective cloud systems in weather and climate models. Since CRMs resolve the mesoscale to large scales of motion (i.e., 10 km to global) they explicitly address the cloud system problem. By explicitly representing organized convection, CRMs bypass restrictive assumptions associated with convective parameterization such as the scale gap between cumulus and large-scale motion. Dynamical models provide insight into the physical mechanisms involved with scale interaction and convective organization. Multiscale CRMs simulate convective cloud systems in computational domains up to global and have been applied in place of contemporary convective parameterizations in global models. Multiscale CRMs pose a new challenge for model validation, which is met in an integrated approach involving CRMs, operational prediction systems, observational measurements, and dynamical models in a new international project: the Year of Tropical Convection, which has an emphasis on organized tropical convection and its global effects.

Dynamics from Seconds to Hours in Hodgkin-Huxley Model with Time-Dependent Ion Concentrations and Buffer Reservoirs

PubMed Central

Hübel, Niklas; Dahlem, Markus A.

2014-01-01

The classical Hodgkin-Huxley (HH) model neglects the time-dependence of ion concentrations in spiking dynamics. The dynamics is therefore limited to a time scale of milliseconds, which is determined by the membrane capacitance multiplied by the resistance of the ion channels, and by the gating time constants. We study slow dynamics in an extended HH framework that includes time-dependent ion concentrations, pumps, and buffers. Fluxes across the neuronal membrane change intra- and extracellular ion concentrations, whereby the latter can also change through contact to reservoirs in the surroundings. Ion gain and loss of the system is identified as a bifurcation parameter whose essential importance was not realized in earlier studies. Our systematic study of the bifurcation structure and thus the phase space structure helps to understand activation and inhibition of a new excitability in ion homeostasis which emerges in such extended models. Also modulatory mechanisms that regulate the spiking rate can be explained by bifurcations. The dynamics on three distinct slow times scales is determined by the cell volume-to-surface-area ratio and the membrane permeability (seconds), the buffer time constants (tens of seconds), and the slower backward buffering (minutes to hours). The modulatory dynamics and the newly emerging excitable dynamics corresponds to pathological conditions observed in epileptiform burst activity, and spreading depression in migraine aura and stroke, respectively. PMID:25474648

Dynamic trapping near a quantum critical point

NASA Astrophysics Data System (ADS)

Kolodrubetz, Michael; Katz, Emanuel; Polkovnikov, Anatoli

2015-02-01

The study of dynamics in closed quantum systems has been revitalized by the emergence of experimental systems that are well-isolated from their environment. In this paper, we consider the closed-system dynamics of an archetypal model: spins driven across a second-order quantum critical point, which are traditionally described by the Kibble-Zurek mechanism. Imbuing the driving field with Newtonian dynamics, we find that the full closed system exhibits a robust new phenomenon—dynamic critical trapping—in which the system is self-trapped near the critical point due to efficient absorption of field kinetic energy by heating the quantum spins. We quantify limits in which this phenomenon can be observed and generalize these results by developing a Kibble-Zurek scaling theory that incorporates the dynamic field. Our findings can potentially be interesting in the context of early universe physics, where the role of the driving field is played by the inflaton or a modulus field.

Automatic network coupling analysis for dynamical systems based on detailed kinetic models.

PubMed

Lebiedz, Dirk; Kammerer, Julia; Brandt-Pollmann, Ulrich

2005-10-01

We introduce a numerical complexity reduction method for the automatic identification and analysis of dynamic network decompositions in (bio)chemical kinetics based on error-controlled computation of a minimal model dimension represented by the number of (locally) active dynamical modes. Our algorithm exploits a generalized sensitivity analysis along state trajectories and subsequent singular value decomposition of sensitivity matrices for the identification of these dominant dynamical modes. It allows for a dynamic coupling analysis of (bio)chemical species in kinetic models that can be exploited for the piecewise computation of a minimal model on small time intervals and offers valuable functional insight into highly nonlinear reaction mechanisms and network dynamics. We present results for the identification of network decompositions in a simple oscillatory chemical reaction, time scale separation based model reduction in a Michaelis-Menten enzyme system and network decomposition of a detailed model for the oscillatory peroxidase-oxidase enzyme system.

Dynamical tunneling versus fast diffusion for a non-convex Hamiltonian

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

Pittman, S. M.; Tannenbaum, E.; Heller, E. J.

This paper attempts to resolve the issue of the nature of the 0.01-0.1 cm{sup −1} peak splittings observed in high-resolution IR spectra of polyatomic molecules. One hypothesis is that these splittings are caused by dynamical tunneling, a quantum-mechanical phenomenon whereby energy flows between two disconnected regions of phase-space across dynamical barriers. However, a competing classical mechanism for energy flow is Arnol’d diffusion, which connects different regions of phase-space by a resonance network known as the Arnol’d web. The speed of diffusion is bounded by the Nekhoroshev theorem, which guarantees stability on exponentially long time scales if the Hamiltonian is steep.more » Here we consider a non-convex Hamiltonian that contains the characteristics of a molecular Hamiltonian, but does not satisfy the Nekhoroshev theorem. The diffusion along the Arnol’d web is expected to be fast for a non-convex Hamiltonian. While fast diffusion is an unlikely competitor for longtime energy flow in molecules, we show how dynamical tunneling dominates compared to fast diffusion in the nearly integrable regime for a non-convex Hamiltonian, as well as present a new kind of dynamical tunneling.« less

Asymptotic theory of time-varying social networks with heterogeneous activity and tie allocation.

PubMed

Ubaldi, Enrico; Perra, Nicola; Karsai, Márton; Vezzani, Alessandro; Burioni, Raffaella; Vespignani, Alessandro

2016-10-24

The dynamic of social networks is driven by the interplay between diverse mechanisms that still challenge our theoretical and modelling efforts. Amongst them, two are known to play a central role in shaping the networks evolution, namely the heterogeneous propensity of individuals to i) be socially active and ii) establish a new social relationships with their alters. Here, we empirically characterise these two mechanisms in seven real networks describing temporal human interactions in three different settings: scientific collaborations, Twitter mentions, and mobile phone calls. We find that the individuals' social activity and their strategy in choosing ties where to allocate their social interactions can be quantitatively described and encoded in a simple stochastic network modelling framework. The Master Equation of the model can be solved in the asymptotic limit. The analytical solutions provide an explicit description of both the system dynamic and the dynamical scaling laws characterising crucial aspects about the evolution of the networks. The analytical predictions match with accuracy the empirical observations, thus validating the theoretical approach. Our results provide a rigorous dynamical system framework that can be extended to include other processes shaping social dynamics and to generate data driven predictions for the asymptotic behaviour of social networks.

Asymptotic theory of time-varying social networks with heterogeneous activity and tie allocation

NASA Astrophysics Data System (ADS)

Ubaldi, Enrico; Perra, Nicola; Karsai, Márton; Vezzani, Alessandro; Burioni, Raffaella; Vespignani, Alessandro

2016-10-01

The dynamic of social networks is driven by the interplay between diverse mechanisms that still challenge our theoretical and modelling efforts. Amongst them, two are known to play a central role in shaping the networks evolution, namely the heterogeneous propensity of individuals to i) be socially active and ii) establish a new social relationships with their alters. Here, we empirically characterise these two mechanisms in seven real networks describing temporal human interactions in three different settings: scientific collaborations, Twitter mentions, and mobile phone calls. We find that the individuals’ social activity and their strategy in choosing ties where to allocate their social interactions can be quantitatively described and encoded in a simple stochastic network modelling framework. The Master Equation of the model can be solved in the asymptotic limit. The analytical solutions provide an explicit description of both the system dynamic and the dynamical scaling laws characterising crucial aspects about the evolution of the networks. The analytical predictions match with accuracy the empirical observations, thus validating the theoretical approach. Our results provide a rigorous dynamical system framework that can be extended to include other processes shaping social dynamics and to generate data driven predictions for the asymptotic behaviour of social networks.

Force Dynamics During T Cell Activation

NASA Astrophysics Data System (ADS)

Garcia, David A.; Upadhyaya, Arpita

T cell activation is an essential step in the adaptive immune response. The binding of the T cell receptor (TCR) with antigen triggers signaling cascades and cell spreading. Physical forces exerted on the TCR by the cytoskeleton have been shown to induce signaling events. While cellular forces are known to depend on the mechanical properties of the cytoskeleton, the biophysical mechanisms underlying force induced activation of TCR-antigen interactions unknown. Here, we use traction force microscopy to measure the force dynamics of activated Jurkat T cells. The movements of beads embedded in an elastic gel serve as a non-invasive reporter of cytoskeletal and molecular motor dynamics. We examined the statistical structure of the force profiles throughout the cell during signaling activation. We found two spatially distinct active regimes of force generation characterized by different time scales. Typically, the interior of the cells was found to be more active than the periphery. Inhibition of myosin motor activity altered the correlation time of the bead displacements indicating additional sources of stochastic force generation. Our results indicate a complex interaction between myosin activity and actin polymerization dynamics in producing cellular forces in immune cells.

Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling.

