Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory.

PubMed

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-13

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Systematic parameter inference in stochastic mesoscopic modeling

NASA Astrophysics Data System (ADS)

Lei, Huan; Yang, Xiu; Li, Zhen; Karniadakis, George Em

2017-02-01

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are "sparse". The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.

Power output and carrier dynamics studies of perovskite solar cells under working conditions.

PubMed

Yu, Man; Wang, Hao-Yi; Hao, Ming-Yang; Qin, Yujun; Fu, Li-Min; Zhang, Jian-Ping; Ai, Xi-Cheng

2017-08-02

Perovskite solar cells have emerged as promising photovoltaic systems with superb power conversion efficiency. For the practical application of perovskite devices, the greatest concerns are the power output density and the related dynamics under working conditions. In this study, the working conditions of planar and mesoscopic perovskite solar cells are simulated and the power output density evolutions with the working voltage are highlighted. The planar device exhibits higher capability of outputting power than the mesoscopic one. The transient photoelectric conversion dynamics are investigated under the open circuit, short circuit and working conditions. It is found that the power output and dynamic processes are correlated intrinsically, which suggests that the power output is the competitive result of the charge carrier recombination and transport. The present work offers a unique view to elucidating the relationship between the power output and the charge carrier dynamics for perovskite solar cells in a comprehensive manner, which would be beneficial to their future practical applications.

Isotropic stochastic rotation dynamics

NASA Astrophysics Data System (ADS)

Mühlbauer, Sebastian; Strobl, Severin; Pöschel, Thorsten

2017-12-01

Stochastic rotation dynamics (SRD) is a widely used method for the mesoscopic modeling of complex fluids, such as colloidal suspensions or multiphase flows. In this method, however, the underlying Cartesian grid defining the coarse-grained interaction volumes induces anisotropy. We propose an isotropic, lattice-free variant of stochastic rotation dynamics, termed iSRD. Instead of Cartesian grid cells, we employ randomly distributed spherical interaction volumes. This eliminates the requirement of a grid shift, which is essential in standard SRD to maintain Galilean invariance. We derive analytical expressions for the viscosity and the diffusion coefficient in relation to the model parameters, which show excellent agreement with the results obtained in iSRD simulations. The proposed algorithm is particularly suitable to model systems bound by walls of complex shape, where the domain cannot be meshed uniformly. The presented approach is not limited to SRD but is applicable to any other mesoscopic method, where particles interact within certain coarse-grained volumes.

Direct construction of mesoscopic models from microscopic simulations

NASA Astrophysics Data System (ADS)

Lei, Huan; Caswell, Bruce; Karniadakis, George Em

2010-02-01

Starting from microscopic molecular-dynamics (MD) simulations of constrained Lennard-Jones (LJ) clusters (with constant radius of gyration Rg ), we construct two mesoscopic models [Langevin dynamics and dissipative particle dynamics (DPD)] by coarse graining the LJ clusters into single particles. Both static and dynamic properties of the coarse-grained models are investigated and compared with the MD results. The effective mean force field is computed as a function of the intercluster distance, and the corresponding potential scales linearly with the number of particles per cluster and the temperature. We verify that the mean force field can reproduce the equation of state of the atomistic systems within a wide density range but the radial distribution function only within the dilute and the semidilute regime. The friction force coefficients for both models are computed directly from the time-correlation function of the random force field of the microscopic system. For high density or a large cluster size the friction force is overestimated and the diffusivity underestimated due to the omission of many-body effects as a result of the assumed pairwise form of the coarse-grained force field. When the many-body effect is not as pronounced (e.g., smaller Rg or semidilute system), the DPD model can reproduce the dynamic properties of the MD system.

Systematic parameter inference in stochastic mesoscopic modeling

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

Lei, Huan; Yang, Xiu; Li, Zhen

2017-02-01

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the priormore » knowledge that the coefficients are “sparse”. The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.« less

Mesoscopic Rigid Body Modelling of the Extracellular Matrix Self-Assembly.

PubMed

Wong, Hua; Prévoteau-Jonquet, Jessica; Baud, Stéphanie; Dauchez, Manuel; Belloy, Nicolas

2018-06-11

The extracellular matrix (ECM) plays an important role in supporting tissues and organs. It even has a functional role in morphogenesis and differentiation by acting as a source of active molecules (matrikines). Many diseases are linked to dysfunction of ECM components and fragments or changes in their structures. As such it is a prime target for drugs. Because of technological limitations for observations at mesoscopic scales, the precise structural organisation of the ECM is not well-known, with sparse or fuzzy experimental observables. Based on the Unity3D game and physics engines, along with rigid body dynamics, we propose a virtual sandbox to model large biological molecules as dynamic chains of rigid bodies interacting together to gain insight into ECM components behaviour in the mesoscopic range. We have preliminary results showing how parameters such as fibre flexibility or the nature and number of interactions between molecules can induce different structures in the basement membrane. Using the Unity3D game engine and virtual reality headset coupled with haptic controllers, we immerse the user inside the corresponding simulation. Untrained users are able to navigate a complex virtual sandbox crowded with large biomolecules models in a matter of seconds.

Simulating the frontal instability of lock-exchange density currents with dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Li, Yanggui; Geng, Xingguo; Wang, Heping; Zhuang, Xin; Ouyang, Jie

2016-06-01

The frontal instability of lock-exchange density currents is numerically investigated using dissipative particle dynamics (DPD) at the mesoscopic particle level. For modeling two-phase flow, the “color” repulsion model is adopted to describe binary fluids according to Rothman-Keller method. The present DPD simulation can reproduce the flow phenomena of lock-exchange density currents, including the lobe-and-cleft instability that appears at the head, as well as the formation of coherent billow structures at the interface behind the head due to the growth of Kelvin-Helmholtz instability. Furthermore, through the DPD simulation, some small-scale characteristics can be observed, which are difficult to be captured in macroscopic simulation and experiment.

Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size.

PubMed

Schwalger, Tilo; Deger, Moritz; Gerstner, Wulfram

2017-04-01

Neural population equations such as neural mass or field models are widely used to study brain activity on a large scale. However, the relation of these models to the properties of single neurons is unclear. Here we derive an equation for several interacting populations at the mesoscopic scale starting from a microscopic model of randomly connected generalized integrate-and-fire neuron models. Each population consists of 50-2000 neurons of the same type but different populations account for different neuron types. The stochastic population equations that we find reveal how spike-history effects in single-neuron dynamics such as refractoriness and adaptation interact with finite-size fluctuations on the population level. Efficient integration of the stochastic mesoscopic equations reproduces the statistical behavior of the population activities obtained from microscopic simulations of a full spiking neural network model. The theory describes nonlinear emergent dynamics such as finite-size-induced stochastic transitions in multistable networks and synchronization in balanced networks of excitatory and inhibitory neurons. The mesoscopic equations are employed to rapidly integrate a model of a cortical microcircuit consisting of eight neuron types, which allows us to predict spontaneous population activities as well as evoked responses to thalamic input. Our theory establishes a general framework for modeling finite-size neural population dynamics based on single cell and synapse parameters and offers an efficient approach to analyzing cortical circuits and computations.

Mesoscopic modeling for nucleic acid chain dynamics

PubMed Central

Sales-Pardo, M.; Guimerà, R.; Moreira, A. A.; Widom, J.; Amaral, L. A. N.

2007-01-01

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin—a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop—studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands. PMID:16089566

Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics

NASA Astrophysics Data System (ADS)

Rakesh, L.

2009-09-01

Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the hydrocarbon "tail" and their hydrophilic head groups. We find that, for the surfactants, the aqueous solubility of anti-inflammatory molecules increases linearly with increasing surfactant concentration. In particular, we observed a 10-fold increase in the solubility of anti-inflammatory drugs relative to that in the aqueous buffer upon the addition of 100 mM dodecyltrimethyl ammonium bromide -DTAB.

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.

Statewide mesoscopic simulation for Wyoming.

DOT National Transportation Integrated Search

2013-10-01

This study developed a mesoscopic simulator which is capable of representing both city-level and statewide roadway : networks. The key feature of such models are the integration of (i) a traffic flow model which is efficient enough to : scale to larg...

The persistent current and energy spectrum on a driven mesoscopic LC-circuit with Josephson junction

NASA Astrophysics Data System (ADS)

Pahlavanias, Hassan

2018-03-01

The quantum theory for a mesoscopic electric circuit including a Josephson junction with charge discreteness is studied. By considering coupling energy of the mesoscopic capacitor in Josephson junction device, a Hamiltonian describing the dynamics of a quantum mesoscopic electric LC-circuit with charge discreteness is introduced. We first calculate the persistent current on a quantum driven ring including Josephson junction. Then we obtain the persistent current and energy spectrum of a quantum mesoscopic electrical circuit which includes capacitor, inductor, time-dependent external source and Josephson junction.

Coarse-grained hydrodynamics from correlation functions

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

Palmer, Bruce

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configuration from a molecular dynamics simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilbrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is applied to some simple hydrodynamic cases to determine the feasibility of applying this to realistic nanoscale systems.

Porting LAMMPS to GPUs.

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

Brown, William Michael; Plimpton, Steven James; Wang, Peng

2010-03-01

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

Structure of rigid polymers confined to nanoparticles: Molecular dynamics simulations insight

DOE PAGES

Maskey, Sabina; Lane, J. Matthew D.; Perahia, Dvora; ...

2016-02-04

Nanoparticles (NPs) grafted with organic layers form hybrids able to retain their unique properties through integration into the mesoscopic scale. The organic layer structure and response often determine the functionality of the hybrids on the mesoscopic length scale. Using molecular dynamics (MD) simulations, we probe the conformation of luminescent rigid polymers, dialkyl poly(p-phenylene ethynylene)s (PPE), end-grafted onto a silica nanoparticle in different solvents as the molecular weights and polymer coverages are varied. We find that, in contrast to NP-grafted flexible polymers, the chains are fully extended independent of the solvent. In toluene and decane, which are good solvents, the graftedmore » PPEs chains assume a similar conformation to that observed in dilute solutions. In water, which is a poor solvent for the PPEs, the polymer chains form one large cluster but remain extended. The radial distribution of the chains around the core of the nanoparticle is homogeneous in good solvents, whereas in poor solvents clusters are formed independent of molecular weights and coverages. As a result, the clustering is distinctively different from the response of grafted flexible and semiflexible polymers.« less

Josephson junction in the quantum mesoscopic electric circuits with charge discreteness

NASA Astrophysics Data System (ADS)

Pahlavani, H.

2018-04-01

A quantum mesoscopic electrical LC-circuit with charge discreteness including a Josephson junction is considered and a nonlinear Hamiltonian that describing the dynamic of such circuit is introduced. The quantum dynamical behavior (persistent current probability) is studied in the charge and phase regimes by numerical solution approaches. The time evolution of charge and current, number-difference and the bosonic phase and also the energy spectrum of a quantum mesoscopic electric LC-circuit with charge discreteness that coupled with a Josephson junction device are investigated. We show the role of the coupling energy and the electrostatic Coulomb energy of the Josephson junction in description of the quantum behavior and the spectral properties of a quantum mesoscopic electrical LC-circuits with charge discreteness.

Dissipative particle dynamics parameterization and simulations to predict negative volume excess and structure of PEG and water mixtures

NASA Astrophysics Data System (ADS)

Kacar, Gokhan

2017-12-01

We report the results of dissipative particle dynamics (DPD) parameterization and simulations of a mixture of hydrophilic polymer, PEG 400, and water which are known to exhibit negative volume excess property upon mixing. The addition of a Morse potential to the conventional DPD potential mimics the hydrogen bond attraction, where the parameterization takes the internal chemistry of the beads into account. The results indicate that the mixing of PEG and water are maintained by the influence of hydrogen bonds, and the mesoscopic structure is characterized by the trade-off of enthalpic and entropic effects.

Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size

PubMed Central

Gerstner, Wulfram

2017-01-01

Neural population equations such as neural mass or field models are widely used to study brain activity on a large scale. However, the relation of these models to the properties of single neurons is unclear. Here we derive an equation for several interacting populations at the mesoscopic scale starting from a microscopic model of randomly connected generalized integrate-and-fire neuron models. Each population consists of 50–2000 neurons of the same type but different populations account for different neuron types. The stochastic population equations that we find reveal how spike-history effects in single-neuron dynamics such as refractoriness and adaptation interact with finite-size fluctuations on the population level. Efficient integration of the stochastic mesoscopic equations reproduces the statistical behavior of the population activities obtained from microscopic simulations of a full spiking neural network model. The theory describes nonlinear emergent dynamics such as finite-size-induced stochastic transitions in multistable networks and synchronization in balanced networks of excitatory and inhibitory neurons. The mesoscopic equations are employed to rapidly integrate a model of a cortical microcircuit consisting of eight neuron types, which allows us to predict spontaneous population activities as well as evoked responses to thalamic input. Our theory establishes a general framework for modeling finite-size neural population dynamics based on single cell and synapse parameters and offers an efficient approach to analyzing cortical circuits and computations. PMID:28422957

Flexible histone tails in a new mesoscopic oligonucleosome model.

PubMed

Arya, Gaurav; Zhang, Qing; Schlick, Tamar

2006-07-01

We describe a new mesoscopic model of oligonucleosomes that incorporates flexible histone tails. The nucleosome cores are modeled using the discrete surface-charge optimization model, which treats the nucleosome as an electrostatic surface represented by hundreds of point charges; the linker DNAs are treated using a discrete elastic chain model; and the histone tails are modeled using a bead/chain hydrodynamic approach as chains of connected beads where each bead represents five protein residues. Appropriate charges and force fields are assigned to each histone chain so as to reproduce the electrostatic potential, structure, and dynamics of the corresponding atomistic histone tails at different salt conditions. The dynamics of resulting oligonucleosomes at different sizes and varying salt concentrations are simulated by Brownian dynamics with complete hydrodynamic interactions. The analyses demonstrate that the new mesoscopic model reproduces experimental results better than its predecessors, which modeled histone tails as rigid entities. In particular, our model with flexible histone tails: correctly accounts for salt-dependent conformational changes in the histone tails; yields the experimentally obtained values of histone-tail mediated core/core attraction energies; and considers the partial shielding of electrostatic repulsion between DNA linkers as a result of the spatial distribution of histone tails. These effects are crucial for regulating chromatin structure but are absent or improperly treated in models with rigid histone tails. The development of this model of oligonucleosomes thus opens new avenues for studying the role of histone tails and their variants in mediating gene expression through modulation of chromatin structure.

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

NASA Astrophysics Data System (ADS)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

ProtoMD: A prototyping toolkit for multiscale molecular dynamics

NASA Astrophysics Data System (ADS)

Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.

2016-05-01

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.

Mesoscopic fluctuations and intermittency in aging dynamics

NASA Astrophysics Data System (ADS)

Sibani, P.

2006-01-01

Mesoscopic aging systems are characterized by large intermittent noise fluctuations. In a record dynamics scenario (Sibani P. and Dall J., Europhys. Lett., 64 (2003) 8) these events, quakes, are treated as a Poisson process with average αln (1 + t/tw), where t is the observation time, tw is the age and α is a parameter. Assuming for simplicity that quakes constitute the only source of de-correlation, we present a model for the probability density function (PDF) of the configuration autocorrelation function. Beside α, the model has the average quake size 1/q as a parameter. The model autocorrelation PDF has a Gumbel-like shape, which approaches a Gaussian for large t/tw and becomes sharply peaked in the thermodynamic limit. Its average and variance, which are given analytically, depend on t/tw as a power law and a power law with a logarithmic correction, respectively. Most predictions are in good agreement with data from the literature and with the simulations of the Edwards-Anderson spin-glass carried out as a test.

Revealing mesoscopic structural universality with diffusion.

PubMed

Novikov, Dmitry S; Jensen, Jens H; Helpern, Joseph A; Fieremans, Els

2014-04-08

Measuring molecular diffusion is widely used for characterizing materials and living organisms noninvasively. This characterization relies on relations between macroscopic diffusion metrics and structure at the mesoscopic scale commensurate with the diffusion length. Establishing such relations remains a fundamental challenge, hindering progress in materials science, porous media, and biomedical imaging. Here we show that the dynamical exponent in the time dependence of the diffusion coefficient distinguishes between the universality classes of the mesoscopic structural complexity. Our approach enables the interpretation of diffusion measurements by objectively selecting and modeling the most relevant structural features. As an example, the specific values of the dynamical exponent allow us to identify the relevant mesoscopic structure affecting MRI-measured water diffusion in muscles and in brain, and to elucidate the structural changes behind the decrease of diffusion coefficient in ischemic stroke.

Mesoscopic modeling of structural and thermodynamic properties of fluids confined by rough surfaces.

PubMed

Terrón-Mejía, Ketzasmin A; López-Rendón, Roberto; Gama Goicochea, Armando

2015-10-21

The interfacial and structural properties of fluids confined by surfaces of different geometries are studied at the mesoscopic scale using dissipative particle dynamics simulations in the grand canonical ensemble. The structure of the surfaces is modeled by a simple function, which allows us to simulate readily different types of surfaces through the choice of three parameters only. The fluids we have modeled are confined either by two smooth surfaces or by symmetrically and asymmetrically structured walls. We calculate structural and thermodynamic properties such as the density, temperature and pressure profiles, as well as the interfacial tension profiles for each case and find that a structural order-disorder phase transition occurs as the degree of surface roughness increases. However, the magnitude of the interfacial tension is insensitive to the structuring of the surfaces and depends solely on the magnitude of the solid-fluid interaction. These results are important for modern nanotechnology applications, such as in the enhanced recovery of oil, and in the design of porous materials with specifically tailored properties.

Coarse-grained hydrodynamics from correlation functions

NASA Astrophysics Data System (ADS)

Palmer, Bruce

2018-02-01

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is demonstrated on a discrete particle simulation of diffusion with a spatially dependent diffusion coefficient. Correlation functions are calculated from the particle simulation and the spatially varying diffusion coefficient is recovered using a fitting procedure.

Regular and irregular dynamics of spin-polarized wavepackets in a mesoscopic quantum dot at the edge of topological insulator

NASA Astrophysics Data System (ADS)

Khomitsky, D. V.; Chubanov, A. A.; Konakov, A. A.

2016-12-01

The dynamics of Dirac-Weyl spin-polarized wavepackets driven by a periodic electric field is considered for the electrons in a mesoscopic quantum dot formed at the edge of the two-dimensional HgTe/CdTe topological insulator with Dirac-Weyl massless energy spectra, where the motion of carriers is less sensitive to disorder and impurity potentials. It is observed that the interplay of strongly coupled spin and charge degrees of freedom creates the regimes of irregular dynamics in both coordinate and spin channels. The border between the regular and irregular regimes determined by the strength and frequency of the driving field is found analytically within the quasiclassical approach by means of the Ince-Strutt diagram for the Mathieu equation, and is supported by full quantum-mechanical simulations of the driven dynamics. The investigation of quasienergy spectrum by Floquet approach reveals the presence of non-Poissonian level statistics, which indicates the possibility of chaotic quantum dynamics and corresponds to the areas of parameters for irregular regimes within the quasiclassical approach. We find that the influence of weak disorder leads to partial suppression of the dynamical chaos. Our findings are of interest both for progress in the fundamental field of quantum chaotic dynamics and for further experimental and technological applications of spindependent phenomena in nanostructures based on topological insulators.

Regular and irregular dynamics of spin-polarized wavepackets in a mesoscopic quantum dot at the edge of topological insulator

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

Khomitsky, D. V., E-mail: khomitsky@phys.unn.ru; Chubanov, A. A.; Konakov, A. A.

2016-12-15

The dynamics of Dirac–Weyl spin-polarized wavepackets driven by a periodic electric field is considered for the electrons in a mesoscopic quantum dot formed at the edge of the two-dimensional HgTe/CdTe topological insulator with Dirac–Weyl massless energy spectra, where the motion of carriers is less sensitive to disorder and impurity potentials. It is observed that the interplay of strongly coupled spin and charge degrees of freedom creates the regimes of irregular dynamics in both coordinate and spin channels. The border between the regular and irregular regimes determined by the strength and frequency of the driving field is found analytically within themore » quasiclassical approach by means of the Ince–Strutt diagram for the Mathieu equation, and is supported by full quantum-mechanical simulations of the driven dynamics. The investigation of quasienergy spectrum by Floquet approach reveals the presence of non-Poissonian level statistics, which indicates the possibility of chaotic quantum dynamics and corresponds to the areas of parameters for irregular regimes within the quasiclassical approach. We find that the influence of weak disorder leads to partial suppression of the dynamical chaos. Our findings are of interest both for progress in the fundamental field of quantum chaotic dynamics and for further experimental and technological applications of spindependent phenomena in nanostructures based on topological insulators.« less

Revealing mesoscopic structural universality with diffusion

PubMed Central

Novikov, Dmitry S.; Jensen, Jens H.; Helpern, Joseph A.; Fieremans, Els

2014-01-01

Measuring molecular diffusion is widely used for characterizing materials and living organisms noninvasively. This characterization relies on relations between macroscopic diffusion metrics and structure at the mesoscopic scale commensurate with the diffusion length. Establishing such relations remains a fundamental challenge, hindering progress in materials science, porous media, and biomedical imaging. Here we show that the dynamical exponent in the time dependence of the diffusion coefficient distinguishes between the universality classes of the mesoscopic structural complexity. Our approach enables the interpretation of diffusion measurements by objectively selecting and modeling the most relevant structural features. As an example, the specific values of the dynamical exponent allow us to identify the relevant mesoscopic structure affecting MRI-measured water diffusion in muscles and in brain, and to elucidate the structural changes behind the decrease of diffusion coefficient in ischemic stroke. PMID:24706873

Dissipative particle dynamics simulation on the self-assembly and disassembly of pH-sensitive polymeric micelle with coating repair agent

NASA Astrophysics Data System (ADS)

Wang, Xiumin; Gao, Jianbang; Wang, Zhikun; Xu, Jianchang; Li, Chunling; Sun, Shuangqing; Hu, Songqing

2017-10-01

Dissipative particle dynamics (DPD) simulations were applied to investigate the coating repair agent dicyclopentadience (DCPD) in pH-sensitive micelles. The results show micelles self-assembled from triblock copolymers with strong hydrophobic interaction are not conducive to loading DCPD, and only micelles with weak interaction parameter can encapsulate DCPD well. After protonation, the structure of micelle was disassembled and DCPD beads have a stronger ability to shrink polymer chains and exposed to water. This work provides mesoscopic insight into self-assembly and disassembly of desired agent-loaded micelle, and might be useful for the design of new materials for agent delivery.

Reaction rates for mesoscopic reaction-diffusion kinetics

DOE PAGES

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2015-02-23

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In thismore » paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. Finally, we show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results.« less

Reaction rates for mesoscopic reaction-diffusion kinetics

PubMed Central

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2016-01-01

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In this paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. We show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results. PMID:25768640

Integrodifferential formulations of the continuous-time random walk for solute transport subject to bimolecular A +B →0 reactions: From micro- to mesoscopic

NASA Astrophysics Data System (ADS)

Hansen, Scott K.; Berkowitz, Brian

2015-03-01

We develop continuous-time random walk (CTRW) equations governing the transport of two species that annihilate when in proximity to one another. In comparison with catalytic or spontaneous transformation reactions that have been previously considered in concert with CTRW, both species have spatially variant concentrations that require consideration. We develop two distinct formulations. The first treats transport and reaction microscopically, potentially capturing behavior at sharp fronts, but at the cost of being strongly nonlinear. The second, mesoscopic, formulation relies on a separation-of-scales technique we develop to separate microscopic-scale reaction and upscaled transport. This simplifies the governing equations and allows treatment of more general reaction dynamics, but requires stronger smoothness assumptions of the solution. The mesoscopic formulation is easily tractable using an existing solution from the literature (we also provide an alternative derivation), and the generalized master equation (GME) for particles undergoing A +B →0 reactions is presented. We show that this GME simplifies, under appropriate circumstances, to both the GME for the unreactive CTRW and to the advection-dispersion-reaction equation. An additional major contribution of this work is on the numerical side: to corroborate our development, we develop an indirect particle-tracking-partial-integro-differential-equation (PIDE) hybrid verification technique which could be applicable widely in reactive anomalous transport. Numerical simulations support the mesoscopic analysis.

Mesoscale Thermodynamic Analysis of Atomic-Scale Dislocation-Obstacle Interactions Simulated by Molecular Dynamics

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

Monet, Giath; Bacon, David J; Osetskiy, Yury N

2010-01-01

Given the time and length scales in molecular dynamics (MD) simulations of dislocation-defect interactions, quantitative MD results cannot be used directly in larger scale simulations or compared directly with experiment. A method to extract fundamental quantities from MD simulations is proposed here. The first quantity is a critical stress defined to characterise the obstacle resistance. This mesoscopic parameter, rather than the obstacle 'strength' designed for a point obstacle, is to be used for an obstacle of finite size. At finite temperature, our analyses of MD simulations allow the activation energy to be determined as a function of temperature. The resultsmore » confirm the proportionality between activation energy and temperature that is frequently observed by experiment. By coupling the data for the activation energy and the critical stress as functions of temperature, we show how the activation energy can be deduced at a given value of the critical stress.« less

Probing eukaryotic cell mechanics via mesoscopic simulations

PubMed Central

Shang, Menglin; Lim, Chwee Teck

2017-01-01

Cell mechanics has proven to be important in many biological processes. Although there is a number of experimental techniques which allow us to study mechanical properties of cell, there is still a lack of understanding of the role each sub-cellular component plays during cell deformations. We present a new mesoscopic particle-based eukaryotic cell model which explicitly describes cell membrane, nucleus and cytoskeleton. We employ Dissipative Particle Dynamics (DPD) method that provides us with the unified framework for modeling of a cell and its interactions in the flow. Data from micropipette aspiration experiments were used to define model parameters. The model was validated using data from microfluidic experiments. The validated model was then applied to study the impact of the sub-cellular components on the cell viscoelastic response in micropipette aspiration and microfluidic experiments. PMID:28922399

Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

PubMed Central

Ayton, Gary S.; Lyman, Edward

2014-01-01

An overall multiscale simulation strategy for large scale coarse-grain simulations of membrane protein systems is presented. The protein is modeled as a heterogeneous elastic network, while the lipids are modeled using the hybrid analytic-systematic (HAS) methodology, where in both cases atomistic level information obtained from molecular dynamics simulation is used to parameterize the model. A feature of this approach is that from the outset liposome length scales are employed in the simulation (i.e., on the order of ½ a million lipids plus protein). A route to develop highly coarse-grained models from molecular-scale information is proposed and results for N-BAR domain protein remodeling of a liposome are presented. PMID:20158037

Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison

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

Dahlen, Oda, E-mail: oda.dahlen@ntnu.no; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no

Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimentalmore » data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones.« less

Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond

PubMed Central

Ge, Hao; Qian, Hong

2011-01-01

A theory for an non-equilibrium phase transition in a driven biochemical network is presented. The theory is based on the chemical master equation (CME) formulation of mesoscopic biochemical reactions and the mathematical method of large deviations. The large deviations theory provides an analytical tool connecting the macroscopic multi-stability of an open chemical system with the multi-scale dynamics of its mesoscopic counterpart. It shows a corresponding non-equilibrium phase transition among multiple stochastic attractors. As an example, in the canonical phosphorylation–dephosphorylation system with feedback that exhibits bistability, we show that the non-equilibrium steady-state (NESS) phase transition has all the characteristics of classic equilibrium phase transition: Maxwell construction, a discontinuous first-derivative of the ‘free energy function’, Lee–Yang's zero for a generating function and a critical point that matches the cusp in nonlinear bifurcation theory. To the biochemical system, the mathematical analysis suggests three distinct timescales and needed levels of description. They are (i) molecular signalling, (ii) biochemical network nonlinear dynamics, and (iii) cellular evolution. For finite mesoscopic systems such as a cell, motions associated with (i) and (iii) are stochastic while that with (ii) is deterministic. Both (ii) and (iii) are emergent properties of a dynamic biochemical network. PMID:20466813

A mesoscopic bridging scale method for fluids and coupling dissipative particle dynamics with continuum finite element method

PubMed Central

Kojic, Milos; Filipovic, Nenad; Tsuda, Akira

2012-01-01

A multiscale procedure to couple a mesoscale discrete particle model and a macroscale continuum model of incompressible fluid flow is proposed in this study. We call this procedure the mesoscopic bridging scale (MBS) method since it is developed on the basis of the bridging scale method for coupling molecular dynamics and finite element models [G.J. Wagner, W.K. Liu, Coupling of atomistic and continuum simulations using a bridging scale decomposition, J. Comput. Phys. 190 (2003) 249–274]. We derive the governing equations of the MBS method and show that the differential equations of motion of the mesoscale discrete particle model and finite element (FE) model are only coupled through the force terms. Based on this coupling, we express the finite element equations which rely on the Navier–Stokes and continuity equations, in a way that the internal nodal FE forces are evaluated using viscous stresses from the mesoscale model. The dissipative particle dynamics (DPD) method for the discrete particle mesoscale model is employed. The entire fluid domain is divided into a local domain and a global domain. Fluid flow in the local domain is modeled with both DPD and FE method, while fluid flow in the global domain is modeled by the FE method only. The MBS method is suitable for modeling complex (colloidal) fluid flows, where continuum methods are sufficiently accurate only in the large fluid domain, while small, local regions of particular interest require detailed modeling by mesoscopic discrete particles. Solved examples – simple Poiseuille and driven cavity flows illustrate the applicability of the proposed MBS method. PMID:23814322

Role of weakest links and system-size scaling in multiscale modeling of stochastic plasticity

NASA Astrophysics Data System (ADS)

Ispánovity, Péter Dusán; Tüzes, Dániel; Szabó, Péter; Zaiser, Michael; Groma, István

2017-02-01

Plastic deformation of crystalline and amorphous matter often involves intermittent local strain burst events. To understand the physical background of the phenomenon a minimal stochastic mesoscopic model was introduced, where details of the microstructure evolution are statistically represented in terms of a fluctuating local yield threshold. In the present paper we propose a method for determining the corresponding yield stress distribution for the case of crystal plasticity from lower scale discrete dislocation dynamics simulations which we combine with weakest link arguments. The success of scale linking is demonstrated by comparing stress-strain curves obtained from the resulting mesoscopic and the underlying discrete dislocation models in the microplastic regime. As shown by various scaling relations they are statistically equivalent and behave identically in the thermodynamic limit. The proposed technique is expected to be applicable to different microstructures and also to amorphous materials.

Variable speed limit strategies analysis with mesoscopic traffic flow model based on complex networks

NASA Astrophysics Data System (ADS)

Li, Shu-Bin; Cao, Dan-Ni; Dang, Wen-Xiu; Zhang, Lin

As a new cross-discipline, the complexity science has penetrated into every field of economy and society. With the arrival of big data, the research of the complexity science has reached its summit again. In recent years, it offers a new perspective for traffic control by using complex networks theory. The interaction course of various kinds of information in traffic system forms a huge complex system. A new mesoscopic traffic flow model is improved with variable speed limit (VSL), and the simulation process is designed, which is based on the complex networks theory combined with the proposed model. This paper studies effect of VSL on the dynamic traffic flow, and then analyzes the optimal control strategy of VSL in different network topologies. The conclusion of this research is meaningful to put forward some reasonable transportation plan and develop effective traffic management and control measures to help the department of traffic management.

Continuum mesoscopic framework for multiple interacting species and processes on multiple site types and/or crystallographic planes.

PubMed

Chatterjee, Abhijit; Vlachos, Dionisios G

2007-07-21

While recently derived continuum mesoscopic equations successfully bridge the gap between microscopic and macroscopic physics, so far they have been derived only for simple lattice models. In this paper, general deterministic continuum mesoscopic equations are derived rigorously via nonequilibrium statistical mechanics to account for multiple interacting surface species and multiple processes on multiple site types and/or different crystallographic planes. Adsorption, desorption, reaction, and surface diffusion are modeled. It is demonstrated that contrary to conventional phenomenological continuum models, microscopic physics, such as the interaction potential, determines the final form of the mesoscopic equation. Models of single component diffusion and binary diffusion of interacting particles on single-type site lattice and of single component diffusion on complex microporous materials' lattices consisting of two types of sites are derived, as illustrations of the mesoscopic framework. Simplification of the diffusion mesoscopic model illustrates the relation to phenomenological models, such as the Fickian and Maxwell-Stefan transport models. It is demonstrated that the mesoscopic equations are in good agreement with lattice kinetic Monte Carlo simulations for several prototype examples studied.

Diffusional correlations among multiple active sites in a single enzyme.

PubMed

Echeverria, Carlos; Kapral, Raymond

2014-04-07

Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

Patient-specific modeling and analysis of dynamic behavior of individual sickle red blood cells under hypoxic conditions

NASA Astrophysics Data System (ADS)

Li, Xuejin; Du, E.; Li, Zhen; Tang, Yu-Hang; Lu, Lu; Dao, Ming; Karniadakis, George

2015-11-01

Sickle cell anemia is an inherited blood disorder exhibiting heterogeneous morphology and abnormal dynamics under hypoxic conditions. We developed a time-dependent cell model that is able to simulate the dynamic processes of repeated sickling and unsickling of red blood cells (RBCs) under physiological conditions. By using the kinetic cell model with parameters derived from patient-specific data, we present a mesoscopic computational study of the dynamic behavior of individual sickle RBCs flowing in a microfluidic channel with multiple microgates. We investigate how individual sickle RBCs behave differently from healthy ones in channel flow, and analyze the alteration of cellular behavior and response to single-cell capillary obstruction induced by cell rheologic rigidification and morphological change due to cell sickling under hypoxic conditions. We also simulate the flow dynamics of sickle RBCs treated with hydroxyurea (HU) and quantify the relative enhancement of hemodynamic performance of HU. This work was supported by the National Institutes of Health (NIH) Grant U01HL114476.

Static and dynamic light scattering by red blood cells: A numerical study.

PubMed

Mauer, Johannes; Peltomäki, Matti; Poblete, Simón; Gompper, Gerhard; Fedosov, Dmitry A

2017-01-01

Light scattering is a well-established experimental technique, which gains more and more popularity in the biological field because it offers the means for non-invasive imaging and detection. However, the interpretation of light-scattering signals remains challenging due to the complexity of most biological systems. Here, we investigate static and dynamic scattering properties of red blood cells (RBCs) using two mesoscopic hydrodynamics simulation methods-multi-particle collision dynamics and dissipative particle dynamics. Light scattering is studied for various membrane shear elasticities, bending rigidities, and RBC shapes (e.g., biconcave and stomatocyte). Simulation results from the two simulation methods show good agreement, and demonstrate that the static light scattering of a diffusing RBC is not very sensitive to the changes in membrane properties and moderate alterations in cell shapes. We also compute dynamic light scattering of a diffusing RBC, from which dynamic properties of RBCs such as diffusion coefficients can be accessed. In contrast to static light scattering, the dynamic measurements can be employed to differentiate between the biconcave and stomatocytic RBC shapes and generally allow the differentiation based on the membrane properties. Our simulation results can be used for better understanding of light scattering by RBCs and the development of new non-invasive methods for blood-flow monitoring.

Static and dynamic light scattering by red blood cells: A numerical study

PubMed Central

Mauer, Johannes; Peltomäki, Matti; Poblete, Simón; Gompper, Gerhard

2017-01-01

Light scattering is a well-established experimental technique, which gains more and more popularity in the biological field because it offers the means for non-invasive imaging and detection. However, the interpretation of light-scattering signals remains challenging due to the complexity of most biological systems. Here, we investigate static and dynamic scattering properties of red blood cells (RBCs) using two mesoscopic hydrodynamics simulation methods—multi-particle collision dynamics and dissipative particle dynamics. Light scattering is studied for various membrane shear elasticities, bending rigidities, and RBC shapes (e.g., biconcave and stomatocyte). Simulation results from the two simulation methods show good agreement, and demonstrate that the static light scattering of a diffusing RBC is not very sensitive to the changes in membrane properties and moderate alterations in cell shapes. We also compute dynamic light scattering of a diffusing RBC, from which dynamic properties of RBCs such as diffusion coefficients can be accessed. In contrast to static light scattering, the dynamic measurements can be employed to differentiate between the biconcave and stomatocytic RBC shapes and generally allow the differentiation based on the membrane properties. Our simulation results can be used for better understanding of light scattering by RBCs and the development of new non-invasive methods for blood-flow monitoring. PMID:28472125

A mesoscopic simulation of static and dynamic wetting using many-body dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Ghorbani, Najmeh; Pishevar, Ahmadreza

2018-01-01

A many-body dissipative particle dynamics simulation is applied here to pave the way for investigating the behavior of mesoscale droplets after impact on horizontal solid substrates. First, hydrophobic and hydrophilic substrates are simulated through tuning the solid-liquid interfacial interaction parameters of an innovative conservative force model. The static contact angles are calculated on homogeneous and several patterned surfaces and compared with the predicted values by the Cassie's law in order to verify the model. The results properly evaluate the amount of increase in surface superhydrophobicity as a result of surface patterning. Then drop impact phenomenon is studied by calculating the spreading factor and dimensionless height versus dimensionless time and the comparisons made between the results and the experimental values for three different static contact angles. The results show the capability of the procedure in calculating the amount of maximum spreading factor, which is a significant concept in ink-jet printing and coating process.

Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer†

PubMed Central

Song, Yuhua; Guallar, Victor; Baker, Nathan A.