PubMed

Liu, Hui; Dong, Peng; Ioannou, Maria S; Li, Li; Shea, Jamien; Pasolli, H Amalia; Grimm, Jonathan B; Rivlin, Patricia K; Lavis, Luke D; Koyama, Minoru; Liu, Zhe

2018-01-09

Our ability to unambiguously image and track individual molecules in live cells is limited by packing of multiple copies of labeled molecules within the resolution limit. Here we devise a universal genetic strategy to precisely control copy number of fluorescently labeled molecules in a cell. This system has a dynamic range of ∼10,000-fold, enabling sparse labeling of proteins expressed at different abundance levels. Combined with photostable labels, this system extends the duration of automated single-molecule tracking by two orders of magnitude. We demonstrate long-term imaging of synaptic vesicle dynamics in cultured neurons as well as in intact zebrafish. We found axon initial segment utilizes a "waterfall" mechanism gating synaptic vesicle transport polarity by promoting anterograde transport processivity. Long-time observation also reveals that transcription factor hops between clustered binding sites in spatially restricted subnuclear regions, suggesting that topological structures in the nucleus shape local gene activities by a sequestering mechanism. This strategy thus greatly expands the spatiotemporal length scales of live-cell single-molecule measurements, enabling new experiments to quantitatively understand complex control of molecular dynamics in vivo.

Rapid microfluidic mixing and liquid jets for studying biomolecular chemical dynamics

NASA Astrophysics Data System (ADS)

Langley, Daniel; Abbey, Brian

2018-01-01

X-ray Free-Electron Lasers (XFELs) offer a unique opportunity to study the structural dynamics of proteins on a femtosecond time-scale. To realize the full potential of XFEL sources for studying time-resolved biomolecular processes however, requires the optimization and development of devices that can both act as a trigger and a delivery mechanism for the system of interest. Here we present numerical simulations and actual devices exploring the conditions required for the development of successful mixing and injection devices for tracking the molecular dynamics of proteins in solution on micro to nanosecond timescales using XFELs. The mechanism for combining reagents employs a threefold combination of pico-liter volumes, lamination and serpentine mixing. Focusing and delivering the sample in solution is achieved using the Gas Dynamic Virtual Nozzle (GDVN), which was specifically developed to produce a micrometer diameter, in-vacuum liquid jet. We explore the influence of parameters such as flow rate and gas pressure on the mixing time and jet stability, and explore the formation of rapid homogeneously mixed jets for `mix-and-inject' liquid scattering experiments at Synchrotron and XFEL facilities.

Ab Initio Calculations of Ultrashort Carrier Dynamics in Two-Dimensional Materials: Valley Depolarization in Single-Layer WSe2

NASA Astrophysics Data System (ADS)

Molina-Sánchez, Alejandro; Sangalli, Davide; Wirtz, Ludger; Marini, Andrea

2017-08-01

In single-layer WSe$_2$, a paradigmatic semiconducting transition metal dichalcogenide, a circularly polarized laser field can selectively excite electronic transitions in one of the inequivalent $K^{\\pm}$ valleys. Such selective valley population corresponds to a pseudospin polarization. This can be used as a degree of freedom in a valleytronic device provided that the time scale for its depolarization is sufficiently large. Yet, the mechanism behind the valley depolarization still remains heavily debated. Recent time-dependent Kerr experiments have provided an accurate way to visualize the valley dynamics by measuring the rotation of a linearly polarized probe pulse applied after a circularly polarized pump pulse. We present here a clear, accurate and parameter-free description of the valley dynamics. By using an atomistic, ab initio, approach we fully disclose the elemental mechanisms that dictate the depolarization effects. Our results are in excellent agreement with recent time-dependent Kerr experiments. We explain the Kerr dynamics and its temperature dependence in terms of electron-phonon mediated processes that induce spin-flip inter-valley transitions.

A dynamic subgrid scale model for Large Eddy Simulations based on the Mori-Zwanzig formalism

NASA Astrophysics Data System (ADS)

Parish, Eric J.; Duraisamy, Karthik

2017-11-01

The development of reduced models for complex multiscale problems remains one of the principal challenges in computational physics. The optimal prediction framework of Chorin et al. [1], which is a reformulation of the Mori-Zwanzig (M-Z) formalism of non-equilibrium statistical mechanics, provides a framework for the development of mathematically-derived reduced models of dynamical systems. Several promising models have emerged from the optimal prediction community and have found application in molecular dynamics and turbulent flows. In this work, a new M-Z-based closure model that addresses some of the deficiencies of existing methods is developed. The model is constructed by exploiting similarities between two levels of coarse-graining via the Germano identity of fluid mechanics and by assuming that memory effects have a finite temporal support. The appeal of the proposed model, which will be referred to as the 'dynamic-MZ-τ' model, is that it is parameter-free and has a structural form imposed by the mathematics of the coarse-graining process (rather than the phenomenological assumptions made by the modeler, such as in classical subgrid scale models). To promote the applicability of M-Z models in general, two procedures are presented to compute the resulting model form, helping to bypass the tedious error-prone algebra that has proven to be a hindrance to the construction of M-Z-based models for complex dynamical systems. While the new formulation is applicable to the solution of general partial differential equations, demonstrations are presented in the context of Large Eddy Simulation closures for the Burgers equation, decaying homogeneous turbulence, and turbulent channel flow. The performance of the model and validity of the underlying assumptions are investigated in detail.

Persistence of Soil Organic Carbon can be Explained as an Emergent Property of Microbial Ecology and Population Dynamics

NASA Astrophysics Data System (ADS)

Woolf, D.; Lehmann, J.

2016-12-01

The exchange of carbon between soils and the atmosphere represents an important uncertainty in climate predictions. Current Earth system models apply soil organic matter (SOM) models based on independent carbon pools with 1st order decomposition dynamics. It has been widely argued over the last decade that such models do not accurately describe soil processes and mechanisms. For example, the long term persistence of soil organic carbon (SOC) is only adequately described by such models by the post hoc assumption of passive or inert carbon pools. Further, such 1st order models also fail to account for microbially-mediated dynamics such as priming interactions. These shortcomings may limit their applicability to long term predictions under conditions of global environmental change. In addition to incorporating recent conceptual advances in the mechanisms of SOM decomposition and protection, next-generation SOM models intended for use in Earth system models need to meet further quality criteria. Namely, that they should (a) accurately describe historical data from long term trials and the current global distribution of soil organic carbon, (b) be computationally efficient for large number of iterations involved in climate modeling, and (c) have sufficiently simple parameterization that they can be run on spatially-explicit data available at global scale under varying conditions of global change over long time scales. Here we show that linking fundamental ecological principles and microbial population dynamics to SOC turnover rates results in a dynamic model that meets all of these quality criteria. This approach simultaneously eliminates the need to postulate biogeochemically-implausible passive or inert pools, instead showing how SOM persistence emerges from ecological principles, while also reproducing observed priming interactions.

Towards a comprehensive understanding of emerging dynamics and function of pancreatic islets: A complex network approach. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

NASA Astrophysics Data System (ADS)

Loppini, Alessandro

2018-03-01

Complex network theory represents a comprehensive mathematical framework to investigate biological systems, ranging from sub-cellular and cellular scales up to large-scale networks describing species interactions and ecological systems. In their exhaustive and comprehensive work [1], Gosak et al. discuss several scenarios in which the network approach was able to uncover general properties and underlying mechanisms of cells organization and regulation, tissue functions and cell/tissue failure in pathology, by the study of chemical reaction networks, structural networks and functional connectivities.

Geometry can provide long-range mechanical guidance for embryogenesis

PubMed Central

Dicko, Mahamar; Saramito, Pierre

2017-01-01

Downstream of gene expression, effectors such as the actomyosin contractile machinery drive embryo morphogenesis. During Drosophila embryonic axis extension, actomyosin has a specific planar-polarised organisation, which is responsible for oriented cell intercalation. In addition to these cell rearrangements, cell shape changes also contribute to tissue deformation. While cell-autonomous dynamics are well described, understanding the tissue-scale behaviour challenges us to solve the corresponding mechanical problem at the scale of the whole embryo, since mechanical resistance of all neighbouring epithelia will feedback on individual cells. Here we propose a novel numerical approach to compute the whole-embryo dynamics of the actomyosin-rich apical epithelial surface. We input in the model specific patterns of actomyosin contractility, such as the planar-polarisation of actomyosin in defined ventro-lateral regions of the embryo. Tissue strain rates and displacements are then predicted over the whole embryo surface according to the global balance of stresses and the material behaviour of the epithelium. Epithelia are modelled using a rheological law that relates the rate of deformation to the local stresses and actomyosin anisotropic contractility. Predicted flow patterns are consistent with the cell flows observed when imaging Drosophila axis extension in toto, using light sheet microscopy. The agreement between model and experimental data indicates that the anisotropic contractility of planar-polarised actomyosin in the ventro-lateral germband tissue can directly cause the tissue-scale deformations of the whole embryo. The three-dimensional mechanical balance is dependent on the geometry of the embryo, whose curved surface is taken into account in the simulations. Importantly, we find that to reproduce experimental flows, the model requires the presence of the cephalic furrow, a fold located anteriorly of the extending tissues. The presence of this geometric feature, through the global mechanical balance, guides the flow and orients extension towards the posterior end. PMID:28346461

Bio-inspired energy-harvesting mechanisms and patterns of dynamic soaring.