2008-01-01

Salicylate, an amphiphilic molecule and a popular member of non-steroidal antiinflammatory drug family, is known to affect hearing through reduction of the electromechanical coupling in the outer hair cells of the ear. This reduction of electromotility by salicylate has been widely studied but the molecular mechanism of the phenomenon is still unknown. In this study, we investigated one aspect of salicylate’s action; namely, the perturbation of electrical and mechanical membrane properties by salicylate in the absence of cytoskeletal or membrane-bound motor proteins such as prestin. In particular, we simulated the interaction of salicylate with a dipalmitoylphosphatidylcholine (DPPC) bilayer via atomically-detailed molecular dynamics simulations to observe the effect of salicylate on the microscopic and mesoscopic properties of the bilayer. The results demonstrate that salicylate interacts with the bilayer by associating at the water-DPPC interface in a nearly perpendicular orientation and penetrating more deeply into the bilayer than either sodium or chloride. This association has several affects on the membrane properties. First, binding of salicylate to the membrane displaces chloride from the bilayer-water interface. Second, salicylate influences the electrostatic potential and dielectric properties of the bilayer, with significant changes at the water-lipid bilayer interface. Third, salicylate association results in structural changes including decreased head group area per lipid and increased lipid tail order. However, salicylate does not significantly alter the mechanical properties of the DPPC bilayer; bulk compressibility, area compressibility, and bending modulus were only perturbed by small, statistically-insignificant amounts, by the presence of salicylate. The observations from these simulations are in qualitative agreement with experimental data and support the conclusion that salicylate influences the electrical but not the mechanical properties of DPPC membranes. PMID:16216066

On an aggregation in birth-and-death stochastic dynamics

NASA Astrophysics Data System (ADS)

Finkelshtein, Dmitri; Kondratiev, Yuri; Kutoviy, Oleksandr; Zhizhina, Elena

2014-06-01

We consider birth-and-death stochastic dynamics of particle systems with attractive interaction. The heuristic generator of the dynamics has a constant birth rate and density-dependent decreasing death rate. The corresponding statistical dynamics is constructed. Using the Vlasov-type scaling we derive the limiting mesoscopic evolution and prove that this evolution propagates chaos. We study a nonlinear non-local kinetic equation for the first correlation function (density of population). The existence of uniformly bounded solutions as well as solutions growing inside of a bounded domain and expanding in the space are shown. These solutions describe two regimes in the mesoscopic system: regulation and aggregation.

The Lowe-Andersen thermostat as an alternative to the dissipative particle dynamics in the mesoscopic simulation of entangled polymers.

PubMed

Khani, Shaghayegh; Yamanoi, Mikio; Maia, Joao

2013-05-07

Dissipative Particle Dynamics (DPD) has shown a great potential in studying the dynamics and rheological properties of soft matter; however, it is associated with deficiencies in describing the characteristics of entangled polymer melts. DPD deficiencies are usually correlated to the time integrating method and the unphysical bond crossings due to utilization of soft potentials. One shortcoming of DPD thermostat is the inability to produce real values of Schmidt number for fluids. In order to overcome this, an alternative Lowe-Anderson (LA) method, which successfully stabilizes the temperature, is used in the present work. Additionally, a segmental repulsive potential was introduced to avoid unphysical bond crossings. The performance of the method in simulating polymer systems is discussed by monitoring the static and dynamic characteristics of polymer chains and the results from the LA method are compared to standard DPD simulations. The performance of the model is evaluated on capturing the main shear flow properties of entangled polymer systems. Finally the linear and nonlinear viscoelastic properties of such systems are discussed.

Hydrodynamics of confined colloidal fluids in two dimensions

NASA Astrophysics Data System (ADS)

Sané, Jimaan; Padding, Johan T.; Louis, Ard A.

2009-05-01

We apply a hybrid molecular dynamics and mesoscopic simulation technique to study the dynamics of two-dimensional colloidal disks in confined geometries. We calculate the velocity autocorrelation functions and observe the predicted t-1 long-time hydrodynamic tail that characterizes unconfined fluids, as well as more complex oscillating behavior and negative tails for strongly confined geometries. Because the t-1 tail of the velocity autocorrelation function is cut off for longer times in finite systems, the related diffusion coefficient does not diverge but instead depends logarithmically on the overall size of the system. The Langevin equation gives a poor approximation to the velocity autocorrelation function at both short and long times.

Integrated corridor management (ICM) analysis, modeling, and simulation (AMS) for Minneapolis site : model calibration and validation report.

DOT National Transportation Integrated Search

2010-02-01

This technical report documents the calibration and validation of the baseline (2008) mesoscopic model for the I-394 Minneapolis, Minnesota, Pioneer Site. DynusT was selected as the mesoscopic model for analyzing operating conditions in the I-394 cor...

Mesoscopic simulations of shock-to-detonation transition in reactive liquid high explosive

NASA Astrophysics Data System (ADS)

Maillet, J. B.; Bourasseau, E.; Desbiens, N.; Vallverdu, G.; Stoltz, G.

2011-12-01

An extension of the model described in a previous work (see Maillet J. B. et al., EPL, 78 (2007) 68001) based on Dissipative Particle Dynamics is presented and applied to a liquid high explosive (HE), with thermodynamic properties mimicking those of liquid nitromethane. Large scale nonequilibrium simulations of reacting liquid HE with model kinetic under sustained shock conditions allow a better understanding of the shock-to-detonation transition in homogeneous explosives. Moreover, the propagation of the reactive wave appears discontinuous since ignition points in the shocked material can be activated by the compressive waves emitted from the onset of chemical reactions.

Fully printable transparent monolithic solid-state dye-sensitized solar cell with mesoscopic indium tin oxide counter electrode.

PubMed

Yang, Ying; Ri, Kwangho; Rong, Yaoguang; Liu, Linfeng; Liu, Tongfa; Hu, Min; Li, Xiong; Han, Hongwei

2014-09-07

We present a new transparent monolithic mesoscopic solid-state dye-sensitized solar cell based on trilamellar films of mesoscopic TiO2 nanocrystalline photoanode, a ZrO2 insulating layer and an indium tin oxide counter electrode (ITO-CE), which were screen-printed layer by layer on a single substrate. When the thickness of the ITO-CE was optimized to 2.1 μm, this very simple and fully printable solid-state DSSC with D102 dye and spiro-OMeTAD hole transport materials presents efficiencies of 1.73% when irradiated from the front side and 1.06% when irradiated from the rear side under a standard simulated sunlight condition (AM 1.5 Global, 100 mW cm(-2)). Higher parameters could be expected with a better transparent mesoscopic counter electrode and hole conductor for the printable monolithic mesoscopic solid-state DSSC.

A molecular dynamics simulation study of dynamic process and mesoscopic structure in liquid mixture systems

NASA Astrophysics Data System (ADS)

Yang, Peng

The focus of this dissertation is the Molecular Dynamics (MD) simulation study of two different systems. In thefirst system, we study the dynamic process of graphene exfoliation, particularly graphene dispersion using ionic surfactants (Chapter 2). In the second system, we investigate the mesoscopic structure of binary solute/ionic liquid (IL) mixtures through the comparison between simulations and corresponding experiments (Chapter 3 and 4). In the graphene exfoliation study, we consider two separation mechanisms: changing the interlayer distance and sliding away the relative distance of two single-layer graphene sheets. By calculating the energy barrier as a function of separation (interlayer or sliding-away) distance and performing sodium dodecyl sulfate (SDS) structure analysis around graphene surface in SDS surfactant/water + bilayer graphene mixture systems, we find that the sliding-away mechanism is the dominant, feasible separation process. In this process, the SDS-graphene interaction gradually replaces the graphene-graphene Van der Waals (VdW) interaction, and decreases the energy barrier until almost zero at critical SDS concentration. In solute/IL study, we investigate nonpolar (CS2) and dipolar (CH 3CN) solute/IL mixture systems. MD simulation shows that at low concentrations, IL is nanosegregated into an ionic network and nonpolar domain. It is also found that CS2 molecules tend to be localized into the nonpolar domain, while CH3CN interacts with nonpolar domain as well as with the charged head groups in the ionic network because of its amphiphilicity. At high concentrations, CH3CN molecules eventually disrupt the nanostructural organization. This dissertation is organized in four chapters: (1) introduction to graphene, ionic liquids and the methodology of MD; (2) MD simulation of graphene exfoliation; (3) Nanostructural organization in acetonitrile/IL mixtures; (4) Nanostructural organization in carbon disulfide/IL mixtures; (5) Conclusions. Results of MD simulations of liquid mixture systems car-ried out in this research explain observed experiments and show the details of nanostructural organizations in small solute molecules/IL mixture. Additionally, the research successfully reveals the correct mechanism of graphene exfoliation process in liquid solution. (This will be summarized in Chapter 5.) The research presented in this dissertation enhances our understanding of the microscopic behaviors in complex liquid systems as well as the theoretical method to explore them.

Transferable Coarse-Grained Models for Ionic Liquids.

PubMed

Wang, Yanting; Feng, Shulu; Voth, Gregory A

2009-04-14

The effective force coarse-graining (EF-CG) method was applied to the imidazolium-based nitrate ionic liquids with various alkyl side-chain lengths. The nonbonded EF-CG forces for the ionic liquid with a short side chain were extended to generate the nonbonded forces for the ionic liquids with longer side chains. The EF-CG force fields for the ionic liquids exhibit very good transferability between different systems at various temperatures and are suitable for investigating the mesoscopic structural properties of this class of ionic liquids. The good additivity and ease of manipulation of the EF-CG force fields can allow for an inverse design methodology of ionic liquids at the coarse-grained level. With the EF-CG force field, the molecular dynamics (MD) simulation at a very large scale has been performed to check the significance of finite size effects on the structural properties. From these MD simulation results, it can be concluded that the finite size effect on the phenomenon of ionic liquid spatial heterogeneity (Wang, Y.; Voth, G. A. J. Am. Chem. Soc. 2005, 127, 12192) is small and that this phenomenon is indeed a nanostructural behavior which leads to the experimentally observed mesoscopic heterogeneous structure of ionic liquids.

Thermal coupling effect on the vortex dynamics of superconducting thin films: time-dependent Ginzburg–Landau simulations

NASA Astrophysics Data System (ADS)

Jing, Ze; Yong, Huadong; Zhou, Youhe

2018-05-01

In this paper, vortex dynamics of superconducting thin films are numerically investigated by the generalized time-dependent Ginzburg–Landau (TDGL) theory. Interactions between vortex motion and the motion induced energy dissipation is considered by solving the coupled TDGL equation and the heat diffusion equation. It is found that thermal coupling has significant effects on the vortex dynamics of superconducting thin films. Branching in the vortex penetration path originates from the coupling between vortex motion and the motion induced energy dissipation. In addition, the environment temperature, the magnetic field ramp rate and the geometry of the superconducting film also greatly influence the vortex dynamic behaviors. Our results provide new insights into the dynamics of superconducting vortices, and give a mesoscopic understanding on the channeling and branching of vortex penetration paths during flux avalanches.

The adiabatic piston: a perpetuum mobile in the mesoscopic realm

NASA Astrophysics Data System (ADS)

Crosignani, Bruno; Porto, Paolo; Conti, Claudio

2004-03-01

A detailed analysis of the adiabatic-piston problem reveals, for a finely-tuned choice of the spatial dimensions of the system, peculiar dynamical features that challenge the statement that an isolated system necessarily reaches a time-independent equilibrium state. In particular, the piston behaves like a perpetuum mobile, i.e., it never comes to a stop but keeps wandering, undergoing sizeable oscillations around the position corresponding to maximum entropy; this has remarkable implications on the entropy changes of a mesoscopic isolated system and on the limits of validity of the second law of thermodynamics in the mesoscopic realm.

Mesoscopic model for binary fluids

NASA Astrophysics Data System (ADS)

Echeverria, C.; Tucci, K.; Alvarez-Llamoza, O.; Orozco-Guillén, E. E.; Morales, M.; Cosenza, M. G.

2017-10-01

We propose a model for studying binary fluids based on the mesoscopic molecular simulation technique known as multiparticle collision, where the space and state variables are continuous, and time is discrete. We include a repulsion rule to simulate segregation processes that does not require calculation of the interaction forces between particles, so binary fluids can be described on a mesoscopic scale. The model is conceptually simple and computationally efficient; it maintains Galilean invariance and conserves the mass and energy in the system at the micro- and macro-scale, whereas momentum is conserved globally. For a wide range of temperatures and densities, the model yields results in good agreement with the known properties of binary fluids, such as the density profile, interface width, phase separation, and phase growth. We also apply the model to the study of binary fluids in crowded environments with consistent results.

Study on the Reduced Traffic Congestion Method Based on Dynamic Guidance Information

NASA Astrophysics Data System (ADS)

Li, Shu-Bin; Wang, Guang-Min; Wang, Tao; Ren, Hua-Ling; Zhang, Lin

2018-05-01

This paper studies how to generate the reasonable information of travelers’ decision in real network. This problem is very complex because the travelers’ decision is constrained by different human behavior. The network conditions can be predicted by using the advanced dynamic OD (Origin-Destination, OD) estimation techniques. Based on the improved mesoscopic traffic model, the predictable dynamic traffic guidance information can be obtained accurately. A consistency algorithm is designed to investigate the travelers’ decision by simulating the dynamic response to guidance information. The simulation results show that the proposed method can provide the best guidance information. Further, a case study is conducted to verify the theoretical results and to draw managerial insights into the potential of dynamic guidance strategy in improving traffic performance. Supported by National Natural Science Foundation of China under Grant Nos. 71471104, 71771019, 71571109, and 71471167; The University Science and Technology Program Funding Projects of Shandong Province under Grant No. J17KA211; The Project of Public Security Department of Shandong Province under Grant No. GATHT2015-236; The Major Social and Livelihood Special Project of Jinan under Grant No. 20150905

OpenRBC: Redefining the Frontier of Red Blood Cell Simulations at Protein Resolution

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Lu, Lu; Li, He; Grinberg, Leopold; Sachdeva, Vipin; Evangelinos, Constantinos; Karniadakis, George

We present a from-scratch development of OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment - simulating an entire mammal red blood cell lipid bilayer and cytoskeleton modeled by 4 million mesoscopic particles - on a single shared memory node. To achieve this, we invented an adaptive spatial searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse 3D space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation. The algorithm enables the construction of a lattice-free cell list, i.e. the key spatial searching data structure in our code, in O (N) time and space space with cells whose position and shape adapts automatically to the local density and curvature. The code implements NUMA/NUCA-aware OpenMP parallelization and achieves perfect scaling with up to hundreds of hardware threads. The code outperforms a legacy solver by more than 8 times in time-to-solution and more than 20 times in problem size, thus providing a new venue for probing the cytomechanics of red blood cells. This work was supported by the Department of Energy (DOE) Collaboratory on Mathematics for Mesoscopic Model- ing of Materials (CM4). YHT acknowledges partial financial support from an IBM Ph.D. Scholarship Award.

Communication: Anion-specific response of mesoscopic organization in ionic liquids upon pressurization

NASA Astrophysics Data System (ADS)

Lo Celso, Fabrizio; Triolo, Alessandro; Gontrani, Lorenzo; Russina, Olga

2018-06-01

One of the outstanding features of ionic liquids is their inherently hierarchical structural organization at mesoscopic spatial scales. Recently experimental and computational studies showed the fading of this feature when pressurising. Here we use simulations to show that this effect is not general: appropriate anion choice leads to an obstinate resistance against pressurization.

Viscoelastic representation of surface waves in patchy saturated poroelastic media

NASA Astrophysics Data System (ADS)

Zhang, Yu; Xu, Yixian; Xia, Jianghai; Ping, Ping; Zhang, Shuangxi

2014-08-01

Wave-induced flow is observed as the dominated factor for P wave propagation at seismic frequencies. This mechanism has a mesoscopic scale nature. The inhomogeneous unsaturated patches are regarded larger than the pore size, but smaller than the wavelength. Surface wave, e.g., Rayleigh wave, which propagates along the free surface, generated by the interfering of body waves is also affected by the mesoscopic loss mechanisms. Recent studies have reported that the effect of the wave-induced flow in wave propagation shows a relaxation behavior. Viscoelastic equivalent relaxation function associated with the wave mode can describe the kinetic nature of the attenuation. In this paper, the equivalent viscoelastic relaxation functions are extended to take into account the free surface for the Rayleigh surface wave propagation in patchy saturated poroelastic media. Numerical results for the frequency-dependent velocity and attenuation and the time-dependent dynamical responses for the equivalent Rayleigh surface wave propagation along an interface between vacuum and patchy saturated porous media are reported in the low-frequency range (0.1-1,000 Hz). The results show that the dispersion and attenuation and kinetic characteristics of the mesoscopic loss effect for the surface wave can be effectively represented in the equivalent viscoelastic media. The simulation of surface wave propagation within mesoscopic patches requires solving Biot's differential equations in very small grid spaces, involving the conversion of the fast P wave energy diffusion into the Biot slow wave. This procedure requires a very large amount of computer consumption. An efficient equivalent approach for this patchy saturated poroelastic media shows a more convenient way to solve the single phase viscoelastic differential equations.

Mesoscopic interactions and species coexistence in evolutionary game dynamics of cyclic competitions.

PubMed

Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

2014-12-15

Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species.

A Lattice-Boltzmann model to simulate diffractive nonlinear ultrasound beam propagation in a dissipative fluid medium

NASA Astrophysics Data System (ADS)

Abdi, Mohamad; Hajihasani, Mojtaba; Gharibzadeh, Shahriar; Tavakkoli, Jahan

2012-12-01

Ultrasound waves have been widely used in diagnostic and therapeutic medical applications. Accurate and effective simulation of ultrasound beam propagation and its interaction with tissue has been proved to be important. The nonlinear nature of the ultrasound beam propagation, especially in the therapeutic regime, plays an important role in the mechanisms of interaction with tissue. There are three main approaches in current computational fluid dynamics (CFD) methods to model and simulate nonlinear ultrasound beams: macroscopic, mesoscopic and microscopic approaches. In this work, a mesoscopic CFD method based on the Lattice-Boltzmann model (LBM) was investigated. In the developed method, the Boltzmann equation is evolved to simulate the flow of a Newtonian fluid with the collision model instead of solving the Navier-Stokes, continuity and state equations which are used in conventional CFD methods. The LBM has some prominent advantages over conventional CFD methods, including: (1) its parallel computational nature; (2) taking microscopic boundaries into account; and (3) capability of simulating in porous and inhomogeneous media. In our proposed method, the propagating medium is discretized with a square grid in 2 dimensions with 9 velocity vectors for each node. Using the developed model, the nonlinear distortion and shock front development of a finiteamplitude diffractive ultrasonic beam in a dissipative fluid medium was computed and validated against the published data. The results confirm that the LBM is an accurate and effective approach to model and simulate nonlinearity in finite-amplitude ultrasound beams with Mach numbers of up to 0.01 which, among others, falls within the range of therapeutic ultrasound regime such as high intensity focused ultrasound (HIFU) beams. A comparison between the HIFU nonlinear beam simulations using the proposed model and pseudospectral methods in a 2D geometry is presented.

A mesoscopic approach for draping simulation of preforms manufactured by direct fibre placement

NASA Astrophysics Data System (ADS)

Engelfried, Mathias; Fial, Julian; Tartler, Manuel; Böhler, Patrick; Hägele, Dominik; Middendorf, Peter

2017-10-01

The draping of preforms made by automated fibre placement is a suitable way to generate complex, three-dimensional preforms. The absence of weaving or sewing yarns leads to a high tendency towards defects, such as gaps. To predict those defects a detailed simulation model of the material is necessary. This work deals with a method to describe the inter-ply friction of preforms that consists of carbon fibre yarns joined by a thermoplastic binder. Therefore, a friction model which is customised to the partial presence of molten binder is proposed. This model is used in a mesoscopic draping simulation and is validated by draping experiments.

Entropy production in mesoscopic stochastic thermodynamics: nonequilibrium kinetic cycles driven by chemical potentials, temperatures, and mechanical forces

NASA Astrophysics Data System (ADS)

Qian, Hong; Kjelstrup, Signe; Kolomeisky, Anatoly B.; Bedeaux, Dick

2016-04-01

Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport, diffusion, thermochemical, thermomechanical and mechanochemical fluxes. In the present review, we introduce a mesoscopic stochastic formulation of NET by analyzing entropy production in several simple examples. The fundamental role of nonequilibrium steady-state cycle kinetics is emphasized. The statistical mechanics of Onsager’s reciprocal relations in this context is elucidated. Chemomechanical, thermomechanical, and enzyme-catalyzed thermochemical energy transduction processes are discussed. It is argued that mesoscopic stochastic NET in phase space provides a rigorous mathematical basis of fundamental concepts needed for understanding complex processes in chemistry, physics and biology. This theory is also relevant for nanoscale technological advances.

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

PubMed

Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Scheraga, Harold A

2009-03-10

The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster.

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

PubMed Central

Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Scheraga, Harold A.

2009-01-01

The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster. PMID:20161452

Simulating immiscible multi-phase flow and wetting with 3D stochastic rotation dynamics (SRD)

NASA Astrophysics Data System (ADS)

Hiller, Thomas; Sanchez de La Lama, Marta; Herminghaus, Stephan; Brinkmann, Martin

2013-11-01

We use a variant of the mesoscopic particle method stochastic rotation dynamics (SRD) to simulate immiscible multi-phase flow on the pore and sub-pore scale in three dimensions. As an extension to the multi-color SRD method, first proposed by Inoue et al., we present an implementation that accounts for complex wettability on heterogeneous surfaces. In order to demonstrate the versatility of this algorithm, we consider immiscible two-phase flow through a model porous medium (disordered packing of spherical beads) where the substrate exhibits different spatial wetting patterns. We show that these patterns have a significant effect on the interface dynamics. Furthermore, the implementation of angular momentum conservation into the SRD algorithm allows us to extent the applicability of SRD also to micro-fluidic systems. It is now possible to study e.g. the internal flow behaviour of a droplet depending on the driving velocity of the surrounding bulk fluid or the splitting of droplets by an obstacle.

Numerical modeling of interface displacement in heterogeneously wetting porous media

NASA Astrophysics Data System (ADS)

Hiller, T.; Brinkmann, M.; Herminghaus, S.

2013-12-01

We use the mesoscopic particle method stochastic rotation dynamics (SRD) to simulate immiscible multi-phase flow on the pore and sub-pore scale in three dimensions. As an extension to the standard SRD method, we present an approach on implementing complex wettability on heterogeneous surfaces. We use 3D SRD to simulate immiscible two-phase flow through a model porous medium (disordered packing of spherical beads) where the substrate exhibits different spatial wetting patterns. The simulations are designed to resemble experimental measurements of capillary pressure saturation. We show that the correlation length of the wetting patterns influences the temporal evolution of the interface and thus percolation, residual saturation and work dissipated during the fluid displacement. Our numerical results are in qualitatively good agreement with the experimental data. Besides of modeling flow in porous media, our SRD implementation allows us to address various questions of interfacial dynamics, e.g. the formation of capillary bridges between spherical beads or droplets in microfluidic applications to name only a few.

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity

PubMed Central

Liang, Jie; Qian, Hong

2010-01-01

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand “complex behavior” and complexity theory, and from which important biological insight can be gained. PMID:24999297

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity.

PubMed

Liang, Jie; Qian, Hong

2010-01-01

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand "complex behavior" and complexity theory, and from which important biological insight can be gained.

Dissipative particle dynamics of diffusion-NMR requires high Schmidt-numbers

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

Azhar, Mueed; Greiner, Andreas; Korvink, Jan G., E-mail: jan.korvink@kit.edu, E-mail: david.kauzlaric@imtek.uni-freiburg.de

We present an efficient mesoscale model to simulate the diffusion measurement with nuclear magnetic resonance (NMR). On the level of mesoscopic thermal motion of fluid particles, we couple the Bloch equations with dissipative particle dynamics (DPD). Thereby we establish a physically consistent scaling relation between the diffusion constant measured for DPD-particles and the diffusion constant of a real fluid. The latter is based on a splitting into a centre-of-mass contribution represented by DPD, and an internal contribution which is not resolved in the DPD-level of description. As a consequence, simulating the centre-of-mass contribution with DPD requires high Schmidt numbers. Aftermore » a verification for fundamental pulse sequences, we apply the NMR-DPD method to NMR diffusion measurements of anisotropic fluids, and of fluids restricted by walls of microfluidic channels. For the latter, the free diffusion and the localisation regime are considered.« less

"Active" drops as phantom models for living cells: a mesoscopic particle-based approach.

PubMed

Dallavalle, Marco; Lugli, Francesca; Rapino, Stefania; Zerbetto, Francesco

2016-04-21

Drops and biological cells share some morphological features and visco-elastic properties. The modelling of drops by mesoscopic non-atomistic models has been carried out to a high degree of success in recent years. We extend such treatment and discuss a simple, drop-like model to describe the interactions of the outer layer of cells with the surfaces of materials. Cells are treated as active mechanical objects that are able to generate adhesion forces. They appear with their true size and are made of "parcels of fluids" or beads. The beads are described by (very) few quantities/parameters related to fundamental chemical forces such as hydrophilicity and lipophilicity that represent an average of the properties of a patch of material or an area of the cell(s) surface. The investigation of adhesion dynamics, motion of individual cells, and the collective behavior of clusters of cells on materials is possible. In the simulations, the drops become active soft matter objects and different from regular droplets they do not fuse when in contact, their trajectories are not Brownian, and they can be forced "to secrete" molecules, to name some of the properties targeted by the modeling. The behavior that emerges from the simulations allows ascribing some cell properties to their mechanics, which are related to their biological features.

Many-Body Effects in the Mesoscopic x-Ray Edge Problem

NASA Astrophysics Data System (ADS)

Hentschel, M.; R"Oder, G.; Ullmo, D.

Many-body phenomena, a key interest in the investigation ofbulk solid state systems, are studied here in the context of the x-ray edge problem for mesoscopic systems. We investigate the many-body effects associated with the sudden perturbation following the x-ray excition of a core electron into the conduction band. For small systems with dimensions at the nanoscale we find considerable deviations from the well-understood metallic case where Anderson orthogonality catastrophe and the Mahan-Nozières-DeDominicis response cause characteristic deviations of the photoabsorption cross section from the naive expectation. Whereas the K-edge is typically rounded in metallic systems, we find a slightly peaked K-edge in generic mesoscopic systems with chaotic-coherent electron dynamics. Thus the behavior of the photoabsorption cross section at threshold depends on the system size and is different for the metallic and the mesoscopic case.

Tunable quasiparticle trapping in Meissner and vortex states of mesoscopic superconductors.

PubMed

Taupin, M; Khaymovich, I M; Meschke, M; Mel'nikov, A S; Pekola, J P

2016-03-16

Nowadays, superconductors serve in numerous applications, from high-field magnets to ultrasensitive detectors of radiation. Mesoscopic superconducting devices, referring to those with nanoscale dimensions, are in a special position as they are easily driven out of equilibrium under typical operating conditions. The out-of-equilibrium superconductors are characterized by non-equilibrium quasiparticles. These extra excitations can compromise the performance of mesoscopic devices by introducing, for example, leakage currents or decreased coherence time in quantum devices. By applying an external magnetic field, one can conveniently suppress or redistribute the population of excess quasiparticles. In this article, we present an experimental demonstration and a theoretical analysis of such effective control of quasiparticles, resulting in electron cooling both in the Meissner and vortex states of a mesoscopic superconductor. We introduce a theoretical model of quasiparticle dynamics, which is in quantitative agreement with the experimental data.

Tunable quasiparticle trapping in Meissner and vortex states of mesoscopic superconductors

PubMed Central

Taupin, M.; Khaymovich, I. M.; Meschke, M.; Mel'nikov, A. S.; Pekola, J. P.

2016-01-01

Nowadays, superconductors serve in numerous applications, from high-field magnets to ultrasensitive detectors of radiation. Mesoscopic superconducting devices, referring to those with nanoscale dimensions, are in a special position as they are easily driven out of equilibrium under typical operating conditions. The out-of-equilibrium superconductors are characterized by non-equilibrium quasiparticles. These extra excitations can compromise the performance of mesoscopic devices by introducing, for example, leakage currents or decreased coherence time in quantum devices. By applying an external magnetic field, one can conveniently suppress or redistribute the population of excess quasiparticles. In this article, we present an experimental demonstration and a theoretical analysis of such effective control of quasiparticles, resulting in electron cooling both in the Meissner and vortex states of a mesoscopic superconductor. We introduce a theoretical model of quasiparticle dynamics, which is in quantitative agreement with the experimental data. PMID:26980225

Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations

NASA Astrophysics Data System (ADS)

Flegg, Mark B.; Hellander, Stefan; Erban, Radek

2015-05-01

In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a "ghost cell" in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: Δt → 0 and h is fixed; Δt → 0 and h → 0 such that √{ Δt } / h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.

Mesoscopic Physics of Electronic and Optical Systems

NASA Astrophysics Data System (ADS)

Hentschel, Martina

2005-10-01

The progress in fabricating and controlling mesoscopic samples opens the possibility to investigate many-body phenomena on the nanoscopic scale, for example in quantum dots or nanoparticles. We recently studied the many-body signatures in the photoabsorption cross-section of those systems. Two counteracting many-body effects (Anderson's orthogonality catastrophe and Mahan's exciton) lead to deviations from the naively expected cross-section and to Fermi-edge singularities in the form of a peaked or rounded edge. We found that mesoscopic-coherent systems can show a many-body response that differs considerably from macroscopic samples. The reason for this lies in the finite number of particles and the lack of rotational symmetry in generic mesoscopic systems. The properties of mesoscopic systems crucially depend on whether the corresponding classical systems possess chaotic or integrable dynamics. Signatures of the underlying classical dynamics in quantum-mechanical behavior are searched for in the field of quantum chaos. We study it in the context of optical microresonators-billiards where reflection at hard walls is replaced by confinement due to total internal reflection. The relation between the simple ray model and the wave description (that has to be used when the wavelength becomes comparable to the system size) is called ``ray-wave correspondence.'' It can be established in both real and phase space. For the latter we generalized the concept of Husimi functions to dielectric boundaries. Although the ray model provides a qualitative understanding of the system properties even into the wave limit, semiclassical corrections of the ray picture are necessary in order to establish quantitative correspondence.

Direct experimental observation of mesoscopic fluorous domains in fluorinated room temperature ionic liquids

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

Lo Celso, F.; Yoshida, Y.; Castiglione, F.

Fluorinated room temperature ionic liquids (FRTILs) represent a class of solvent media that are attracting great attention due to their IL-specific properties as well as features stemming from their fluorous nature. Medium-to-long fluorous tails constitute a well-defined apolar moiety in the otherwise polar environment. Similarly to the case of alkyl tails, such chains are expected to result in the formation of self-assembled fluorous domains. So far, however, no direct experimental observation has been made of the existence of such structural heterogeneities on the nm scale. We report here the first experimental evidence of the existence of mesoscopic spatial segregation ofmore » fluorinated domains, on the basis of highly complementary X-ray and neutron scattering data sets (highlighting the importance of the latter probe) and NMR spectroscopy. Data are interpreted using atomistic molecular dynamics simulations, emphasizing the existence of a self-assembly mechanism that delivers segregated fluorous domains, where preferential solubilisation of fluorinated compounds can occur, thus paving the way for several smart applications.« less

The Complexity of Dynamics in Small Neural Circuits

PubMed Central

Panzeri, Stefano

2016-01-01

Mean-field approximations are a powerful tool for studying large neural networks. However, they do not describe well the behavior of networks composed of a small number of neurons. In this case, major differences between the mean-field approximation and the real behavior of the network can arise. Yet, many interesting problems in neuroscience involve the study of mesoscopic networks composed of a few tens of neurons. Nonetheless, mathematical methods that correctly describe networks of small size are still rare, and this prevents us to make progress in understanding neural dynamics at these intermediate scales. Here we develop a novel systematic analysis of the dynamics of arbitrarily small networks composed of homogeneous populations of excitatory and inhibitory firing-rate neurons. We study the local bifurcations of their neural activity with an approach that is largely analytically tractable, and we numerically determine the global bifurcations. We find that for strong inhibition these networks give rise to very complex dynamics, caused by the formation of multiple branching solutions of the neural dynamics equations that emerge through spontaneous symmetry-breaking. This qualitative change of the neural dynamics is a finite-size effect of the network, that reveals qualitative and previously unexplored differences between mesoscopic cortical circuits and their mean-field approximation. The most important consequence of spontaneous symmetry-breaking is the ability of mesoscopic networks to regulate their degree of functional heterogeneity, which is thought to help reducing the detrimental effect of noise correlations on cortical information processing. PMID:27494737

Static and dynamic properties of smoothed dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Alizadehrad, Davod; Fedosov, Dmitry A.

2018-03-01

In this paper, static and dynamic properties of the smoothed dissipative particle dynamics (SDPD) method are investigated. We study the effect of method parameters on SDPD fluid properties, such as structure, speed of sound, and transport coefficients, and show that a proper choice of parameters leads to a well-behaved and accurate fluid model. In particular, the speed of sound, the radial distribution function (RDF), shear-thinning of viscosity, the mean-squared displacement (〈R2 〉 ∝ t), and the Schmidt number (Sc ∼ O (103) - O (104)) can be controlled, such that the model exhibits a fluid-like behavior for a wide range of temperatures in simulations. Furthermore, in addition to the consideration of fluid density variations for fluid compressibility, a more challenging test of incompressibility is performed by considering the Poisson ratio and divergence of velocity field in an elongational flow. Finally, as an example of complex-fluid flow, we present the applicability and validity of the SDPD method with an appropriate choice of parameters for the simulation of cellular blood flow in irregular geometries. In conclusion, the results demonstrate that the SDPD method is able to approximate well a nearly incompressible fluid behavior, which includes hydrodynamic interactions and consistent thermal fluctuations, thereby providing, a powerful approach for simulations of complex mesoscopic systems.

Multiscale Analysis of Structurally-Graded Microstructures Using Molecular Dynamics, Discrete Dislocation Dynamics and Continuum Crystal Plasticity

NASA Technical Reports Server (NTRS)

Saether, Erik; Hochhalter, Jacob D.; Glaessgen, Edward H.; Mishin, Yuri

2014-01-01

A multiscale modeling methodology is developed for structurally-graded material microstructures. Molecular dynamic (MD) simulations are performed at the nanoscale to determine fundamental failure mechanisms and quantify material constitutive parameters. These parameters are used to calibrate material processes at the mesoscale using discrete dislocation dynamics (DD). Different grain boundary interactions with dislocations are analyzed using DD to predict grain-size dependent stress-strain behavior. These relationships are mapped into crystal plasticity (CP) parameters to develop a computationally efficient finite element-based DD/CP model for continuum-level simulations and complete the multiscale analysis by predicting the behavior of macroscopic physical specimens. The present analysis is focused on simulating the behavior of a graded microstructure in which grain sizes are on the order of nanometers in the exterior region and transition to larger, multi-micron size in the interior domain. This microstructural configuration has been shown to offer improved mechanical properties over homogeneous coarse-grained materials by increasing yield stress while maintaining ductility. Various mesoscopic polycrystal models of structurally-graded microstructures are generated, analyzed and used as a benchmark for comparison between multiscale DD/CP model and DD predictions. A final series of simulations utilize the DD/CP analysis method exclusively to study macroscopic models that cannot be analyzed by MD or DD methods alone due to the model size.

Nonlinear Acoustic Experiments Involving Landmine Detection: Connections with Mesoscopic Elasticity and Slow Dynamics in Geomaterials

NASA Astrophysics Data System (ADS)

Korman, Murray S.; Sabatier, James M.

2006-05-01

The vibration interaction between the top-plate of a buried VS 2.2 plastic, anti-tank landmine and the soil above it appears to exhibit similar characteristics to the nonlinear mesoscopic/nanoscale effects that are observed in geomaterials like rocks or granular materials. [J. Acoust. Soc. Am. 116, 3354-3369 (2004)]. When airborne sound at two primary frequencies f1 and f2 (closely spaced near resonance) undergo acoustic-to-seismic coupling, (A/S), interactions with the mine and soil generate combination frequencies | n f1 ± m f2 | which affect the surface vibration velocity. Profiles at f1, f2, f1 -(f2 - f1) and f2 +(f2 - f1) exhibit single peaks whereas other combination frequencies may involve higher order modes. A family of increasing amplitude tuning curves, involving the surface vibration over the landmine, exhibits a linear relationship between the peak particle velocity and corresponding resonant frequency. Subsequent decreasing amplitude tuning curves exhibit hysteresis effects. New experiments for a buried VS 1.6 anti-tank landmine and a "plastic drum head" mine simulant behave similarly. Slow dynamics explains the amplitude difference in tuning curves for first sweeping upward and then downward through resonance, provided the soil modulus drops after periods of high strain. [Support by U.S. Army RDECOM CERDEC, NVESD, Fort Belvoir, VA.

Controlling the quantum dynamics of a mesoscopic spin bath in diamond

PubMed Central

de Lange, Gijs; van der Sar, Toeno; Blok, Machiel; Wang, Zhi-Hui; Dobrovitski, Viatcheslav; Hanson, Ronald

2012-01-01

Understanding and mitigating decoherence is a key challenge for quantum science and technology. The main source of decoherence for solid-state spin systems is the uncontrolled spin bath environment. Here, we demonstrate quantum control of a mesoscopic spin bath in diamond at room temperature that is composed of electron spins of substitutional nitrogen impurities. The resulting spin bath dynamics are probed using a single nitrogen-vacancy (NV) centre electron spin as a magnetic field sensor. We exploit the spin bath control to dynamically suppress dephasing of the NV spin by the spin bath. Furthermore, by combining spin bath control with dynamical decoupling, we directly measure the coherence and temporal correlations of different groups of bath spins. These results uncover a new arena for fundamental studies on decoherence and enable novel avenues for spin-based magnetometry and quantum information processing. PMID:22536480

Effects of finite size on spin glass dynamics

NASA Astrophysics Data System (ADS)

Sato, Tetsuya; Komatsu, Katsuyoshi

2010-12-01

In spite of comprehensive studies to clarify a variety of interesting phenomena of spin glasses, their understanding has been insufficiently established. To overcome such a problem, fabrication of a mesoscopic spin glass system, whose dynamics can be observed over the entire range to the equilibrium, is useful. In this review the challenges of research that has been performed up to now in this direction and our recent related studies are introduced. We have established to study the spin glass behaviour in terms of droplet picture using nanofabricated mesoscopic samples to some extent, but some problems that should be clarified have been left. Finally, the direction of some new studies is proposed to solve the problems.

Computational Model of Population Dynamics Based on the Cell Cycle and Local Interactions

NASA Astrophysics Data System (ADS)

Oprisan, Sorinel Adrian; Oprisan, Ana

2005-03-01

Our study bridges cellular (mesoscopic) level interactions and global population (macroscopic) dynamics of carcinoma. The morphological differences and transitions between well and smooth defined benign tumors and tentacular malignat tumors suggest a theoretical analysis of tumor invasion based on the development of mathematical models exhibiting bifurcations of spatial patterns in the density of tumor cells. Our computational model views the most representative and clinically relevant features of oncogenesis as a fight between two distinct sub-systems: the immune system of the host and the neoplastic system. We implemented the neoplastic sub-system using a three-stage cell cycle: active, dormant, and necrosis. The second considered sub-system consists of cytotoxic active (effector) cells — EC, with a very broad phenotype ranging from NK cells to CTL cells, macrophages, etc. Based on extensive numerical simulations, we correlated the fractal dimensions for carcinoma, which could be obtained from tumor imaging, with the malignat stage. Our computational model was able to also simulate the effects of surgical, chemotherapeutical, and radiotherapeutical treatments.

Particle Based Simulations of Complex Systems with MP2C : Hydrodynamics and Electrostatics

NASA Astrophysics Data System (ADS)

Sutmann, Godehard; Westphal, Lidia; Bolten, Matthias

2010-09-01

Particle based simulation methods are well established paths to explore system behavior on microscopic to mesoscopic time and length scales. With the development of new computer architectures it becomes more and more important to concentrate on local algorithms which do not need global data transfer or reorganisation of large arrays of data across processors. This requirement strongly addresses long-range interactions in particle systems, i.e. mainly hydrodynamic and electrostatic contributions. In this article, emphasis is given to the implementation and parallelization of the Multi-Particle Collision Dynamics method for hydrodynamic contributions and a splitting scheme based on Multigrid for electrostatic contributions. Implementations are done for massively parallel architectures and are demonstrated for the IBM Blue Gene/P architecture Jugene in Jülich.

Adaptive resolution simulation of an atomistic protein in MARTINI water

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

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

2014-02-07

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

Adaptive resolution simulation of an atomistic protein in MARTINI water.

PubMed

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

2014-02-07

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

Mesoscopic modeling and parameter estimation of a lithium-ion battery based on LiFePO4/graphite

NASA Astrophysics Data System (ADS)

Jokar, Ali; Désilets, Martin; Lacroix, Marcel; Zaghib, Karim

2018-03-01

A novel numerical model for simulating the behavior of lithium-ion batteries based on LiFePO4(LFP)/graphite is presented. The model is based on the modified Single Particle Model (SPM) coupled to a mesoscopic approach for the LFP electrode. The model comprises one representative spherical particle as the graphite electrode, and N LFP units as the positive electrode. All the SPM equations are retained to model the negative electrode performance. The mesoscopic model rests on non-equilibrium thermodynamic conditions and uses a non-monotonic open circuit potential for each unit. A parameter estimation study is also carried out to identify all the parameters needed for the model. The unknown parameters are the solid diffusion coefficient of the negative electrode (Ds,n), reaction-rate constant of the negative electrode (Kn), negative and positive electrode porosity (εn&εn), initial State-Of-Charge of the negative electrode (SOCn,0), initial partial composition of the LFP units (yk,0), minimum and maximum resistance of the LFP units (Rmin&Rmax), and solution resistance (Rcell). The results show that the mesoscopic model can simulate successfully the electrochemical behavior of lithium-ion batteries at low and high charge/discharge rates. The model also describes adequately the lithiation/delithiation of the LFP particles, however, it is computationally expensive compared to macro-based models.

Postcoalescence evolution of growth stress in polycrystalline films.

PubMed

González-González, A; Polop, C; Vasco, E

2013-02-01

The growth stress generated once grains coalesce in Volmer-Weber-type thin films is investigated by time-multiscale simulations comprising complementary modules of (i) finite-element modeling to address the interactions between grains happening at atomic vibration time scales (~0.1 ps), (ii) dynamic scaling to account for the surface stress relaxation via morphology changes at surface diffusion time scales (~μs-ms), and (iii) the mesoscopic rate equation approach to simulate the bulk stress relaxation at deposition time scales (~sec-h). On the basis of addressing the main experimental evidence reported so far on the topic dealt with, the simulation results provide key findings concerning the interplay between anisotropic grain interactions at complementary space scales, deposition conditions (such as flux and mobility), and mechanisms of stress accommodation-relaxation, which underlies the origin, nature and spatial distribution, and the flux dependence of the postcoalescence growth stress.

Thermally induced magnetic relaxation in square artificial spin ice.

PubMed

Andersson, M S; Pappas, S D; Stopfel, H; Östman, E; Stein, A; Nordblad, P; Mathieu, R; Hjörvarsson, B; Kapaklis, V

2016-11-24

The properties of natural and artificial assemblies of interacting elements, ranging from Quarks to Galaxies, are at the heart of Physics. The collective response and dynamics of such assemblies are dictated by the intrinsic dynamical properties of the building blocks, the nature of their interactions and topological constraints. Here we report on the relaxation dynamics of the magnetization of artificial assemblies of mesoscopic spins. In our model nano-magnetic system - square artificial spin ice - we are able to control the geometrical arrangement and interaction strength between the magnetically interacting building blocks by means of nano-lithography. Using time resolved magnetometry we show that the relaxation process can be described using the Kohlrausch law and that the extracted temperature dependent relaxation times of the assemblies follow the Vogel-Fulcher law. The results provide insight into the relaxation dynamics of mesoscopic nano-magnetic model systems, with adjustable energy and time scales, and demonstrates that these can serve as an ideal playground for the studies of collective dynamics and relaxations.

Thermally induced magnetic relaxation in square artificial spin ice

NASA Astrophysics Data System (ADS)

Andersson, M. S.; Pappas, S. D.; Stopfel, H.; Östman, E.; Stein, A.; Nordblad, P.; Mathieu, R.; Hjörvarsson, B.; Kapaklis, V.

2016-11-01

The properties of natural and artificial assemblies of interacting elements, ranging from Quarks to Galaxies, are at the heart of Physics. The collective response and dynamics of such assemblies are dictated by the intrinsic dynamical properties of the building blocks, the nature of their interactions and topological constraints. Here we report on the relaxation dynamics of the magnetization of artificial assemblies of mesoscopic spins. In our model nano-magnetic system - square artificial spin ice - we are able to control the geometrical arrangement and interaction strength between the magnetically interacting building blocks by means of nano-lithography. Using time resolved magnetometry we show that the relaxation process can be described using the Kohlrausch law and that the extracted temperature dependent relaxation times of the assemblies follow the Vogel-Fulcher law. The results provide insight into the relaxation dynamics of mesoscopic nano-magnetic model systems, with adjustable energy and time scales, and demonstrates that these can serve as an ideal playground for the studies of collective dynamics and relaxations.

Local Chain Segregation and Entanglements in a Confined Polymer Melt

NASA Astrophysics Data System (ADS)

Lee, Nam-Kyung; Diddens, Diddo; Meyer, Hendrik; Johner, Albert

2017-02-01

The reptation mechanism, introduced by de Gennes and Edwards, where a polymer diffuses along a fluffy tube, defined by the constraints imposed by its surroundings, convincingly describes the relaxation of long polymers in concentrated solutions and melts. We propose that the scale for the tube diameter is set by local chain segregation, which we study analytically. We show that the concept of local segregation is especially operational for confined geometries, where segregation extends over mesoscopic domains, drastically reducing binary contacts, and provide an estimate of the entanglement length. Our predictions are quantitatively supported by extensive molecular dynamics simulations on systems consisting of long, entangled chains.

Definitions of state variables and state space for brain-computer interface : Part 2. Extraction and classification of feature vectors.

PubMed

Freeman, Walter J

2007-06-01

The hypothesis is proposed that the central dynamics of the action-perception cycle has five steps: emergence from an existing macroscopic brain state of a pattern that predicts a future goal state; selection of a mesoscopic frame for action control; execution of a limb trajectory by microscopic spike activity; modification of microscopic cortical spike activity by sensory inputs; construction of mesoscopic perceptual patterns; and integration of a new macroscopic brain state. The basis is the circular causality between microscopic entities (neurons) and the mesoscopic and macroscopic entities (populations) self-organized by axosynaptic interactions. Self-organization of neural activity is bidirectional in all cortices. Upwardly the organization of mesoscopic percepts from microscopic spike input predominates in primary sensory areas. Downwardly the organization of spike outputs that direct specific limb movements is by mesoscopic fields constituting plans to achieve predicted goals. The mesoscopic fields in sensory and motor cortices emerge as frames within macroscopic activity. Part 1 describes the action-perception cycle and its derivative reflex arc qualitatively. Part 2 describes the perceptual limb of the arc from microscopic MSA to mesoscopic wave packets, and from these to macroscopic EEG and global ECoG fields that express experience-dependent knowledge in successive states. These macroscopic states are conceived to embed and control mesoscopic frames in premotor and motor cortices that are observed in local ECoG and LFP of frontoparietal areas. The fields sampled by ECoG and LFP are conceived as local patterns of neural activity in which trajectories of multiple spike activities (MSA) emerge that control limb movements. Mesoscopic frames are located by use of the analytic signal from the Hilbert transform after band pass filtering. The state variables in frames are measured to construct feature vectors by which to describe and classify frame patterns. Evidence is cited to justify use of linear analysis. The aim of the review is to enable researchers to conceive and identify goal-oriented states in brain activity for use as commands, in order to relegate the details of execution to adaptive control devices outside the brain.

Graphene Foam: Uniaxial Tension Behavior and Fracture Mode Based on a Mesoscopic Model.

PubMed

Pan, Douxing; Wang, Chao; Wang, Tzu-Chiang; Yao, Yugui

2017-09-26

Because of the combined advantages of both porous materials and two-dimensional (2D) graphene sheets, superior mechanical properties of three-dimensional (3D) graphene foams have received much attention from material scientists and energy engineers. Here, a 2D mesoscopic graphene model (Modell. Simul. Mater. Sci. Eng. 2011, 19, 054003), was expanded into a 3D bonded graphene foam system by utilizing physical cross-links and van der Waals forces acting among different mesoscopic graphene flakes by considering the debonding behavior, to evaluate the uniaxial tension behavior and fracture mode based on in situ SEM tensile testing (Carbon 2015, 85, 299). We reasonably reproduced a multipeak stress-strain relationship including its obvious yielding plateau and a ductile fracture mode near 45° plane from the tensile direction including the corresponding fracture morphology. Then, a power scaling law of tensile elastic modulus with mass density and an anisotropic strain-dependent Poisson's ratio were both deduced. The mesoscopic physical mechanism of tensile deformation was clearly revealed through the local stress state and evolution of mesostructure. The fracture feature of bonded graphene foam and its thermodynamic state were directly navigated to the tearing pattern of mesoscopic graphene flakes. This study provides an effective way to understand the mesoscopic physical nature of 3D graphene foams, and hence it may contribute to the multiscale computations of micro/meso/macromechanical performances and optimal design of advanced graphene-foam-based materials.

Ballistic Resistance of Honeycomb Sandwich Panels under In-Plane High-Velocity Impact

PubMed Central

Yang, Shu; Wang, Dong; Yang, Li-Jun

2013-01-01

The dynamic responses of honeycomb sandwich panels (HSPs) subjected to in-plane projectile impact were studied by means of explicit nonlinear finite element simulations using LS-DYNA. The HSPs consisted of two identical aluminum alloy face-sheets and an aluminum honeycomb core featuring three types of unit cell configurations (regular, rectangular-shaped, and reentrant hexagons). The ballistic resistances of HSPs with the three core configurations were first analyzed. It was found that the HSP with the reentrant auxetic honeycomb core has the best ballistic resistance, due to the negative Poisson's ratio effect of the core. Parametric studies were then carried out to clarify the influences of both macroscopic (face-sheet and core thicknesses, core relative density) and mesoscopic (unit cell angle and size) parameters on the ballistic responses of the auxetic HSPs. Numerical results show that the perforation resistant capabilities of the auxetic HSPs increase as the values of the macroscopic parameters increase. However, the mesoscopic parameters show nonmonotonic effects on the panels' ballistic capacities. The empirical equations for projectile residual velocities were formulated in terms of impact velocity and the structural parameters. It was also found that the blunter projectiles result in higher ballistic limits of the auxetic HSPs. PMID:24187526

Ballistic resistance of honeycomb sandwich panels under in-plane high-velocity impact.

PubMed

Qi, Chang; Yang, Shu; Wang, Dong; Yang, Li-Jun

2013-01-01

The dynamic responses of honeycomb sandwich panels (HSPs) subjected to in-plane projectile impact were studied by means of explicit nonlinear finite element simulations using LS-DYNA. The HSPs consisted of two identical aluminum alloy face-sheets and an aluminum honeycomb core featuring three types of unit cell configurations (regular, rectangular-shaped, and reentrant hexagons). The ballistic resistances of HSPs with the three core configurations were first analyzed. It was found that the HSP with the reentrant auxetic honeycomb core has the best ballistic resistance, due to the negative Poisson's ratio effect of the core. Parametric studies were then carried out to clarify the influences of both macroscopic (face-sheet and core thicknesses, core relative density) and mesoscopic (unit cell angle and size) parameters on the ballistic responses of the auxetic HSPs. Numerical results show that the perforation resistant capabilities of the auxetic HSPs increase as the values of the macroscopic parameters increase. However, the mesoscopic parameters show nonmonotonic effects on the panels' ballistic capacities. The empirical equations for projectile residual velocities were formulated in terms of impact velocity and the structural parameters. It was also found that the blunter projectiles result in higher ballistic limits of the auxetic HSPs.

Mesoscopic Effects in an Agent-Based Bargaining Model in Regular Lattices

PubMed Central

Poza, David J.; Santos, José I.; Galán, José M.; López-Paredes, Adolfo

2011-01-01

The effect of spatial structure has been proved very relevant in repeated games. In this work we propose an agent based model where a fixed finite population of tagged agents play iteratively the Nash demand game in a regular lattice. The model extends the multiagent bargaining model by Axtell, Epstein and Young [1] modifying the assumption of global interaction. Each agent is endowed with a memory and plays the best reply against the opponent's most frequent demand. We focus our analysis on the transient dynamics of the system, studying by computer simulation the set of states in which the system spends a considerable fraction of the time. The results show that all the possible persistent regimes in the global interaction model can also be observed in this spatial version. We also find that the mesoscopic properties of the interaction networks that the spatial distribution induces in the model have a significant impact on the diffusion of strategies, and can lead to new persistent regimes different from those found in previous research. In particular, community structure in the intratype interaction networks may cause that communities reach different persistent regimes as a consequence of the hindering diffusion effect of fluctuating agents at their borders. PMID:21408019

Mesoscopic effects in an agent-based bargaining model in regular lattices.

PubMed

Poza, David J; Santos, José I; Galán, José M; López-Paredes, Adolfo

2011-03-09

The effect of spatial structure has been proved very relevant in repeated games. In this work we propose an agent based model where a fixed finite population of tagged agents play iteratively the Nash demand game in a regular lattice. The model extends the multiagent bargaining model by Axtell, Epstein and Young modifying the assumption of global interaction. Each agent is endowed with a memory and plays the best reply against the opponent's most frequent demand. We focus our analysis on the transient dynamics of the system, studying by computer simulation the set of states in which the system spends a considerable fraction of the time. The results show that all the possible persistent regimes in the global interaction model can also be observed in this spatial version. We also find that the mesoscopic properties of the interaction networks that the spatial distribution induces in the model have a significant impact on the diffusion of strategies, and can lead to new persistent regimes different from those found in previous research. In particular, community structure in the intratype interaction networks may cause that communities reach different persistent regimes as a consequence of the hindering diffusion effect of fluctuating agents at their borders.

Cavity-assisted mesoscopic transport of fermions: Coherent and dissipative dynamics

NASA Astrophysics Data System (ADS)

Hagenmüller, David; Schütz, Stefan; Schachenmayer, Johannes; Genes, Claudiu; Pupillo, Guido

2018-05-01

We study the interplay between charge transport and light-matter interactions in a confined geometry by considering an open, mesoscopic chain of two-orbital systems resonantly coupled to a single bosonic mode close to its vacuum state. We introduce and benchmark different methods based on self-consistent solutions of nonequilibrium Green's functions and numerical simulations of the quantum master equation, and derive both analytical and numerical results. It is shown that in the dissipative regime where the cavity photon decay rate is the largest parameter, the light-matter coupling is responsible for a steady-state current enhancement scaling with the cooperativity parameter. We further identify different regimes of interest depending on the ratio between the cavity decay rate and the electronic bandwidth. Considering the situation where the lower band has a vanishing bandwidth, we show that for a high-finesse cavity, the properties of the resonant Bloch state in the upper band are transferred to the lower one, giving rise to a delocalized state along the chain. Conversely, in the dissipative regime with low-cavity quality factors, we find that the current enhancement is due to a collective decay of populations from the upper to the lower band.

Characterizing granular networks using topological metrics

NASA Astrophysics Data System (ADS)

Dijksman, Joshua A.; Kovalcinova, Lenka; Ren, Jie; Behringer, Robert P.; Kramar, Miroslav; Mischaikow, Konstantin; Kondic, Lou

2018-04-01

We carry out a direct comparison of experimental and numerical realizations of the exact same granular system as it undergoes shear jamming. We adjust the numerical methods used to optimally represent the experimental settings and outcomes up to microscopic contact force dynamics. Measures presented here range from microscopic through mesoscopic to systemwide characteristics of the system. Topological properties of the mesoscopic force networks provide a key link between microscales and macroscales. We report two main findings: (1) The number of particles in the packing that have at least two contacts is a good predictor for the mechanical state of the system, regardless of strain history and packing density. All measures explored in both experiments and numerics, including stress-tensor-derived measures and contact numbers depend in a universal manner on the fraction of nonrattler particles, fNR. (2) The force network topology also tends to show this universality, yet the shape of the master curve depends much more on the details of the numerical simulations. In particular we show that adding force noise to the numerical data set can significantly alter the topological features in the data. We conclude that both fNR and topological metrics are useful measures to consider when quantifying the state of a granular system.

cDF Theory Software for mesoscopic modeling of equilibrium and transport phenomena

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

2015-12-01

The approach is based on classical Density Functional Theory ((cDFT) coupled with the Poisson-Nernst-Planck (PNP) transport kinetics model and quantum mechanical description of short-range interaction and elementary transport processes. The model we proposed and implemented is fully atomistic, taking into account pairwise short-range and manybody long-range interactions. But in contrast to standard molecular dynamics (MD) simulations, where long-range manybody interactions are evaluated as a sum of pair-wise atom-atom contributions, we include them analytically based on wellestablished theories of electrostatic and excluded volume interactions in multicomponent systems. This feature of the PNP/cDFT approach allows us to reach well beyond the length-scalesmore » accessible to MD simulations, while retaining the essential physics of interatomic interactions from first principles and in a parameter-free fashion.« less

Alignment of cell division axes in directed epithelial cell migration

NASA Astrophysics Data System (ADS)

Marel, Anna-Kristina; Podewitz, Nils; Zorn, Matthias; Oskar Rädler, Joachim; Elgeti, Jens

2014-11-01

Cell division is an essential dynamic event in tissue remodeling during wound healing, cancer and embryogenesis. In collective migration, tensile stresses affect cell shape and polarity, hence, the orientation of the cell division axis is expected to depend on cellular flow patterns. Here, we study the degree of orientation of cell division axes in migrating and resting epithelial cell sheets. We use microstructured channels to create a defined scenario of directed cell invasion and compare this situation to resting but proliferating cell monolayers. In experiments, we find a strong alignment of the axis due to directed flow while resting sheets show very weak global order, but local flow gradients still correlate strongly with the cell division axis. We compare experimental results with a previously published mesoscopic particle based simulation model. Most of the observed effects are reproduced by the simulations.

Seismoelectric effects due to mesoscopic heterogeneities

NASA Astrophysics Data System (ADS)

Jougnot, Damien; Rubino, J. GermáN.; Carbajal, Marina Rosas; Linde, Niklas; Holliger, Klaus

2013-05-01

While the seismic effects of wave-induced fluid flow due to mesoscopic heterogeneities have been studied for several decades, the role played by these types of heterogeneities on seismoelectric phenomena is largely unexplored. To address this issue, we have developed a novel methodological framework which allows for the coupling of wave-induced fluid flow, as inferred through numerical oscillatory compressibility tests, with the pertinent seismoelectric conversion mechanisms. Simulating the corresponding response of a water-saturated sandstone sample containing mesoscopic fractures, we demonstrate for the first time that these kinds of heterogeneities can produce measurable seismoelectric signals under typical laboratory conditions. Given that this phenomenon is sensitive to key hydraulic and mechanical properties, we expect that the results of this pilot study will stimulate further exploration on this topic in several domains of the Earth, environmental, and engineering sciences.

Thermally induced magnetic relaxation in square artificial spin ice

DOE PAGES

Andersson, M. S.; Pappas, S. D.; Stopfel, H.; ...

2016-11-24

The properties of natural and artificial assemblies of interacting elements, ranging from Quarks to Galaxies, are at the heart of Physics. The collective response and dynamics of such assemblies are dictated by the intrinsic dynamical properties of the building blocks, the nature of their interactions and topological constraints. Here in this paper, we report on the relaxation dynamics of the magnetization of artificial assemblies of mesoscopic spins. In our model nano-magnetic system $-$ square artificial spin ice $-$ we are able to control the geometrical arrangement and interaction strength between the magnetically interacting building blocks by means of nano-lithography. Usingmore » time resolved magnetometry we show that the relaxation process can be described using the Kohlrausch law and that the extracted temperature dependent relaxation times of the assemblies follow the Vogel-Fulcher law. The results provide insight into the relaxation dynamics of mesoscopic nano-magnetic model systems, with adjustable energy and time scales, and demonstrates that these can serve as an ideal playground for the studies of collective dynamics and relaxations.« less

Thermally induced magnetic relaxation in square artificial spin ice

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

Andersson, M. S.; Pappas, S. D.; Stopfel, H.

The properties of natural and artificial assemblies of interacting elements, ranging from Quarks to Galaxies, are at the heart of Physics. The collective response and dynamics of such assemblies are dictated by the intrinsic dynamical properties of the building blocks, the nature of their interactions and topological constraints. Here in this paper, we report on the relaxation dynamics of the magnetization of artificial assemblies of mesoscopic spins. In our model nano-magnetic system $-$ square artificial spin ice $-$ we are able to control the geometrical arrangement and interaction strength between the magnetically interacting building blocks by means of nano-lithography. Usingmore » time resolved magnetometry we show that the relaxation process can be described using the Kohlrausch law and that the extracted temperature dependent relaxation times of the assemblies follow the Vogel-Fulcher law. The results provide insight into the relaxation dynamics of mesoscopic nano-magnetic model systems, with adjustable energy and time scales, and demonstrates that these can serve as an ideal playground for the studies of collective dynamics and relaxations.« less

Lattice Boltzmann model capable of mesoscopic vorticity computation

NASA Astrophysics Data System (ADS)

Peng, Cheng; Guo, Zhaoli; Wang, Lian-Ping

2017-11-01

It is well known that standard lattice Boltzmann (LB) models allow the strain-rate components to be computed mesoscopically (i.e., through the local particle distributions) and as such possess a second-order accuracy in strain rate. This is one of the appealing features of the lattice Boltzmann method (LBM) which is of only second-order accuracy in hydrodynamic velocity itself. However, no known LB model can provide the same quality for vorticity and pressure gradients. In this paper, we design a multiple-relaxation time LB model on a three-dimensional 27-discrete-velocity (D3Q27) lattice. A detailed Chapman-Enskog analysis is presented to illustrate all the necessary constraints in reproducing the isothermal Navier-Stokes equations. The remaining degrees of freedom are carefully analyzed to derive a model that accommodates mesoscopic computation of all the velocity and pressure gradients from the nonequilibrium moments. This way of vorticity calculation naturally ensures a second-order accuracy, which is also proven through an asymptotic analysis. We thus show, with enough degrees of freedom and appropriate modifications, the mesoscopic vorticity computation can be achieved in LBM. The resulting model is then validated in simulations of a three-dimensional decaying Taylor-Green flow, a lid-driven cavity flow, and a uniform flow passing a fixed sphere. Furthermore, it is shown that the mesoscopic vorticity computation can be realized even with single relaxation parameter.

On the crystallization of polymer composites with inorganic fullerene-like particles.

PubMed

Enyashin, Andrey N; Glazyrina, Polina Yu

2012-05-21

The effect of a sulfide fullerene-like particle embedded into a polymer has been studied by molecular dynamics simulations on the nanosecond time scale using a mesoscopic Van der Waals force field evaluated for the case of a spherical particle. Even in this approach, neglecting the atomistic features of the surface, the inorganic particle acts as a nucleation agent facilitating the crystallization of the polymeric sample. A consideration of the Van der Waals force field of multi-walled sulfide nanoparticles suggests that in the absence of chemical interactions the size of the nanoparticle is dominating for the adhesion strength, while the number of sulfide layers composing the cage does not play a role.

Theory of the Bloch oscillating transistor

NASA Astrophysics Data System (ADS)

Hassel, J.; Seppä, H.

2005-01-01

The Bloch oscillating transistor (BOT) is a device in which single electron current through a normal tunnel junction enhances Cooper pair current in a mesoscopic Josephson junction, leading to signal amplification. In this article we develop a theory in which the BOT dynamics is described as a two-level system. The theory is used to predict current-voltage characteristics and small-signal response. The transition from stable operation into the hysteretic regime is studied. By identifying the two-level switching noise as the main source of fluctuations, the expressions for equivalent noise sources and the noise temperature are derived. The validity of the model is tested by comparing the results with simulations and experiments.

MESOSCOPIC MODELING OF STOCHASTIC REACTION-DIFFUSION KINETICS IN THE SUBDIFFUSIVE REGIME

PubMed Central

BLANC, EMILIE; ENGBLOM, STEFAN; HELLANDER, ANDREAS; LÖTSTEDT, PER

2017-01-01

Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model of subdiffusion into an accurate and consistent reaction-subdiffusion computational framework. Two different possible models of chemical reaction are revealed and some basic dynamic properties are derived. In certain cases those mesoscopic models have a direct interpretation at the macroscopic level as fractional partial differential equations in a bounded time interval. Through analysis and numerical experiments we estimate the macroscopic effects of reactions under subdiffusive mixing. The models display properties observed also in experiments: for a short time interval the behavior of the diffusion and the reaction is ordinary, in an intermediate interval the behavior is anomalous, and at long times the behavior is ordinary again. PMID:29046618

Vortex-slip transitions in superconducting a-NbGe mesoscopic channels

NASA Astrophysics Data System (ADS)

Kokubo, N.; Sorop, T. G.; Besseling, R.; Kes, P. H.

2006-06-01

Intriguing and novel physical aspects related to the vortex flow dynamics have been recently observed in mesoscopic channel devices of a-NbGe with NbN channel edges. In this work we have systematically studied the flow properties of vortices confined in such mesoscopic channels as a function of the magnetic field history, using dc-transport and mode-locking (ML) measurements. As opposed to the field-down situation, in the field-up case a kink anomaly in the dc I-V curves is detected. The mode-locking measurements reveal that this anomaly is, in fact, a flow induced vortex slip transition: by increasing the external drive (either dc or ac) a sudden change occurs from n to n+2 moving vortex rows in the channel. The observed features can be explained in terms of an interplay between field focusing due to screening currents and a change in the predominant pinning mechanism.

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.

Quantifying the biophysical characteristics of Plasmodium-falciparum-parasitized red blood cells in microcirculation

PubMed Central

Fedosov, D. A.; Caswell, B.; Suresh, S.; Karniadakis, G. E.

2011-01-01

The pathogenicity of Plasmodium falciparum (Pf) malaria results from the stiffening of red blood cells (RBCs) and its ability to adhere to endothelial cells (cytoadherence). The dynamics of Pf-parasitized RBCs is studied by three-dimensional mesoscopic simulations of flow in cylindrical capillaries in order to predict the flow resistance enhancement at different parasitemia levels. In addition, the adhesive dynamics of Pf-RBCs is explored for various parameters revealing several types of cell dynamics such as firm adhesion, very slow slipping along the wall, and intermittent flipping. The parasite inside the RBC is modeled explicitly in order to capture phenomena such as “hindered tumbling” motion of the RBC and the sudden transition from firm RBC cytoadherence to flipping on the endothelial surface. These predictions are in quantitative agreement with recent experimental observations, and thus the three-dimensional modeling method presented here provides new capabilities for guiding and interpreting future in vitro and in vivo studies of malaria. PMID:21173269

Imaging of super-fast dynamics and flow instabilities of superconducting vortices

DOE PAGES

Embon, L.; Anahory, Y.; Jelić, Ž. L.; ...

2017-07-20

Quantized magnetic vortices driven by electric current determine key electromagnetic properties of superconductors. And while the dynamic behavior of slow vortices has been thoroughly investigated, the physics of ultrafast vortices under strong currents remains largely unexplored. Here, we use a nanoscale scanning superconducting quantum interference device to image vortices penetrating into a superconducting Pb film at rates of tens of GHz and moving with velocities of up to tens of km/s, which are not only much larger than the speed of sound but also exceed the pair-breaking speed limit of superconducting condensate. These experiments reveal formation of mesoscopic vortex channelsmore » which undergo cascades of bifurcations as the current and magnetic field increase. Our numerical simulations predict metamorphosis of fast Abrikosov vortices into mixed Abrikosov-Josephson vortices at even higher velocities. Our work offers an insight into the fundamental physics of dynamic vortex states of superconductors at high current densities, crucial for many applications.« less

Microstructure-based hyperelastic models for closed-cell solids

PubMed Central

Wyatt, Hayley

2017-01-01

For cellular bodies involving large elastic deformations, mesoscopic continuum models that take into account the interplay between the geometry and the microstructural responses of the constituents are developed, analysed and compared with finite-element simulations of cellular structures with different architecture. For these models, constitutive restrictions for the physical plausibility of the material responses are established, and global descriptors such as nonlinear elastic and shear moduli and Poisson’s ratio are obtained from the material characteristics of the constituents. Numerical results show that these models capture well the mechanical responses of finite-element simulations for three-dimensional periodic structures of neo-Hookean material with closed cells under large tension. In particular, the mesoscopic models predict the macroscopic stiffening of the structure when the stiffness of the cell-core increases. PMID:28484340

Microstructure-based hyperelastic models for closed-cell solids.

PubMed

Mihai, L Angela; Wyatt, Hayley; Goriely, Alain

2017-04-01

For cellular bodies involving large elastic deformations, mesoscopic continuum models that take into account the interplay between the geometry and the microstructural responses of the constituents are developed, analysed and compared with finite-element simulations of cellular structures with different architecture. For these models, constitutive restrictions for the physical plausibility of the material responses are established, and global descriptors such as nonlinear elastic and shear moduli and Poisson's ratio are obtained from the material characteristics of the constituents. Numerical results show that these models capture well the mechanical responses of finite-element simulations for three-dimensional periodic structures of neo-Hookean material with closed cells under large tension. In particular, the mesoscopic models predict the macroscopic stiffening of the structure when the stiffness of the cell-core increases.

Microstructure-based hyperelastic models for closed-cell solids

NASA Astrophysics Data System (ADS)

Mihai, L. Angela; Wyatt, Hayley; Goriely, Alain

2017-04-01

For cellular bodies involving large elastic deformations, mesoscopic continuum models that take into account the interplay between the geometry and the microstructural responses of the constituents are developed, analysed and compared with finite-element simulations of cellular structures with different architecture. For these models, constitutive restrictions for the physical plausibility of the material responses are established, and global descriptors such as nonlinear elastic and shear moduli and Poisson's ratio are obtained from the material characteristics of the constituents. Numerical results show that these models capture well the mechanical responses of finite-element simulations for three-dimensional periodic structures of neo-Hookean material with closed cells under large tension. In particular, the mesoscopic models predict the macroscopic stiffening of the structure when the stiffness of the cell-core increases.

Modeling and simulation of the debonding process of composite solid propellants

NASA Astrophysics Data System (ADS)

Feng, Tao; Xu, Jin-sheng; Han, Long; Chen, Xiong

2017-07-01

In order to study the damage evolution law of composite solid propellants, the molecular dynamics particle filled algorithm was used to establish the mesoscopic structure model of HTPB(Hydroxyl-terminated polybutadiene) propellants. The cohesive element method was employed for the adhesion interface between AP(Ammonium perchlorate) particle and HTPB matrix and the bilinear cohesive zone model was used to describe the mechanical response of the interface elements. The inversion analysis method based on Hooke-Jeeves optimization algorithm was employed to identify the parameters of cohesive zone model(CZM) of the particle/binder interface. Then, the optimized parameters were applied to the commercial finite element software ABAQUS to simulate the damage evolution process for AP particle and HTPB matrix, including the initiation, development, gathering and macroscopic crack. Finally, the stress-strain simulation curve was compared with the experiment curves. The result shows that the bilinear cohesive zone model can accurately describe the debonding and fracture process between the AP particles and HTPB matrix under the uniaxial tension loading.

Physics at the FMQT’08 conference

NASA Astrophysics Data System (ADS)

Špička, V.; Nieuwenhuizen, Th. M.; Keefe, P. D.

2010-01-01

This paper summarizes the recent state of the art of the following topics presented at the FQMT’08 conference: Foundations of quantum physics, Quantum measurement; Quantum noise, decoherence and dephasing; Cold atoms and Bose-Einstein condensation; Physics of quantum computing and information; Nonequilibrium quantum statistical mechanics; Quantum, mesoscopic and partly classical thermodynamics; Mesoscopic, nano-electro-mechanical systems and optomechanical systems; Spins systems and their dynamics, Brownian motion and molecular motors; Physics of biological systems, and Relevant experiments from the nanoscale to the macroscale. To all these subjects an introduction is given and the recent literature is overviewed. The paper contains some 680 references in total.

Mesoscopic electrohydrodynamic simulations of binary colloidal suspensions.

PubMed

Rivas, Nicolas; Frijters, Stefan; Pagonabarraga, Ignacio; Harting, Jens

2018-04-14

A model is presented for the solution of electrokinetic phenomena of colloidal suspensions in fluid mixtures. We solve the discrete Boltzmann equation with a Bhatnagar-Gross-Krook collision operator using the lattice Boltzmann method to simulate binary fluid flows. Solvent-solvent and solvent-solute interactions are implemented using a pseudopotential model. The Nernst-Planck equation, describing the kinetics of dissolved ion species, is solved using a finite difference discretization based on the link-flux method. The colloids are resolved on the lattice and coupled to the hydrodynamics and electrokinetics through appropriate boundary conditions. We present the first full integration of these three elements. The model is validated by comparing with known analytic solutions of ionic distributions at fluid interfaces, dielectric droplet deformations, and the electrophoretic mobility of colloidal suspensions. Its possibilities are explored by considering various physical systems, such as breakup of charged and neutral droplets and colloidal dynamics at either planar or spherical fluid interfaces.

Mesoscopic electrohydrodynamic simulations of binary colloidal suspensions

NASA Astrophysics Data System (ADS)

Rivas, Nicolas; Frijters, Stefan; Pagonabarraga, Ignacio; Harting, Jens

2018-04-01

A model is presented for the solution of electrokinetic phenomena of colloidal suspensions in fluid mixtures. We solve the discrete Boltzmann equation with a Bhatnagar-Gross-Krook collision operator using the lattice Boltzmann method to simulate binary fluid flows. Solvent-solvent and solvent-solute interactions are implemented using a pseudopotential model. The Nernst-Planck equation, describing the kinetics of dissolved ion species, is solved using a finite difference discretization based on the link-flux method. The colloids are resolved on the lattice and coupled to the hydrodynamics and electrokinetics through appropriate boundary conditions. We present the first full integration of these three elements. The model is validated by comparing with known analytic solutions of ionic distributions at fluid interfaces, dielectric droplet deformations, and the electrophoretic mobility of colloidal suspensions. Its possibilities are explored by considering various physical systems, such as breakup of charged and neutral droplets and colloidal dynamics at either planar or spherical fluid interfaces.

NMR relaxometric probing of ionic liquid dynamics and diffusion under mesoscopic confinement within bacterial cellulose ionogels

NASA Astrophysics Data System (ADS)

Smith, Chip J.; Gehrke, Sascha; Hollóczki, Oldamur; Wagle, Durgesh V.; Heitz, Mark P.; Baker, Gary A.