PubMed

Liu, Duo-Neng; Hou, Zhong-Xi; Guo, Zheng; Yang, Xi-Xiang; Gao, Xian-Zhong

2017-01-30

Albatrosses can make use of the dynamic soaring technique extracting energy from the wind field to achieve large-scale movement without a flap, which stimulates interest in effortless flight with small unmanned aerial vehicles (UAVs). However, mechanisms of energy harvesting in terms of the energy transfer from the wind to the flyer (albatross or UAV) are still indeterminate and controversial when using different reference frames in previous studies. In this paper, the classical four-phase Rayleigh cycle, includes sequentially upwind climb, downwind turn, downwind dive and upwind turn, is introduced in analyses of energy gain with the albatross's equation of motions and the simulated trajectory in dynamic soaring. Analytical and numerical results indicate that the energy gain in the air-relative frame mostly originates from large wind gradients at lower part of the climb and dive, while the energy gain in the inertial frame comes from the lift vector inclined to the wind speed direction during the climb, dive and downwind turn at higher altitude. These two energy-gain mechanisms are not equivalent in terms of energy sources and reference frames but have to be simultaneously satisfied in terms of the energy-neutral dynamic soaring cycle. For each reference frame, energy-loss phases are necessary to connect energy-gain ones. Based on these four essential phases in dynamic soaring and the albatrosses' flight trajectory, different dynamic soaring patterns are schematically depicted and corresponding optimal trajectories are computed. The optimal dynamic soaring trajectories are classified into two closed patterns including 'O' shape and '8' shape, and four travelling patterns including 'Ω' shape, 'α' shape, 'C' shape and 'S' shape. The correlation among these patterns are analysed and discussed. The completeness of the classification for different patterns is confirmed by listing and summarising dynamic soaring trajectories shown in studies over the past decades.

Critical transition to bistability arising from hidden degrees of freedom in origami structures

NASA Astrophysics Data System (ADS)

Cohen, Itai; Silverberg, Jesse; Na, Jun-Hee; Evans, Arthur; Liu, Bin; Hull, Thomas; Santangelo, Christian; Lang, Robert; Hayward, Ryan

2015-03-01

Origami, the traditional art of paper folding, is now being used to design responsive, dynamic, and customizable mechanical metamaterials. The remarkable abilities of these origami-inspired devices emerge from a predefined crease pattern, which couples kinematic folding constraints to the geometric placement of creases. In spite of this progress, a generalized physical understanding of origami remains elusive due to the challenge in determining whether local kinematic constraints are globally compatible, and an incomplete understanding of how bending and crease plasticity found in real materials contribute to the overall mechanical response. Here, we show experimentally and theoretically that the traditional square twist, whose crease pattern has zero degrees of freedom (DOF) and therefore should not be foldable, is nevertheless able to be folded by accessing higher energy scale deformations associated with bending. Due to the separation of bending and crease energy scales, these hidden DOF lead to a geometrically-driven critical bifurcation between mono- and bistability. The scale-free geometric underpinnings of this physical phenomenon suggest a generalized design principle that can be useful for fabricating micro- and nanoscale mechanical switches.

Dynamical Scaling Relations and the Angular Momentum Problem in the FIRE Simulations

NASA Astrophysics Data System (ADS)

Schmitz, Denise; Hopkins, Philip F.; Quataert, Eliot; Keres, Dusan; Faucher-Giguere, Claude-Andre

2015-01-01

Simulations are an extremely important tool with which to study galaxy formation and evolution. However, even state-of-the-art simulations still fail to accurately predict important galaxy properties such as star formation rates and dynamical scaling relations. One possible explanation is the inadequacy of sub-grid models to capture the range of stellar feedback mechanisms which operate below the resolution limit of simulations. FIRE (Feedback in Realistic Environments) is a set of high-resolution cosmological galaxy simulations run using the code GIZMO. It includes more realistic models for various types of feedback including radiation pressure, supernovae, stellar winds, and photoionization and photoelectric heating. Recent FIRE results have demonstrated good agreement with the observed stellar mass-halo mass relation as well as more realistic star formation histories than previous simulations. We investigate the effects of FIRE's improved feedback prescriptions on the simulation "angular momentum problem," i.e., whether FIRE can reproduce observed scaling relations between galaxy stellar mass and rotational/dispersion velocities.

Ion-Neutral Coupling in Solar Prominence

NASA Technical Reports Server (NTRS)

Gilbert, H.; DeVore, C. R.; Karpen, J.; Kucera, T.; Antiochos, S.; Kawashima, R.

2011-01-01

Coupling between ions and neutrals in magnetized plasmas is fundamentally important to many aspects of heliophysics, including our ionosphere, the solar chromosphere, the solar wind interaction with planetary atmospheres, and the interface between the heliosphere and the interstellar medium. Ion-neutral coupling also plays a major role in the physics of solar prominences. By combining theory, modeling, and observations we are working toward a better understanding of the structure and dynamics of partially ionized prominence plasma. Two key questions are addressed in the present work: 1) what physical mechanism(s) sets the cross-field scale of prominence threads? 2) Are ion-neutral interactions responsible for the vertical flows and structure in prominences? We present initial results from a study investigating what role ion-neutral interactions play in prominence dynamics and structure. This research was supported by NASA.

Shock-induced poration, cholesterol flip-flop and small interfering RNA transfection in a phospholipid membrane: Multimillion atom, microsecond molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Choubey, Amit

Biological cell membranes provide mechanical stability to cells and understanding their structure, dynamics and mechanics are important biophysics problems. Experiments coupled with computational methods such as molecular dynamics (MD) have provided insight into the physics of membranes. We use long-time and large-scale MD simulations to study the structure, dynamics and mechanical behavior of membranes. We investigate shock-induced collapse of nanobubbles in water using MD simulations based on a reactive force field. We observe a focused jet at the onset of bubble shrinkage and a secondary shock wave upon bubble collapse. The jet length scales linearly with the nanobubble radius, as observed in experiments on micron-to-millimeter size bubbles. Shock induces dramatic structural changes, including an ice-VII-like structural motif at a particle velocity of 1 km/s. The incipient ice VII formation and the calculated Hugoniot curve are in good agreement with experimental results. We also investigate molecular mechanisms of poration in lipid bilayers due to shock-induced collapse of nanobubbles. Our multimillion-atom MD simulations reveal that the jet impact generates shear flow of water on bilayer leaflets and pressure gradients across them. This transiently enhances the bilayer permeability by creating nanopores through which water molecules translocate rapidly across the bilayer. Effects of nanobubble size and temperature on the porosity of lipid bilayers are examined. The second research project focuses on cholesterol (CHOL) dynamics in phospholipid bilayers. Several experimental and computational studies have been performed on lipid bilayers consisting of dipalmitoylphosphatidylcholine (DPPC) and CHOL molecules. CHOL interleaflet transport (flip-flop) plays an important role in interleaflet coupling and determining CHOL flip-flop rate has been elusive. Various studies report that the rate ranges between milliseconds to seconds. We calculate CHOL flip-flop rates by performing a 15 mus all-atom MD simulation of a DPPC-CHOL bilayer. We find that the CHOL flip-flop rates are on the sub microsecond timescale. These results are verified by performing various independent parallel replica (PR) simulations. Our PR simulations provide significant boost in sampling of the flip-flop events. We observe that the CHOL flip-flop can induce membrane order, regulate membrane-bending energy, and facilitate membrane relaxation. The rapid flip-flop rates reported here have important implications for the role of CHOL in mechanical properties of cell membranes, formation of domains, and maintaining CHOL concentration asymmetry in plasma membrane. Our PR approach can reach submillisecond time scales and bridge the gap between MD simulations and Nuclear Magnetic Resonance (NMR) experiments on CHOL flip-flop dynamics in membranes. The last project deals with transfection barriers encountered by a bare small interfering RNA (siRNA) in a phospholipid bilayer. SiRNA molecules play a pivotal role in therapeutic applications. A key limitation to the widespread implementation of siRNA-based therapeutics is the difficulty of delivering siRNA-based drugs to cells. We have examined structural and mechanical barriers to siRNA passage across a phospholipid bilayer using all-atom MD simulations. We find that the electrostatic interaction between the anionic siRNA and head groups of phospholipid molecules induces a phase transformation from the liquid crystalline to ripple phase. Steered MD simulations reveal that the siRNA transfection through the ripple phase requires a force of ˜ 1.5 nN.

Counter-intuitive features of the dynamic topography unveiled by tectonically realistic 3D numerical models of mantle-lithosphere interactions

NASA Astrophysics Data System (ADS)

Burov, Evgueni; Gerya, Taras

2013-04-01

It has been long assumed that the dynamic topography associated with mantle-lithosphere interactions should be characterized by long-wavelength features (> 1000 km) correlating with morphology of mantle flow and expanding beyond the scale of tectonic processes. For example, debates on the existence of mantle plumes largely originate from interpretations of expected signatures of plume-induced topography that are compared to the predictions of analytical and numerical models of plume- or mantle-lithosphere interactions (MLI). Yet, most of the large-scale models treat the lithosphere as a homogeneous stagnant layer. We show that in continents, the dynamic topography is strongly affected by rheological properties and layered structure of the lithosphere. For that we reconcile mantle- and tectonic-scale models by introducing a tectonically realistic continental plate model in 3D large-scale plume-mantle-lithosphere interaction context. This model accounts for stratified structure of continental lithosphere, ductile and frictional (Mohr-Coulomb) plastic properties and thermodynamically consistent density variations. The experiments reveal a number of important differences from the predictions of the conventional models. In particular, plate bending, mechanical decoupling of crustal and mantle layers and intra-plate tension-compression instabilities result in transient topographic signatures such as alternating small-scale surface features that could be misinterpreted in terms of regional tectonics. Actually thick ductile lower crustal layer absorbs most of the "direct" dynamic topography and the features produced at surface are mostly controlled by the mechanical instabilities in the upper and intermediate crustal layers produced by MLI-induced shear and bending at Moho and LAB. Moreover, the 3D models predict anisotropic response of the lithosphere even in case of isotropic solicitations by axisymmetric mantle upwellings such as plumes. In particular, in presence of small (i.e. insufficient to produce solely any significant deformation) uniaxial extensional tectonic stress field, the plume-produced surface and LAB features have anisotropic linear shapes perpendicular to the far-field tectonic forces, typical for continental rifts. Compressional field results in singular sub-linear folds above the plume head, perpendicular to the direction of compression. Small bi-axial tectonic stress fields (compression in one direction and extension in the orthogonal direction) result in oblique, almost linear segmented normal or inverse faults with strike-slip components (or visa verse , strike-slip faults with normal or inverse components)

Cetane Scale Evaluation and Possible Modification.