2018-05-01

Bacterial cellulose ionogels (BCIGs) represent a new class of material comprising a significant content of entrapped ionic liquid (IL) within a porous network formed from crystalline cellulose microfibrils. BCIGs suggest unique opportunities in separations, optically active materials, solid electrolytes, and drug delivery due to the fact that they can contain as much as 99% of an IL phase by weight, coupled with an inherent flexibility, high optical transparency, and the ability to control ionogel cross-sectional shape and size. To allow for the tailoring of BCIGs for a multitude of applications, it is necessary to better understand the underlying principles of the mesoscopic confinement within these ionogels. Toward this, we present a study of the structural, relaxation, and diffusional properties of the ILs, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([emim][Tf2N]) and 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([bmpy][Tf2N]), using 1H and 19F NMR T1 relaxation times, rotational correlation times, and diffusion ordered spectroscopy (DOSY) diffusion coefficients, accompanied by molecular dynamics (MD) simulations. We observed that the cation methyl groups in both ILs were primary points of interaction with the cellulose chains and, while the pore size in cellulose is rather large, [emim]+ diffusion was slowed by ˜2-fold, whereas [Tf2N]- diffusion was unencumbered by incorporation in the ionogel. While MD simulations of [bmpy][Tf2N] confinement at the interface showed a diffusion coefficient decrease roughly 3-fold compared to the bulk liquid, DOSY measurements did not reveal any significant changes in diffusion. This suggests that the [bmpy][Tf2N] alkyl chains dominate diffusion through formation of apolar domains. This is in contrast to [emim][Tf2N] where delocalized charge appears to preclude apolar domain formation, allowing interfacial effects to be manifested at a longer range in [emim][Tf2N].

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective

PubMed Central

Srivastava, Ashutosh; Sinha, Somdatta

2014-01-01

Proteins in thermophilic organisms remain stable and function optimally at high temperatures. Owing to their important applicability in many industrial processes, such thermostable proteins have been studied extensively, and several structural factors attributed to their enhanced stability. How these factors render the emergent property of thermostability to proteins, even in situations where no significant changes occur in their three-dimensional structures in comparison to their mesophilic counter-parts, has remained an intriguing question. In this study we treat Lipase A from Bacillus subtilis and its six thermostable mutants in a unified manner and address the problem with a combined complex network-based analysis and molecular dynamic studies to find commonality in their properties. The Protein Contact Networks (PCN) of the wild-type and six mutant Lipase A structures developed at a mesoscopic scale were analyzed at global network and local node (residue) level using network parameters and community structure analysis. The comparative PCN analysis of all proteins pointed towards important role of specific residues in the enhanced thermostability. Network analysis results were corroborated with finer-scale molecular dynamics simulations at both room and high temperatures. Our results show that this combined approach at two scales can uncover small but important changes in the local conformations that add up to stabilize the protein structure in thermostable mutants, even when overall conformation differences among them are negligible. Our analysis not only supports the experimentally determined stabilizing factors, but also unveils the important role of contacts, distributed throughout the protein, that lead to thermostability. We propose that this combined mesoscopic-network and fine-grained molecular dynamics approach is a convenient and useful scheme not only to study allosteric changes leading to protein stability in the face of negligible over-all conformational changes due to mutations, but also in other molecular networks where change in function does not accompany significant change in the network structure. PMID:25122499

Parameterization of a mesoscopic model for the self-assembly of linear sodium alkyl sulfates

NASA Astrophysics Data System (ADS)

Mai, Zhaohuan; Couallier, Estelle; Rakib, Mohammed; Rousseau, Bernard

2014-05-01

A systematic approach to develop mesoscopic models for a series of linear anionic surfactants (CH3(CH2)n - 1OSO3Na, n = 6, 9, 12, 15) by dissipative particle dynamics (DPD) simulations is presented in this work. The four surfactants are represented by coarse-grained models composed of the same head group and different numbers of identical tail beads. The transferability of the DPD model over different surfactant systems is carefully checked by adjusting the repulsive interaction parameters and the rigidity of surfactant molecules, in order to reproduce key equilibrium properties of the aqueous micellar solutions observed experimentally, including critical micelle concentration (CMC) and average micelle aggregation number (Nag). We find that the chain length is a good index to optimize the parameters and evaluate the transferability of the DPD model. Our models qualitatively reproduce the essential properties of these surfactant analogues with a set of best-fit parameters. It is observed that the logarithm of the CMC value decreases linearly with the surfactant chain length, in agreement with Klevens' rule. With the best-fit and transferable set of parameters, we have been able to calculate the free energy contribution to micelle formation per methylene unit of -1.7 kJ/mol, very close to the experimentally reported value.

Mesoscopic chaos mediated by Drude electron-hole plasma in silicon optomechanical oscillators

PubMed Central

Wu, Jiagui; Huang, Shu-Wei; Huang, Yongjun; Zhou, Hao; Yang, Jinghui; Liu, Jia-Ming; Yu, Mingbin; Lo, Guoqiang; Kwong, Dim-Lee; Duan, Shukai; Wei Wong, Chee

2017-01-01

Chaos has revolutionized the field of nonlinear science and stimulated foundational studies from neural networks, extreme event statistics, to physics of electron transport. Recent studies in cavity optomechanics provide a new platform to uncover quintessential architectures of chaos generation and the underlying physics. Here, we report the generation of dynamical chaos in silicon-based monolithic optomechanical oscillators, enabled by the strong and coupled nonlinearities of two-photon absorption induced Drude electron–hole plasma. Deterministic chaotic oscillation is achieved, and statistical and entropic characterization quantifies the chaos complexity at 60 fJ intracavity energies. The correlation dimension D2 is determined at 1.67 for the chaotic attractor, along with a maximal Lyapunov exponent rate of about 2.94 times the fundamental optomechanical oscillation for fast adjacent trajectory divergence. Nonlinear dynamical maps demonstrate the subharmonics, bifurcations and stable regimes, along with distinct transitional routes into chaos. This provides a CMOS-compatible and scalable architecture for understanding complex dynamics on the mesoscopic scale. PMID:28598426

Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

PubMed

Thomas, Philipp; Matuschek, Hannes; Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen's system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA's performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license.

Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion

PubMed Central

Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen’s system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA’s performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license. PMID:22723865

Small angle neutron scattering from 1-alkyl-3-methylimidazolium hexafluorophosphate ionic liquids ([Cnmim][PF6], n=4, 6, and 8)

NASA Astrophysics Data System (ADS)

Hardacre, Christopher; Holbrey, John D.; Mullan, Claire L.; Youngs, Tristan G. A.; Bowron, Daniel T.

2010-08-01

The presence of local anisotropy in the bulk, isotropic, and ionic liquid phases—leading to local mesoscopic inhomogeneity—with nanoscale segregation and expanding nonpolar domains on increasing the length of the cation alkyl-substituents has been proposed on the basis of molecular dynamics (MD) simulations. However, there has been little conclusive experimental evidence for the existence of intermediate mesoscopic structure between the first/second shell correlations shown by neutron scattering on short chain length based materials and the mesophase structure of the long chain length ionic liquid crystals. Herein, small angle neutron scattering measurements have been performed on selectively H/D-isotopically substituted 1-alkyl-3-methylimidazolium hexafluorophosphate ionic liquids with butyl, hexyl, and octyl substituents. The data show the unambiguous existence of a diffraction peak in the low-Q region for all three liquids which moves to longer distances (lower Q), sharpens, and increases in intensity with increasing length of the alkyl substituent. It is notable, however, that this peak occurs at lower values of Q (longer length scale) than predicted in any of the previously published MD simulations of ionic liquids, and that the magnitude of the scattering from this peak is comparable with that from the remainder of the amorphous ionic liquid. This strongly suggests that the peak arises from the second coordination shells of the ions along the vector of alkyl-chain substituents as a consequence of increasing the anisotropy of the cation, and that there is little or no long-range correlated nanostructure in these ionic liquids.

Numerical Simulation of the Perrin-Like Experiments

ERIC Educational Resources Information Center

Mazur, Zygmunt; Grech, Dariusz

2008-01-01

A simple model of the random Brownian walk of a spherical mesoscopic particle in viscous liquids is proposed. The model can be solved analytically and simulated numerically. The analytic solution gives the known Einstein-Smoluchowski diffusion law r[superscript 2] = 2Dt, where the diffusion constant D is expressed by the mass and geometry of a…

PRATHAM: Parallel Thermal Hydraulics Simulations using Advanced Mesoscopic Methods

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

Joshi, Abhijit S; Jain, Prashant K; Mudrich, Jaime A

2012-01-01

At the Oak Ridge National Laboratory, efforts are under way to develop a 3D, parallel LBM code called PRATHAM (PaRAllel Thermal Hydraulic simulations using Advanced Mesoscopic Methods) to demonstrate the accuracy and scalability of LBM for turbulent flow simulations in nuclear applications. The code has been developed using FORTRAN-90, and parallelized using the message passing interface MPI library. Silo library is used to compact and write the data files, and VisIt visualization software is used to post-process the simulation data in parallel. Both the single relaxation time (SRT) and multi relaxation time (MRT) LBM schemes have been implemented in PRATHAM.more » To capture turbulence without prohibitively increasing the grid resolution requirements, an LES approach [5] is adopted allowing large scale eddies to be numerically resolved while modeling the smaller (subgrid) eddies. In this work, a Smagorinsky model has been used, which modifies the fluid viscosity by an additional eddy viscosity depending on the magnitude of the rate-of-strain tensor. In LBM, this is achieved by locally varying the relaxation time of the fluid.« less

Exact and approximate stochastic simulation of intracellular calcium dynamics.

PubMed

Wieder, Nicolas; Fink, Rainer H A; Wegner, Frederic von

2011-01-01

In simulations of chemical systems, the main task is to find an exact or approximate solution of the chemical master equation (CME) that satisfies certain constraints with respect to computation time and accuracy. While Brownian motion simulations of single molecules are often too time consuming to represent the mesoscopic level, the classical Gillespie algorithm is a stochastically exact algorithm that provides satisfying results in the representation of calcium microdomains. Gillespie's algorithm can be approximated via the tau-leap method and the chemical Langevin equation (CLE). Both methods lead to a substantial acceleration in computation time and a relatively small decrease in accuracy. Elimination of the noise terms leads to the classical, deterministic reaction rate equations (RRE). For complex multiscale systems, hybrid simulations are increasingly proposed to combine the advantages of stochastic and deterministic algorithms. An often used exemplary cell type in this context are striated muscle cells (e.g., cardiac and skeletal muscle cells). The properties of these cells are well described and they express many common calcium-dependent signaling pathways. The purpose of the present paper is to provide an overview of the aforementioned simulation approaches and their mutual relationships in the spectrum ranging from stochastic to deterministic algorithms.

Fiber lubrication: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Liu, Hongyi

Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence of water increases the attractive interaction energy of the diblock copolymer on the cellulose surface, compared with that on the PP surface. Water decreases the interaction energy of the triblock copolymer on the cellulose surface, compared with that on the PP surface. MesoDyn was adopted to investigate the self-assembled morphology of the triblock copolymer, in aqueous solution, confined and sheared at solid-liquid interfaces. In a bulk aqueous solution, when the polymer concentration reached 10% v/v, micelles were observed with PPO blocks in the core and PEO blocks in the shell of the micelles. At the concentrations of 25% and 50%, worm-like micelles and irregular cylinders were observed in solutions, respectively. The micelles were formed faster in aqueous solutions confined by cellulose surfaces than that in the bulk. The formed micelles were broken under shearing, which led to a depletion of polymers at the interfaces. During the shearing on the PP surfaces, the polymers were adsorbed on the surfaces protecting the PP surfaces. This simulation study in the fiber lubrication was in good agreement with the experimental results and so provided an approach to visualize the polymer configuration at the liquid-solid interface, predict the lubricant-surface systems, and theoretically guide the experiments of designing new/efficient lubricants for fibers.

Probing eukaryotic cell mechanics via mesoscopic simulations

NASA Astrophysics Data System (ADS)

Pivkin, Igor V.; Lykov, Kirill; Nematbakhsh, Yasaman; Shang, Menglin; Lim, Chwee Teck

2017-11-01

We developed a new mesoscopic particle based eukaryotic cell model which takes into account cell membrane, cytoskeleton and nucleus. The breast epithelial cells were used in our studies. To estimate the viscoelastic properties of cells and to calibrate the computational model, we performed micropipette aspiration experiments. The model was then validated using data from microfluidic experiments. Using the validated model, we probed contributions of sub-cellular components to whole cell mechanics in micropipette aspiration and microfluidics experiments. We believe that the new model will allow to study in silico numerous problems in the context of cell biomechanics in flows in complex domains, such as capillary networks and microfluidic devices.

Phase diagrams of block copolymer melts by dissipative particle dynamics simulations

NASA Astrophysics Data System (ADS)

Gavrilov, Alexey A.; Kudryavtsev, Yaroslav V.; Chertovich, Alexander V.

2013-12-01

Phase diagrams for monodisperse and polydisperse diblock copolymer melts and a random multiblock copolymer melt are constructed using dissipative particle dynamics simulations. A thorough visual analysis and calculation of the static structure factor in several hundreds of points at each of the diagrams prove the ability of mesoscopic molecular dynamics to predict the phase behavior of polymer systems as effectively as the self-consistent field-theory and Monte Carlo simulations do. It is demonstrated that the order-disorder transition (ODT) curve for monodisperse diblocks can be precisely located by a spike in the dependence of the mean square pressure fluctuation on χN, where χ is the Flory-Huggins parameter and N is the chain length. For two other copolymer types, the continuous ODTs are observed. Large polydispersity of both blocks obeying the Flory distribution in length does not shift the ODT curve but considerably narrows the domains of the cylindrical and lamellar phases partially replacing them with the wormlike micelle and perforated lamellar phases, respectively. Instead of the pure 3d-bicontinuous phase in monodisperse diblocks, which could be identified as the gyroid, a coexistence of the 3d phase and cylindrical micelles is detected in polydisperse diblocks. The lamellar domain spacing D in monodisperse diblocks follows the strong-segregation theory prediction, D/N1/2 ˜ (χN)1/6, whereas in polydisperse diblocks it is almost independent of χN at χN < 100. Completely random multiblock copolymers cannot form ordered microstructures other than lamellas at any composition.

Particle-based membrane model for mesoscopic simulation of cellular dynamics

NASA Astrophysics Data System (ADS)

Sadeghi, Mohsen; Weikl, Thomas R.; Noé, Frank

2018-01-01

We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.

Mesoscopic Community Structure of Financial Markets Revealed by Price and Sign Fluctuations.

PubMed

Almog, Assaf; Besamusca, Ferry; MacMahon, Mel; Garlaschelli, Diego

2015-01-01

The mesoscopic organization of complex systems, from financial markets to the brain, is an intermediate between the microscopic dynamics of individual units (stocks or neurons, in the mentioned cases), and the macroscopic dynamics of the system as a whole. The organization is determined by "communities" of units whose dynamics, represented by time series of activity, is more strongly correlated internally than with the rest of the system. Recent studies have shown that the binary projections of various financial and neural time series exhibit nontrivial dynamical features that resemble those of the original data. This implies that a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. Here, we explore whether the binary signatures of multiple time series can replicate the same complex community organization of the financial market, as the original weighted time series. We adopt a method that has been specifically designed to detect communities from cross-correlation matrices of time series data. Our analysis shows that the simpler binary representation leads to a community structure that is almost identical with that obtained using the full weighted representation. These results confirm that binary projections of financial time series contain significant structural information.

Melting dynamics of ice in the mesoscopic regime

PubMed Central

Citroni, Margherita; Fanetti, Samuele; Falsini, Naomi; Foggi, Paolo; Bini, Roberto

2017-01-01

How does a crystal melt? How long does it take for melt nuclei to grow? The melting mechanisms have been addressed by several theoretical and experimental works, covering a subnanosecond time window with sample sizes of tens of nanometers and thus suitable to determine the onset of the process but unable to unveil the following dynamics. On the other hand, macroscopic observations of phase transitions, with millisecond or longer time resolution, account for processes occurring at surfaces and time limited by thermal contact with the environment. Here, we fill the gap between these two extremes, investigating the melting of ice in the entire mesoscopic regime. A bulk ice Ih or ice VI sample is homogeneously heated by a picosecond infrared pulse, which delivers all of the energy necessary for complete melting. The evolution of melt/ice interfaces thereafter is monitored by Mie scattering with nanosecond resolution, for all of the time needed for the sample to reequilibrate. The growth of the liquid domains, over distances of micrometers, takes hundreds of nanoseconds, a time orders of magnitude larger than expected from simple H-bond dynamics. PMID:28536197

Magnetic susceptibility, nanorheology, and magnetoviscosity of magnetic nanoparticles in viscoelastic environments

NASA Astrophysics Data System (ADS)

Ilg, Patrick; Evangelopoulos, Apostolos E. A. S.

2018-03-01

While magnetic nanoparticles suspended in Newtonian solvents (ferrofluids) have been intensively studied in recent years, the effects of viscoelasticity of the surrounding medium on the nanoparticle dynamics are much less understood. Here we investigate a mesoscopic model for the orientational dynamics of isolated magnetic nanoparticles subject to external fields, viscous and viscoelastic friction, as well as the corresponding random torques. We solve the model analytically in the overdamped limit for weak viscoelasticity. By comparison to Brownian dynamics simulations we establish the limits of validity of the analytical solution. We find that viscoelasticity not only slows down the magnetization relaxation, shifts the peak of the imaginary magnetic susceptibility χ″ to lower frequencies, and increases the magnetoviscosity but also leads to nonexponential relaxation and a broadening of χ″. The model we study also allows us to test a recent proposal for using magnetic susceptibility measurements as a nanorheological tool using a variant of the Germant-DiMarzio-Bishop relation. We find for the present model and certain parameter ranges that the relation of the magnetic susceptibility to the shear modulus is satisfied to a good approximation.

Anomalous properties of the acoustic excitations in glasses on the mesoscopic length scale.

PubMed

Monaco, Giulio; Mossa, Stefano

2009-10-06

The low-temperature thermal properties of dielectric crystals are governed by acoustic excitations with large wavelengths that are well described by plane waves. This is the Debye model, which rests on the assumption that the medium is an elastic continuum, holds true for acoustic wavelengths large on the microscopic scale fixed by the interatomic spacing, and gradually breaks down on approaching it. Glasses are characterized as well by universal low-temperature thermal properties that are, however, anomalous with respect to those of the corresponding crystalline phases. Related universal anomalies also appear in the low-frequency vibrational density of states and, despite a longstanding debate, remain poorly understood. By using molecular dynamics simulations of a model monatomic glass of extremely large size, we show that in glasses the structural disorder undermines the Debye model in a subtle way: The elastic continuum approximation for the acoustic excitations breaks down abruptly on the mesoscopic, medium-range-order length scale of approximately 10 interatomic spacings, where it still works well for the corresponding crystalline systems. On this scale, the sound velocity shows a marked reduction with respect to the macroscopic value. This reduction turns out to be closely related to the universal excess over the Debye model prediction found in glasses at frequencies of approximately 1 THz in the vibrational density of states or at temperatures of approximately 10 K in the specific heat.

Modeling snow-crystal growth: a three-dimensional mesoscopic approach.

PubMed

Gravner, Janko; Griffeath, David

2009-01-01

We introduce a three-dimensional, computationally feasible, mesoscopic model for snow-crystal growth, based on diffusion of vapor, anisotropic attachment, and a boundary layer. Several case studies are presented that faithfully replicate most observed snow-crystal morphology, an unusual achievement for a mathematical model. In particular, many of the most striking physical specimens feature both facets and branches, and our model provides an explanation for this phenomenon. We also duplicate many other observed traits, including ridges, ribs, sandwich plates, and hollow columns, as well as various dynamic instabilities. The concordance of observed phenomena suggests that the ingredients in our model are the most important ones in the development of physical snow crystals.

Active matter model of Myxococcus xanthus aggregation

NASA Astrophysics Data System (ADS)

Patch, Adam; Bahar, Fatmagul; Liu, Guannan; Thutupalli, Shashi; Welch, Roy; Yllanes, David; Shaevitz, Joshua; Marchetti, M. Cristina

Myxococcus xanthus is a soil-dwelling bacterium that exhibits several fascinating collective behaviors including streaming, swarming, and generation of fruiting bodies. A striking feature of M. xanthus is that it periodically reverses its motility direction. The first stage of fruiting body formation is characterized by the aggregation of cells on a surface into round mesoscopic structures. Experiments have shown that this aggregation relies heavily on regulation of the reversal rate and local mechanical interactions, suggesting motility-induced phase separation may play an important role. We have adapted self-propelled particle models to include cell reversal and motility suppression resulting from sporulation observed in aggregates. Using 2D molecular dynamics simulations, we map the phase behavior in the space of Péclet number and local density and examine the kinetics of aggregation for comparison to experiments.

Dynamic Behavior of Engineered Lattice Materials

PubMed Central

Hawreliak, J. A.; Lind, J.; Maddox, B.; Barham, M.; Messner, M.; Barton, N.; Jensen, B. J.; Kumar, M.

2016-01-01

Additive manufacturing (AM) is enabling the fabrication of materials with engineered lattice structures at the micron scale. These mesoscopic structures fall between the length scale associated with the organization of atoms and the scale at which macroscopic structures are constructed. Dynamic compression experiments were performed to study the emergence of behavior owing to the lattice periodicity in AM materials on length scales that approach a single unit cell. For the lattice structures, both bend and stretch dominated, elastic deflection of the structure was observed ahead of the compaction of the lattice, while no elastic deformation was observed to precede the compaction in a stochastic, random structure. The material showed lattice characteristics in the elastic response of the material, while the compaction was consistent with a model for compression of porous media. The experimental observations made on arrays of 4 × 4 × 6 lattice unit cells show excellent agreement with elastic wave velocity calculations for an infinite periodic lattice, as determined by Bloch wave analysis, and finite element simulations. PMID:27321697

Probing entropic repulsion through mesoscopic simulations

NASA Astrophysics Data System (ADS)

Vaiwala, Rakesh; Thaokar, Rochish

2017-11-01

Following the publication of Freund's work on entropic pressure (Freund L., Proc. Natl. Acad. Sci. U.S.A., 110 (2013) 2047), which states that the undulation pressure for a biomembrane confined between two parallel rigid walls decays linearly with wall separation (d), different contradictory views on the pressure law evolved; some supporting Helfrich's prediction that the entropic pressure scales as 1/d3 . Attempts were made to resolve this stark contradiction by distinct groups of researchers. In this work, using dissipative particle dynamics simulations it has been shown for the first time that the height fluctuations are suppressed by wall confinement. An analysis of the fluctuation spectrum reveals that the entropic loss manifests as a membrane tension for a membrane that conserves its local area, and this fact is confirmed by the rise in stresses with an increase in wall confinement. Furthermore, we theorize a pressure law, which interestingly is congruous with Freund's prediction that the entropic pressure scales as 1/d .

Mesoscopic modeling of multi-physicochemical transport phenomena in porous media

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

Kang, Qinjin; Wang, Moran; Mukherjee, Partha P

2009-01-01

We present our recent progress on mesoscopic modeling of multi-physicochemical transport phenomena in porous media based on the lattice Boltzmann method. Simulation examples include injection of CO{sub 2} saturated brine into a limestone rock, two-phase behavior and flooding phenomena in polymer electrolyte fuel cells, and electroosmosis in homogeneously charged porous media. It is shown that the lattice Boltzmann method can account for multiple, coupled physicochemical processes in these systems and can shed some light on the underlying physics occuning at the fundamental scale. Therefore, it can be a potential powerful numerical tool to analyze multi-physicochemical processes in various energy, earth,more » and environmental systems.« less

Localization and elasticity in entangled polymer liquids as a mesoscopic glass transition

NASA Astrophysics Data System (ADS)

Schweizer, Kenneth

2010-03-01

The reptation-tube model is widely viewed as the correct zeroth order model for entangled linear polymer dynamics under quiescent conditions. Its key ansatz is the existence of a mesoscopic dynamical length scale that prohibits transverse chain motion beyond a tube diameter of order 3-10 nm. However, the theory is phenomenological and lacks a microscopic foundation, and many fundamental questions remain unanswered. These include: (i) where does the confining tube field come from and can it be derived from statistical mechanics? (ii) what is the microscopic origin of the magnitude, and power law scaling with concentration and packing length, of the plateau shear modulus? (iii) is the tube diameter time-dependent? (iv) does the confinement field contribute to elasticity ? (v) do entanglement constraints have a finite strength? Building on our new force-level theories for the dynamical crossover and activated barrier hopping in glassy colloidal suspensions and polymer melts, a first principles self-consistent theory has been developed for entangled polymers. Its basic physical elements, and initial results that address the questions posed above, will be presented. The key idea is that beyond a critical degree of polymerization, the chain connectivity and excluded volume induced intermolecular correlation hole drives temporary localization on an intermediate length scale resulting in a mesoscopic ``ideal kinetic glass transition.'' Large scale isotropic motion is effectively quenched due to the emergence of chain length dependent entropic barriers. However, the barrier height is not infinite, resulting in softening of harmonic localization at large displacements, temporal increase of the confining length scale, and a finite strength of entanglement constraints which can be destroyed by applied stress.

PREFACE: Advanced many-body and statistical methods in mesoscopic systems

NASA Astrophysics Data System (ADS)

Anghel, Dragos Victor; Sabin Delion, Doru; Sorin Paraoanu, Gheorghe

2012-02-01

It has increasingly been realized in recent times that the borders separating various subfields of physics are largely artificial. This is the case for nanoscale physics, physics of lower-dimensional systems and nuclear physics, where the advanced techniques of many-body theory developed in recent times could provide a unifying framework for these disciplines under the general name of mesoscopic physics. Other fields, such as quantum optics and quantum information, are increasingly using related methods. The 6-day conference 'Advanced many-body and statistical methods in mesoscopic systems' that took place in Constanta, Romania, between 27 June and 2 July 2011 was, we believe, a successful attempt at bridging an impressive list of topical research areas: foundations of quantum physics, equilibrium and non-equilibrium quantum statistics/fractional statistics, quantum transport, phases and phase transitions in mesoscopic systems/superfluidity and superconductivity, quantum electromechanical systems, quantum dissipation, dephasing, noise and decoherence, quantum information, spin systems and their dynamics, fundamental symmetries in mesoscopic systems, phase transitions, exactly solvable methods for mesoscopic systems, various extension of the random phase approximation, open quantum systems, clustering, decay and fission modes and systematic versus random behaviour of nuclear spectra. This event brought together participants from seventeen countries and five continents. Each of the participants brought considerable expertise in his/her field of research and, at the same time, was exposed to the newest results and methods coming from the other, seemingly remote, disciplines. The talks touched on subjects that are at the forefront of topical research areas and we hope that the resulting cross-fertilization of ideas will lead to new, interesting results from which everybody will benefit. We are grateful for the financial and organizational support from IFIN-HH, Ovidius University (where the conference took place), the Academy of Romanian Scientists and the Romanian National Authority for Scientific Research. This conference proceedings volume brings together some of the invited and contributed talks of the conference. The hope of the editors is that they will constitute reference material for applying many-body techniques to problems in mesoscopic and nuclear physics. We thank all the participants for their contribution to the success of this conference. D V Anghel and D S Delion IFIN-HH, Bucharest, Romania G S Paraoanu Aalto University, Finland Conference photograph

Spatial and mesoscopic fluctuations in glassy dynamics

NASA Astrophysics Data System (ADS)

Chamon, Claudio C.; Cugliandolo, Leticia F.

2004-05-01

One of the striking properties of a glassy system is that many material properties depend on its age, i.e., the time since the system entered its glassy phase. In this this talk we shall review some recent progress (work in collaboration with H. E. Castillo, P. Charbonneau, J. L. Iguain, M. P. Kennett, D. R. Reichman and M. Sellitto) in understanding local aging, through the study of local observable quantities, which reveal that there are spatial heterogeneities and fluctuations in the aging process of macroscopic systems. We show that a number of universal properties are shared by many non-equilibrium systems, both with and without quenched disorder, such as the 3D Edwards-Anderson model and some kinetically constrained non-interacting 2D and 3D spin models, for example. Similar scaling relations are found for mesoscopic sample-to-sample fluctuations of global quantities in small size systems. We discuss how the emergence of a symmetry in aging systems, time-reparametrization invariance, could be responsible for the observed universal behavior of the local and mesoscopic non-equilibrium fluctuations.

The Superstatistical Nature and Interoccurrence Time of Atmospheric Mercury Concentration Fluctuations

NASA Astrophysics Data System (ADS)

Carbone, F.; Bruno, A. G.; Naccarato, A.; De Simone, F.; Gencarelli, C. N.; Sprovieri, F.; Hedgecock, I. M.; Landis, M. S.; Skov, H.; Pfaffhuber, K. A.; Read, K. A.; Martin, L.; Angot, H.; Dommergue, A.; Magand, O.; Pirrone, N.

2018-01-01

The probability density function (PDF) of the time intervals between subsequent extreme events in atmospheric Hg0 concentration data series from different latitudes has been investigated. The Hg0 dynamic possesses a long-term memory autocorrelation function. Above a fixed threshold Q in the data, the PDFs of the interoccurrence time of the Hg0 data are well described by a Tsallis q-exponential function. This PDF behavior has been explained in the framework of superstatistics, where the competition between multiple mesoscopic processes affects the macroscopic dynamics. An extensive parameter μ, encompassing all possible fluctuations related to mesoscopic phenomena, has been identified. It follows a χ2 distribution, indicative of the superstatistical nature of the overall process. Shuffling the data series destroys the long-term memory, the distributions become independent of Q, and the PDFs collapse on to the same exponential distribution. The possible central role of atmospheric turbulence on extreme events in the Hg0 data is highlighted.

Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion

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

Del Razo, Mauricio; Pan, Wenxiao; Qian, Hong

2014-05-30

The currently existing theory of fluorescence correlation spectroscopy (FCS) is based on the linear fluctuation theory originally developed by Einstein, Onsager, Lax, and others as a phenomenological approach to equilibrium fluctuations in bulk solutions. For mesoscopic reaction-diffusion systems with nonlinear chemical reactions among a small number of molecules, a situation often encountered in single-cell biochemistry, it is expected that FCS time correlation functions of a reaction-diffusion system can deviate from the classic results of Elson and Magde [Biopolymers (1974) 13:1-27]. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems there are no closedmore » solutions; therefore, stochastic Monte-Carlo simulations are carried out. We show that the deviation is small for a simple bimolecular reaction; the most significant deviations occur when the number of molecules is small and of the same order. Extending Delbrück-Gillespie’s theory for stochastic nonlinear reactions with rapidly stirring to reaction-diffusion systems provides a mesoscopic model for chemical and biochemical reactions at nanometric and mesoscopic level such as a single biological cell.« less

Hierarchical Theoretical Methods for Understanding and Predicting Anisotropic Thermal Transport Release in Rocket Propellant Formulations

DTIC Science & Technology

2016-12-08

mesoscopic models of interfaces and interphases, and microstructure-resolved representative volume element simulations. Atomic simulations were...title and subtitle with volume number and part number, if applicable. On classified documents, enter the title classification in parentheses. 5a...careful prediction of the pressure- volume -temperature equation of state, pressure- and temperature-dependent crystal and liquid thermal and transport

Mesoscopic Community Structure of Financial Markets Revealed by Price and Sign Fluctuations

PubMed Central

Almog, Assaf; Besamusca, Ferry; MacMahon, Mel; Garlaschelli, Diego

2015-01-01

The mesoscopic organization of complex systems, from financial markets to the brain, is an intermediate between the microscopic dynamics of individual units (stocks or neurons, in the mentioned cases), and the macroscopic dynamics of the system as a whole. The organization is determined by “communities” of units whose dynamics, represented by time series of activity, is more strongly correlated internally than with the rest of the system. Recent studies have shown that the binary projections of various financial and neural time series exhibit nontrivial dynamical features that resemble those of the original data. This implies that a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. Here, we explore whether the binary signatures of multiple time series can replicate the same complex community organization of the financial market, as the original weighted time series. We adopt a method that has been specifically designed to detect communities from cross-correlation matrices of time series data. Our analysis shows that the simpler binary representation leads to a community structure that is almost identical with that obtained using the full weighted representation. These results confirm that binary projections of financial time series contain significant structural information. PMID:26226226

Dynamics of microemulsions bridged with hydrophobically end-capped star polymers studied by neutron spin-echo

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

Hoffmann, I., E-mail: ingo.hoffmann@tu-berlin.de; Institut Max von Laue-Paul Langevin; Malo de Molina, Paula

2014-01-21

The mesoscopic dynamical properties of oil-in-water microemulsions (MEs) bridged with telechelic polymers of different number of arms and with different lengths of hydrophobic stickers were studied with neutron spin-echo (NSE) probing the dynamics in the size range of individual ME droplets. These results then were compared to those of dynamicic light scattering (DLS) which allow to investigate the dynamics on a much larger length scale. Studies were performed as a function of the polymer concentration, number of polymer arms, and length of the hydrophobic end-group. In general it is observed that the polymer bridging has a rather small influence onmore » the local dynamics, despite the fact that the polymer addition leads to an increase of viscosity by several orders of magnitude. In contrast to results from rheology and DLS, where the dynamics on much larger length and time scales are observed, NSE shows that the linear polymer is more efficient in arresting the motion of individual ME droplets. This finding can be explained by a simple simulation, merely by the fact that the interconnection of droplets becomes more efficient with a decreasing number of arms. This means that the dynamics observed on the short and on the longer length scale depend in an opposite way on the number of arms and hydrophobic stickers.« less

Cooperation of sperm in two dimensions: synchronization, attraction, and aggregation through hydrodynamic interactions.

PubMed

Yang, Yingzi; Elgeti, Jens; Gompper, Gerhard

2008-12-01

Sperm swimming at low Reynolds number have strong hydrodynamic interactions when their concentration is high in vivo or near substrates in vitro. The beating tails not only propel the sperm through a fluid, but also create flow fields through which sperm interact with each other. We study the hydrodynamic interaction and cooperation of sperm embedded in a two-dimensional fluid by using a particle-based mesoscopic simulation method, multiparticle collision dynamics. We analyze the sperm behavior by investigating the relationship between the beating-phase difference and the relative sperm position, as well as the energy consumption. Two effects of hydrodynamic interaction are found, synchronization and attraction. With these hydrodynamic effects, a multisperm system shows swarm behavior with a power-law dependence of the average cluster size on the width of the distribution of beating frequencies.

Adsorption of poly(ethylene succinate) chain onto graphene nanosheets: A molecular simulation.

PubMed

Kelich, Payam; Asadinezhad, Ahmad

2016-09-01

Understanding the interaction between single polymer chain and graphene nanosheets at local and global length scales is essential for it underlies the mesoscopic properties of polymer nanocomposites. A computational attempt was then performed using atomistic molecular dynamics simulation to gain physical insights into behavior of a model aliphatic polyester, poly(ethylene succinate), single chain near graphene nanosheets, where the effects of the polymer chain length, graphene functionalization, and temperature on conformational properties of the polymer were studied comparatively. Graphene functionalization was carried out through extending the parameters set of an all-atom force field. The results showed a significant conformational transition of the polymer chain from three-dimensional statistical coil, in initial state, to two-dimensional fold, in final state, during adsorption on graphene. The conformational order, overall shape, end-to-end separation statistics, and mobility of the polymer chain were found to be influenced by the graphene functionalization, temperature, and polymer chain length. Furthermore, the polymer chain dynamics mode during adsorption on graphene was observed to transit from normal diffusive to slow subdiffusive mode. The findings from this computational study could shed light on the physics of the early stages of aliphatic polyester chain organization induced by graphene. Copyright © 2016 Elsevier Inc. All rights reserved.

The influence of mesoscopic confinement on the dynamics of imidazolium-based room temperature ionic liquids in polyether sulfone membranes.

PubMed

Thomaz, Joseph E; Bailey, Heather E; Fayer, Michael D

2017-11-21

The structural dynamics of a series of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (C n mimNTf 2 , n = 2, 4, 6, 10: ethyl-Emim; butyl-Bmim; hexyl-Hmim; decyl-Dmim) room temperature ionic liquids confined in the pores of polyether sulfone (PES 200) membranes with an average pore size of ∼350 nm and in the bulk liquids were studied. Time correlated single photon counting measurements of the fluorescence of the fluorophore coumarin 153 (C153) were used to observe the time-dependent Stokes shift (solvation dynamics). The solvation dynamics of C153 in the ionic liquids are multiexponential decays. The multiexponential functional form of the decays was confirmed as the slowest decay component of each bulk liquid matches the slowest component of the liquid dynamics measured by optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments, which is single exponential. The fact that the slowest component of the Stokes shift matches the OHD-OKE data in all four liquids identifies this component of the solvation dynamics as arising from the complete structural randomization of the liquids. Although the pores in the PES membranes are large, confinement on the mesoscopic length scale results in substantial slowing of the dynamics, a factor of ∼4, for EmimNTf 2 , with the effect decreasing as the chain length increases. By DmimNTf 2 , the dynamics are virtually indistinguishable from those in the bulk liquid. The rotation relaxation of C153 in the four bulk liquids was also measured and showed strong coupling between the C153 probe and its environment.

The influence of mesoscopic confinement on the dynamics of imidazolium-based room temperature ionic liquids in polyether sulfone membranes

NASA Astrophysics Data System (ADS)

Thomaz, Joseph E.; Bailey, Heather E.; Fayer, Michael D.