DTIC Science & Technology

1987-12-23

Rings dw dTk Trec - r~k, mr( Tk2 - )- 0.65). The mass flow (Mb) is found by examining dt dO each pair of adjacent volumes in turn. The mass and...Engine Dynamics for 1960. the Diagnosis of Deficient Energy Conver- 37. S. Furahama, and T. Tada, "On the Flow of the sion", Ph.D Thesis, Mechanical

Evaluation of reactive force fields for prediction of the thermo-mechanical properties of cellulose Iâ

Treesearch

Fernando L. Dri; Xiawa Wu; Robert J. Moon; Ashlie Martini; Pablo D. Zavattieri

2015-01-01

Molecular dynamics simulation is commonly used to study the properties of nanocellulose-based materials at the atomic scale. It is well known that the accuracy of these simulations strongly depends on the force field that describes energetic interactions. However, since there is no force field developed specifically for cellulose, researchers utilize models...

Introduction to Time-Resolved Spectroscopy: Nanosecond Transient Absorption and Time-Resolved Fluorescence of Eosin B

ERIC Educational Resources Information Center

Farr, Erik P.; Quintana, Jason C.; Reynoso, Vanessa; Ruberry, Josiah D.; Shin, Wook R.; Swartz, Kevin R.

2018-01-01

Here we present a new undergraduate laboratory that will introduce the concepts of time-resolved spectroscopy and provide insight into the natural time scales on which chemical dynamics occur through direct measurement. A quantitative treatment of the acquired data will provide a deeper understanding of the role of quantum mechanics and various…

From Theory to Air Force Practice: Applications and Non-Binary Extensions of Probabilistic Model-Building Genetic Algorithms

DTIC Science & Technology

2006-05-31

dynamics (MD) and kinetic Monte Carlo ( KMC ) procedures. In 2D surface modeling our calculations project speedups of 9 orders of magnitude at 300 degrees...programming is used to perform customized statistical mechanics by bridging the different time scales of MD and KMC quickly and well. Speedups in

Dynamic adaptive chemistry for turbulent flame simulations

NASA Astrophysics Data System (ADS)

Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.

2013-02-01

The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.

Multiple Scale Analysis of the Dynamic State Index (DSI)

NASA Astrophysics Data System (ADS)

Müller, A.; Névir, P.

2016-12-01

The Dynamic State Index (DSI) is a novel parameter that indicates local deviations of the atmospheric flow field from a stationary, inviscid and adiabatic solution of the primitive equations of fluid mechanics. This is in contrast to classical methods, which often diagnose deviations from temporal or spatial mean states. We show some applications of the DSI to atmospheric flow phenomena on different scales. The DSI is derived from the Energy-Vorticity-Theory (EVT) which is based on two global conserved quantities, the total energy and Ertel's potential enstrophy. Locally, these global quantities lead to the Bernoulli function and the PV building together with the potential temperature the DSI.If the Bernoulli function and the PV are balanced, the DSI vanishes and the basic state is obtained. Deviations from the basic state provide an indication of diabatic and non-stationary weather events. Therefore, the DSI offers a tool to diagnose and even prognose different atmospheric events on different scales.On synoptic scale, the DSI can help to diagnose storms and hurricanes, where also the dipole structure of the DSI plays an important role. In the scope of the collaborative research center "Scaling Cascades in Complex Systems" we show high correlations between the DSI and precipitation on convective scale. Moreover, we compare the results with reduced models and different spatial resolutions.

Order reduction, identification and localization studies of dynamical systems

NASA Astrophysics Data System (ADS)

Ma, Xianghong

In this thesis methods are developed for performing order reduction, system identification and induction of nonlinear localization in complex mechanical dynamic systems. General techniques are proposed for constructing low-order models of linear and nonlinear mechanical systems; in addition, novel mechanical designs are considered for inducing nonlinear localization phenomena for the purpose of enhancing their dynamical performance. The thesis is in three major parts. In the first part, the transient dynamics of an impulsively loaded multi-bay truss is numerically computed by employing the Direct Global Matrix (DGM) approach. The approach is applicable to large-scale flexible structures with periodicity. Karhunen-Loeve (K-L) decomposition is used to discretize the dynamics of the truss and to create the low-order models of the truss. The leading order K-L modes are recovered by an experiment, which shows the feasibility of K-L based order reduction technique. In the second part of the thesis, nonlinear localization in dynamical systems is studied through two applications. In the seismic base isolation study, it is shown that the dynamics are sensitive to the presence of nonlinear elements and that passive motion confinement can be induced under proper design. In the coupled rod system, numerical simulation of the transient dynamics shows that a nonlinear backlash spring can induce either nonlinear localization or delocalization in the form of beat phenomena. K-L decomposition and poincare maps are utilized to study the nonlinear effects. The study shows that nonlinear localization can be induced in complex structures through backlash. In the third and final part of the thesis, a new technique based on Green!s function method is proposed to identify the dynamics of practical bolted joints. By modeling the difference between the dynamics of the bolted structure and the corresponding unbolted one, one constructs a nonparametric model for the joint dynamics. Two applications are given with a bolted beam and a truss joint in order to show the applicability of the technique.

Advances in the mechanical modeling of filamentous actin and its cross-linked networks on multiple scales.

PubMed

Unterberger, Michael J; Holzapfel, Gerhard A

2014-11-01

The protein actin is a part of the cytoskeleton and, therefore, responsible for the mechanical properties of the cells. Starting with the single molecule up to the final structure, actin creates a hierarchical structure of several levels exhibiting a remarkable behavior. The hierarchy spans several length scales and limitations in computational power; therefore, there is a call for different mechanical modeling approaches for the different scales. On the molecular level, we may consider each atom in molecular dynamics simulations. Actin forms filaments by combining the molecules into a double helix. In a model, we replace molecular subdomains using coarse-graining methods, allowing the investigation of larger systems of several atoms. These models on the nanoscale inform continuum mechanical models of large filaments, which are based on worm-like chain models for polymers. Assemblies of actin filaments are connected with cross-linker proteins. Models with discrete filaments, so-called Mikado models, allow us to investigate the dependence of the properties of networks on the parameters of the constituents. Microstructurally motivated continuum models of the networks provide insights into larger systems containing cross-linked actin networks. Modeling of such systems helps to gain insight into the processes on such small scales. On the other hand, they call for verification and hence trigger the improvement of established experiments and the development of new methods.

On the scale dependence of earthquake stress drop

NASA Astrophysics Data System (ADS)

Cocco, Massimo; Tinti, Elisa; Cirella, Antonella

2016-10-01

We discuss the debated issue of scale dependence in earthquake source mechanics with the goal of providing supporting evidence to foster the adoption of a coherent interpretative framework. We examine the heterogeneous distribution of source and constitutive parameters during individual ruptures and their scaling with earthquake size. We discuss evidence that slip, slip-weakening distance and breakdown work scale with seismic moment and are interpreted as scale dependent parameters. We integrate our estimates of earthquake stress drop, computed through a pseudo-dynamic approach, with many others available in the literature for both point sources and finite fault models. We obtain a picture of the earthquake stress drop scaling with seismic moment over an exceptional broad range of earthquake sizes (-8 < MW < 9). Our results confirm that stress drop values are scattered over three order of magnitude and emphasize the lack of corroborating evidence that stress drop scales with seismic moment. We discuss these results in terms of scale invariance of stress drop with source dimension to analyse the interpretation of this outcome in terms of self-similarity. Geophysicists are presently unable to provide physical explanations of dynamic self-similarity relying on deterministic descriptions of micro-scale processes. We conclude that the interpretation of the self-similar behaviour of stress drop scaling is strongly model dependent. We emphasize that it relies on a geometric description of source heterogeneity through the statistical properties of initial stress or fault-surface topography, in which only the latter is constrained by observations.

Rheology and microstructure of filled polymer melts

NASA Astrophysics Data System (ADS)

Anderson, Benjamin John

The states of particle dispersion in polymer nanocomposite melts are studied through rheological characterization of nanocomposite melt mechanical properties and small angle X-ray scattering measurement of the particle microstructure. The particle microstructure probed with scattering is related to bulk flow mechanics to determine the origin of slow dynamics in these complex dispersions: whether a gel or glass transition or a slowing down of dispersing phase dynamics. These studies were conducted to understand polymer mediated particle-particle interactions and potential particle-polymer phase separation. The phase behavior of the dispersion will be governed by enthalpic and entropic contributions. A variety of phases are expected: homogeneous fluid, phase separated, or non-equilibrium gel. The effects of dispersion control parameters, namely particle volume fraction, polymer molecular weight, and polymer-particle surface affinity, on the phase behavior of 44 nm silica dispersions are studied in low molecular weight polyethylene oxide (PEO), polyethylene oxide dimethylether (PEODME), and polytetrahydrofuran (PTHF). Scattering measurements of the particle second virial coefficient in PEO melts indicates repulsive particles by a value slightly greater than unity. In PEO nanocomposites, dispersion dynamics slow down witnessed by a plateau in the elastic modulus as the particle separation approaches the length scale of the polymer radius of gyration. As the polymer molecular weight is increased, the transition shifts to lower particle volume fractions. Below polymer entanglement, the slow dynamics mimics that of a colloidal glass by the appearance of two relaxation times in the viscous modulus that display power law scaling with volume fraction. Above entanglement, the slow dynamics is qualitatively different resembling the behavior of a gelled suspension yet lacking any sign of scattering from particle agglomerates. As polymer molecular weight is increased at a fixed volume fraction, two strain yielding events emerge. Further particle loading leads to the formation of a particle-polymer network and the onset of brittle mechanical behavior. The performance of PEO nanocomposites is contrasted by PEODME and PTHF nanocomposites where a change in the polymer segment-surface activity changes the slow dynamics of the nanocomposite and the microstructure of particles in the melt. Slow dynamics and the particle microstructure indicate a gelled suspension as volume fraction is raised with particles in or near contact and support the turning on of particle attractions in the melt.

Electroencephalographic field influence on calcium momentum waves.

PubMed

Ingber, Lester; Pappalepore, Marco; Stesiak, Ronald R

2014-02-21

Macroscopic electroencephalographic (EEG) fields can be an explicit top-down neocortical mechanism that directly drives bottom-up processes that describe memory, attention, and other neuronal processes. The top-down mechanism considered is macrocolumnar EEG firings in neocortex, as described by a statistical mechanics of neocortical interactions (SMNI), developed as a magnetic vector potential A. The bottom-up process considered is Ca(2+) waves prominent in synaptic and extracellular processes that are considered to greatly influence neuronal firings. Here, the complimentary effects are considered, i.e., the influence of A on Ca(2+) momentum, p. The canonical momentum of a charged particle in an electromagnetic field, Π=p+qA (SI units), is calculated, where the charge of Ca(2+) is q=-2e, e is the magnitude of the charge of an electron. Calculations demonstrate that macroscopic EEG A can be quite influential on the momentum p of Ca(2+) ions, in both classical and quantum mechanics. Molecular scales of Ca(2+) wave dynamics are coupled with A fields developed at macroscopic regional scales measured by coherent neuronal firing activity measured by scalp EEG. The project has three main aspects: fitting A models to EEG data as reported here, building tripartite models to develop A models, and studying long coherence times of Ca(2+) waves in the presence of A due to coherent neuronal firings measured by scalp EEG. The SMNI model supports a mechanism wherein the p+qA interaction at tripartite synapses, via a dynamic centering mechanism (DCM) to control background synaptic activity, acts to maintain short-term memory (STM) during states of selective attention. © 2013 Published by Elsevier Ltd. All rights reserved.

Scaling Symmetries in Elastic-Plastic Dynamic Cavity Expansion Equations Using the Isovector Method

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

Albright, Eric Jason; Ramsey, Scott D.; Schmidt, Joseph H.

Cavity-expansion approximations are widely-used in the study of penetration mechanics and indentation phenomena. We apply the isovector method to a well-established model in the literature for elastic-plastic cavity-expansion to systematically demonstrate the existence of Lie symmetries corresponding to scale-invariant solutions. Here we use the symmetries obtained from the equations of motion to determine compatible auxiliary conditions describing the cavity wall trajectory and the elastic-plastic material interface. The admissible conditions are then compared with specific similarity solutions in the literature.

Contributions to the understanding of large-scale coherent structures in developing free turbulent shear flows

NASA Technical Reports Server (NTRS)

Liu, J. T. C.

1986-01-01

Advances in the mechanics of boundary layer flow are reported. The physical problems of large scale coherent structures in real, developing free turbulent shear flows, from the nonlinear aspects of hydrodynamic stability are addressed. The presence of fine grained turbulence in the problem, and its absence, lacks a small parameter. The problem is presented on the basis of conservation principles, which are the dynamics of the problem directed towards extracting the most physical information, however, it is emphasized that it must also involve approximations.

Scaling Symmetries in Elastic-Plastic Dynamic Cavity Expansion Equations Using the Isovector Method

DOE PAGES

Albright, Eric Jason; Ramsey, Scott D.; Schmidt, Joseph H.; ...

2017-09-16

Cavity-expansion approximations are widely-used in the study of penetration mechanics and indentation phenomena. We apply the isovector method to a well-established model in the literature for elastic-plastic cavity-expansion to systematically demonstrate the existence of Lie symmetries corresponding to scale-invariant solutions. Here we use the symmetries obtained from the equations of motion to determine compatible auxiliary conditions describing the cavity wall trajectory and the elastic-plastic material interface. The admissible conditions are then compared with specific similarity solutions in the literature.

Hysteresis, regime shifts, and non-stationarity in aquifer recharge-storage-discharge systems

NASA Astrophysics Data System (ADS)

Klammler, Harald; Jawitz, James; Annable, Michael; Hatfield, Kirk; Rao, Suresh

2016-04-01

Based on physical principles and geological information we develop a parsimonious aquifer model for Silver Springs, one of the largest karst springs in Florida. The model structure is linear and time-invariant with recharge, aquifer head (storage) and spring discharge as dynamic variables at the springshed (landscape) scale. Aquifer recharge is the hydrological driver with trends over a range of time scales from seasonal to multi-decadal. The freshwater-saltwater interaction is considered as a dynamic storage mechanism. Model results and observed time series show that aquifer storage causes significant rate-dependent hysteretic behavior between aquifer recharge and discharge. This leads to variable discharge per unit recharge over time scales up to decades, which may be interpreted as a gradual and cyclic regime shift in the aquifer drainage behavior. Based on field observations, we further amend the aquifer model by assuming vegetation growth in the spring run to be inversely proportional to stream velocity and to hinder stream flow. This simple modification introduces non-linearity into the dynamic system, for which we investigate the occurrence of rate-independent hysteresis and of different possible steady states with respective regime shifts between them. Results may contribute towards explaining observed non-stationary behavior potentially due to hydrological regime shifts (e.g., triggered by gradual, long-term changes in recharge or single extreme events) or long-term hysteresis (e.g., caused by aquifer storage). This improved understanding of the springshed hydrologic response dynamics is fundamental for managing the ecological, economic and social aspects at the landscape scale.

Cosmological Higgs-Axion Interplay for a Naturally Small Electroweak Scale.

PubMed

Espinosa, J R; Grojean, C; Panico, G; Pomarol, A; Pujolàs, O; Servant, G

2015-12-18

Recently, a new mechanism to generate a naturally small electroweak scale has been proposed. It exploits the coupling of the Higgs boson to an axionlike field and a long era in the early Universe where the axion unchains a dynamical screening of the Higgs mass. We present a new realization of this idea with the new feature that it leaves no sign of new physics at the electroweak scale, and up to a rather large scale, 10^{9}  GeV, except for two very light and weakly coupled axionlike states. One of the scalars can be a viable dark matter candidate. Such a cosmological Higgs-axion interplay could be tested with a number of experimental strategies.

NGH: A Dynamic Factor in Deep Water Sediments & the Geological Record

NASA Astrophysics Data System (ADS)

Max, M. D.; Johnson, A. H.

2012-12-01

Prior to identification of natural gas hydrate (NGH) in marine sediments, gravity and tectonic forces were the recognized dynamic forces that could cause disruption in deep marine sediments. NGH introduces a new dynamic factor into continental slope and rise sediments as well as sediments in the deeper parts of some continental shelves. Two critical elements interplay to provide for a slow acting, long-term NGH-dynamic cyclical system. First, NGH forms spontaneously from dissolved natural gas generally in a passive manner without causing any other than very subtle alterations to the megascopic sediment structure. When NGH forms in either dispersed form in muddy sediments or in concentrated form in veins or nodules or in porosity in sandy sediments, it increases overall mechanical strength. Second, when it dissociates, mechanical strength weakens to the point where shear strengths can approach zero. Because the chemical reaction of NGH is highly reversible, changes in sea level that affect pressure, and changes in seafloor temperature can alter rapidly the tendency of NGH to either crystallize or dissociate, with consequent structural and morphological effects. The cyclicity of the Earth's climate introduces a mechanism for periodically injecting overpressured gas into marine sediments as the gas hydrate stability zones (GHSZ) undergoes changes to its thickness and depth. Natural climate change has the potential to produce overpressured natural gas converted from NGH in marine sediments periodically. In-place disruption would consist of disrupted sandy beds, chaotic textures on all scales, intrusion effects, limited mass flow features, dramatic sediment mixing not related to large scale movement and sediment redeposition from fluidized beds. Mobilization would involve larger scale sediment mass flow effects that would be indistinguishable from olistostromic melanges postulated to be initiated by tectonic or gravitational forces. The earliest interpretation of this fluidization type of large scale sediment disruption in the later part of the 1900s identified them as tectonic in origin. Subsequently, in the 1970s, it was recognized that the features were more likely a product of soft sediment deformation whose initiator might be gravity or tectonic forces, of 'tectonosedimentary' origin. The action of the NGH cycle to initiate sedimentary disruption may more readily explain many of these features in the geological record. Drill core taken across seismic reflection sediment redeposition features that otherwise show no tectonic activity related movement in abandoned GHSZ could provide important evidence for the long-term geological action of the NGH cycle.

Physics of base-pairing dynamics in DNA

NASA Astrophysics Data System (ADS)

Manghi, Manoel; Destainville, Nicolas

2016-05-01

As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque-driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain orientational degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain orientational degrees of freedom can be integrated out, and the quasi-static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

Online Low-Rank Representation Learning for Joint Multi-subspace Recovery and Clustering.