2017-11-01

The structural dynamics of a series of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (CnmimNTf2, n = 2, 4, 6, 10: ethyl—Emim; butyl—Bmim; hexyl—Hmim; decyl—Dmim) room temperature ionic liquids confined in the pores of polyether sulfone (PES 200) membranes with an average pore size of ˜350 nm and in the bulk liquids were studied. Time correlated single photon counting measurements of the fluorescence of the fluorophore coumarin 153 (C153) were used to observe the time-dependent Stokes shift (solvation dynamics). The solvation dynamics of C153 in the ionic liquids are multiexponential decays. The multiexponential functional form of the decays was confirmed as the slowest decay component of each bulk liquid matches the slowest component of the liquid dynamics measured by optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments, which is single exponential. The fact that the slowest component of the Stokes shift matches the OHD-OKE data in all four liquids identifies this component of the solvation dynamics as arising from the complete structural randomization of the liquids. Although the pores in the PES membranes are large, confinement on the mesoscopic length scale results in substantial slowing of the dynamics, a factor of ˜4, for EmimNTf2, with the effect decreasing as the chain length increases. By DmimNTf2, the dynamics are virtually indistinguishable from those in the bulk liquid. The rotation relaxation of C153 in the four bulk liquids was also measured and showed strong coupling between the C153 probe and its environment.

Multiscale simulation of molecular processes in cellular environments.

PubMed

Chiricotto, Mara; Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone

2016-11-13

We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Numerical methods for multi-scale modeling of non-Newtonian flows

NASA Astrophysics Data System (ADS)

Symeonidis, Vasileios

This work presents numerical methods for the simulation of Non-Newtonian fluids in the continuum as well as the mesoscopic level. The former is achieved with Direct Numerical Simulation (DNS) spectral h/p methods, while the latter employs the Dissipative Particle Dynamics (DPD) technique. Physical results are also presented as a motivation for a clear understanding of the underlying numerical approaches. The macroscopic simulations employ two non-Newtonian models, namely the Reiner-Ravlin (RR) and the viscoelastic FENE-P model. (1) A spectral viscosity method defined by two parameters ε, M is used to stabilize the FENE-P conformation tensor c. Convergence studies are presented for different combinations of these parameters. Two boundary conditions for the tensor c are also investigated. (2) Agreement is achieved with other works for Stokes flow of a two-dimensional cylinder in a channel. Comparison of the axial normal stress and drag coefficient on the cylinder is presented. Further, similar results from unsteady two- and three-dimensional turbulent flows past a flat plate in a channel are shown. (3) The RR problem is formulated for nearly incompressible flows, with the introduction of a mathematically equivalent tensor formulation. A spectral viscosity method and polynomial over-integration are studied. Convergence studies, including a three-dimensional channel flow with a parallel slot, investigate numerical problems arising from elemental boundaries and sharp corners. (4) The round hole pressure problem is presented for Newtonian and RR fluids in geometries with different hole sizes. Comparison with experimental data is made for the Newtonian case. The flaw in the experimental assumptions of undisturbed pressure opposite the hole is revealed, while good agreement with the data is shown. The Higashitani-Pritchard kinematical theory for RR, fluids is recovered for round holes and an approximate formula for the RR Stokes hole pressure is presented. The mesoscopic simulations assume bead-spring representations of polymer chains and investigate different integrating schemes of the DPD equations and different intra-polymer force combinations. (1) A novel family of time-staggered integrators is presented, taking advantage of the time-scale disparity between polymer-solvent and solvent-solvent interactions. Convergence tests for relaxation parameters for the velocity-Verlet and Lowe's schemes are presented. (2) Wormlike chains simulating lambda- DNA molecules subject to constant shear are studied, and direct comparison with Brownian Dynamics and experimental results is made. The effect of the number of beads per chain is examined through the extension autocorrelation function. (3) The Schmidt number (Sc) for each numerical scheme is investigated and the dependence on the scheme's parameters is shown. Re-visiting the wormlike chain problem under shear, we recover a better agreement with the experimental data through proper adjustment of Sc.

Computational methods for diffusion-influenced biochemical reactions.

PubMed

Dobrzynski, Maciej; Rodríguez, Jordi Vidal; Kaandorp, Jaap A; Blom, Joke G

2007-08-01

We compare stochastic computational methods accounting for space and discrete nature of reactants in biochemical systems. Implementations based on Brownian dynamics (BD) and the reaction-diffusion master equation are applied to a simplified gene expression model and to a signal transduction pathway in Escherichia coli. In the regime where the number of molecules is small and reactions are diffusion-limited predicted fluctuations in the product number vary between the methods, while the average is the same. Computational approaches at the level of the reaction-diffusion master equation compute the same fluctuations as the reference result obtained from the particle-based method if the size of the sub-volumes is comparable to the diameter of reactants. Using numerical simulations of reversible binding of a pair of molecules we argue that the disagreement in predicted fluctuations is due to different modeling of inter-arrival times between reaction events. Simulations for a more complex biological study show that the different approaches lead to different results due to modeling issues. Finally, we present the physical assumptions behind the mesoscopic models for the reaction-diffusion systems. Input files for the simulations and the source code of GMP can be found under the following address: http://www.cwi.nl/projects/sic/bioinformatics2007/

Quantum approach of mesoscopic magnet dynamics with spin transfer torque

NASA Astrophysics Data System (ADS)

Wang, Yong; Sham, L. J.

2013-05-01

We present a theory of magnetization dynamics driven by spin-polarized current in terms of the quantum master equation. In the spin coherent state representation, the master equation becomes a Fokker-Planck equation, which naturally includes the spin transfer and quantum fluctuation. The current electron scattering state is correlated to the magnet quantum states, giving rise to quantum correction to the electron transport properties in the usual semiclassical theory. In the large-spin limit, the magnetization dynamics is shown to obey the Hamilton-Jacobi equation or the Hamiltonian canonical equations.

Mesoscopic model for the viscosities of nematic liquid crystals.

PubMed

Chrzanowska, A; Kröger, M; Sellers, S

1999-10-01

Based on the definition of the mesoscopic concept by Blenk et al. [Physica A 174, 119 (1991); J. Noneq. Therm. 16, 67 (1991); Mol. Cryst. Liq. Cryst. 204, 133 (1991)] an approach to calculate the Leslie viscosity coefficients for nematic liquid crystals is presented. The approach rests upon the mesoscopic stress tensor, whose structure is assumed similar to the macroscopic Leslie viscous stress. The proposed form is also the main dissipation part of the mesoscopic Navier-Stokes equation. On the basis of the correspondence between microscopic and mesoscopic scales a mean-field mesoscopic potential is introduced. It allows us to obtain the stress tensor angular velocity of the free rotating molecules with the help of the orientational Fokker-Planck equation. The macroscopic stress tensor is calculated as an average of the mesoscopic counterpart. Appropriate relations among mesoscopic viscosities have been found. The mesoscopic analysis results are shown to be consistent with the diffusional model of Kuzuu-Doi and Osipov-Terentjev with the exception of the shear viscosity alpha(4). In the nematic phase alpha(4) is shown to have two contributions: isotropic and nematic. There exists an indication that the influence of the isotropic part is dominant over the nematic part. The so-called microscopic stress tensor used in the microscopic theories is shown to be the mean-field potential-dependent representation of the mesoscopic stress tensor. In the limiting case of total alignment the Leslie coefficients are estimated for the diffusional and mesoscopic models. They are compared to the results of the affine transformation model of the perfectly ordered systems. This comparison shows disagreement concerning the rotational viscosity, whereas the coefficients characteristic for the symmetric part of the viscous stress tensor remain the same. The difference is caused by the hindered diffusion in the affine model case.

Continuation through Singularity of Continuum Multiphase Algorithms

DTIC Science & Technology

2013-03-01

capturing simulation of two-phase flow ; a singularity- free mesoscopic simulation that bridges atomic and continuum scales; and a physics-based closure...for free surface flow . The full two-way coupling was found to be irrelevant to the overall objective of developing a closure model to allow...The method can be used for the study of single species free - surface flow , for instance, in the case of pinch-off of a liquid thread during the

Dynamic and structural evidence of mesoscopic aggregation in phosphonium ionic liquids

NASA Astrophysics Data System (ADS)

Cosby, T.; Vicars, Z.; Heres, M.; Tsunashima, K.; Sangoro, J.

2018-05-01

Mesoscopic aggregation in aprotic ionic liquids due to the microphase separation of polar and non-polar components is expected to correlate strongly with the physicochemical properties of ionic liquids and therefore their potential applications. The most commonly cited experimental evidence of such aggregation is the observation of a low-q pre-peak in the x-ray and neutron scattering profiles, attributed to the polarity alternation of polar and apolar phases. In this work, a homologous series of phosphonium ionic liquids with the bis(trifluoromethylsulfonyl)imide anion and systematically varying alkyl chain lengths on the phosphonium cation are investigated by small and wide-angle x-ray scattering, dynamic-mechanical spectroscopy, and broadband dielectric spectroscopy. A comparison of the real space correlation distance corresponding to the pre-peak and the presence or absence of the slow sub-α dielectric relaxation previously associated with the motion of mesoscale aggregates reveals a disruption of mesoscale aggregates with increasing symmetry of the quaternary phosphonium cation. These findings contribute to the broader understanding of the interplay of molecular structures, mesoscale aggregation, and physicochemical properties in aprotic ionic liquids.

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.

Formation of a disordered solid via a shock-induced transition in a dense particle suspension

NASA Astrophysics Data System (ADS)

Petel, Oren E.; Frost, David L.; Higgins, Andrew J.; Ouellet, Simon

2012-02-01

Shock wave propagation in multiphase media is typically dominated by the relative compressibility of the two components of the mixture. The difference in the compressibility of the components results in a shock-induced variation in the effective volume fraction of the suspension tending toward the random-close-packing limit for the system, and a disordered solid can take form within the suspension. The present study uses a Hugoniot-based model to demonstrate this variation in the volume fraction of the solid phase as well as a simple hard-sphere model to investigate the formation of disordered structures within uniaxially compressed model suspensions. Both models are discussed in terms of available experimental plate impact data in dense suspensions. Through coordination number statistics of the mesoscopic hard-sphere model, comparisons are made with the trends of the experimental pressure-volume fraction relationship to illustrate the role of these disordered structures in the bulk properties of the suspensions. A criterion for the dynamic stiffening of suspensions under high-rate dynamic loading is suggested as an analog to quasi-static jamming based on the results of the simulations.

DNA denaturation bubbles: free-energy landscape and nucleation/closure rates.

PubMed

Sicard, François; Destainville, Nicolas; Manghi, Manoel

2015-01-21

The issue of the nucleation and slow closure mechanisms of non-superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (respectively, closure) of an approximately 10 base-pair bubble, in agreement with experiments, are associated with the crossing of a free-energy barrier of 22 kBT (respectively, 13 kBT) at room temperature T. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, and thus to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the millisecond range. Contrary to small breathing bubbles, those more than 4 base-pair bubbles are of biological relevance, for example, when a pre-existing state of denaturation is required by specific DNA-binding proteins.

cDPD: A new dissipative particle dynamics method for modeling electrokinetic phenomena at the mesoscale

NASA Astrophysics Data System (ADS)

Deng, Mingge; Li, Zhen; Borodin, Oleg; Karniadakis, George Em

2016-10-01

We develop a "charged" dissipative particle dynamics (cDPD) model for simulating mesoscopic electrokinetic phenomena governed by the stochastic Poisson-Nernst-Planck and the Navier-Stokes equations. Specifically, the transport equations of ionic species are incorporated into the DPD framework by introducing extra degrees of freedom and corresponding evolution equations associated with each DPD particle. Diffusion of ionic species driven by the ionic concentration gradient, electrostatic potential gradient, and thermal fluctuations is captured accurately via pairwise fluxes between DPD particles. The electrostatic potential is obtained by solving the Poisson equation on the moving DPD particles iteratively at each time step. For charged surfaces in bounded systems, an effective boundary treatment methodology is developed for imposing both the correct hydrodynamic and electrokinetics boundary conditions in cDPD simulations. To validate the proposed cDPD model and the corresponding boundary conditions, we first study the electrostatic structure in the vicinity of a charged solid surface, i.e., we perform cDPD simulations of the electrostatic double layer and show that our results are in good agreement with the well-known mean-field theoretical solutions. We also simulate the electrostatic structure and capacity densities between charged parallel plates in salt solutions with different salt concentrations. Moreover, we employ the proposed methodology to study the electro-osmotic and electro-osmotic/pressure-driven flows in a micro-channel. In the latter case, we simulate the dilute poly-electrolyte solution drifting by electro-osmotic flow in a micro-channel, hence demonstrating the flexibility and capability of this method in studying complex fluids with electrostatic interactions at the micro- and nano-scales.

Molecular simulation of the effect of cholesterol on lipid-mediated protein-protein interactions.

PubMed

de Meyer, Frédérick J-M; Rodgers, Jocelyn M; Willems, Thomas F; Smit, Berend

2010-12-01

Experiments and molecular simulations have shown that the hydrophobic mismatch between proteins and membranes contributes significantly to lipid-mediated protein-protein interactions. In this article, we discuss the effect of cholesterol on lipid-mediated protein-protein interactions as function of hydrophobic mismatch, protein diameter and protein cluster size, lipid tail length, and temperature. To do so, we study a mesoscopic model of a hydrated bilayer containing lipids and cholesterol in which proteins are embedded, with a hybrid dissipative particle dynamics-Monte Carlo method. We propose a mechanism by which cholesterol affects protein interactions: protein-induced, cholesterol-enriched, or cholesterol-depleted lipid shells surrounding the proteins affect the lipid-mediated protein-protein interactions. Our calculations of the potential of mean force between proteins and protein clusters show that the addition of cholesterol dramatically reduces repulsive lipid-mediated interactions between proteins (protein clusters) with positive mismatch, but does not affect attractive interactions between proteins with negative mismatch. Cholesterol has only a modest effect on the repulsive interactions between proteins with different mismatch. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Pinning-Depinning Mechanisms of the Contact Line during Evaporation of Microdroplets on Rough Surfaces: A Lattice Boltzmann Simulation.

PubMed

Yuan, Wu-Zhi; Zhang, Li-Zhi

2018-06-22

In this study, pinning and depinning of the contact line during droplet evaporation on the rough surfaces with randomly distributed structures is theoretically analyzed and numerically investigated. A fast Fourier transformation (FFT) method is used to generate the rough surfaces, whose skewness ( Sk), kurtosis ( K), and root-mean-square ( Rq) are obtained from real surfaces. A thermal multiphase LB model is proposed to simulate the isothermal pinning and depinning processes. The evaporation processes are recorded with the variations in contact angle, contact radius, and drop shape. It is found that the drops sitting on rough surfaces show different behavior from those on smoother surfaces. The former shows a pinned contact line during almost the whole lifetime. By contrast, the latter experiences a stick-slip-jump behavior until the drop disappears. At mesoscopic scale, the pinning of the contact line is actually a slow motion rather than a complete immobilization at the sharp edges. The dynamic equilibrium is achieved by the self-adjustment of the contact line according to each edge.

Stochastic effects in a thermochemical system with Newtonian heat exchange.

PubMed

Nowakowski, B; Lemarchand, A

2001-12-01

We develop a mesoscopic description of stochastic effects in the Newtonian heat exchange between a diluted gas system and a thermostat. We explicitly study the homogeneous Semenov model involving a thermochemical reaction and neglecting consumption of reactants. The master equation includes a transition rate for the thermal transfer process, which is derived on the basis of the statistics for inelastic collisions between gas particles and walls of the thermostat. The main assumption is that the perturbation of the Maxwellian particle velocity distribution can be neglected. The transition function for the thermal process admits a continuous spectrum of temperature changes, and consequently, the master equation has a complicated integro-differential form. We perform Monte Carlo simulations based on this equation to study the stochastic effects in the Semenov system in the explosive regime. The dispersion of ignition times is calculated as a function of system size. For sufficiently small systems, the probability distribution of temperature displays transient bimodality during the ignition period. The results of the stochastic description are successfully compared with those of direct simulations of microscopic particle dynamics.

An NMR database for simulations of membrane dynamics.

PubMed

Leftin, Avigdor; Brown, Michael F

2011-03-01

Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations. Copyright © 2010 Elsevier B.V. All rights reserved.

Conformational State Distributions and Catalytically Relevant Dynamics of a Hinge-Bending Enzyme Studied by Single-Molecule FRET and a Coarse-Grained Simulation

PubMed Central

Gabba, Matteo; Poblete, Simón; Rosenkranz, Tobias; Katranidis, Alexandros; Kempe, Daryan; Züchner, Tina; Winkler, Roland G.; Gompper, Gerhard; Fitter, Jörg

2014-01-01

Over the last few decades, a view has emerged showing that multidomain enzymes are biological machines evolved to harness stochastic kicks of solvent particles into highly directional functional motions. These intrinsic motions are structurally encoded, and Nature makes use of them to catalyze chemical reactions by means of ligand-induced conformational changes and states redistribution. Such mechanisms align reactive groups for efficient chemistry and stabilize conformers most proficient for catalysis. By combining single-molecule Förster resonance energy transfer measurements with normal mode analysis and coarse-grained mesoscopic simulations, we obtained results for a hinge-bending enzyme, namely phosphoglycerate kinase (PGK), which support and extend these ideas. From single-molecule Förster resonance energy transfer, we obtained insight into the distribution of conformational states and the dynamical properties of the domains. The simulations allowed for the characterization of interdomain motions of a compact state of PGK. The data show that PGK is intrinsically a highly dynamic system sampling a wealth of conformations on timescales ranging from nanoseconds to milliseconds and above. Functional motions encoded in the fold are performed by the PGK domains already in its ligand-free form, and substrate binding is not required to enable them. Compared to other multidomain proteins, these motions are rather fast and presumably not rate-limiting in the enzymatic reaction. Ligand binding slightly readjusts the orientation of the domains and feasibly locks the protein motions along a preferential direction. In addition, the functionally relevant compact state is stabilized by the substrates, and acts as a prestate to reach active conformations by means of Brownian motions. PMID:25418172

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.

An analytical model accounting for tip shape evolution during atom probe analysis of heterogeneous materials.

PubMed

Rolland, N; Larson, D J; Geiser, B P; Duguay, S; Vurpillot, F; Blavette, D

2015-12-01

An analytical model describing the field evaporation dynamics of a tip made of a thin layer deposited on a substrate is presented in this paper. The difference in evaporation field between the materials is taken into account in this approach in which the tip shape is modeled at a mesoscopic scale. It was found that the non-existence of sharp edge on the surface is a sufficient condition to derive the morphological evolution during successive evaporation of the layers. This modeling gives an instantaneous and smooth analytical representation of the surface that shows good agreement with finite difference simulations results, and a specific regime of evaporation was highlighted when the substrate is a low evaporation field phase. In addition, the model makes it possible to calculate theoretically the tip analyzed volume, potentially opening up new horizons for atom probe tomographic reconstruction. Copyright © 2015 Elsevier B.V. All rights reserved.

Hydrodynamic effects on phase transition in active matter

NASA Astrophysics Data System (ADS)

Gidituri, Harinadha; Akella, V. S.; Panchagnula, Mahesh; Vedantam, Srikanth; Multiphase flow physics lab Team

2017-11-01

Organized motion of active (self-propelled) objects are ubiquitous in nature. The objective of this study to investigate the effect of hydrodynamics on the coherent structures in active and passive particle mixtures. We use a mesoscopic method Dissipative Particle Dynamics (DPD). The system shows three different states viz. meso-turbulent (disordered state), polar flock and vortical (ordered state) for different values of activity and volume fraction of active particles. From our numerical simulations we construct a phase diagram between activity co-efficient, volume fraction and viscosity of the passive fluid. Transition from vortical to polar is triggered by increasing the viscosity of passive fluid which causes strong short-range hydrodynamic interactions. However, as the viscosity of the fluid decreases, both vortical and meso-turbulent states transition to polar flock phase. We also calculated the diffusion co-efficients via mean square displacement (MSD) for passive and active particles. We observe ballistic and diffusive regimes in the present system.

Direct extraction of electron parameters from magnetoconductance analysis in mesoscopic ring array structures

NASA Astrophysics Data System (ADS)

Sawada, A.; Faniel, S.; Mineshige, S.; Kawabata, S.; Saito, K.; Kobayashi, K.; Sekine, Y.; Sugiyama, H.; Koga, T.

2018-05-01

We report an approach for examining electron properties using information about the shape and size of a nanostructure as a measurement reference. This approach quantifies the spin precession angles per unit length directly by considering the time-reversal interferences on chaotic return trajectories within mesoscopic ring arrays (MRAs). Experimentally, we fabricated MRAs using nanolithography in InGaAs quantum wells which had a gate-controllable spin-orbit interaction (SOI). As a result, we observed an Onsager symmetry related to relativistic magnetic fields, which provided us with indispensable information for the semiclassical billiard ball simulation. Our simulations, developed based on the real-space formalism of the weak localization/antilocalization effect including the degree of freedom for electronic spin, reproduced the experimental magnetoconductivity (MC) curves with high fidelity. The values of five distinct electron parameters (Fermi wavelength, spin precession angles per unit length for two different SOIs, impurity scattering length, and phase coherence length) were thereby extracted from a single MC curve. The methodology developed here is applicable to wide ranges of nanomaterials and devices, providing a diagnostic tool for exotic properties of two-dimensional electron systems.

Viscous and thermal modelling of thermoplastic composites forming process

NASA Astrophysics Data System (ADS)

Guzman, Eduardo; Liang, Biao; Hamila, Nahiene; Boisse, Philippe

2016-10-01

Thermoforming thermoplastic prepregs is a fast manufacturing process. It is suitable for automotive composite parts manufacturing. The simulation of thermoplastic prepreg forming is achieved by alternate thermal and mechanical analyses. The thermal properties are obtained from a mesoscopic analysis and a homogenization procedure. The forming simulation is based on a viscous-hyperelastic approach. The thermal simulations define the coefficients of the mechanical model that depend on the temperature. The forming simulations modify the boundary conditions and the internal geometry of the thermal analyses. The comparison of the simulation with an experimental thermoforming of a part representative of automotive applications shows the efficiency of the approach.

Imaging electron wave functions inside open quantum rings.

PubMed

Martins, F; Hackens, B; Pala, M G; Ouisse, T; Sellier, H; Wallart, X; Bollaert, S; Cappy, A; Chevrier, J; Bayot, V; Huant, S

2007-09-28

Combining scanning gate microscopy (SGM) experiments and simulations, we demonstrate low temperature imaging of the electron probability density |Psi|(2)(x,y) in embedded mesoscopic quantum rings. The tip-induced conductance modulations share the same temperature dependence as the Aharonov-Bohm effect, indicating that they originate from electron wave function interferences. Simulations of both |Psi|(2)(x,y) and SGM conductance maps reproduce the main experimental observations and link fringes in SGM images to |Psi|(2)(x,y).

Mesoscopic Model — Advanced Simulation of Microforming Processes

NASA Astrophysics Data System (ADS)

Geißdörfer, Stefan; Engel, Ulf; Geiger, Manfred

2007-04-01

Continued miniaturization in many fields of forming technology implies the need for a better understanding of the effects occurring while scaling down from conventional macroscopic scale to microscale. At microscale, the material can no longer be regarded as a homogeneous continuum because of the presence of only a few grains in the deformation zone. This leads to a change in the material behaviour resulting among others in a large scatter of forming results. A correlation between the integral flow stress of the workpiece and the scatter of the process factors on the one hand and the mean grain size and its standard deviation on the other hand has been observed in experiments. The conventional FE-simulation of scaled down processes is not able to consider the size-effects observed such as the actual reduction of the flow stress, the increasing scatter of the process factors and a local material flow being different to that obtained in the case of macroparts. For that reason, a new simulation model has been developed taking into account all the size-effects. The present paper deals with the theoretical background of the new mesoscopic model, its characteristics like synthetic grain structure generation and the calculation of micro material properties — based on conventional material properties. The verification of the simulation model is done by carrying out various experiments with different mean grain sizes and grain structures but the same geometrical dimensions of the workpiece.

Low-noise current amplifier based on mesoscopic Josephson junction.

PubMed

Delahaye, J; Hassel, J; Lindell, R; Sillanpää, M; Paalanen, M; Seppä, H; Hakonen, P

2003-02-14

We used the band structure of a mesoscopic Josephson junction to construct low-noise amplifiers. By taking advantage of the quantum dynamics of a Josephson junction, i.e., the interplay of interlevel transitions and the Coulomb blockade of Cooper pairs, we created transistor-like devices, Bloch oscillating transistors, with considerable current gain and high-input impedance. In these transistors, the correlated supercurrent of Cooper pairs is controlled by a small base current made up of single electrons. Our devices reached current and power gains on the order of 30 and 5, respectively. The noise temperature was estimated to be around 1 kelvin, but noise temperatures of less than 0.1 kelvin can be realistically achieved. These devices provide quantum-electronic building blocks that will be useful at low temperatures in low-noise circuit applications with an intermediate impedance level.

Out-of-equilibrium spin transport in mesoscopic superconductors.

PubMed

Quay, C H L; Aprili, M

2018-08-06

The excitations in conventional superconductors, Bogoliubov quasi-particles, are spin-[Formula: see text] fermions but their charge is energy-dependent and, in fact, zero at the gap edge. Therefore, in superconductors (unlike normal metals) spin and charge degrees of freedom may be separated. In this article, we review spin injection into conventional superconductors and focus on recent experiments on mesoscopic superconductors. We show how quasi-particle spin transport and out-of-equilibrium spin-dependent superconductivity can be triggered using the Zeeman splitting of the quasi-particle density of states in thin-film superconductors with small spin-mixing scattering. Finally, we address the spin dynamics and the feedback of quasi-particle spin imbalances on the amplitude of the superconducting energy gap.This article is part of the theme issue 'Andreev bound states'. © 2018 The Author(s).

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

NASA Astrophysics Data System (ADS)

Katsoulakis, Markos A.; Vlachos, Dionisios G.

2003-11-01

We derive a hierarchy of successively coarse-grained stochastic processes and associated coarse-grained Monte Carlo (CGMC) algorithms directly from the microscopic processes as approximations in larger length scales for the case of diffusion of interacting particles on a lattice. This hierarchy of models spans length scales between microscopic and mesoscopic, satisfies a detailed balance, and gives self-consistent fluctuation mechanisms whose noise is asymptotically identical to the microscopic MC. Rigorous, detailed asymptotics justify and clarify these connections. Gradient continuous time microscopic MC and CGMC simulations are compared under far from equilibrium conditions to illustrate the validity of our theory and delineate the errors obtained by rigorous asymptotics. Information theory estimates are employed for the first time to provide rigorous error estimates between the solutions of microscopic MC and CGMC, describing the loss of information during the coarse-graining process. Simulations under periodic boundary conditions are used to verify the information theory error estimates. It is shown that coarse-graining in space leads also to coarse-graining in time by q2, where q is the level of coarse-graining, and overcomes in part the hydrodynamic slowdown. Operation counting and CGMC simulations demonstrate significant CPU savings in continuous time MC simulations that vary from q3 for short potentials to q4 for long potentials. Finally, connections of the new coarse-grained stochastic processes to stochastic mesoscopic and Cahn-Hilliard-Cook models are made.

Mesoscopic Modeling of the Encapsulation of Capsaicin by Lecithin/Chitosan Liposomal Nanoparticles.

PubMed

Terrón-Mejía, Ketzasmin A; Martínez-Benavidez, Evelin; Higuera-Ciapara, Inocencio; Virués, Claudia; Hernández, Javier; Domínguez, Zaira; Argüelles-Monal, Waldo; Goycoolea, Francisco M; López-Rendón, Roberto; Gama Goicochea, Armando

2018-06-12

The transport of hydrophobic drugs in the human body exhibits complications due to the low solubility of these compounds. With the purpose of enhancing the bioavailability and biodistribution of such drugs, recent studies have reported the use of amphiphilic molecules, such as phospholipids, for the synthesis of nanoparticles or nanocapsules. Given that phospholipids can self-assemble in liposomes or micellar structures, they are ideal candidates to function as vehicles of hydrophobic molecules. In this work, we report mesoscopic simulations of nanoliposomes, constituted by lecithin and coated with a shell of chitosan. The stability of such structures and the efficiency of the encapsulation of capsaicin, as well as the internal and superficial distribution of capsaicin and chitosan inside the nanoliposome, were analyzed. The characterization of the system was carried out through density maps and the potentials of mean force for the lecithin-capsaicin, lecithin-chitosan, and capsaicin-chitosan interactions. The results of these simulations show that chitosan is deposited on the surface of the nanoliposome, as has been reported in some experimental works. It was also observed that a nanoliposome of approximately 18 nm in diameter is stable during the simulation. The deposition behavior was found to be influenced by a pattern of N-acetylation of chitosan.

REPERTOIRE OF MESOSCOPIC CORTICAL ACTIVITY IS NOT REDUCED DURING ANESTHESIA

PubMed Central

HUDETZ, ANTHONY G.; VIZUETE, JEANNETTE A.; PILLAY, SIVESHIGAN; MASHOUR, GEORGE A.

2016-01-01

Consciousness has been linked to the repertoire of brain states at various spatiotemporal scales. Anesthesia is thought to modify consciousness by altering information integration in cortical and thalamocortical circuits. At a mesoscopic scale, neuronal populations in the cortex form synchronized ensembles whose characteristics are presumably state-dependent but this has not been rigorously tested. In this study, spontaneous neuronal activity was recorded with 64-contact microelectrode arrays in primary visual cortex of chronically instrumented, unrestrained rats under stepwise decreasing levels of desflurane anesthesia (8%, 6%, 4%, and 2% inhaled concentrations) and wakefulness (0% concentration). Negative phases of the local field potentials formed compact, spatially contiguous activity patterns (CAPs) that were not due to chance. The number of CAPs was 120% higher in wakefulness and deep anesthesia associated with burst-suppression than at intermediate levels of consciousness. The frequency distribution of CAP sizes followed a power–law with slope −1.5 in relatively deep anesthesia (8–6%) but deviated from that at the lighter levels. Temporal variance and entropy of CAP sizes were lowest in wakefulness (76% and 24% lower at 0% than at 8% desflurane, respectively) but changed little during recovery of consciousness. CAPs categorized by K-means clustering were conserved at all anesthesia levels and wakefulness, although their proportion changed in a state-dependent manner. These observations yield new knowledge about the dynamic landscape of ongoing population activity in sensory cortex at graded levels of anesthesia. The repertoire of population activity and self-organized criticality at the mesoscopic scale do not appear to contribute to anesthetic suppression of consciousness, which may instead depend on large-scale effects, more subtle dynamic properties, or changes outside of primary sensory cortex. PMID:27751957

Repertoire of mesoscopic cortical activity is not reduced during anesthesia.

PubMed

Hudetz, Anthony G; Vizuete, Jeannette A; Pillay, Siveshigan; Mashour, George A

2016-12-17

Consciousness has been linked to the repertoire of brain states at various spatiotemporal scales. Anesthesia is thought to modify consciousness by altering information integration in cortical and thalamocortical circuits. At a mesoscopic scale, neuronal populations in the cortex form synchronized ensembles whose characteristics are presumably state-dependent but this has not been rigorously tested. In this study, spontaneous neuronal activity was recorded with 64-contact microelectrode arrays in primary visual cortex of chronically instrumented, unrestrained rats under stepwise decreasing levels of desflurane anesthesia (8%, 6%, 4%, and 2% inhaled concentrations) and wakefulness (0% concentration). Negative phases of the local field potentials formed compact, spatially contiguous activity patterns (CAPs) that were not due to chance. The number of CAPs was 120% higher in wakefulness and deep anesthesia associated with burst-suppression than at intermediate levels of consciousness. The frequency distribution of CAP sizes followed a power-law with slope -1.5 in relatively deep anesthesia (8-6%) but deviated from that at the lighter levels. Temporal variance and entropy of CAP sizes were lowest in wakefulness (76% and 24% lower at 0% than at 8% desflurane, respectively) but changed little during recovery of consciousness. CAPs categorized by K-means clustering were conserved at all anesthesia levels and wakefulness, although their proportion changed in a state-dependent manner. These observations yield new knowledge about the dynamic landscape of ongoing population activity in sensory cortex at graded levels of anesthesia. The repertoire of population activity and self-organized criticality at the mesoscopic scale do not appear to contribute to anesthetic suppression of consciousness, which may instead depend on large-scale effects, more subtle dynamic properties, or changes outside of primary sensory cortex. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

Cavity QED with hybrid nanocircuits: from atomic-like physics to condensed matter phenomena

NASA Astrophysics Data System (ADS)

Cottet, Audrey; Dartiailh, Matthieu C.; Desjardins, Matthieu M.; Cubaynes, Tino; Contamin, Lauriane C.; Delbecq, Matthieu; Viennot, Jérémie J.; Bruhat, Laure E.; Douçot, Benoit; Kontos, Takis

2017-11-01

Circuit QED techniques have been instrumental in manipulating and probing with exquisite sensitivity the quantum state of superconducting quantum bits coupled to microwave cavities. Recently, it has become possible to fabricate new devices in which the superconducting quantum bits are replaced by hybrid mesoscopic circuits combining nanoconductors and metallic reservoirs. This mesoscopic QED provides a new experimental playground to study the light-matter interaction in electronic circuits. Here, we present the experimental state of the art of mesoscopic QED and its theoretical description. A first class of experiments focuses on the artificial atom limit, where some quasiparticles are trapped in nanocircuit bound states. In this limit, the circuit QED techniques can be used to manipulate and probe electronic degrees of freedom such as confined charges, spins, or Andreev pairs. A second class of experiments uses cavity photons to reveal the dynamics of electron tunneling between a nanoconductor and fermionic reservoirs. For instance, the Kondo effect, the charge relaxation caused by grounded metallic contacts, and the photo-emission caused by voltage-biased reservoirs have been studied. The tunnel coupling between nanoconductors and fermionic reservoirs also enable one to obtain split Cooper pairs, or Majorana bound states. Cavity photons represent a qualitatively new tool to study these exotic condensed matter states.

Cavity QED with hybrid nanocircuits: from atomic-like physics to condensed matter phenomena.

PubMed

Cottet, Audrey; Dartiailh, Matthieu C; Desjardins, Matthieu M; Cubaynes, Tino; Contamin, Lauriane C; Delbecq, Matthieu; Viennot, Jérémie J; Bruhat, Laure E; Douçot, Benoit; Kontos, Takis

2017-11-01

Circuit QED techniques have been instrumental in manipulating and probing with exquisite sensitivity the quantum state of superconducting quantum bits coupled to microwave cavities. Recently, it has become possible to fabricate new devices in which the superconducting quantum bits are replaced by hybrid mesoscopic circuits combining nanoconductors and metallic reservoirs. This mesoscopic QED provides a new experimental playground to study the light-matter interaction in electronic circuits. Here, we present the experimental state of the art of mesoscopic QED and its theoretical description. A first class of experiments focuses on the artificial atom limit, where some quasiparticles are trapped in nanocircuit bound states. In this limit, the circuit QED techniques can be used to manipulate and probe electronic degrees of freedom such as confined charges, spins, or Andreev pairs. A second class of experiments uses cavity photons to reveal the dynamics of electron tunneling between a nanoconductor and fermionic reservoirs. For instance, the Kondo effect, the charge relaxation caused by grounded metallic contacts, and the photo-emission caused by voltage-biased reservoirs have been studied. The tunnel coupling between nanoconductors and fermionic reservoirs also enable one to obtain split Cooper pairs, or Majorana bound states. Cavity photons represent a qualitatively new tool to study these exotic condensed matter states.

Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry.

PubMed

Kalay, Ziya

2011-08-01

How small can a macroscopic object be made without losing its intended function? Obviously, the smallest possible size is determined by the size of an atom, but it is not so obvious how many atoms are required to assemble an object so small, and yet that performs the same function as its macroscopic counterpart. In this review, we are concerned with objects of intermediate nature, lying between the microscopic and the macroscopic world. In physics and chemistry literature, this regime in-between is often called mesoscopic, and is known to bear interesting and counterintuitive features. After a brief introduction to the concept of mesoscopic systems from the perspective of physics, we discuss the functional aspects of mesoscopic architectures in cell biology, and supramolecular chemistry through many examples from the literature. We argue that the biochemistry of the cell is largely regulated by mesoscopic functional architectures; however, the significance of mesoscopic phenomena seems to be quite underappreciated in biological sciences. With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry.

Poroelastic finite difference modeling of seismic attenuation and dispersion due to mesoscopic-scale heterogeneity

NASA Astrophysics Data System (ADS)

Masson, Y. J.; Pride, S. R.

2007-03-01

Seismic attenuation and dispersion are numerically determined for computer-generated porous materials that contain arbitrary amounts of mesoscopic-scale heterogeneity in the porous continuum properties. The local equations used to determine the poroelastic response within such materials are those of Biot (1962). Upon applying a step change in stress to samples containing mesoscopic-scale heterogeneity, the poroelastic response is determined using finite difference modeling, and the average strain throughout the sample computed, along with the effective complex and frequency-dependent elastic moduli of the sample. The ratio of the imaginary and real parts of these moduli determines the attenuation as a function of frequency associated with the modes of applied stress (pure compression and pure shear). By having a wide range of heterogeneity present, there exists a wide range of relaxation frequencies in the response with the result that the curves of attenuation as a function of frequency are broader than in existing analytical theories based on a single relaxation frequency. Analytical explanations are given for the various high-frequency and low-frequency asymptotic behavior observed in the numerical simulations. It is also shown that the overall level of attenuation of a given sample is proportional to the square of the incompressibility contrasts locally present.