PubMed

Li, Bo; Liu, Risheng; Cao, Junjie; Zhang, Jie; Lai, Yu-Kun; Liua, Xiuping

2017-10-06

Benefiting from global rank constraints, the lowrank representation (LRR) method has been shown to be an effective solution to subspace learning. However, the global mechanism also means that the LRR model is not suitable for handling large-scale data or dynamic data. For large-scale data, the LRR method suffers from high time complexity, and for dynamic data, it has to recompute a complex rank minimization for the entire data set whenever new samples are dynamically added, making it prohibitively expensive. Existing attempts to online LRR either take a stochastic approach or build the representation purely based on a small sample set and treat new input as out-of-sample data. The former often requires multiple runs for good performance and thus takes longer time to run, and the latter formulates online LRR as an out-ofsample classification problem and is less robust to noise. In this paper, a novel online low-rank representation subspace learning method is proposed for both large-scale and dynamic data. The proposed algorithm is composed of two stages: static learning and dynamic updating. In the first stage, the subspace structure is learned from a small number of data samples. In the second stage, the intrinsic principal components of the entire data set are computed incrementally by utilizing the learned subspace structure, and the low-rank representation matrix can also be incrementally solved by an efficient online singular value decomposition (SVD) algorithm. The time complexity is reduced dramatically for large-scale data, and repeated computation is avoided for dynamic problems. We further perform theoretical analysis comparing the proposed online algorithm with the batch LRR method. Finally, experimental results on typical tasks of subspace recovery and subspace clustering show that the proposed algorithm performs comparably or better than batch methods including the batch LRR, and significantly outperforms state-of-the-art online methods.

Structural and Dynamic Insights into the Mechanism of Allosteric Signal Transmission in ERK2-Mediated MKP3 Activation.

PubMed

Lu, Chang; Liu, Xin; Zhang, Chen-Song; Gong, Haipeng; Wu, Jia-Wei; Wang, Zhi-Xin

2017-11-21

The mitogen-activated protein kinases (MAPKs) are key components of cellular signal transduction pathways, which are down-regulated by the MAPK phosphatases (MKPs). Catalytic activity of the MKPs is controlled both by their ability to recognize selective MAPKs and by allosteric activation upon binding to MAPK substrates. Here, we use a combination of experimental and computational techniques to elucidate the molecular mechanism for the ERK2-induced MKP3 activation. Mutational and kinetic study shows that the 334 FNFM 337 motif in the MKP3 catalytic domain is essential for MKP3-mediated ERK2 inactivation and is responsible for ERK2-mediated MKP3 activation. The long-term molecular dynamics (MD) simulations further reveal a complete dynamic process in which the catalytic domain of MKP3 gradually changes to a conformation that resembles an active MKP catalytic domain over the time scale of the simulation, providing a direct time-dependent observation of allosteric signal transmission in ERK2-induced MKP3 activation.

Mesoscopic Modeling of Blood Clotting: Coagulation Cascade and Platelets Adhesion

NASA Astrophysics Data System (ADS)

Yazdani, Alireza; Li, Zhen; Karniadakis, George

2015-11-01

The process of clot formation and growth at a site on a blood vessel wall involve a number of multi-scale simultaneous processes including: multiple chemical reactions in the coagulation cascade, species transport and flow. To model these processes we have incorporated advection-diffusion-reaction (ADR) of multiple species into an extended version of Dissipative Particle Dynamics (DPD) method which is considered as a coarse-grained Molecular Dynamics method. At the continuum level this is equivalent to the Navier-Stokes equation plus one advection-diffusion equation for each specie. The chemistry of clot formation is now understood to be determined by mechanisms involving reactions among many species in dilute solution, where reaction rate constants and species diffusion coefficients in plasma are known. The role of blood particulates, i.e. red cells and platelets, in the clotting process is studied by including them separately and together in the simulations. An agonist-induced platelet activation mechanism is presented, while platelets adhesive dynamics based on a stochastic bond formation/dissociation process is included in the model.

Hysteresis, nucleation and growth phenomena in spin-crossover solids

NASA Astrophysics Data System (ADS)

Ridier, Karl; Molnár, Gábor; Salmon, Lionel; Nicolazzi, William; Bousseksou, Azzedine

2017-12-01

The observation and the study of first-order phase transitions in cooperative spin-crossover (SCO) solids exhibiting hysteresis behaviours are of particular interest and currently constitute a burgeoning area in the field of bistable molecular materials. The understanding and the control of the transition mechanisms (nucleation and growth processes) and their dynamics within the hysteresis region appear to be a general and appealing problem from a fundamental point of view and for technological applications as well. This review reports on the recent progresses and most important findings made on the spatiotemporal dynamics of the spin transition in SCO solids, particularly through the universal nucleation and growth process. Both thermally induced and light-induced spin transitions are discussed. We open up this review to the central question of the evolution of the transition mechanisms and dynamics in SCO nano-objects, which constitute promising systems to reach ultra-fast switching, and the experimental issues inherent to such studies at the micro- and nanometric scale.

Mapping the dynamics of force transduction at cell–cell junctions of epithelial clusters

PubMed Central

Ng, Mei Rosa; Besser, Achim; Brugge, Joan S; Danuser, Gaudenz

2014-01-01

Force transduction at cell-cell adhesions regulates tissue development, maintenance and adaptation. We developed computational and experimental approaches to quantify, with both sub-cellular and multi-cellular resolution, the dynamics of force transmission in cell clusters. Applying this technology to spontaneously-forming adherent epithelial cell clusters, we found that basal force fluctuations were coupled to E-cadherin localization at the level of individual cell-cell junctions. At the multi-cellular scale, cell-cell force exchange depended on the cell position within a cluster, and was adaptive to reconfigurations due to cell divisions or positional rearrangements. Importantly, force transmission through a cell required coordinated modulation of cell-matrix adhesion and actomyosin contractility in the cell and its neighbors. These data provide insights into mechanisms that could control mechanical stress homeostasis in dynamic epithelial tissues, and highlight our methods as a resource for the study of mechanotransduction in cell-cell adhesions. DOI: http://dx.doi.org/10.7554/eLife.03282.001 PMID:25479385

Cavitation instability in bulk metallic glasses

NASA Astrophysics Data System (ADS)

Dai, L. H.; Huang, X.; Ling, Z.

2015-09-01

Recent experiments have shown that fracture surfaces of bulk metallic glasses (BMGs) usually exhibit an intriguing nanoscale corrugation like fractographic feature mediated by nanoscale void formation. We attribute the onset of this nanoscale corrugation to TTZs (tension transformation zones) mediated cavitation. In our recent study, the spall experiments of Zr-based BMG using a single-stage light gas gun were performed. To uncover the mechanisms of the spallation damage nucleation and evolution, the samples were designed to be subjected to dynamic tensile loadings of identical amplitude but with different durations by making use of the multi-stress pulse and the double-flyer techniques. It is clearly revealed that the macroscopic spall fracture in BMGs originates from the nucleation, growth and coalescence of micro-voids. Then, a microvoid nucleation model of BMGs based on free volume theory is proposed, which indicates that the nucleation of microvoids at the early stage of spallation in BMGs is resulted from diffusion and coalescence of free volume. Furthermore, a theoretical model of void growth in BMGs undergoing remote dynamic hydrostatic tension is developed. The critical condition of cavitation instability is obtained. It is found that dynamic void growth in BMGs can be well controlled by a dimensionless inertial number characterizing the competition between intrinsic and extrinsic time scales. To unveil the atomic-level mechanism of cavitation, a systematic molecular dynamics (MD) simulation of spallation behaviour of a binary metallic glass with different impact velocities was performed. It is found that micro-void nucleation is determined TTZs while the growth is controlled by shear transformation zones (STZs) at atomic scale.

Biofilm attachment reduction on bioinspired, dynamic, micro-wrinkling surfaces

NASA Astrophysics Data System (ADS)

Epstein, Alexander K.; Hong, Donggyoon; Kim, Philseok; Aizenberg, Joanna

2013-09-01

Most bacteria live in multicellular communities known as biofilms that are adherent to surfaces in our environment, from sea beds to plumbing systems. Biofilms are often associated with clinical infections, nosocomial deaths and industrial damage such as bio-corrosion and clogging of pipes. As mature biofilms are extremely challenging to eradicate once formed, prevention is advantageous over treatment. However, conventional surface chemistry strategies are either generally transient, due to chemical masking, or toxic, as in the case of leaching marine antifouling paints. Inspired by the nonfouling skins of echinoderms and other marine organisms, which possess highly dynamic surface structures that mechanically frustrate bio-attachment, we have developed and tested a synthetic platform based on both uniaxial mechanical strain and buckling-induced elastomer microtopography. Bacterial biofilm attachment to the dynamic substrates was studied under an array of parameters, including strain amplitude and timescale (1-100 mm s-1), surface wrinkle length scale, bacterial species and cell geometry, and growth time. The optimal conditions for achieving up to ˜ 80% Pseudomonas aeruginosa biofilm reduction after 24 h growth and ˜ 60% reduction after 48 h were combinatorially elucidated to occur at 20% strain amplitude, a timescale of less than ˜ 5 min between strain cycles and a topography length scale corresponding to the cell dimension of ˜ 1 μm. Divergent effects on the attachment of P. aeruginosa, Staphylococcus aureus and Escherichia coli biofilms showed that the dynamic substrate also provides a new means of species-specific biofilm inhibition, or inversely, selection for a desired type of bacteria, without reliance on any toxic or transient surface chemical treatments.