A mesoscopic reaction rate model for shock initiation of multi-component PBX explosives.

PubMed

Liu, Y R; Duan, Z P; Zhang, Z Y; Ou, Z C; Huang, F L

2016-11-05

The primary goal of this research is to develop a three-term mesoscopic reaction rate model that consists of a hot-spot ignition, a low-pressure slow burning and a high-pressure fast reaction terms for shock initiation of multi-component Plastic Bonded Explosives (PBX). Thereinto, based on the DZK hot-spot model for a single-component PBX explosive, the hot-spot ignition term as well as its reaction rate is obtained through a "mixing rule" of the explosive components; new expressions for both the low-pressure slow burning term and the high-pressure fast reaction term are also obtained by establishing the relationships between the reaction rate of the multi-component PBX explosive and that of its explosive components, based on the low-pressure slow burning term and the high-pressure fast reaction term of a mesoscopic reaction rate model. Furthermore, for verification, the new reaction rate model is incorporated into the DYNA2D code to simulate numerically the shock initiation process of the PBXC03 and the PBXC10 multi-component PBX explosives, and the numerical results of the pressure histories at different Lagrange locations in explosive are found to be in good agreements with previous experimental data. Copyright © 2016 Elsevier B.V. All rights reserved.

Fluctuations and differential contraction during regeneration of Hydra vulgaris tissue toroids

NASA Astrophysics Data System (ADS)

Krahe, Michael; Wenzel, Iris; Lin, Kao-Nung; Fischer, Julia; Goldmann, Joseph; Kästner, Markus; Fütterer, Claus

2013-03-01

We studied regenerating bilayered tissue toroids dissected from Hydra vulgaris polyps and relate our macroscopic observations to the dynamics of force-generating mesoscopic cytoskeletal structures. Tissue fragments undergo a specific toroid-spheroid folding process leading to complete regeneration towards a new organism. The time scale of folding is too fast for biochemical signalling or morphogenetic gradients, which forced us to assume purely mechanical self-organization. The initial pattern selection dynamics was studied by embedding toroids into hydro-gels, allowing us to observe the deformation modes over longer periods of time. We found increasing mechanical fluctuations which break the toroidal symmetry, and discuss the evolution of their power spectra for various gel stiffnesses. Our observations are related to single-cell studies which explain the mechanical feasibility of the folding process. In addition, we observed switching of cells from a tissue bound to a migrating state after folding failure as well as in tissue injury. We found a supra-cellular actin ring assembled along the toroid's inner edge. Its contraction can lead to the observed folding dynamics as we could confirm by finite element simulations. This actin ring in the inner cell layer is assembled by myosin-driven length fluctuations of supra-cellular F-actin bundles (myonemes) in the outer cell layer. This paper is dedicated to Malcolm Steinberg.

a Numerical Investigation of the Jamming Transition in Traffic Flow on Diluted Planar Networks

NASA Astrophysics Data System (ADS)

Achler, Gabriele; Barra, Adriano

In order to develop a toy model for car's traffic in cities, in this paper we analyze, by means of numerical simulations, the transition among fluid regimes and a congested jammed phase of the flow of kinetically constrained hard spheres in planar random networks similar to urban roads. In order to explore as timescales as possible, at a microscopic level we implement an event driven dynamics as the infinite time limit of a class of already existing model (Follow the Leader) on an Erdos-Renyi two-dimensional graph, the crossroads being accounted by standard Kirchoff density conservations. We define a dynamical order parameter as the ratio among the moving spheres versus the total number and by varying two control parameters (density of the spheres and coordination number of the network) we study the phase transition. At a mesoscopic level it respects an, again suitable, adapted version of the Lighthill-Whitham model, which belongs to the fluid-dynamical approach to the problem. At a macroscopic level, the model seems to display a continuous transition from a fluid phase to a jammed phase when varying the density of the spheres (the amount of cars in a city-like scenario) and a discontinuous jump when varying the connectivity of the underlying network.

A review of progress in the physics of open quantum systems: theory and experiment.

PubMed

Rotter, I; Bird, J P

2015-11-01

This report on progress explores recent advances in our theoretical and experimental understanding of the physics of open quantum systems (OQSs). The study of such systems represents a core problem in modern physics that has evolved to assume an unprecedented interdisciplinary character. OQSs consist of some localized, microscopic, region that is coupled to an external environment by means of an appropriate interaction. Examples of such systems may be found in numerous areas of physics, including atomic and nuclear physics, photonics, biophysics, and mesoscopic physics. It is the latter area that provides the main focus of this review, an emphasis that is driven by the capacity that exists to subject mesoscopic devices to unprecedented control. We thus provide a detailed discussion of the behavior of mesoscopic devices (and other OQSs) in terms of the projection-operator formalism, according to which the system under study is considered to be comprised of a localized region (Q), embedded into a well-defined environment (P) of scattering wavefunctions (with Q   +   P   =   1). The Q subspace must be treated using the concepts of non-Hermitian physics, and of particular interest here is: the capacity of the environment to mediate a coupling between the different states of Q; the role played by the presence of exceptional points (EPs) in the spectra of OQSs; the influence of EPs on the rigidity of the wavefunction phases, and; the ability of EPs to initiate a dynamical phase transition (DPT). EPs are singular points in the continuum, at which two resonance states coalesce, that is where they exhibit a non-avoided crossing. DPTs occur when the quantum dynamics of the open system causes transitions between non-analytically connected states, as a function of some external control parameter. Much like conventional phase transitions, the behavior of the system on one side of the DPT does not serve as a reliable indicator of that on the other. In addition to discussing experiments on mesoscopic quantum point contacts that provide evidence of the environmentally-mediated coupling of quantum states, we also review manifestations of DPTs in mesoscopic devices and other systems. These experiments include observations of resonance-trapping behavior in microwave cavities and open quantum dots, phase lapses in tunneling through single-electron transistors, and spin swapping in atomic ensembles. Other possible manifestations of this phenomenon are presented, including various superradiant phenomena in low-dimensional semiconductors. From these discussions a generic picture of OQSs emerges in which the environmentally-mediated coupling between different quantum states plays a critical role in governing the system behavior. The ability to control or manipulate this interaction may even lead to new applications in photonics and electronics.

Nonmonotonic diffusion in crowded environments

PubMed Central

Putzel, Gregory Garbès; Tagliazucchi, Mario; Szleifer, Igal

2015-01-01

We study the diffusive motion of particles among fixed spherical crowders. The diffusers interact with the crowders through a combination of a hard-core repulsion and a short-range attraction. The long-time effective diffusion coefficient of the diffusers is found to depend non-monotonically on the strength of their attraction to the crowders. That is, for a given concentration of crowders, a weak attraction to the crowders enhances diffusion. We show that this counterintuitive fact can be understood in terms of the mesoscopic excess chemical potential landscape experienced by the diffuser. The roughness of this excess chemical potential landscape quantitatively captures the nonmonotonic dependence of the diffusion rate on the strength of crowder-diffuser attraction; thus it is a purely static predictor of dynamic behavior. The mesoscopic view given here provides a unified explanation for enhanced diffusion effects that have been found in various systems of technological and biological interest. PMID:25302920

Efficient Tuning of Optical Properties and Morphology of Mesoscopic CdS via a Facile Route

NASA Astrophysics Data System (ADS)

Aslam, Samia; Mustafa, Faiza; Jamil, Ayesha; Abbas, Ghazanfar; Raza, Rizwan; Ahmad, Muhammad Ashfaq

2018-03-01

A facile and simple synthetic route has been employed to synthesize rod-shaped optically efficient cadmium sulfide (CdS) mesoscopic structures using high concentrations of cetyl trimethyl ammonium bromide (CTAB) as the stabilizing agent. The mesoscopic structures were characterized using x-ray diffaractometer (XRD), scanning electron microscopy, UV-visible, photoluminescence (PL), and Fourier transform and infrared (FTIR) spectroscopy. It was found that, if the concentration of CTAB is significantly higher than its critical micelle concentration, the nucleation of CdS mesoscopic structures resulted in rod-like structures. The size of the mesoscopic structures initially increased and then decreased with band gaps 2.5-2.7 eV. XRD analysis showed that the samples had a pure cubic phase confirming the particle size. The values of Urbach energy for the absorption tail states were determined and found to be in agreement with the single crystal. PL spectra showed sharp green emission peaks in the 530-nm to 560-nm wavelength range. FTIR spectra showed the adsorption mode of CTAB onto the CdS mesoscopic structures. A possible mechanism of formation of rod-shaped CdS mesoscopic structures is also elucidated.

Mesoscopic pairing without superconductivity

NASA Astrophysics Data System (ADS)

Hofmann, Johannes

2017-12-01

We discuss pairing signatures in mesoscopic nanowires with a variable attractive pairing interaction. Depending on the wire length, density, and interaction strength, these systems realize a simultaneous bulk-to-mesoscopic and BCS-BEC crossover, which we describe in terms of the parity parameter that quantifies the odd-even energy difference and generalizes the bulk Cooper pair binding energy to mesoscopic systems. We show that the parity parameter can be extracted from recent measurements of conductance oscillations in SrTiO3 nanowires by Cheng et al. [Nature (London) 521, 196 (2015), 10.1038/nature14398], where it marks the critical magnetic field that separates pair and single-particle currents. Our results place the experiment in the fluctuation-dominated mesoscopic regime on the BCS side of the crossover.

Multi Length Scale Finite Element Design Framework for Advanced Woven Fabrics

NASA Astrophysics Data System (ADS)

Erol, Galip Ozan

Woven fabrics are integral parts of many engineering applications spanning from personal protective garments to surgical scaffolds. They provide a wide range of opportunities in designing advanced structures because of their high tenacity, flexibility, high strength-to-weight ratios and versatility. These advantages result from their inherent multi scale nature where the filaments are bundled together to create yarns while the yarns are arranged into different weave architectures. Their highly versatile nature opens up potential for a wide range of mechanical properties which can be adjusted based on the application. While woven fabrics are viable options for design of various engineering systems, being able to understand the underlying mechanisms of the deformation and associated highly nonlinear mechanical response is important and necessary. However, the multiscale nature and relationships between these scales make the design process involving woven fabrics a challenging task. The objective of this work is to develop a multiscale numerical design framework using experimentally validated mesoscopic and macroscopic length scale approaches by identifying important deformation mechanisms and recognizing the nonlinear mechanical response of woven fabrics. This framework is exercised by developing mesoscopic length scale constitutive models to investigate plain weave fabric response under a wide range of loading conditions. A hyperelastic transversely isotropic yarn material model with transverse material nonlinearity is developed for woven yarns (commonly used in personal protection garments). The material properties/parameters are determined through an inverse method where unit cell finite element simulations are coupled with experiments. The developed yarn material model is validated by simulating full scale uniaxial tensile, bias extension and indentation experiments, and comparing to experimentally observed mechanical response and deformation mechanisms. Moreover, mesoscopic unit cell finite elements are coupled with a design-of-experiments method to systematically identify the important yarn material properties for the macroscale response of various weave architectures. To demonstrate the macroscopic length scale approach, two new material models for woven fabrics were developed. The Planar Material Model (PMM) utilizes two important deformation mechanisms in woven fabrics: (1) yarn elongation, and (2) relative yarn rotation due to shear loads. The yarns' uniaxial tensile response is modeled with a nonlinear spring using constitutive relations while a nonlinear rotational spring is implemented to define fabric's shear stiffness. The second material model, Sawtooth Material Model (SMM) adopts the sawtooth geometry while recognizing the biaxial nature of woven fabrics by implementing the interactions between the yarns. Material properties/parameters required by both PMM and SMM can be directly determined from standard experiments. Both macroscopic material models are implemented within an explicit finite element code and validated by comparing to the experiments. Then, the developed macroscopic material models are compared under various loading conditions to determine their accuracy. Finally, the numerical models developed in the mesoscopic and macroscopic length scales are linked thus demonstrating the new systematic design framework involving linked mesoscopic and macroscopic length scale modeling approaches. The approach is demonstrated with both Planar and Sawtooth Material Models and the simulation results are verified by comparing the results obtained from meso and macro models.

Finite element modelling of woven composite failure modes at the mesoscopic scale: deterministic versus stochastic approaches

NASA Astrophysics Data System (ADS)

Roirand, Q.; Missoum-Benziane, D.; Thionnet, A.; Laiarinandrasana, L.

2017-09-01

Textile composites are composed of 3D complex architecture. To assess the durability of such engineering structures, the failure mechanisms must be highlighted. Examinations of the degradation have been carried out thanks to tomography. The present work addresses a numerical damage model dedicated to the simulation of the crack initiation and propagation at the scale of the warp yarns. For the 3D woven composites under study, loadings in tension and combined tension and bending were considered. Based on an erosion procedure of broken elements, the failure mechanisms have been modelled on 3D periodic cells by finite element calculations. The breakage of one element was determined using a failure criterion at the mesoscopic scale based on the yarn stress at failure. The results were found to be in good agreement with the experimental data for the two kinds of macroscopic loadings. The deterministic approach assumed a homogeneously distributed stress at failure all over the integration points in the meshes of woven composites. A stochastic approach was applied to a simple representative elementary periodic cell. The distribution of the Weibull stress at failure was assigned to the integration points using a Monte Carlo simulation. It was shown that this stochastic approach allowed more realistic failure simulations avoiding the idealised symmetry due to the deterministic modelling. In particular, the stochastic simulations performed have shown several variations of the stress as well as strain at failure and the failure modes of the yarn.

Band and Correlated Insulators of Cold Fermions in a Mesoscopic Lattice

NASA Astrophysics Data System (ADS)

Lebrat, Martin; Grišins, Pjotrs; Husmann, Dominik; Häusler, Samuel; Corman, Laura; Giamarchi, Thierry; Brantut, Jean-Philippe; Esslinger, Tilman

2018-01-01

We investigate the transport properties of neutral, fermionic atoms passing through a one-dimensional quantum wire containing a mesoscopic lattice. The lattice is realized by projecting individually controlled, thin optical barriers on top of a ballistic conductor. Building an increasingly longer lattice, one site after another, we observe and characterize the emergence of a band insulating phase, demonstrating control over quantum-coherent transport. We explore the influence of atom-atom interactions and show that the insulating state persists as contact interactions are tuned from moderately to strongly attractive. Using bosonization and classical Monte Carlo simulations, we analyze such a model of interacting fermions and find good qualitative agreement with the data. The robustness of the insulating state supports the existence of a Luther-Emery liquid in the one-dimensional wire. Our work realizes a tunable, site-controlled lattice Fermi gas strongly coupled to reservoirs, which is an ideal test bed for nonequilibrium many-body physics.

Spatial confinement governs orientational order in patchy particles

NASA Astrophysics Data System (ADS)

Iwashita, Yasutaka; Kimura, Yasuyuki

2016-06-01

Orientational order in condensed matter plays a key role in determining material properties such as ferromagnetism, viscoelasticity or birefringence. We studied purely orientational ordering in closely-packed one-patch colloidal particles confined between flat substrates, where the particles can only rotate and are ordered via the sticky interaction between the patches. For the first time, we experimentally realized a rich variety of mesoscopic patterns through orientational ordering of colloids by controlling patch size and confinement thickness. The combination of experiment and numerical simulation reveals the decisive role of confinement: An ordered state(s) is selected from the (meta)stable options in bulk when it is commensurate with the system geometry and boundary conditions; otherwise, frustration induces a unique order. Our study offers a new means of systematic control over mesoscopic structures via orientational ordering in patchy particles. The system would also possess unique functionalities through the rotational response of the particles to external stimuli.

Local dynamic nuclear polarization using quantum point contacts

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

Wald, K.R.; Kouwenhoven, L.P.; McEuen, P.L.

1994-08-15

We have used quantum point contacts (QPCs) to locally create and probe dynamic nuclear polarization (DNP) in GaAs heterostructures in the quantum Hall regime. DNP is created via scattering between spin-polarized Landau level electrons and the Ga and As nuclear spins, and it leads to hysteresis in the dc transport characteristics. The nuclear origin of this hysteresis is demonstrated by nuclear magnetic resonance (NMR). Our results show that QPCs can be used to create and probe local nuclear spin populations, opening up new possibilities for mesoscopic NMR experiments.

Molecular simulations of lipid-mediated protein-protein interactions.

PubMed

de Meyer, Frédérick Jean-Marie; Venturoli, Maddalena; Smit, Berend

2008-08-01

Recent experimental results revealed that lipid-mediated interactions due to hydrophobic forces may be important in determining the protein topology after insertion in the membrane, in regulating the protein activity, in protein aggregation and in signal transduction. To gain insight into the lipid-mediated interactions between two intrinsic membrane proteins, we developed a mesoscopic model of a lipid bilayer with embedded proteins, which we studied with dissipative particle dynamics. Our calculations of the potential of mean force between transmembrane proteins show that hydrophobic forces drive long-range protein-protein interactions and that the nature of these interactions depends on the length of the protein hydrophobic segment, on the three-dimensional structure of the protein and on the properties of the lipid bilayer. To understand the nature of the computed potentials of mean force, the concept of hydrophilic shielding is introduced. The observed protein interactions are interpreted as resulting from the dynamic reorganization of the system to maintain an optimal hydrophilic shielding of the protein and lipid hydrophobic parts, within the constraint of the flexibility of the components. Our results could lead to a better understanding of several membrane processes in which protein interactions are involved.

Ionic transport through sub-10 nm diameter hydrophobic high-aspect ratio nanopores: experiment, theory and simulation

PubMed Central

Balme, Sébastien; Picaud, Fabien; Manghi, Manoel; Palmeri, John; Bechelany, Mikhael; Cabello-Aguilar, Simon; Abou-Chaaya, Adib; Miele, Philippe; Balanzat, Emmanuel; Janot, Jean Marc

2015-01-01

Fundamental understanding of ionic transport at the nanoscale is essential for developing biosensors based on nanopore technology and new generation high-performance nanofiltration membranes for separation and purification applications. We study here ionic transport through single putatively neutral hydrophobic nanopores with high aspect ratio (of length L = 6 μm with diameters ranging from 1 to 10 nm) and with a well controlled cylindrical geometry. We develop a detailed hybrid mesoscopic theoretical approach for the electrolyte conductivity inside nanopores, which considers explicitly ion advection by electro-osmotic flow and possible flow slip at the pore surface. By fitting the experimental conductance data we show that for nanopore diameters greater than 4 nm a constant weak surface charge density of about 10−2 C m−2 needs to be incorporated in the model to account for conductance plateaus of a few pico-siemens at low salt concentrations. For tighter nanopores, our analysis leads to a higher surface charge density, which can be attributed to a modification of ion solvation structure close to the pore surface, as observed in the molecular dynamics simulations we performed. PMID:26036687

Mesoscopic Simulations of Adsorption and Association of PEO-PPO-PEO Triblock Copolymers on a Hydrophobic Surface: From Mushroom Hemisphere to Rectangle Brush.

PubMed

Song, Xianyu; Zhao, Shuangliang; Fang, Shenwen; Ma, Yongzhang; Duan, Ming

2016-11-08

The dissipative particle dynamics (DPD) method is used to investigate the adsorption behavior of PEO-PPO-PEO triblock copolymers at the liquid/solid interface. The effect of molecular architecture on the self-assembled monolayer adsorption of PEO-PPO-PEO triblock copolymers on hydrophobic surfaces is elucidated by the adsorption process, film properties, and adsorption morphologies. The adsorption thicknesses on hydrophobic surfaces and the diffusion coefficient as well as the aggregation number of Pluronic copolymers in aqueous solution observed in our simulations agree well with previous experimental and numerical observations. The radial distribution function revealed that the ability of self-assembly on hydrophobic surfaces is P123 > P84 > L64 > P105 > F127, which increased with the EO ratio of the Pluronic copolymers. Moreover, the shape parameter and the degree of anisotropy increase with increasing molecular weight and mole ratio of PO of the Pluronic copolymers. Depending on the conformation of different Pluronic copolymers, the morphology transition of three regimes on hydrophobic surfaces is present: mushroom or hemisphere, progressively semiellipsoid, and rectangle brush regimes induced by decreasing molecular weight and mole ratio of EO of Pluronic copolymers.

Effective properties of dispersed phase reinforced composite materials with perfect and imperfect interfaces

NASA Astrophysics Data System (ADS)

Han, Ru

This thesis focuses on the analysis of dispersed phase reinforced composite materials with perfect as well as imperfect interfaces using the Boundary Element Method (BEM). Two problems of interest are considered, namely, to determine the limitations in the use of effective properties and the analysis of failure progression at the inclusion-matrix interface. The effective moduli (effective Young's modulus, effective Poisson's ratio, effective shear modulus, and effective bulk modulus) of composite materials can be determined at the mesoscopic level using three-dimensional parallel BEM simulations. By comparing the mesoscopic BEM results and the macroscopic results based on effective properties, limitations in the effective property approach can be determined. Decohesion is an important failure mode associated with fiber-reinforced composite materials. Analysis of failure progression at the fiber-matrix interface in fiber-reinforced composite materials is considered using a softening decohesion model consistent with thermodynamic concepts. In this model, the initiation of failure is given directly by a failure criterion. Damage is interpreted by the development of a discontinuity of displacement. The formulation describing the potential development of damage is governed by a discrete decohesive constitutive equation. Numerical simulations are performed using the direct boundary element method. Incremental decohesion simulations illustrate the progressive evolution of debonding zones and the propagation of cracks along the interfaces. The effect of decohesion on the macroscopic response of composite materials is also investigated.

Mesoscopic structural phase progression in photo-excited VO 2 revealed by time-resolved x-ray diffraction microscopy

DOE PAGES

Zhu, Yi; Cai, Zhonghou; Chen, Pice; ...

2016-02-26

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase seperated regions. The ability to simultanousely track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of- the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO 2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation ismore » initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO 2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, which is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO 2. Lastly, the direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.« less

Mesoscopic structural phase progression in photo-excited VO2 revealed by time-resolved x-ray diffraction microscopy

NASA Astrophysics Data System (ADS)

Zhu, Yi; Cai, Zhonghou; Chen, Pice; Zhang, Qingteng; Highland, Matthew J.; Jung, Il Woong; Walko, Donald A.; Dufresne, Eric M.; Jeong, Jaewoo; Samant, Mahesh G.; Parkin, Stuart S. P.; Freeland, John W.; Evans, Paul G.; Wen, Haidan

2016-02-01

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase separated regions. The ability to simultaneously track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of-the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation is initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, and is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO2. The direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.

Mesoscopic structural phase progression in photo-excited VO2 revealed by time-resolved x-ray diffraction microscopy.

PubMed

Zhu, Yi; Cai, Zhonghou; Chen, Pice; Zhang, Qingteng; Highland, Matthew J; Jung, Il Woong; Walko, Donald A; Dufresne, Eric M; Jeong, Jaewoo; Samant, Mahesh G; Parkin, Stuart S P; Freeland, John W; Evans, Paul G; Wen, Haidan

2016-02-26

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase separated regions. The ability to simultaneously track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of-the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation is initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, and is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO2. The direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.

Mesoscopic homogenization of semi-insulating GaAs by two-step post growth annealing

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

Hoffmann, B.; Jurisch, M.; Koehler, A.

1996-12-31

Mesoscopic homogenization of the electrical properties of s.i. LEC-GaAs is commonly realized by thermal treatment of the crystals including the steps of dissolution of arsenic precipitates, homogenization of excess As and re-precipitation by creating a controlled supersaturation. Caused by the inhomogeneous distribution of dislocations and the corresponding cellular structure along and across LEC-grown crystals a proper choice of the time-temperature program is necessary to minimize fluctuations of mesoscopic homogeneity. A modified two-step ingot annealing process is demonstrated to ensure the homogeneous distribution of mesoscopic homogeneity.

Influence of system size and solvent flow on the distribution of wormlike micelles in a contraction-expansion geometry

NASA Astrophysics Data System (ADS)

Stukan, M. R.; Boek, E. S.; Padding, J. T.; Crawshaw, J. P.

2008-05-01

Viscoelastic wormlike micelles are formed by surfactants assembling into elongated cylindrical structures. These structures respond to flow by aligning, breaking and reforming. Their response to the complex flow fields encountered in porous media is particularly rich. Here we use a realistic mesoscopic Brownian Dynamics model to investigate the flow of a viscoelastic surfactant (VES) fluid through individual pores idealized as a step expansion-contraction of size around one micron. In a previous study, we assumed the flow field to be Newtonian. Here we extend the work to include the non-Newtonian flow field previously obtained by experiment. The size of the simulations is also increased so that the pore is much larger than the radius of gyration of the micelles. For the non-Newtonian flow field at the higher flow rates in relatively large pores, the density of the micelles becomes markedly non-uniform. In this case, we find that the density in the large, slowly moving entry corner regions is substantially increased.

Fast relaxations in foam

NASA Astrophysics Data System (ADS)

Krishan, Kapilanjan; Helal, Ahmed; Höhler, Reinhard; Cohen-Addad, Sylvie

2010-07-01

Aqueous foams present an anomalous macroscopic viscoelastic response at high frequency, previously shown to arise from collective relaxations in the disordered bubble packing. We demonstrate experimentally how these mesoscopic dynamics are in turn tuned by physico-chemical processes on the scale of the gas-liquid interfaces. Two specific local dissipation processes are identified, and we show how the rigidity of the interfaces selects the dominant one, depending on the choice of the surfactant.

Four dimensional chaos and intermittency in a mesoscopic model of the electroencephalogram.

PubMed

Dafilis, Mathew P; Frascoli, Federico; Cadusch, Peter J; Liley, David T J

2013-06-01

The occurrence of so-called four dimensional chaos in dynamical systems represented by coupled, nonlinear, ordinary differential equations is rarely reported in the literature. In this paper, we present evidence that Liley's mesoscopic theory of the electroencephalogram (EEG), which has been used to describe brain activity in a variety of clinically relevant contexts, possesses a chaotic attractor with a Kaplan-Yorke dimension significantly larger than three. This accounts for simple, high order chaos for a physiologically admissible parameter set. Whilst the Lyapunov spectrum of the attractor has only one positive exponent, the contracting dimensions are such that the integer part of the Kaplan-Yorke dimension is three, thus giving rise to four dimensional chaos. A one-parameter bifurcation analysis with respect to the parameter corresponding to extracortical input is conducted, with results indicating that the origin of chaos is due to an inverse period doubling cascade. Hence, in the vicinity of the high order, strange attractor, the model is shown to display intermittent behavior, with random alternations between oscillatory and chaotic regimes. This phenomenon represents a possible dynamical justification of some of the typical features of clinically established EEG traces, which can arise in the case of burst suppression in anesthesia and epileptic encephalopathies in early infancy.

Smoothed dissipative particle dynamics with angular momentum conservation

NASA Astrophysics Data System (ADS)

Müller, Kathrin; Fedosov, Dmitry A.; Gompper, Gerhard

2015-01-01

Smoothed dissipative particle dynamics (SDPD) combines two popular mesoscopic techniques, the smoothed particle hydrodynamics and dissipative particle dynamics (DPD) methods, and can be considered as an improved dissipative particle dynamics approach. Despite several advantages of the SDPD method over the conventional DPD model, the original formulation of SDPD by Español and Revenga (2003) [9], lacks angular momentum conservation, leading to unphysical results for problems where the conservation of angular momentum is essential. To overcome this limitation, we extend the SDPD method by introducing a particle spin variable such that local and global angular momentum conservation is restored. The new SDPD formulation (SDPD+a) is directly derived from the Navier-Stokes equation for fluids with spin, while thermal fluctuations are incorporated similarly to the DPD method. We test the new SDPD method and demonstrate that it properly reproduces fluid transport coefficients. Also, SDPD with angular momentum conservation is validated using two problems: (i) the Taylor-Couette flow with two immiscible fluids and (ii) a tank-treading vesicle in shear flow with a viscosity contrast between inner and outer fluids. For both problems, the new SDPD method leads to simulation predictions in agreement with the corresponding analytical theories, while the original SDPD method fails to capture properly physical characteristics of the systems due to violation of angular momentum conservation. In conclusion, the extended SDPD method with angular momentum conservation provides a new approach to tackle fluid problems such as multiphase flows and vesicle/cell suspensions, where the conservation of angular momentum is essential.

Nonlinear Acoustic Landmine Detection: Profiling Soil Surface Vibrations and Modeling Mesoscopic Elastic Behavior

DTIC Science & Technology

2007-05-04

TITLE AND SUBTITLE Nonlinear Acoustic Landmine Detection: Profiling Soil Surface Vibrations and Modeling Mesoscopic Elastic Behavior 6. AUTHOR(S...project report; no. 352 (2007) NONLINEAR ACOUSTIC LANDMINE DETECTION: PROFILING SOIL SURFACE VIBRATIONS AND MODELING MESOSCOPIC ELASTIC... model (Caughey 1966). Nonlinear acoustic landmine detection experiments are performed in the anechoic chamber facility using both a buried acrylic

CHAIRMAN'S FOREWORD: First International Symposium on Advanced Nanodevices and Nanotechnology

NASA Astrophysics Data System (ADS)

Aoyagi, Yoshinobu; Goodnick, Stephen M.

2008-03-01

This volume of Journal of Physics: Conference Series contains selected papers from the First International Symposium on Advanced Nanodevices and Nanotechnology. This conference is a merging of the two previous series New Phenomena in Mesoscopic Structures and the Surfaces and Interfaces of Mesoscopic Devices. This year's conference was held 2-7 December 2007 at the Waikoloa Beach Marriott on the Kohala coast of the big island of Hawaii. The scope of ISANN spans nano-fabrication through complex phase coherent mesoscopic systems including nano-transistors and nano-scale characterization. Topics of interest included: Nano-scale fabrication (high-resolution electron lithography, FIB nano-patterning SFM lithography, SFM stimulated growth, novel patterning, nano-imprint lithography, special etching, and SAMs) Nano-characterization (SFM characterization, BEEM, optical studies of nanostructures, tunneling, properties of discrete impurities, phase coherence, noise, THz studies, electro-luminescence in small structures) Nano-devices (ultra-scaled FETs, quantum SETs, RTDs, ferromagnetic, and spin devices, superlattice arrays, IR detectors with quantum dots and wires, quantum point contacts, non-equilibrium transport, simulation, ballistic transport, molecular electronic devices, carbon nanotubes, spin selection devices, spin-coupled quantum dots, nano-magnetics) Quantum coherent transport (quantum Hall effect, ballistic quantum systems, quantum computing implementations and theory, magnetic spin systems, quantum NEMs) Mesoscopic structures (quantum wires and dots, chaos, non-equilibrium transport, instabilities, nano-electro-mechanical systems, mesoscopic Josephson effects, phase coherence and breaking, Kondo effect) Systems of nano-devices (QCAs, systolic SET processors, quantum neural nets, adaptive effects in circuits, molecular circuits, NEMs) Nanomaterials (nanotubes, nanowires, organic and molecular materials, self-assembled nanowires, organic devices) Nano-bio-electronics (electronic properties of biological structures on the nanoscale) We were very pleased and honored to have the opportunity to organize the first International Symposium on Advanced Nanodevices and Nanotechnology. The conference benefited from 14 invited speakers, whose topics spanned the above list, and a total of 90 registered attendees. The largest contingent was from Japan, followed closely by the USA. We wish to particularly thank the sponsors for the meeting: Arizona State University on the US side, and the Japan Society for the Promotion of Science, through their 151 Committee, on the Japanese side. We would also like to thank Dr Koji Ishibashi, of RIKEN, for his assistance in the organization of the conference, and Professor David K Ferry for serving as the Editor for the ISANN Proceedings. Yoshinobu Aoyagi and Stephen M Goodnick Conference Co-Chairs

Multi-Dimensional, Mesoscopic Monte Carlo Simulations of Inhomogeneous Reaction-Drift-Diffusion Systems on Graphics-Processing Units

PubMed Central

Vigelius, Matthias; Meyer, Bernd

2012-01-01

For many biological applications, a macroscopic (deterministic) treatment of reaction-drift-diffusion systems is insufficient. Instead, one has to properly handle the stochastic nature of the problem and generate true sample paths of the underlying probability distribution. Unfortunately, stochastic algorithms are computationally expensive and, in most cases, the large number of participating particles renders the relevant parameter regimes inaccessible. In an attempt to address this problem we present a genuine stochastic, multi-dimensional algorithm that solves the inhomogeneous, non-linear, drift-diffusion problem on a mesoscopic level. Our method improves on existing implementations in being multi-dimensional and handling inhomogeneous drift and diffusion. The algorithm is well suited for an implementation on data-parallel hardware architectures such as general-purpose graphics processing units (GPUs). We integrate the method into an operator-splitting approach that decouples chemical reactions from the spatial evolution. We demonstrate the validity and applicability of our algorithm with a comprehensive suite of standard test problems that also serve to quantify the numerical accuracy of the method. We provide a freely available, fully functional GPU implementation. Integration into Inchman, a user-friendly web service, that allows researchers to perform parallel simulations of reaction-drift-diffusion systems on GPU clusters is underway. PMID:22506001

Viscous electron flow in mesoscopic two-dimensional electron gas

NASA Astrophysics Data System (ADS)

Gusev, G. M.; Levin, A. D.; Levinson, E. V.; Bakarov, A. K.

2018-02-01

We report electrical and magneto transport measurements in mesoscopic size, two-dimensional (2D) electron gas in a GaAs quantum well. Remarkably, we find that the probe configuration and sample geometry strongly affects the temperature evolution of local resistance. We attribute all transport properties to the presence of hydrodynamic effects. Experimental results confirm the theoretically predicted significance of viscous flow in mesoscopic devices.

Multidimensional dynamic piezoresponse measurements. Unraveling local relaxation behavior in relaxor-ferroelectrics via big data

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

Vasudevan, Rama K.; Zhang, Shujun; Okatan, Mahmut Baris

Compositional and charge disorder in ferroelectric relaxors lies at the heart of the unusual properties of these systems, such as aging and non-ergodicity, polarization rotations, and a host of temperature and field-driven phase transitions. However, much information about the field-dynamics of the polarization in the prototypical ferroelectric relaxor (1-x)Pb(Mg 1/3Nb 2/3)O 3-xPbTiO 3 (PMN-xPT) remains unprobed at the mesoscopic level. We use a piezoresponse force microscopy-based dynamic multimodal relaxation spectroscopy technique, enabling the study of ferroelectric switching and polarization relaxation at mesoscopic length scales, and carry out measurements on a PMN-0.28PT sample with minimal polishing. Results indicate that beyond amore » threshold DC bias the average relaxation increases as the system attempts to relax to the previous state. Phenomenological fitting reveals the presence of mesoscale heterogeneity in relaxation amplitudes and clearly suggests the presence of two distinct amplitudes. Independent component analysis reveals the presence of a disorder component of the relaxation, which is found to be strongly anti-correlated with the maximum piezoresponse at that location, suggesting smaller disorder effects where the polarization reversal is large and vice versa. The disorder in the relaxation amplitudes is postulated to arise from rhombohedral and field-induced tetragonal phase in the crystal, with each phase associated with its own relaxation amplitude. As a result, these studies highlight the crucial importance of the mixture of ferroelectric phases in the compositions in proximity of the morphotropic phase boundary in governing the local response and further highlight the ability of PFM voltage and time spectroscopies, in conjunction with big-data multivariate analyses, to locally map disorder and correlate it with parameters governing the dynamic behavior.« less

Multidimensional dynamic piezoresponse measurements. Unraveling local relaxation behavior in relaxor-ferroelectrics via big data

DOE PAGES

Vasudevan, Rama K.; Zhang, Shujun; Okatan, Mahmut Baris; ...

2015-08-19

Compositional and charge disorder in ferroelectric relaxors lies at the heart of the unusual properties of these systems, such as aging and non-ergodicity, polarization rotations, and a host of temperature and field-driven phase transitions. However, much information about the field-dynamics of the polarization in the prototypical ferroelectric relaxor (1-x)Pb(Mg 1/3Nb 2/3)O 3-xPbTiO 3 (PMN-xPT) remains unprobed at the mesoscopic level. We use a piezoresponse force microscopy-based dynamic multimodal relaxation spectroscopy technique, enabling the study of ferroelectric switching and polarization relaxation at mesoscopic length scales, and carry out measurements on a PMN-0.28PT sample with minimal polishing. Results indicate that beyond amore » threshold DC bias the average relaxation increases as the system attempts to relax to the previous state. Phenomenological fitting reveals the presence of mesoscale heterogeneity in relaxation amplitudes and clearly suggests the presence of two distinct amplitudes. Independent component analysis reveals the presence of a disorder component of the relaxation, which is found to be strongly anti-correlated with the maximum piezoresponse at that location, suggesting smaller disorder effects where the polarization reversal is large and vice versa. The disorder in the relaxation amplitudes is postulated to arise from rhombohedral and field-induced tetragonal phase in the crystal, with each phase associated with its own relaxation amplitude. As a result, these studies highlight the crucial importance of the mixture of ferroelectric phases in the compositions in proximity of the morphotropic phase boundary in governing the local response and further highlight the ability of PFM voltage and time spectroscopies, in conjunction with big-data multivariate analyses, to locally map disorder and correlate it with parameters governing the dynamic behavior.« less

On the Reduction of Molecular Degrees of Freedom in Computer Simulations

NASA Astrophysics Data System (ADS)

Lyubartsev, Alexander P.; Laaksonen, Aatto

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

Effect of short-chain branching on interfacial polymer structure and dynamics under shear flow.

PubMed

Jeong, Sohdam; Kim, Jun Mo; Cho, Soowon; Baig, Chunggi

2017-11-22

We present a detailed analysis on the effect of short-chain branches on the structure and dynamics of interfacial chains using atomistic nonequilibrium molecular dynamics simulations of confined polyethylene melts in a wide range of shear rates. The intrinsically fast random motions of the short branches constantly disturb the overall chain conformation, leading to a more compact and less deformed chain structure of the short-chain branched (SCB) polymer against the imposed flow field in comparison with the corresponding linear polymer. Moreover, such highly mobile short branches along the backbone of the SCB polymer lead to relatively weaker out-of-plane wagging dynamics of interfacial chains, with highly curvy backbone structures in the intermediate flow regime. In conjunction with the contribution of short branches (as opposed to that of the backbone) to the total interfacial friction between the chains and the wall, the SCB polymer shows a nearly constant behavior in the degree of slip (d s ) with respect to shear rate in the weak-to-intermediate flow regimes. On the contrary, in the strong flow regime where irregular chain rotation and tumbling dynamics occur via intensive dynamical collisions between interfacial chains and the wall, an enhancement effect on the chain detachment from the wall, caused by short branches, leads to a steeper increase in d s for the SCB polymer than for the linear polymer. Remarkably, the SCB chains at the interface exhibit two distinct types of rolling mechanisms along the backbone, with a half-dumbbell mesoscopic structure at strong flow fields, in addition to the typical hairpin-like tumbling behavior displayed by the linear chains.

Charactrisation of particle assemblies by 3D cross correlation light scattering and diffusing wave spectroscopy

NASA Astrophysics Data System (ADS)

Scheffold, Frank

2014-08-01

To characterize the structural and dynamic properties of soft materials and small particles, information on the relevant mesoscopic length scales is required. Such information is often obtained from traditional static and dynamic light scattering (SLS/DLS) experiments in the single scattering regime. In many dense systems, however, these powerful techniques frequently fail due to strong multiple scattering of light. Here I will discuss some experimental innovations that have emerged over the last decade. New methods such as 3D static and dynamic light scattering (3D LS) as well as diffusing wave spectroscopy (DWS) can cover a much extended range of experimental parameters ranging from dilute polymer solutions, colloidal suspensions to extremely opaque viscoelastic emulsions.

Nonlinear dynamics and cavity cooling of levitated nanoparticles

NASA Astrophysics Data System (ADS)

Fonseca, P. Z. G.; Aranas, E. B.; Millen, J.; Monteiro, T. S.; Barker, P. F.

2016-09-01

We investigate a dynamic nonlinear optomechanical system, comprising a nanosphere levitated in a hybrid electro-optical trap. An optical cavity offers readout of both linear-in-position and quadratic-in-position (nonlinear) light-matter coupling, whilst simultaneously cooling the nanosphere, for indefinite periods of time and in high vacuum. Through the rich sideband structure displayed by the cavity output we can observe cooling of the linear and non-linear particle's motion. Here we present an experimental setup which allows full control over the cavity resonant frequencies, and shows cooling of the particle's motion as a function of the detuning. This work paves the way to strong-coupled quantum dynamics between a cavity and a mesoscopic object largely decoupled from its environment.

Mesoscopic Dynamical Differences from Quantum State Preparation in a Bose-Hubbard Trimer

NASA Astrophysics Data System (ADS)

Olsen, M. K.; Neely, T. W.; Bradley, A. S.

2018-06-01

Conventional wisdom is that quantum effects will tend to disappear as the number of quanta in a system increases, and the evolution of a system will become closer to that described by mean-field classical equations. In this Letter we combine newly developed theoretical and experimental techniques to propose and analyze an experiment using a Bose-Hubbard trimer where the opposite is the case. We find that differences in the preparation of a centrally evacuated trimer can lead to readily observable differences in the subsequent dynamics which increase with system size. Importantly, these differences can be detected by the simple measurements of atomic number.

Chaos and generalised multistability in a mesoscopic model of the electroencephalogram

NASA Astrophysics Data System (ADS)

Dafilis, Mathew P.; Frascoli, Federico; Cadusch, Peter J.; Liley, David T. J.

2009-06-01

We present evidence for chaos and generalised multistability in a mesoscopic model of the electroencephalogram (EEG). Two limit cycle attractors and one chaotic attractor were found to coexist in a two-dimensional plane of the ten-dimensional volume of initial conditions. The chaotic attractor was found to have a moderate value of the largest Lyapunov exponent (3.4 s -1 base e) with an associated Kaplan-Yorke (Lyapunov) dimension of 2.086. There are two different limit cycles appearing in conjunction with this particular chaotic attractor: one multiperiodic low amplitude limit cycle whose largest spectral peak is within the alpha band (8-13 Hz) of the EEG; and another multiperiodic large-amplitude limit cycle which may correspond to epilepsy. The cause of the coexistence of these structures is explained with a one-parameter bifurcation analysis. Each attractor has a basin of differing complexity: the large-amplitude limit cycle has a basin relatively uncomplicated in its structure while the small-amplitude limit cycle and chaotic attractor each have much more finely structured basins of attraction, but none of the basin boundaries appear to be fractal. The basins of attraction for the chaotic and small-amplitude limit cycle dynamics apparently reside within each other. We briefly discuss the implications of these findings in the context of theoretical attempts to understand the dynamics of brain function and behaviour.

Modeling of multiphase flow with solidification and chemical reaction in materials processing

NASA Astrophysics Data System (ADS)

Wei, Jiuan

Understanding of multiphase flow and related heat transfer and chemical reactions are the keys to increase the productivity and efficiency in industrial processes. The objective of this thesis is to utilize the computational approaches to investigate the multiphase flow and its application in the materials processes, especially in the following two areas: directional solidification, and pyrolysis and synthesis. In this thesis, numerical simulations will be performed for crystal growth of several III-V and II-VI compounds. The effects of Prandtl and Grashof numbers on the axial temperature profile, the solidification interface shape, and melt flow are investigated. For the material with high Prandtl and Grashof numbers, temperature field and growth interface will be significantly influenced by melt flow, resulting in the complicated temperature distribution and curved interface shape, so it will encounter tremendous difficulty using a traditional Bridgman growth system. A new design is proposed to reduce the melt convection. The geometric configuration of top cold and bottom hot in the melt will dramatically reduce the melt convection. The new design has been employed to simulate the melt flow and heat transfer in crystal growth with large Prandtl and Grashof numbers and the design parameters have been adjusted. Over 90% of commercial solar cells are made from silicon and directional solidification system is the one of the most important method to produce multi-crystalline silicon ingots due to its tolerance to feedstock impurities and lower manufacturing cost. A numerical model is developed to simulate the silicon ingot directional solidification process. Temperature distribution and solidification interface location are presented. Heat transfer and solidification analysis are performed to determine the energy efficiency of the silicon production furnace. Possible improvements are identified. The silicon growth process is controlled by adjusting heating power and moving the side insulation layer upward. It is possible to produce high quality crystal with a good combination of heating and cooling. SiC based ceramic materials fabricated by polymer pyrolysis and synthesis becomes a promising candidate for nuclear applications. To obtain high uniformity of microstructure/concentration fuel without crack at high operating temperature, it is important to understand transport phenomena in material processing at different scale levels. In our prior work, a system level model based on reactive porous media theory was developed to account for the pyrolysis process in uranium-ceramic nuclear fabrication In this thesis, a particle level mesoscopic model based on the Smoothed Particle Hydrodynamics (SPH) is developed for modeling the synthesis of filler U3O8 particles and SiC matrix. The system-level model provides the thermal boundary conditions needed in the particle level simulation. The evolution of particle concentration and structure as well as composition of composite produced will be investigated. Since the process temperature and heat flux play the important roles in material quality and uniformity, the effects of heating rate at different directions, filler particle size and distribution on uniformity and microstructure of the final product are investigated. Uncertainty issue is also discussed. For the multiphase flow with directional solidification, a system level based on FVM is established. In this model, melt convection, temperature distribution, phase change and solidification interface can be investigated. For the multiphase flow with chemical reaction, a particle level model based on SPH method is developed to describe the pyrolysis and synthesis process of uranium-ceramic nuclear fuel. Due to its mesh-free nature, SPH can easily handle the problems with multi phases and components, large deformation, chemical reactions and even solidifications. A multi-scale meso-macroscopic approach, which combine a mesoscopic model based on SPH method and macroscopic model based on FVM, FEM and FDM, can be applied to even more complicated system. In the mesoscopic model by SPH method, some fundamental mesoscopic phenomena, such as the microstructure evolution, interface morphology represented by high resolution, particle entrapment in solidification can be studied. In the macroscopic model, the heat transfer, fluid flow, species transport can be modeled, and the simulation results provided the velocity, temperature and species boundary condition necessary for the mesoscopic model. This part falls into the region of future work. (Abstract shortened by UMI.)

A Multimodality Ultramicrospectroscope (MUMS): Nanoscale Imaging with Integrated Spectroscopies for Chemical and Biomolecular Identification

DTIC Science & Technology

2010-11-10

nanoparticles, and nanoshells by making sub 100 nm diameter nanoshells to mesoscopic sized nanoparticles (gold meatballs ) and micron sized nanoshells. In...mesoscopic gold ‘ meatballs ’, gold bipyrimids etc. In addition nanoparticles such as the nanostar demonstrate some of the highest LSPR sensitivity but...20, 535-538 (2008). 64. H. Wang and N. J. Halas, “Mesoscopic Au ‘ Meatball ’ Particles”, Advanced Materials 20, 820-825 (2008). 65. S. Priya

CHAIRMEN'S FOREWORD: The Seventh International Conference on New Phenomena in Mesoscopic Structures & The Fifth International Conference on Surfaces and Interfaces of Mesoscopic Devices

NASA Astrophysics Data System (ADS)

Aoyagi, Yoshinobu; Goodnick, Stephen M.

2006-05-01

This special issue of the Journal of Physics: Conference Series contains the proceedings of the joint Seventh International Conference on New Phenomena in Mesoscopic Structures and Fifth International Conference on Surfaces and Interfaces of Mesoscopic Devices, which was held from November 27th - December 2nd, 2005, at the Ritz Carlton Kapalua, Maui, Hawaii. The string of these conferences dates back to the first one in 1989. Of special importance is that this year's conference was dedicated to Professor Gottfried Landwehr, in recognition of his many outstanding contributions to semiconductor physics. A personal tribute to Prof Landwehr by Dr K von Klitzing leads off this issue. The scope of NPMS-7/SIMD-5 spans nano-fabrication through complex phase coherent mesoscopic systems including nano-transistors and nano-scale characterization. Topics of interest include: •Nanoscale fabrication: high-resolution electron lithography, FIB nano-patterning, scanning- force-microscopy (SFM) lithography, SFM-stimulated growth, novel patterning, nano-imprint lithography, special etching, and self-assembled monolayers •Nanocharacterization: SFM characterization, ballistic-electron emission microscopy (BEEM), optical studies of nanostructures, tunneling, properties of discrete impurities, phase coherence, noise, THz studies, and electro-luminescence in small structures •Nanodevices: ultra-scaled FETs, quantum single-electron transistors (SETS), resonant tunneling diodes, ferromagnetic and spin devices, superlattice arrays, IR detectors with quantum dots and wires, quantum point contacts, non-equilibrium transport, simulation, ballistic transport, molecular electronic devices, carbon nanotubes, spin selection devices, spin-coupled quantum dots, and nanomagnetics •Quantum-coherent transport: the quantum Hall effect, ballistic quantum systems, quantum-computing implementations and theory, and magnetic spin systems •Mesoscopic structures: quantum wires and dots, quantum chaos, non-equilibrium transport, instabilities, nano-electro-mechanical systems, mesoscopic Josephson effects, phase coherence and breaking, and the Kondo effect •Systems of nanodevices: Quantum cellular automata, systolic SET processors, quantum neural nets, adaptive effects in circuits, and molecular circuits •Nanomaterials: nanotubes, nanowires, organic and molecular materials, self-assembled nano wires, and organic devices •Nanobioelectronics: electronic properties of biological structures on the nanoscale. This year's conference was organized by Prof Stephen Goodnick, Arizona State University, and Prof Yoshinobu Aoyagi, Tokyo Institute of Technology. The conference benefited from 14 invited speakers, whose topics spanned the above list, and a total of 97 registered attendees. The largest contingent was from Japan, followed closely by the US. In total, there were 49 from Japan, 31 fiom the US, and 17 from Europe. The organizers want to especially thank the sponsors for the meeting: The Office of Naval Research, the Army Research Office, and Arizona State University on the US side, and the Japan Society for the Promotion of Science, through their 151 Committee, on the Japanese side. PROGRAM COMMITTEE •Prof Gerhard Abstreiter, Technical University of Munich •Prof Tsuneya Ando, Tokyo Institute of Technology •Prof John Barker, University of Glasgow •Prof Jonathan Bird, the University at Buffalo •Prof Robert Blick, University of Wisconsin •Prof David Ferry, Chair, Arizona State University •Dr Yoshiro Hirayama, NTT Basic Research Laboratories •Dr Koji Ishibashi, RIKEN •Prof Carlo Jacoboni, University of Modena •Prof David Janes, Purdue University •Prof Friedl Kuchar, University of Leoben •Prof K. Matsumoto, Osaka University •Prof Wolfgang Porod, Notre Dame University •Prof Michiharu Tabe, Shizuoka University •Prof Joachim Wolter, Eindhoven Institute of Technology •Prof Lukas Worschech, University of Würzburg •Dr Naoki Yokoyama, Fujitsu Research

Lattice Boltzmann method for rain-induced overland flow

NASA Astrophysics Data System (ADS)

Ding, Yu; Liu, Haifei; Peng, Yong; Xing, Liming

2018-07-01

Complex rainfall situations can generate overland flow with complex hydrodynamic characteristics, affecting the surface configuration (i.e. sheet erosion) and environment to varying degrees. Reliable numerical simulations can provide a scientific method for the optimization of environmental management. A mesoscopic numerical method, the lattice Boltzmann method, was employed to simulate overland flows. To deal with complex rainfall, two schemes were introduced to improve the lattice Boltzmann equation and the local equilibrium function, respectively. Four typical cases with differences in rainfall, bed roughness, and slopes were selected to test the accuracy and applicability of the proposed schemes. It was found that the simulated results were in good agreement with the experimental data, analytical values, and the results produced by other models.

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

Müller, Kathrin, E-mail: k.mueller@fz-juelich.de; Fedosov, Dmitry A., E-mail: d.fedosov@fz-juelich.de; Gompper, Gerhard, E-mail: g.gompper@fz-juelich.de

Smoothed dissipative particle dynamics (SDPD) combines two popular mesoscopic techniques, the smoothed particle hydrodynamics and dissipative particle dynamics (DPD) methods, and can be considered as an improved dissipative particle dynamics approach. Despite several advantages of the SDPD method over the conventional DPD model, the original formulation of SDPD by Español and Revenga (2003) [9], lacks angular momentum conservation, leading to unphysical results for problems where the conservation of angular momentum is essential. To overcome this limitation, we extend the SDPD method by introducing a particle spin variable such that local and global angular momentum conservation is restored. The new SDPDmore » formulation (SDPD+a) is directly derived from the Navier–Stokes equation for fluids with spin, while thermal fluctuations are incorporated similarly to the DPD method. We test the new SDPD method and demonstrate that it properly reproduces fluid transport coefficients. Also, SDPD with angular momentum conservation is validated using two problems: (i) the Taylor–Couette flow with two immiscible fluids and (ii) a tank-treading vesicle in shear flow with a viscosity contrast between inner and outer fluids. For both problems, the new SDPD method leads to simulation predictions in agreement with the corresponding analytical theories, while the original SDPD method fails to capture properly physical characteristics of the systems due to violation of angular momentum conservation. In conclusion, the extended SDPD method with angular momentum conservation provides a new approach to tackle fluid problems such as multiphase flows and vesicle/cell suspensions, where the conservation of angular momentum is essential.« less

High Resolution Higher Energy X-ray Microscope for Mesoscopic Materials

NASA Astrophysics Data System (ADS)

Snigireva, I.; Snigirev, A.

2013-10-01

We developed a novel X-ray microscopy technique to study mesoscopically structured materials, employing compound refractive lenses. The easily seen advantage of lens-based methodology is the possibility to retrieve high resolution diffraction pattern and real-space images in the same experimental setup. Methodologically the proposed approach is similar to the studies of crystals by high resolution transmission electron microscopy. The proposed microscope was applied for studying of mesoscopic materials such as natural and synthetic opals, inverted photonic crystals.

Quantum Coherence and Random Fields at Mesoscopic Scales

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

Rosenbaum, Thomas F.

2016-03-01

We seek to explore and exploit model, disordered and geometrically frustrated magnets where coherent spin clusters stably detach themselves from their surroundings, leading to extreme sensitivity to finite frequency excitations and the ability to encode information. Global changes in either the spin concentration or the quantum tunneling probability via the application of an external magnetic field can tune the relative weights of quantum entanglement and random field effects on the mesoscopic scale. These same parameters can be harnessed to manipulate domain wall dynamics in the ferromagnetic state, with technological possibilities for magnetic information storage. Finally, extensions from quantum ferromagnets tomore » antiferromagnets promise new insights into the physics of quantum fluctuations and effective dimensional reduction. A combination of ac susceptometry, dc magnetometry, noise measurements, hole burning, non-linear Fano experiments, and neutron diffraction as functions of temperature, magnetic field, frequency, excitation amplitude, dipole concentration, and disorder address issues of stability, overlap, coherence, and control. We have been especially interested in probing the evolution of the local order in the progression from spin liquid to spin glass to long-range-ordered magnet.« less

Effect of molecular properties on the performance of polymer light-emitting diodes

NASA Astrophysics Data System (ADS)

Ramos, Marta M. D.; Almeida, A. M.; Correia, Helena M. G.; Ribeiro, R. Mendes; Stoneham, A. M.

2004-11-01

The performance of a single layer polymer light-emitting diode depends on several interdependent factors, although recombination between electrons and holes within the polymer layer is believed to play an important role. Our aim is to carry out computer experiments in which bipolar charge carriers are injected in polymer networks made of poly(p-phenylene vinylene) chains randomly oriented. In these simulations, we follow the charge evolution in time from some initial state to the steady state. The intra-molecular properties of the polymer molecules obtained from self-consistent quantum molecular dynamics calculations are used in the mesoscopic model. The purpose of the present work is to clarify the effects of intra-molecular charge mobility and energy disorder on recombination efficiency. In particular, we find that charge mobility along the polymer chains has a serious influence on recombination within the polymer layer. Our results also show that energy disorder due to differences in ionization potential and electron affinity of neighbouring molecules affects mainly recombinations that occur near the electrodes at polymer chains parallel to them.

Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism.

PubMed

Reymer, Anna; Zakrzewska, Krystyna; Lavery, Richard

2018-02-28

Torsional restraints on DNA change in time and space during the life of the cell and are an integral part of processes such as gene expression, DNA repair and packaging. The mechanical behavior of DNA under torsional stress has been studied on a mesoscopic scale, but little is known concerning its response at the level of individual base pairs and the effects of base pair composition. To answer this question, we have developed a geometrical restraint that can accurately control the total twist of a DNA segment during all-atom molecular dynamics simulations. By applying this restraint to four different DNA oligomers, we are able to show that DNA responds to both under- and overtwisting in a very heterogeneous manner. Certain base pair steps, in specific sequence environments, are able to absorb most of the torsional stress, leaving other steps close to their relaxed conformation. This heterogeneity also affects the local torsional modulus of DNA. These findings suggest that modifying torsional stress on DNA could act as a modulator for protein binding via the heterogeneous changes in local DNA structure.

Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism

PubMed Central

Reymer, Anna; Zakrzewska, Krystyna; Lavery, Richard

2018-01-01

Abstract Torsional restraints on DNA change in time and space during the life of the cell and are an integral part of processes such as gene expression, DNA repair and packaging. The mechanical behavior of DNA under torsional stress has been studied on a mesoscopic scale, but little is known concerning its response at the level of individual base pairs and the effects of base pair composition. To answer this question, we have developed a geometrical restraint that can accurately control the total twist of a DNA segment during all-atom molecular dynamics simulations. By applying this restraint to four different DNA oligomers, we are able to show that DNA responds to both under- and overtwisting in a very heterogeneous manner. Certain base pair steps, in specific sequence environments, are able to absorb most of the torsional stress, leaving other steps close to their relaxed conformation. This heterogeneity also affects the local torsional modulus of DNA. These findings suggest that modifying torsional stress on DNA could act as a modulator for protein binding via the heterogeneous changes in local DNA structure. PMID:29267977

Buckling in armored droplets.

PubMed

Sicard, François; Striolo, Alberto

2017-06-29

The buckling mechanism in droplets stabilized by solid particles (armored droplets) is tackled at a mesoscopic level using dissipative particle dynamics simulations. We consider one spherical water droplet in a decane solvent coated with nanoparticle monolayers of two different types: Janus (particles whose surface shows two regions with different wetting properties) and homogeneous. The chosen particles yield comparable initial three-phase contact angles, selected to maximize the adsorption energy at the interface. We study the interplay between the evolution of droplet shape, layering of the particles, and their distribution at the interface when the volume of the droplets is reduced. We show that Janus particles affect strongly the shape of the droplet with the formation of a crater-like depression. This evolution is actively controlled by a close-packed particle monolayer at the curved interface. In contrast, homogeneous particles follow passively the volume reduction of the droplet, whose shape does not deviate too much from spherical, even when a nanoparticle monolayer/bilayer transition is detected at the interface. We discuss how these buckled armored droplets might be of relevance in various applications including potential drug delivery systems and biomimetic design of functional surfaces.

Dynamics and Melting of Finite Plasma Crystals

NASA Astrophysics Data System (ADS)

Ludwig, Patrick; K"Ahlert, Hanno; Baumgartner, Henning; Thomsen, Hauke; Bonitz, Michael

2009-11-01

Interacting few-particle systems in external trapping potentials are of strong current interest since they allow to realize and control strong correlation and quantum effects [1]. Here, we present our recent results on the structural and thermodynamic properties of the crystal-like Wigner phase of complex plasma confined in a 3D harmonic potential. We discuss the linear response of the strongly correlated system to external excitations, which can be described in terms of normal modes [2]. By means of first-principle simulations the details of the melting phase transitions of these mesoscopic systems are systematically analysed with the melting temperatures being determined by a modified Lindemann parameter for the pair distance fluctuations [3]. The critical temperatures turn out to be utmost sensitive to finite size effects (i.e., the exact particle number), and form of the (screened) interaction potential.[4pt] [1] PhD Thesis, P. Ludwig, U Rostock (2008)[0pt] [2] C. Henning et al., J. Phys. A 42, 214023 (2009)[0pt] [3] B"oning et al., Phys. Rev. Lett. 100, 113401 (2008)

Multivariate cross-frequency coupling via generalized eigendecomposition

PubMed Central

Cohen, Michael X

2017-01-01

This paper presents a new framework for analyzing cross-frequency coupling in multichannel electrophysiological recordings. The generalized eigendecomposition-based cross-frequency coupling framework (gedCFC) is inspired by source-separation algorithms combined with dynamics of mesoscopic neurophysiological processes. It is unaffected by factors that confound traditional CFC methods—such as non-stationarities, non-sinusoidality, and non-uniform phase angle distributions—attractive properties considering that brain activity is neither stationary nor perfectly sinusoidal. The gedCFC framework opens new opportunities for conceptualizing CFC as network interactions with diverse spatial/topographical distributions. Five specific methods within the gedCFC framework are detailed, these are validated in simulated data and applied in several empirical datasets. gedCFC accurately recovers physiologically plausible CFC patterns embedded in noise that causes traditional CFC methods to perform poorly. The paper also demonstrates that spike-field coherence in multichannel local field potential data can be analyzed using the gedCFC framework, which provides significant advantages over traditional spike-field coherence analyses. Null-hypothesis testing is also discussed. DOI: http://dx.doi.org/10.7554/eLife.21792.001 PMID:28117662

Solvent effects on the polar network of ionic liquid solutions

NASA Astrophysics Data System (ADS)

Bernardes, Carlos E. S.; Shimizu, Karina; Canongia Lopes, José N.

2015-05-01

Molecular dynamics simulations were used to probe mixtures of ionic liquids (ILs) with common molecular solvents. Four types of systems were considered: (i) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide plus benzene, hexafluorobenzene or 1,2-difluorobenzene mixtures; (ii) choline-based ILs plus ether mixtures (iii) choline-based ILs plus n-alkanol mixtures; and (iv) 1-butyl-3-methylimidazolium nitrate and 1-ethyl-3-methylimidazolium ethyl sulfate aqueous mixtures. The results produced a wealth of structural and aggregation information that highlight the resilience of the polar network of the ILs (formed by clusters of alternating ions and counter-ions) to the addition of different types of molecular solvent. The analysis of the MD data also shows that the intricate balance between different types of interaction (electrostatic, van der Waals, H-bond-like) between the different species present in the mixtures has a profound effect on the morphology of the mixtures at a mesoscopic scale. In the case of the IL aqueous solutions, the present results suggest an alternative interpretation for very recently published x-ray and neutron diffraction data on similar systems.

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.

Numerical Simulations of the Digital Microfluidic Manipulation of Single Microparticles.

PubMed

Lan, Chuanjin; Pal, Souvik; Li, Zhen; Ma, Yanbao

2015-09-08

Single-cell analysis techniques have been developed as a valuable bioanalytical tool for elucidating cellular heterogeneity at genomic, proteomic, and cellular levels. Cell manipulation is an indispensable process for single-cell analysis. Digital microfluidics (DMF) is an important platform for conducting cell manipulation and single-cell analysis in a high-throughput fashion. However, the manipulation of single cells in DMF has not been quantitatively studied so far. In this article, we investigate the interaction of a single microparticle with a liquid droplet on a flat substrate using numerical simulations. The droplet is driven by capillary force generated from the wettability gradient of the substrate. Considering the Brownian motion of microparticles, we utilize many-body dissipative particle dynamics (MDPD), an off-lattice mesoscopic simulation technique, in this numerical study. The manipulation processes (including pickup, transport, and drop-off) of a single microparticle with a liquid droplet are simulated. Parametric studies are conducted to investigate the effects on the manipulation processes from the droplet size, wettability gradient, wetting properties of the microparticle, and particle-substrate friction coefficients. The numerical results show that the pickup, transport, and drop-off processes can be precisely controlled by these parameters. On the basis of the numerical results, a trap-free delivery of a hydrophobic microparticle to a destination on the substrate is demonstrated in the numerical simulations. The numerical results not only provide a fundamental understanding of interactions among the microparticle, the droplet, and the substrate but also demonstrate a new technique for the trap-free immobilization of single hydrophobic microparticles in the DMF design. Finally, our numerical method also provides a powerful design and optimization tool for the manipulation of microparticles in DMF systems.

Colloidal Asphaltene Deposition and Aggregation in Capillary Flow: Experiments and Mesoscopic Simulation

NASA Astrophysics Data System (ADS)

Boek, Edo S.; Ladva, Hemant K.; Crawshaw, John P.; Padding, Johan T.

2008-07-01

The aggregation and deposition of colloidal asphaltene in reservoir rock is a significant problem in the oil industry. To obtain a fundamental understanding of this phenomenon, we have studied the deposition and aggregation of colloidal asphaltene in capillary flow by experiment and simulation. For the simulation, we have used the stochastic rotation dynamics (SRD) method, in which the solvent hydrodynamic emerges from the collisions between the solvent particles, while the Brownian motion emerges naturally from the interactions between the colloidal asphaltene particles and the solvent. The asphaltene colloids interact through a screened Coulomb potential. We vary the well depth ɛ∝ and the flow rate v to obtain Peflow≫1 (hydrodynamic interactions dominate) and Re≪1 (Stokes flow). In the simulations, we impose a pressure drop over the capillary length and measure the corresponding solvent flow rate. We observe that the transient solvent flow rate decreases when the asphaltene particles become more "sticky". For a well depth ɛ∝ = 2kBT, a monolayer deposits on the capillary wall. With an increasing well depth, the capillary becomes totally blocked. The clogging is transient for ɛ∝ = 5kBT, but appears to be permanent for ɛ∝ = 10-20 kBT. We compare our simulation results with flow experiments in glass capillaries, where we use extracted asphaltenes in toluene, reprecipitated with n-heptane. In the experiments, the dynamics of asphaltene precipitation and deposition were monitored in a slot capillary using optical microscopy under flow conditions similar to those used in the simulation. Maintaining a constant flow rate of 5 μL min-1, we found that the pressure drop across the capillary first increased slowly, followed by a sharp increase, corresponding to a complete local blockage of the capillary. Doubling the flow rate to 10 μL min-1, we observe that the initial deposition occurs faster but the deposits are subsequently entrained by the flow. We calculate the change in the dimensionless permeability as a function of time for both experiment and simulation. By matching the experimental and simulation results, we obtain information about (1) the interaction potential well depth for the particular asphaltenes used in the experiments and (2) the flow conditions associated with the asphaltene deposition process.

Spin and Magnetism: Two Transfer Matrix Formulations of a Classical Heisenberg Ring in a Magnetic Field.

DTIC Science & Technology

1998-06-01

determination of the partition function could be attempted. According to Gatteschi et al, however, [Ref. 15] when commenting on the quantum mechanical...1995 15. Gatteschi , D. et al, "Large Clusters of Metal Ions: The Transition from Molecular to Bulk Magnets" Science vol. 265, pp. 1054-1058, August... Gatteschi , D. et al, "Spin Dynamics in Mesoscopic Size Magnetic Systems... ", Phys. Rev. B, vol. 55, no. 21, 01 June, 1997 18. Tejeda, J. etal, "Quantum

Femtojoule-scale all-optical latching and modulation via cavity nonlinear optics.

PubMed

Kwon, Yeong-Dae; Armen, Michael A; Mabuchi, Hideo

2013-11-15

We experimentally characterize Hopf bifurcation phenomena at femtojoule energy scales in a multiatom cavity quantum electrodynamical (cavity QED) system and demonstrate how such behaviors can be exploited in the design of all-optical memory and modulation devices. The data are analyzed by using a semiclassical model that explicitly treats heterogeneous coupling of atoms to the cavity mode. Our results highlight the interest of cavity QED systems for ultralow power photonic signal processing as well as for fundamental studies of mesoscopic nonlinear dynamics.

The Adiabatic Piston and the Second Law of Thermodynamics

NASA Astrophysics Data System (ADS)

Crosignani, Bruno; Di Porto, Paolo; Conti, Claudio

2002-11-01

A detailed analysis of the adiabatic-piston problem reveals peculiar dynamical features that challenge the general belief that isolated systems necessarily reach a static equilibrium state. In particular, the fact that the piston behaves like a perpetuum mobile, i.e., it never stops but keeps wandering, undergoing sizable oscillations, around the position corresponding to maximum entropy, has remarkable implications on the entropy variations of the system and on the validity of the second law when dealing with systems of mesoscopic dimensions.

Hydrodynamically Coupled Brownian Dynamics: A coarse-grain particle-based Brownian dynamics technique with hydrodynamic interactions for modeling self-developing flow of polymer solutions

NASA Astrophysics Data System (ADS)

Ahuja, V. R.; van der Gucht, J.; Briels, W. J.

2018-01-01

We present a novel coarse-grain particle-based simulation technique for modeling self-developing flow of dilute and semi-dilute polymer solutions. The central idea in this paper is the two-way coupling between a mesoscopic polymer model and a phenomenological fluid model. As our polymer model, we choose Responsive Particle Dynamics (RaPiD), a Brownian dynamics method, which formulates the so-called "conservative" and "transient" pair-potentials through which the polymers interact besides experiencing random forces in accordance with the fluctuation dissipation theorem. In addition to these interactions, our polymer blobs are also influenced by the background solvent velocity field, which we calculate by solving the Navier-Stokes equation discretized on a moving grid of fluid blobs using the Smoothed Particle Hydrodynamics (SPH) technique. While the polymers experience this frictional force opposing their motion relative to the background flow field, our fluid blobs also in turn are influenced by the motion of the polymers through an interaction term. This makes our technique a two-way coupling algorithm. We have constructed this interaction term in such a way that momentum is conserved locally, thereby preserving long range hydrodynamics. Furthermore, we have derived pairwise fluctuation terms for the velocities of the fluid blobs using the Fokker-Planck equation, which have been alternatively derived using the General Equation for the Non-Equilibrium Reversible-Irreversible Coupling (GENERIC) approach in Smoothed Dissipative Particle Dynamics (SDPD) literature. These velocity fluctuations for the fluid may be incorporated into the velocity updates for our fluid blobs to obtain a thermodynamically consistent distribution of velocities. In cases where these fluctuations are insignificant, however, these additional terms may well be dropped out as they are in a standard SPH simulation. We have applied our technique to study the rheology of two different concentrations of our model linear polymer solutions. The results show that the polymers and the fluid are coupled very well with each other, showing no lag between their velocities. Furthermore, our results show non-Newtonian shear thinning and the characteristic flattening of the Poiseuille flow profile typically observed for polymer solutions.

Hydrodynamically Coupled Brownian Dynamics: A coarse-grain particle-based Brownian dynamics technique with hydrodynamic interactions for modeling self-developing flow of polymer solutions.

PubMed

Ahuja, V R; van der Gucht, J; Briels, W J

2018-01-21

We present a novel coarse-grain particle-based simulation technique for modeling self-developing flow of dilute and semi-dilute polymer solutions. The central idea in this paper is the two-way coupling between a mesoscopic polymer model and a phenomenological fluid model. As our polymer model, we choose Responsive Particle Dynamics (RaPiD), a Brownian dynamics method, which formulates the so-called "conservative" and "transient" pair-potentials through which the polymers interact besides experiencing random forces in accordance with the fluctuation dissipation theorem. In addition to these interactions, our polymer blobs are also influenced by the background solvent velocity field, which we calculate by solving the Navier-Stokes equation discretized on a moving grid of fluid blobs using the Smoothed Particle Hydrodynamics (SPH) technique. While the polymers experience this frictional force opposing their motion relative to the background flow field, our fluid blobs also in turn are influenced by the motion of the polymers through an interaction term. This makes our technique a two-way coupling algorithm. We have constructed this interaction term in such a way that momentum is conserved locally, thereby preserving long range hydrodynamics. Furthermore, we have derived pairwise fluctuation terms for the velocities of the fluid blobs using the Fokker-Planck equation, which have been alternatively derived using the General Equation for the Non-Equilibrium Reversible-Irreversible Coupling (GENERIC) approach in Smoothed Dissipative Particle Dynamics (SDPD) literature. These velocity fluctuations for the fluid may be incorporated into the velocity updates for our fluid blobs to obtain a thermodynamically consistent distribution of velocities. In cases where these fluctuations are insignificant, however, these additional terms may well be dropped out as they are in a standard SPH simulation. We have applied our technique to study the rheology of two different concentrations of our model linear polymer solutions. The results show that the polymers and the fluid are coupled very well with each other, showing no lag between their velocities. Furthermore, our results show non-Newtonian shear thinning and the characteristic flattening of the Poiseuille flow profile typically observed for polymer solutions.

Decoupling nonclassical nonlinear behavior of elastic wave types

DOE PAGES

Remillieux, Marcel C.; Guyer, Robert A.; Payan, Cedric; ...

2016-03-01

In this Letter, the tensorial nature of the nonequilibrium dynamics in nonlinear mesoscopic elastic materials is evidenced via multimode resonance experiments. In these experiments the dynamic response, including the spatial variations of velocities and strains, is carefully monitored while the sample is vibrated in a purely longitudinal or a purely torsional mode. By analogy with the fact that such experiments can decouple the elements of the linear elastic tensor, we demonstrate that the parameters quantifying the nonequilibrium dynamics of the material differ substantially for a compressional wave and for a shear wave. As a result, this could lead to furthermore » understanding of the nonlinear mechanical phenomena that arise in natural systems as well as to the design and engineering of nonlinear acoustic metamaterials.« less

Multiscale X-ray and Proton Imaging of Bismuth-Tin Solidification

NASA Astrophysics Data System (ADS)

Gibbs, P. J.; Imhoff, S. D.; Morris, C. L.; Merrill, F. E.; Wilde, C. H.; Nedrow, P.; Mariam, F. G.; Fezzaa, K.; Lee, W.-K.; Clarke, A. J.

2014-08-01

The formation of structural patterns during metallic solidification is complex and multiscale in nature, ranging from the nanometer scale, where solid-liquid interface properties are important, to the macroscale, where casting mold filling and intended heat transfer are crucial. X-ray and proton imaging can directly interrogate structure, solute, and fluid flow development in metals from the microscale to the macroscale. X-rays permit high spatio-temporal resolution imaging of microscopic solidification dynamics in thin metal sections. Similarly, high-energy protons permit imaging of mesoscopic and macroscopic solidification dynamics in large sample volumes. In this article, we highlight multiscale x-ray and proton imaging of bismuth-tin alloy solidification to illustrate dynamic measurement of crystal growth rates and solute segregation profiles that can be that can be acquired using these techniques.

Fluctuations in the DNA double helix

NASA Astrophysics Data System (ADS)

Peyrard, M.; López, S. C.; Angelov, D.