Dynamic Voltage-Frequency and Workload Joint Scaling Power Management for Energy Harvesting Multi-Core WSN Node SoC

PubMed Central

Li, Xiangyu; Xie, Nijie; Tian, Xinyue

2017-01-01

This paper proposes a scheduling and power management solution for energy harvesting heterogeneous multi-core WSN node SoC such that the system continues to operate perennially and uses the harvested energy efficiently. The solution consists of a heterogeneous multi-core system oriented task scheduling algorithm and a low-complexity dynamic workload scaling and configuration optimization algorithm suitable for light-weight platforms. Moreover, considering the power consumption of most WSN applications have the characteristic of data dependent behavior, we introduce branches handling mechanism into the solution as well. The experimental result shows that the proposed algorithm can operate in real-time on a lightweight embedded processor (MSP430), and that it can make a system do more valuable works and make more than 99.9% use of the power budget. PMID:28208730

Convection Electric Field Observations by THEMIS and the Van Allen Probes

NASA Astrophysics Data System (ADS)

Califf, S.; Li, X.; Bonnell, J. W.; Wygant, J. R.; Malaspina, D.; Hartinger, M.; Thaller, S. A.

2013-12-01

We present direct electric field measurements made by THEMIS and the Van Allen Probes in the inner magnetosphere, focusing on the large-scale, near-DC convection electric field. The convection electric field drives plasma Earthward from the tail into the inner magnetosphere, playing a critical role in forming the ring current. Although it is normally shielded deep inside the magnetosphere, during storm times this large-scale electric field can penetrate to low L values (L < 3), eroding the plasmasphere and also providing a mechanism for ~100 keV electron injection into the slot region and inner radiation belt. The relationship of the convection electric field with the plasmasphere is also important for understanding the dynamic outer radiation belt, as the plasmapause boundary has been strongly correlated with the dynamic variation of the outer radiation belt electrons.

Multiscale multifractal DCCA and complexity behaviors of return intervals for Potts price model

NASA Astrophysics Data System (ADS)

Wang, Jie; Wang, Jun; Stanley, H. Eugene

2018-02-01

To investigate the characteristics of extreme events in financial markets and the corresponding return intervals among these events, we use a Potts dynamic system to construct a random financial time series model of the attitudes of market traders. We use multiscale multifractal detrended cross-correlation analysis (MM-DCCA) and Lempel-Ziv complexity (LZC) perform numerical research of the return intervals for two significant China's stock market indices and for the proposed model. The new MM-DCCA method is based on the Hurst surface and provides more interpretable cross-correlations of the dynamic mechanism between different return interval series. We scale the LZC method with different exponents to illustrate the complexity of return intervals in different scales. Empirical studies indicate that the proposed return intervals from the Potts system and the real stock market indices hold similar statistical properties.

Dynamic Voltage-Frequency and Workload Joint Scaling Power Management for Energy Harvesting Multi-Core WSN Node SoC.

PubMed

Li, Xiangyu; Xie, Nijie; Tian, Xinyue

2017-02-08

This paper proposes a scheduling and power management solution for energy harvesting heterogeneous multi-core WSN node SoC such that the system continues to operate perennially and uses the harvested energy efficiently. The solution consists of a heterogeneous multi-core system oriented task scheduling algorithm and a low-complexity dynamic workload scaling and configuration optimization algorithm suitable for light-weight platforms. Moreover, considering the power consumption of most WSN applications have the characteristic of data dependent behavior, we introduce branches handling mechanism into the solution as well. The experimental result shows that the proposed algorithm can operate in real-time on a lightweight embedded processor (MSP430), and that it can make a system do more valuable works and make more than 99.9% use of the power budget.

The biology and polymer physics underlying large‐scale chromosome organization

PubMed Central

2017-01-01

Chromosome large‐scale organization is a beautiful example of the interplay between physics and biology. DNA molecules are polymers and thus belong to the class of molecules for which physicists have developed models and formulated testable hypotheses to understand their arrangement and dynamic properties in solution, based on the principles of polymer physics. Biologists documented and discovered the biochemical basis for the structure, function and dynamic spatial organization of chromosomes in cells. The underlying principles of chromosome organization have recently been revealed in unprecedented detail using high‐resolution chromosome capture technology that can simultaneously detect chromosome contact sites throughout the genome. These independent lines of investigation have now converged on a model in which DNA loops, generated by the loop extrusion mechanism, are the basic organizational and functional units of the chromosome. PMID:29105235

Large-scale computations in fluid mechanics; Proceedings of the Fifteenth Summer Seminar on Applied Mathematics, University of California, La Jolla, CA, June 27-July 8, 1983. Parts 1 & 2

NASA Technical Reports Server (NTRS)

Engquist, B. E. (Editor); Osher, S. (Editor); Somerville, R. C. J. (Editor)

1985-01-01

Papers are presented on such topics as the use of semi-Lagrangian advective schemes in meteorological modeling; computation with high-resolution upwind schemes for hyperbolic equations; dynamics of flame propagation in a turbulent field; a modified finite element method for solving the incompressible Navier-Stokes equations; computational fusion magnetohydrodynamics; and a nonoscillatory shock capturing scheme using flux-limited dissipation. Consideration is also given to the use of spectral techniques in numerical weather prediction; numerical methods for the incorporation of mountains in atmospheric models; techniques for the numerical simulation of large-scale eddies in geophysical fluid dynamics; high-resolution TVD schemes using flux limiters; upwind-difference methods for aerodynamic problems governed by the Euler equations; and an MHD model of the earth's magnetosphere.

Coherent structures: Comments on mechanisms

NASA Technical Reports Server (NTRS)

Hunt, J. C. R.

1987-01-01

There is now overwhelming evidence that in most turbulent flows there exist regions moving with the flow where the velocity and vorticity have a characteristic structure. These regions are called coherent structures because within them the large-scale distributions of velocity and/or vorticity remain coherent even as these structures move through the flow and interact with other structures. Since the flow enters and leaves the bounding surfaces of these structures, a useful definition for coherent structures is that they are open volumes with distinctive large-scale vorticity distributions. Possible fruitful directions for the study of the dynamics of coherent structures are suggested. Most coherent structures research to data was concentrated on measurement and kinematical analysis; there is now a welcome move to examine the dynamics of coherent structures, by a variety of different methods. A few of them will be described.

Attenuation of cryocooler induced vibration using multimodal tuned dynamic absorbers

NASA Astrophysics Data System (ADS)

Veprik, Alexander; Babitsky, Vladimir; Tuito, Avi

2017-05-01

Modern infrared imagers often rely on split Stirling linear cryocoolers comprising compressor and expander, the relative position of which is governed by the optical design and packaging constraints. A force couple generated by imbalanced reciprocation of moving components inside both compressor and expander result in cryocooler induced vibration comprising angular and translational tonal components manifesting itself in the form of line of sight jitter and dynamic defocusing. Since linear cryocooler is usually driven at a fixed and precisely adjustable frequency, a tuned dynamic absorber is a well suited tool for vibration control. It is traditionally made in the form of lightweight single degree of freedom undamped mechanical resonator, the frequency of which is essentially matched with the driving frequency or vice versa. Unfortunately, the performance of such a traditional approach is limited in terms of simultaneous attenuating translational and angular components of cooler induced vibration. The authors are enhancing the traditional concept and consider multimodal tuned dynamic absorber made in the form of weakly damped mechanical resonator, where the frequencies of useful dynamic modes are essentially matched with the driving frequency. Dynamic analysis and experimental testing show that the dynamic reactions (forces and moments) produced by such a device may simultaneously attenuate both translational and angular components of cryocoolerinduced vibration. The authors are considering different embodiments and their suitability for different packaging concepts. The outcomes of theoretical predictions are supported by full scale experimentation.

Molecular simulation of dispersion and mechanical stability of organically modified layered silicates in polymer matrices

NASA Astrophysics Data System (ADS)

Fu, Yao-Tsung

The experimental analysis of nanometer-scale separation processes and mechanical properties at buried interfaces in nanocomposites has remained difficult. We have employed molecular dynamics simulation in relation to available experimental data to alleviate such limitations and gain insight into the dispersion and mechanical stability of organically modified layered silicates in hydrophobic polymer matrices. We analyzed cleavage energies of various organically modified silicates as a function of the cation exchange capacity, surfactant head group chemistry, and chain length using MD simulations with the PCFF-PHYLLOSILICATE force field. The range of the cleavage energy is between 25 and 210 mJ/m2 upon the molecular structures and packing of surfactants. As a function of chain length, the cleavage energy indicates local minima for interlayer structures comprised of loosely packed layers of alkyl chains and local maxima for interlayer structures comprised of densely packed layers of alkyl chains between the layers. In addition, the distribution of cationic head groups between the layers in the equilibrium state determines whether large increases in cleavage energy due to Coulomb attraction. We have also examined mechanical bending and failure mechanisms of layered silicates on the nanometer scale using molecular dynamics simulation in comparison to a library of TEM data of polymer nanocomposites. We investigated the energy of single clay lamellae as a function of bending radius and different cation density. The layer energy increases particularly for bending radii below 20 nm and is largely independent of cation exchange capacity. The analysis of TEM images of agglomerated and exfoliated aluminosilicates of different CEC in polymer matrices at small volume fractions showed bending radii in excess of 100 nm due to free volumes in the polymer matrix. At a volume fraction >5%, however, bent clay layers were found with bending radii <20 nm and kinks as a failure mechanism in good agreement with simulation results. We have examined thermal conductivity of organically modified layered silicates using molecular dynamics simulation in comparison to experimental results by laser measurement. The thermal conductivity slightly increased from 0.08 to 0.14 Wm-1K-1 with increasing chain length, related to the gallery spacing and interlayer density of the organic material.

Elucidating the atomistic mechanisms underpinning plasticity in Li-Si nanostructures

NASA Astrophysics Data System (ADS)

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 the behavior of a-Li-Si nanostructures under tensile strain rates ranging from 103 to 108s-1 . We find significant differences in the deformation behavior across the strain rates and discover that the well-known shear transformation zones (widely discussed in the context of amorphous materials) are formed by a "diffusionlike" process. We identify the rotation of the shear transformation zone as a key dissipation mechanism.

North American extreme temperature events and related large scale meteorological patterns: A review of statistical methods, dynamics, modeling, and trends

DOE PAGES

Grotjahn, Richard; Black, Robert; Leung, Ruby; ...

2015-05-22

This paper reviews research approaches and open questions regarding data, statistical analyses, dynamics, modeling efforts, and trends in relation to temperature extremes. Our specific focus is upon extreme events of short duration (roughly less than 5 days) that affect parts of North America. These events are associated with large scale meteorological patterns (LSMPs). Methods used to define extreme events statistics and to identify and connect LSMPs to extreme temperatures are presented. Recent advances in statistical techniques can connect LSMPs to extreme temperatures through appropriately defined covariates that supplements more straightforward analyses. A wide array of LSMPs, ranging from synoptic tomore » planetary scale phenomena, have been implicated as contributors to extreme temperature events. Current knowledge about the physical nature of these contributions and the dynamical mechanisms leading to the implicated LSMPs is incomplete. There is a pressing need for (a) systematic study of the physics of LSMPs life cycles and (b) comprehensive model assessment of LSMP-extreme temperature event linkages and LSMP behavior. Generally, climate models capture the observed heat waves and cold air outbreaks with some fidelity. However they overestimate warm wave frequency and underestimate cold air outbreaks frequency, and underestimate the collective influence of low-frequency modes on temperature extremes. Climate models have been used to investigate past changes and project future trends in extreme temperatures. Overall, modeling studies have identified important mechanisms such as the effects of large-scale circulation anomalies and land-atmosphere interactions on changes in extreme temperatures. However, few studies have examined changes in LSMPs more specifically to understand the role of LSMPs on past and future extreme temperature changes. Even though LSMPs are resolvable by global and regional climate models, they are not necessarily well simulated so more research is needed to understand the limitations of climate models and improve model skill in simulating extreme temperatures and their associated LSMPs. Furthermore, the paper concludes with unresolved issues and research questions.« less

On the Role of Subduction Dynamics on Emplacement of Metamorphic Core Complexes and Geothermal Systems

NASA Astrophysics Data System (ADS)

Roche, V. M.; Sternai, P.; Guillou-Frottier, L.; Menant, A.; Jolivet, L.; Bouchot, V.; Gerya, T.

2017-12-01

Subduction-induced extensional tectonics in back-arc domains results in the development of metamorphic core complexes (MCCs) and low-angle normal faults (detachments) that also control magma ascent and fluid circulation. However, possible links with the genesis of high-enthalpy geothermal resources (HEGRs) remain barely explored, and no unifying mechanism responsible for both the generation of MCCs and emplacement of HEGRs has yet been recognized. Although discussions on the possible role of magmatic intrusions beneath these systems are still active, another source of heat is required when one considers the scale of a geothermal Province. An additional source of heat, for instance, could arise from the deep dynamics implied by large-scale tectonic processes such as subduction. Firstly, we investigate subduction dynamics through 3D numerical geodynamic models involving slab rollback and tearing constrained primarily by, geothermal anomaly measurements from western Turkey. Our results show that subduction-induced extensional tectonics controls the genesis and distribution of crustal-scale thermal domes, analogous to crustal and lithospheric boudinage. The thermal domes weaken the crust, localize deformation and enhance development of crustal-scale detachments. Thus, these thermo-mechanical instabilities primarily trigger and control the distribution of MCCs. In addition, subduction-related asthenospheric return flow and shear heating in the mantle increase the temperature of the Moho by up to 250°C. Such forcing is observed in natural settings such as the Menderes (western Anatolia) and the Basin and Range (Western United States). Secondly, the numerically-obtained subduction-induced thermal signature at the base of the continental crust is then imposed as basal thermal condition for 2D high-resolution crustal models dedicated to the understanding of fluid flow around detachments. Our results show that permeable detachments control the bulk of the heat transport and fluid circulation patterns at shallow depth, thus creating favourable zones for HEGRS, as illustrated in the Menderes Massif and in the Basin & Range province.

Focused Ultrasound-Induced Blood-Brain Barrier Opening: Association with Mechanical Index and Cavitation Index Analyzed by Dynamic Contrast-Enhanced Magnetic-Resonance Imaging

NASA Astrophysics Data System (ADS)

Chu, Po-Chun; Chai, Wen-Yen; Tsai, Chih-Hung; Kang, Shih-Tsung; Yeh, Chih-Kuang; Liu, Hao-Li

2016-09-01

Focused ultrasound (FUS) with microbubbles can temporally open the blood-brain barrier (BBB), and the cavitation activities of microbubbles play a key role in the BBB-opening process. Previous attempts used contrast-enhanced magnetic resonance imaging (CE-MRI) to correlate the mechanical index (MI) with the scale of BBB-opening, but MI only partially gauged acoustic activities, and CE-MRI did not fully explore correlations of pharmacodynamic/pharmacokinetic behaviors. Recently, the cavitation index (CI) has been derived to serve as an indicator of microbubble-ultrasound stable cavitation, and may also serve as a valid indicator to gauge the level of FUS-induced BBB opening. This study investigates the feasibility of gauging FUS-induced BBB opened level via the two indexes, MI and CI, through dynamic contrast-enhanced (DCE)-MRI analysis as well as passive cavitation detection (PCD) analysis. Pharmacodynamic/pharmacokinetic parameters derived from DCE-MRI were characterized to identify the scale of FUS-induced BBB opening. Our results demonstrated that DCE-MRI can successfully access pharmacodynamic/pharmacokinetic BBB-opened behavior, and was highly correlated both with MI and CI, implying the feasibility in using these two indices to gauge the scale of FUS-induced BBB opening. The proposed finding may facilitate the design toward using focused ultrasound as a safe and reliable noninvasive CNS drug delivery.

Centrifuge modeling of rocking-isolated inelastic RC bridge piers

PubMed Central

Loli, Marianna; Knappett, Jonathan A; Brown, Michael J; Anastasopoulos, Ioannis; Gazetas, George

2014-01-01

Experimental proof is provided of an unconventional seismic design concept, which is based on deliberately underdesigning shallow foundations to promote intense rocking oscillations and thereby to dramatically improve the seismic resilience of structures. Termed rocking isolation, this new seismic design philosophy is investigated through a series of dynamic centrifuge experiments on properly scaled models of a modern reinforced concrete (RC) bridge pier. The experimental method reproduces the nonlinear and inelastic response of both the soil-footing interface and the structure. To this end, a novel scale model RC (1:50 scale) that simulates reasonably well the elastic response and the failure of prototype RC elements is utilized, along with realistic representation of the soil behavior in a geotechnical centrifuge. A variety of seismic ground motions are considered as excitations. They result in consistent demonstrably beneficial performance of the rocking-isolated pier in comparison with the one designed conventionally. Seismic demand is reduced in terms of both inertial load and deck drift. Furthermore, foundation uplifting has a self-centering potential, whereas soil yielding is shown to provide a particularly effective energy dissipation mechanism, exhibiting significant resistance to cumulative damage. Thanks to such mechanisms, the rocking pier survived, with no signs of structural distress, a deleterious sequence of seismic motions that caused collapse of the conventionally designed pier. © 2014 The Authors Earthquake Engineering & Structural Dynamics Published by John Wiley & Sons Ltd. PMID:26300573

Focused Ultrasound-Induced Blood-Brain Barrier Opening: Association with Mechanical Index and Cavitation Index Analyzed by Dynamic Contrast-Enhanced Magnetic-Resonance Imaging.

PubMed

Chu, Po-Chun; Chai, Wen-Yen; Tsai, Chih-Hung; Kang, Shih-Tsung; Yeh, Chih-Kuang; Liu, Hao-Li

2016-09-15

Focused ultrasound (FUS) with microbubbles can temporally open the blood-brain barrier (BBB), and the cavitation activities of microbubbles play a key role in the BBB-opening process. Previous attempts used contrast-enhanced magnetic resonance imaging (CE-MRI) to correlate the mechanical index (MI) with the scale of BBB-opening, but MI only partially gauged acoustic activities, and CE-MRI did not fully explore correlations of pharmacodynamic/pharmacokinetic behaviors. Recently, the cavitation index (CI) has been derived to serve as an indicator of microbubble-ultrasound stable cavitation, and may also serve as a valid indicator to gauge the level of FUS-induced BBB opening. This study investigates the feasibility of gauging FUS-induced BBB opened level via the two indexes, MI and CI, through dynamic contrast-enhanced (DCE)-MRI analysis as well as passive cavitation detection (PCD) analysis. Pharmacodynamic/pharmacokinetic parameters derived from DCE-MRI were characterized to identify the scale of FUS-induced BBB opening. Our results demonstrated that DCE-MRI can successfully access pharmacodynamic/pharmacokinetic BBB-opened behavior, and was highly correlated both with MI and CI, implying the feasibility in using these two indices to gauge the scale of FUS-induced BBB opening. The proposed finding may facilitate the design toward using focused ultrasound as a safe and reliable noninvasive CNS drug delivery.