2007-08-01

DNA is not the static entity suggested by the famous double helix structure. It shows large fluctuational openings, in which the bases, which contain the genetic code, are temporarily open. Therefore it is an interesting system to study the effect of nonlinearity on the physical properties of a system. A simple model for DNA, at a mesoscopic scale, can be investigated by computer simulation, in the same spirit as the original work of Fermi, Pasta and Ulam. These calculations raise fundamental questions in statistical physics because they show a temporary breaking of equipartition of energy, regions with large amplitude fluctuations being able to coexist with regions where the fluctuations are very small, even when the model is studied in the canonical ensemble. This phenomenon can be related to nonlinear excitations in the model. The ability of the model to describe the actual properties of DNA is discussed by comparing theoretical and experimental results for the probability that base pairs open an a given temperature in specific DNA sequences. These studies give us indications on the proper description of the effect of the sequence in the mesoscopic model.

Liquid crystals and their interactions with colloidal particles and phospholipid membranes: Molecular simulation studies

NASA Astrophysics Data System (ADS)

Kim, Evelina B.

Experimentally, liquid crystals (LC) can be used as the basis for optical biomolecular sensors that rely on LC ordering. Recently, the use of LC as a reporting medium has been extended to investigations of molecular scale processes at lipid laden aqueous-LC interfaces and at biological cell membranes. In this thesis, we present two related studies where liquid crystals are modelled at different length scales. We examine (a) the behavior of nanoscopic colloidal particles in LC systems, using Monte Carlo (MC) molecular simulations and a mesoscopic dynamic field theory (DyFT); and (b) specific interactions of two types of mesogens with a model phospholipid bilayer, using atomistic molecular dynamics (MD) at the A-nm scale. In (a), we consider colloidal particles suspended in a LC, confined between two walls. We calculate the colloid-substrate and colloid-colloid potentials of mean force (PMF). For the MC simulations, we developed a new technique (ExEDOS or Expanded Ensemble Density Of States) that ensures good sampling of phase space without prior knowledge of the energy landscape of the system. Both results, simulation and DyFT, indicate a repulsive force acting between a colloid and a wall. In contrast, both techniques indicate an overall colloid-colloid attraction and predict a new topology of the disclination lines that arises when the particles approach each other. In (b), we find that mesogens (pentylcyanobiphenyl [5CB] or difluorophenyl-pentylbicyclohexyl [5CF]) preferentially partition from the aqueous phase into a dipalmitoylphosphatidylcholine (DPPC) bilayer. We find highly favorable free energy differences for partitioning (-18kBT for 5CB, -26k BT for 5CF). We also simulated fully hydrated bilayers with embedded 5CB or 5CF at concentrations used in recent experiments (6 mol% and 20 mol%). The presence of mesogens in the bilayer enhances the order of lipid acyl tails and changes the spatial and orientational arrangement of lipid headgroup atoms. A stronger spatial correlation and larger ranges of molecular orientations and positions are observed for 5CB molecules compared to 5CF. At the same time, 5CF molecules were found to bind more strongly to lipid headgroups, thereby slowing the lateral motion of lipid molecules.

SPM investigation of local aging effects in glassy polymers

NASA Astrophysics Data System (ADS)

Crider, Philip

2005-03-01

We investigate the cooperative and heterogeneous nature of glassy dynamics by nanometer-scale probing in a glassy polymer, Polyvinyl-Actetate (PVAc), with a Scanning Force Microscope (SFM). Using ultra-high-vacuum (UHV) Scanning Capacitive Force Microscopy techniques, nanometer-scale capacitive responses are probed. Dielectric relaxation near the glass transition is investigated, and scanning capabilities are utilized to analyze spatial response on a nanometer scale. The results of these studies may yield insight into the understanding of temperature-dependent cooperative length scales, local aging properties, and energy landscape properties of evolving dipole clusters on a mesoscopic scale. Results are used to test the validity and relevance of current models of glassy dynamics.

Fast optical cooling of a nanomechanical cantilever by a dynamical Stark-shift gate.

PubMed

Yan, Leilei; Zhang, Jian-Qi; Zhang, Shuo; Feng, Mang

2015-10-12

The efficient cooling of nanomechanical resonators is essential to exploration of quantum properties of the macroscopic or mesoscopic systems. We propose such a laser-cooling scheme for a nanomechanical cantilever, which works even for the low-frequency mechanical mode and under weak cooling lasers. The cantilever is coupled by a diamond nitrogen-vacancy center under a strong magnetic field gradient and the cooling is assisted by a dynamical Stark-shift gate. Our scheme can effectively enhance the desired cooling efficiency by avoiding the off-resonant and undesired carrier transitions, and thereby cool the cantilever down to the vicinity of the vibrational ground state in a fast fashion.

Fast optical cooling of a nanomechanical cantilever by a dynamical Stark-shift gate

PubMed Central

Yan, Leilei; Zhang, Jian-Qi; Zhang, Shuo; Feng, Mang

2015-01-01

The efficient cooling of nanomechanical resonators is essential to exploration of quantum properties of the macroscopic or mesoscopic systems. We propose such a laser-cooling scheme for a nanomechanical cantilever, which works even for the low-frequency mechanical mode and under weak cooling lasers. The cantilever is coupled by a diamond nitrogen-vacancy center under a strong magnetic field gradient and the cooling is assisted by a dynamical Stark-shift gate. Our scheme can effectively enhance the desired cooling efficiency by avoiding the off-resonant and undesired carrier transitions, and thereby cool the cantilever down to the vicinity of the vibrational ground state in a fast fashion. PMID:26455901

Tailoring of quantum dot emission efficiency by localized surface plasmon polaritons in self-organized mesoscopic rings.

PubMed

Margapoti, Emanuela; Gentili, Denis; Amelia, Matteo; Credi, Alberto; Morandi, Vittorio; Cavallini, Massimiliano

2014-01-21

We report on the tailoring of quantum dot (QD) emission efficiency by localized surface plasmon polaritons in self-organized mesoscopic rings. Ag nanoparticles (NPs) with CdSe QDs embedded in a polymeric matrix are spatially organised in mesoscopic rings and coupled in a tuneable fashion by breath figure formation. The mean distance between NPs and QDs and consequently the intensity of QD photoluminescence, which is enhanced by the coupling of surface plasmons and excitons, are tuned by acting on the NP concentration.

A new transport phenomenon in nanostructures: a mesoscopic analog of the Braess paradox encountered in road networks

PubMed Central

2012-01-01

The Braess paradox, known for traffic and other classical networks, lies in the fact that adding a new route to a congested network in an attempt to relieve congestion can degrade counterintuitively the overall network performance. Recently, we have extended the concept of the Braess paradox to semiconductor mesoscopic networks, whose transport properties are governed by quantum physics. In this paper, we demonstrate theoretically that, alike in classical systems, congestion plays a key role in the occurrence of a Braess paradox in mesoscopic networks. PMID:22913510

What can we learn from noise? — Mesoscopic nonequilibrium statistical physics —

PubMed Central

KOBAYASHI, Kensuke

2016-01-01

Mesoscopic systems — small electric circuits working in quantum regime — offer us a unique experimental stage to explorer quantum transport in a tunable and precise way. The purpose of this Review is to show how they can contribute to statistical physics. We introduce the significance of fluctuation, or equivalently noise, as noise measurement enables us to address the fundamental aspects of a physical system. The significance of the fluctuation theorem (FT) in statistical physics is noted. We explain what information can be deduced from the current noise measurement in mesoscopic systems. As an important application of the noise measurement to statistical physics, we describe our experimental work on the current and current noise in an electron interferometer, which is the first experimental test of FT in quantum regime. Our attempt will shed new light in the research field of mesoscopic quantum statistical physics. PMID:27477456

What can we learn from noise? - Mesoscopic nonequilibrium statistical physics.

PubMed

Kobayashi, Kensuke

2016-01-01

Mesoscopic systems - small electric circuits working in quantum regime - offer us a unique experimental stage to explorer quantum transport in a tunable and precise way. The purpose of this Review is to show how they can contribute to statistical physics. We introduce the significance of fluctuation, or equivalently noise, as noise measurement enables us to address the fundamental aspects of a physical system. The significance of the fluctuation theorem (FT) in statistical physics is noted. We explain what information can be deduced from the current noise measurement in mesoscopic systems. As an important application of the noise measurement to statistical physics, we describe our experimental work on the current and current noise in an electron interferometer, which is the first experimental test of FT in quantum regime. Our attempt will shed new light in the research field of mesoscopic quantum statistical physics.

Electron Waiting Times in Mesoscopic Conductors

NASA Astrophysics Data System (ADS)

Albert, Mathias; Haack, Géraldine; Flindt, Christian; Büttiker, Markus

2012-05-01

Electron transport in mesoscopic conductors has traditionally involved investigations of the mean current and the fluctuations of the current. A complementary view on charge transport is provided by the distribution of waiting times between charge carriers, but a proper theoretical framework for coherent electronic systems has so far been lacking. Here we develop a quantum theory of electron waiting times in mesoscopic conductors expressed by a compact determinant formula. We illustrate our methodology by calculating the waiting time distribution for a quantum point contact and find a crossover from Wigner-Dyson statistics at full transmission to Poisson statistics close to pinch-off. Even when the low-frequency transport is noiseless, the electrons are not equally spaced in time due to their inherent wave nature. We discuss the implications for renewal theory in mesoscopic systems and point out several analogies with level spacing statistics and random matrix theory.

Noise switching at a dynamical critical point in a cavity-conductor hybrid

NASA Astrophysics Data System (ADS)

Armour, Andrew D.; Kubala, Björn; Ankerhold, Joachim

2017-12-01

Coupling a mesoscopic conductor to a microwave cavity can lead to fascinating feedback effects which generate strong correlations between the dynamics of photons and charges. We explore the connection between cavity dynamics and charge transport in a model system consisting of a voltage-biased Josephson junction embedded in a high-Q cavity, focusing on the behavior as the system is tuned through a dynamical critical point. On one side of the critical point the noise is strongly suppressed, signaling the existence of a regime of highly coherent transport, but on the other side it switches abruptly to a much larger value. Using a semiclassical approach we show that this behavior arises because of the strongly nonlinear cavity drive generated by the Cooper pairs. We also uncover an equivalence between charge and photonic current noise in the system which opens up a route to detecting the critical behavior through straightforward microwave measurements.

A material combination principle for highly efficient polymer solar cells investigated by mesoscopic phase heterogeneity

NASA Astrophysics Data System (ADS)

Yan, Han; Li, Denghua; He, Chang; Wei, Zhixiang; Yang, Yanlian; Li, Yongfang

2013-11-01

Organic solar cells have become a promising energy conversion candidate because of their unique advantages. Novel fullerene derivatives, as a common acceptor, can increase power conversion efficiency (PCE) by increasing the open-circuit voltage. As a representative acceptor, Indene-C60 bisadduct (ICBA) can reach high efficiency with poly(3-hexylthiophene) (P3HT). On the other hand, the novel synthesized polymers mainly aimed to broaden the optical absorption range have steadily promoted efficiency to higher than 9%. However, it is challenging to obtain the desired result by simply combining ICBA with other high-efficiency donors. Thus, P3HT or a high-efficiency polymer PBDTTT-C-T (copolymer of thienyl-substituted BDT with substituted TT) is used as donor and PCBM or ICBA as acceptor in this article to clarify the mechanism behind these materials. The optical and photovoltaic properties of the materials are studied for pair-wise combination. Among these four material groups, the highest PCE of 6.2% is obtained for the PBDTTT-C-T/PCBM combination while the lowest PCE of 3.5% is obtained for the PBDTTT-C-T/ICBA combination. The impact of the mesoscopic heterogeneity on the local mesoscopic photoelectric properties is identified by photo-conductive AFM (pc-AFM), and the consistence between the mesoscopic properties and the macroscopic device performances is also observed. Based on these results, an interface combined model is proposed based on the mesoscopic phase heterogeneity. This study provides a new view on the rational selection of photovoltaic materials, where, aside from the traditional energy level and absorption spectrum matching, the matching of mesoscopic heterogeneity must also be considered.Organic solar cells have become a promising energy conversion candidate because of their unique advantages. Novel fullerene derivatives, as a common acceptor, can increase power conversion efficiency (PCE) by increasing the open-circuit voltage. As a representative acceptor, Indene-C60 bisadduct (ICBA) can reach high efficiency with poly(3-hexylthiophene) (P3HT). On the other hand, the novel synthesized polymers mainly aimed to broaden the optical absorption range have steadily promoted efficiency to higher than 9%. However, it is challenging to obtain the desired result by simply combining ICBA with other high-efficiency donors. Thus, P3HT or a high-efficiency polymer PBDTTT-C-T (copolymer of thienyl-substituted BDT with substituted TT) is used as donor and PCBM or ICBA as acceptor in this article to clarify the mechanism behind these materials. The optical and photovoltaic properties of the materials are studied for pair-wise combination. Among these four material groups, the highest PCE of 6.2% is obtained for the PBDTTT-C-T/PCBM combination while the lowest PCE of 3.5% is obtained for the PBDTTT-C-T/ICBA combination. The impact of the mesoscopic heterogeneity on the local mesoscopic photoelectric properties is identified by photo-conductive AFM (pc-AFM), and the consistence between the mesoscopic properties and the macroscopic device performances is also observed. Based on these results, an interface combined model is proposed based on the mesoscopic phase heterogeneity. This study provides a new view on the rational selection of photovoltaic materials, where, aside from the traditional energy level and absorption spectrum matching, the matching of mesoscopic heterogeneity must also be considered. Electronic Supplementary Information (ESI) available. See DOI: 10.1039/c3nr03165a

Multiscale Approach For Simulating Nonlinear Wave Propagation In Materials with Localized Microdamage

NASA Astrophysics Data System (ADS)

Vanaverbeke, Sigfried; Van Den Abeele, Koen

2006-05-01

A multiscale model for the simulation of two-dimensional nonlinear wave propagation in microcracked materials exhibiting hysteretic nonlinearity is presented. We use trigger-like elements with a two state nonlinear stress-strain relation to simulate microcracks at the microlevel. A generalized Preisach space approach, based on the eigenstress-eigenstrain formulation, upscales the microscopic state relation to the mesoscopic level. The macroscopic response of the sample to an arbitrary excitation signal is then predicted using a staggered grid Elastodynamic Finite Integration Technique (EFIT) formalism. We apply the model to investigate spectral changes of a pulsed signal traversing a localized microdamaged region with hysteretic nonlinearity in a plate, and to study the influence of a superficial region with hysteretic nonlinearity on the nonlinear Rayleigh wave propagation.

Nonlinear acoustic experiments involving landmine detection: Connections with mesoscopic elasticity and slow dynamics in geomaterials, Part III

NASA Astrophysics Data System (ADS)

Korman, Murray S.; Sabatier, James M.

2005-09-01

In nonlinear acoustic detection schemes, airborne sound at two primary tones, f1, f2 (closely spaced near an 80-Hz resonance) excites the soil surface over a buried landmine. Due to soil wave interactions with the landmine, a scattered surface profile can be measured by a geophone. Profiles at f1, f2, f1-(f2-f1) and f2+(f2-f1) exhibit single peaks; those at 2f1-(f2-f1), f1+f2 and 2f2+(f2-f1) involve higher order mode shapes for a VS 2.2 plastic, inert, anti-tank landmine, buried at 3.6 cm in sifted loess soil [J. Acoust. Soc. Am. 116, 3354-3369 (2004)]. Near resonance, the bending (softening) of a family of increasing amplitude tuning curves, involving the vibration over the landmine, exhibits a linear relationship between the peak particle velocity and corresponding frequency. Results are similar to nonlinear mesoscopic/nanoscale effects that are observed in granular solids like Berea sandstone. New experiments show that first sweeping up through resonance and then immediately sweeping back down result in different tuning curve behavior that might be explained by ``slow dynamics'' where an effective modulus reduction persists following periods of high strain. Results are similar to those described by TenCate et al. [Phys. Rev. Lett. 85, 1020-1023 (2000)]. [Work supported by U.S. Army RDECOM CERDEC, NVESD.

Nonlinear acoustic experiments involving landmine detection: Connections with mesoscopic elasticity and slow dynamics in geomaterials

NASA Astrophysics Data System (ADS)

Korman, Murray S.; Fenneman, Douglas J.; Sabatier, James M.

2004-10-01

The vibration interaction between the top-plate of a buried VS 1.6 plastic, anti-tank landmine and the soil above it appears to exhibit similar characteristics to the nonlinear mesoscopic/nanoscale effects that are observed in geomaterials like rocks or granular materials. In nonlinear detection schemes, airborne sound at two primary frequencies f1 and f2 (chosen several Hz apart on either side of resonance) undergo acoustic-to-seismic coupling. Interactions with the compliant mine and soil generate combination frequencies that, through scattering, can effect the vibration velocity at the surface. Profiles at f1, f2, f1-(f2-f1) and f2+(f2-f1) exhibit a single peak while profiles at 2f1-(f2-f1), f1+f2 and 2f2+(f2-f1) are attributed to higher order mode shapes. Near resonance (~125 Hz for a mine buried 3.6 cm deep), the bending (softening) of a family of increasing amplitude tuning curves (involving the surface vibration over the landmine) exhibits a linear relationship between the peak particle velocity and corresponding frequency. Subsequent decreasing amplitude tuning curves exhibit hysteresis effects. Slow dynamics explains the amplitude difference in tuning curves for first sweeping upward and then downward through resonance, provided the soil modulus drops after periods of high strain. [Work supported by U.S. Army RDECOM, CERDEC, NVESD, Fort Belvoir, VA.

An effective rate equation approach to reaction kinetics in small volumes: theory and application to biochemical reactions in nonequilibrium steady-state conditions.

PubMed

Grima, R

2010-07-21

Chemical master equations provide a mathematical description of stochastic reaction kinetics in well-mixed conditions. They are a valid description over length scales that are larger than the reactive mean free path and thus describe kinetics in compartments of mesoscopic and macroscopic dimensions. The trajectories of the stochastic chemical processes described by the master equation can be ensemble-averaged to obtain the average number density of chemical species, i.e., the true concentration, at any spatial scale of interest. For macroscopic volumes, the true concentration is very well approximated by the solution of the corresponding deterministic and macroscopic rate equations, i.e., the macroscopic concentration. However, this equivalence breaks down for mesoscopic volumes. These deviations are particularly significant for open systems and cannot be calculated via the Fokker-Planck or linear-noise approximations of the master equation. We utilize the system-size expansion including terms of the order of Omega(-1/2) to derive a set of differential equations whose solution approximates the true concentration as given by the master equation. These equations are valid in any open or closed chemical reaction network and at both the mesoscopic and macroscopic scales. In the limit of large volumes, the effective mesoscopic rate equations become precisely equal to the conventional macroscopic rate equations. We compare the three formalisms of effective mesoscopic rate equations, conventional rate equations, and chemical master equations by applying them to several biochemical reaction systems (homodimeric and heterodimeric protein-protein interactions, series of sequential enzyme reactions, and positive feedback loops) in nonequilibrium steady-state conditions. In all cases, we find that the effective mesoscopic rate equations can predict very well the true concentration of a chemical species. This provides a useful method by which one can quickly determine the regions of parameter space in which there are maximum differences between the solutions of the master equation and the corresponding rate equations. We show that these differences depend sensitively on the Fano factors and on the inherent structure and topology of the chemical network. The theory of effective mesoscopic rate equations generalizes the conventional rate equations of physical chemistry to describe kinetics in systems of mesoscopic size such as biological cells.

Probing equilibrium by nonequilibrium dynamics: Aging in Co/Cr superlattices

NASA Astrophysics Data System (ADS)

Binek, Christian

2013-03-01

Magnetic aging phenomena are investigated in a structurally ordered Co/Cr superlattice through measurements of magnetization relaxation, magnetic susceptibility, and hysteresis at various temperatures above and below the onset of collective magnetic order. We take advantage of the fact that controlled growth of magnetic multilayer thin films via molecular beam epitaxy allows tailoring the intra and inter-layer exchange interaction and thus enables tuning of magnetic properties including the spin-fluctuation spectra. Tailored nanoscale periodicity in Co/Cr multilayers creates mesoscopic spatial magnetic correlations with slow relaxation dynamics when quenching the system into a nonequilibrium state. Magnetization relaxation in weakly correlated spin systems depends on the microscopic spin-flip time of about 10 ns and is therefore a fast process. The spin correlations in our Co/Cr superlattice bring the magnetization dynamics to experimentally better accessible time scales of seconds or hours. In contrast to spin-glasses, where slow dynamics due to disorder and frustration is a well-known phenomenon, we tune and increase relaxation times in ordered structures. This is achieved by increasing spin-spin correlation between mesoscopically correlated regions rather than individual atomic spins, a concept with some similarity to block spin renormalization. Magnetization transients are measured after exposing the Co/Cr heterostructure to a magnetic set field for various waiting times. Scaling analysis reveals an asymptotic power-law behavior in accordance with a full aging scenario. The temperature dependence of the relaxation exponent shows pronounced anomalies at the equilibrium phase transitions of the antiferromagnetic superstructure and the ferromagnetic to paramagnetic transition of the Co layers. The latter leaves only weak fingerprints in the equilibrium magnetic behavior but gives rise to a prominent change in nonequilibrium properties. Our findings suggest that scaling analysis of nonequilibrium data can serve as a probe for weak equilibrium phase transitions. Financial support by NRI, and NSF through EPSCoR, and MRSEC 0820521 is greatly acknowledged.

Mesoscopic Length Scale Controls the Rheology of Dense Suspensions

NASA Astrophysics Data System (ADS)

Bonnoit, Claire; Lanuza, Jose; Lindner, Anke; Clement, Eric

2010-09-01

From the flow properties of dense granular suspensions on an inclined plane, we identify a mesoscopic length scale strongly increasing with volume fraction. When the flowing layer height is larger than this length scale, a diverging Newtonian viscosity is determined. However, when the flowing layer height drops below this scale, we evidence a nonlocal effective viscosity, decreasing as a power law of the flow height. We establish a scaling relation between this mesoscopic length scale and the suspension viscosity. These results support recent theoretical and numerical results implying collective and clustered granular motion when the jamming point is approached from below.

Mesoscopic length scale controls the rheology of dense suspensions.

PubMed

Bonnoit, Claire; Lanuza, Jose; Lindner, Anke; Clement, Eric

2010-09-03

From the flow properties of dense granular suspensions on an inclined plane, we identify a mesoscopic length scale strongly increasing with volume fraction. When the flowing layer height is larger than this length scale, a diverging Newtonian viscosity is determined. However, when the flowing layer height drops below this scale, we evidence a nonlocal effective viscosity, decreasing as a power law of the flow height. We establish a scaling relation between this mesoscopic length scale and the suspension viscosity. These results support recent theoretical and numerical results implying collective and clustered granular motion when the jamming point is approached from below.

A simple quantum mechanical treatment of scattering in nanoscale transistors

NASA Astrophysics Data System (ADS)

Venugopal, R.; Paulsson, M.; Goasguen, S.; Datta, S.; Lundstrom, M. S.

2003-05-01

We present a computationally efficient, two-dimensional quantum mechanical simulation scheme for modeling dissipative electron transport in thin body, fully depleted, n-channel, silicon-on-insulator transistors. The simulation scheme, which solves the nonequilibrium Green's function equations self consistently with Poisson's equation, treats the effect of scattering using a simple approximation inspired by the "Büttiker probes," often used in mesoscopic physics. It is based on an expansion of the active device Hamiltonian in decoupled mode space. Simulation results are used to highlight quantum effects, discuss the physics of scattering and to relate the quantum mechanical quantities used in our model to experimentally measured low field mobilities. Additionally, quantum boundary conditions are rigorously derived and the effects of strong off-equilibrium transport are examined. This paper shows that our approximate treatment of scattering, is an efficient and useful simulation method for modeling electron transport in nanoscale, silicon-on-insulator transistors.

A mesoscopic simulation on distributions of red blood cells in a bifurcating channel

NASA Astrophysics Data System (ADS)

Inoue, Yasuhiro; Takagi, Shu; Matsumoto, Yoichiro

2004-11-01

Transports of red blood cells (RBCs) or particles in bifurcated channels have been attracting renewed interest since the advent of concepts of MEMS for sorting, analyzing, and removing cells or particles from sample medium. In this talk, we present a result on a transport of red blood cells (RBCs) in a bifurcating channel studied by using a mesoscale simulation technique of immiscible droplets, where RBCs have been modeled as immiscible droplets. The distribution of RBCs is represented by the fractional RBC flux into two daughters as a function of volumetric flow ratio between the daughters. The data obtained in our simulations are examined with a theoretical prediction, in which, we assume an exponential distribution for positions of RBCs in the mother channel. The theoretical predictions show a good agreement with simulation results. A non-uniform distribution of RBCs in the mother channel affects disproportional separation of RBC flux at a bifurcation.

Adiabatic coarse-graining and simulations of stochastic biochemical networks

PubMed Central

Sinitsyn, N. A.; Hengartner, Nicolas; Nemenman, Ilya

2009-01-01

We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian fluctuations of the slow ones. Our approach is similar to the Born–Oppenheimer approximation in quantum mechanics and follows from the stochastic path integral representation of the cumulant generating function of reaction events. In applications with a small number of chemical reactions, it produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, interpretable representation and can be used for high-accuracy, low-complexity coarse-grained numerical simulations. As an example, we derive the coarse-grained description for a chain of biochemical reactions and show that the coarse-grained and the microscopic simulations agree, but the former is 3 orders of magnitude faster. PMID:19525397

Effects of nanoparticles on the compatibility of PEO-PMMA block copolymers.

PubMed

Mu, Dan; Li, Jian-Quan; Li, Wei-Dong; Wang, Song

2011-12-01

The compatibility of six kinds of designed poly(ethylene oxide)-block-poly(methyl methacrylate) (PEO-b-PMMA) copolymers was studied at 270, 298 and 400 K via mesoscopic modeling. The values of the order parameters depended on both the structures of the block copolymers and the simulation temperature, while the values of the order parameters of the long chains were higher than those of the short ones; temperature had a more obvious effect on long chains than on the short ones. Plain copolymers doped with poly(ethylene oxide) (PEO) or poly(methyl methacrylate) (PMMA) homopolymer showed different order parameter values. When a triblock copolymer had the same component at both ends and was doped with one of its component polymers as a homopolymer (such as A5B6A5 doped with B6 or A5 homopolymer), the value of its order parameter depended on the simulation temperature. The highest order parameter values were observed for A5B6A5 doped with B6 at 400 K and for A5B6A5 doped with A5 at 270 K. A study of copolymers doped with nanoparticles showed that the mesoscopic phase was influenced by not only the properties of the nanoparticles, such as the size and density, but also the compositions of the copolymers. Increasing the size of the nanoparticles used as a dopant had the most significant effect on the phase morphologies of the copolymers.

The quest for solvable multistate Landau-Zener models

DOE PAGES

Sinitsyn, Nikolai A.; Chernyak, Vladimir Y.

2017-05-24

Recently, integrability conditions (ICs) in mutistate Landau-Zener (MLZ) theory were proposed. They describe common properties of all known solved systems with linearly time-dependent Hamiltonians. Here we show that ICs enable efficient computer assisted search for new solvable MLZ models that span complexity range from several interacting states to mesoscopic systems with many-body dynamics and combinatorially large phase space. This diversity suggests that nontrivial solvable MLZ models are numerous. Additionally, we refine the formulation of ICs and extend the class of solvable systems to models with points of multiple diabatic level crossing.

Systems Biology Approach and Mathematical Modeling for Analyzing Phase-Space Switch During Epithelial-Mesenchymal Transition.

PubMed

Simeoni, Chiara; Dinicola, Simona; Cucina, Alessandra; Mascia, Corrado; Bizzarri, Mariano

2018-01-01

In this report, we aim at presenting a viable strategy for the study of Epithelial-Mesenchymal Transition (EMT) and its opposite Mesenchymal-Epithelial Transition (MET) by means of a Systems Biology approach combined with a suitable Mathematical Modeling analysis. Precisely, it is shown how the presence of a metastable state, that is identified at a mesoscopic level of description, is crucial for making possible the appearance of a phase transition mechanism in the framework of fast-slow dynamics for Ordinary Differential Equations (ODEs).

Signature of phase singularities in diffusive regimes in disordered waveguide lattices: interplay and qualitative analysis

NASA Astrophysics Data System (ADS)

Ghosh, Somnath

2018-05-01

Co-existence and interplay between mesoscopic light dynamics with singular optics in spatially random but temporally coherent disordered waveguide lattices is reported. Two CW light beams of 1.55 micron operating wavelength are launched as inputs to 1D waveguide lattices with controllable weak disorder in refractive index profile. Direct observation of phase singularities in the speckle pattern along the length is numerically demonstrated. Quantitative analysis of onset of such singular behavior and diffusive wave propagation is analyzed for the first time.

Suppression of the "Quasiclassical" proximity gap in correlated-metal--superconductor structures.

PubMed

Nikolić, Branislav K; Freericks, J K; Miller, P

2002-02-18

We study the energy and spatial dependence of the local density of states in a superconductor--correlated-metal--superconductor Josephson junction, where the correlated metal is a non-Fermi liquid (described by the Falicov-Kimball model). Many-body correlations are treated with dynamical mean-field theory, extended to inhomogeneous systems. While quasiclassical theories predict a minigap in the spectrum of a disordered Fermi liquid which is proximity-coupled within a mesoscopic junction, we find that increasing electron correlations destroy any minigap that might be opened in the absence of many-body correlations.

Introscopy in nano- and mesoscopic physics: Single electronics and quantum ballistics

NASA Astrophysics Data System (ADS)

Tkachenko, V. A.; Tkachenko, O. A.; Kvon, Z. D.; Latyshev, A. V.; Aseev, A. L.

2016-09-01

A method is presented to be used in a computational experiment aimed at studying the internal structure of nano- and mesoscopic objects, i.e., conducting subsystems and quantum phenomena in solid submicron objects, which demonstrate an individual behavior of low-temperature resistance.

Fermi edge singularities in the mesoscopic regime: Photoabsorption spectra

NASA Astrophysics Data System (ADS)

Hentschel, Martina; Ullmo, Denis; Baranger, Harold U.

2007-12-01

We study Fermi edge singularities in photoabsorption spectra of generic mesoscopic systems such as quantum dots or nanoparticles. We predict deviations from macroscopic-metallic behavior and propose experimental setups for the observation of these effects. The theory is based on the model of a localized, or rank one, perturbation caused by the (core) hole left behind after the photoexcitation of an electron into the conduction band. The photoabsorption spectra result from the competition between two many-body responses, Anderson’s orthogonality catastrophe and the Mahan-Nozières-DeDominicis contribution. Both mechanisms depend on the system size through the number of particles and, more importantly, fluctuations produced by the coherence characteristic of mesoscopic samples. The latter lead to a modification of the dipole matrix element and trigger one of our key results: a rounded K -edge typically found in metals will turn into a (slightly) peaked edge on average in the mesoscopic regime. We consider in detail the effect of the “bound state” produced by the core hole.

Fracture of disordered solids in compression as a critical phenomenon. I. Statistical mechanics formalism.

PubMed

Toussaint, Renaud; Pride, Steven R

2002-09-01

This is the first of a series of three articles that treats fracture localization as a critical phenomenon. This first article establishes a statistical mechanics based on ensemble averages when fluctuations through time play no role in defining the ensemble. Ensembles are obtained by dividing a huge rock sample into many mesoscopic volumes. Because rocks are a disordered collection of grains in cohesive contact, we expect that once shear strain is applied and cracks begin to arrive in the system, the mesoscopic volumes will have a wide distribution of different crack states. These mesoscopic volumes are the members of our ensembles. We determine the probability of observing a mesoscopic volume to be in a given crack state by maximizing Shannon's measure of the emergent-crack disorder subject to constraints coming from the energy balance of brittle fracture. The laws of thermodynamics, the partition function, and the quantification of temperature are obtained for such cracking systems.

Direct Observation of Individual Charges and Their Dynamics on Graphene by Low-Energy Electron Holography.

PubMed

Latychevskaia, Tatiana; Wicki, Flavio; Longchamp, Jean-Nicolas; Escher, Conrad; Fink, Hans-Werner

2016-09-14

Visualizing individual charges confined to molecules and observing their dynamics with high spatial resolution is a challenge for advancing various fields in science, ranging from mesoscopic physics to electron transfer events in biological molecules. We show here that the high sensitivity of low-energy electrons to local electric fields can be employed to directly visualize individual charged adsorbates and to study their behavior in a quantitative way. This makes electron holography a unique probing tool for directly visualizing charge distributions with a sensitivity of a fraction of an elementary charge. Moreover, spatial resolution in the nanometer range and fast data acquisition inherent to lens-less low-energy electron holography allows for direct visual inspection of charge transfer processes.

Frenetic Bounds on the Entropy Production

NASA Astrophysics Data System (ADS)

Maes, Christian

2017-10-01

We give a systematic derivation of positive lower bounds for the expected entropy production (EP) rate in classical statistical mechanical systems obeying a dynamical large deviation principle. The logic is the same for the return to thermodynamic equilibrium as it is for steady nonequilibria working under the condition of local detailed balance. We recover there recently studied "uncertainty" relations for the EP, appearing in studies about the effectiveness of mesoscopic machines. In general our refinement of the positivity of the expected EP rate is obtained in terms of a positive and even function of the expected current(s) which measures the dynamical activity in the system, a time-symmetric estimate of the changes in the system's configuration. Also underdamped diffusions can be included in the analysis.

Probing the early stages of shock-induced chondritic meteorite formation at the mesoscale

PubMed Central

Rutherford, Michael E.; Chapman, David J.; Derrick, James G.; Patten, Jack R. W.; Bland, Philip A.; Rack, Alexander; Collins, Gareth S.; Eakins, Daniel E.

2017-01-01

Chondritic meteorites are fragments of asteroids, the building blocks of planets, that retain a record of primordial processes. Important in their early evolution was impact-driven lithification, where a porous mixture of millimetre-scale chondrule inclusions and sub-micrometre dust was compacted into rock. In this Article, the shock compression of analogue precursor chondrite material was probed using state of the art dynamic X-ray radiography. Spatially-resolved shock and particle velocities, and shock front thicknesses were extracted directly from the radiographs, representing a greatly enhanced scope of data than could be measured in surface-based studies. A statistical interpretation of the measured velocities showed that mean values were in good agreement with those predicted using continuum-level modelling and mixture theory. However, the distribution and evolution of wave velocities and wavefront thicknesses were observed to be intimately linked to the mesoscopic structure of the sample. This Article provides the first detailed experimental insight into the distribution of extreme states within a shocked powder mixture, and represents the first mesoscopic validation of leading theories concerning the variation in extreme pressure-temperature states during the formation of primordial planetary bodies. PMID:28555619

Electrochemical capacitance modulation in an interacting mesoscopic capacitor induced by internal charge transfer

NASA Astrophysics Data System (ADS)

Liu, Wei; He, Jianhong; Guo, Huazhong; Gao, Jie

2018-04-01

We report experiments on the dynamic response of an interacting mesoscopic capacitor consisting of a quantum dot with two confined spin-split levels of the lowest Landau level. In high magnetic fields, states inside the dot are regulated by a mixture of Coulomb interaction and Landau-level quantization, and electrons distribute on two spatially separated regions. Quantum point contact voltage and magnetic field are employed to manipulate the number and distribution of electrons inside the quantum dot. We find that the periodicity of the electrochemical capacitance oscillations is dominated by the charging energy, and their amplitudes, due to internal charge transfer and strong internal capacitive coupling, show rich variations of modulations. Magnetocapacitance displays a sawtoothlike manner and may differ in tooth directions for different voltages, which, we demonstrate, result from a sawtoothlike electrochemical potential change induced by internal charge transfer and field-sensitive electrostatic potential. We further build a charge stability diagram, which, together with all other capacitance properties, is consistently interpreted in terms of a double-dot model. The demonstrated technique is of interest as a tool for fast and sensitive charge state readout of a double-quantum-dot qubit in the gigahertz frequency quantum electronics.

Domain pinning near a single-grain boundary in tetragonal and rhombohedral lead zirconate titanate films

DOE PAGES

Marincel, Dan M.; Zhang, H. R.; Briston, J.; ...

2015-04-27

The interaction of grain boundaries with ferroelectric domain walls strongly influences the extrinsic contribution to piezoelectric activity in Pb(Zr,Ti)O 3 (PZT), ubiquitous in modern transducers and actuators. However, the fundamental understanding of these phenomena has been limited by complex mechanisms originating from the interplay of atomic-level domain wall pinning, collective domain wall dynamics, and emergent mesoscopic behavior. This contribution utilizes engineered grain boundaries created by depositing epitaxial PZT films with various Zr:Ti ratio onto 24º SrTiO 3 tilt bicrystals. The nonlinear piezoelectric response and surface domain structure across the boundary are investigated using piezoresponse force microscopy whilst cross section domainmore » structure is studied using transmission electron microscopy. The grain boundary reduces domain wall motion over a width of 800±70 nm for PZT 45:55 and 450±30 nm for PZT 52:48. Phase field modeling provides an understanding of the elastic and electric fields associated with the grain boundary and local domain configurations. In conclusion, this study demonstrates that complex mesoscopic behaviors can be explored to complement atomic-level pictures of the material system.« less

Toward a microscopic model of bidirectional synaptic plasticity

PubMed Central

Castellani, Gastone C.; Bazzani, Armando; Cooper, Leon N

2009-01-01

We show that a 2-step phospho/dephosphorylation cycle for the α-amino-3-hydroxy-5-methyl-4-isoxazole proprionic acid receptor (AMPAR), as used in in vivo learning experiments to assess long-term potentiation (LTP) induction and establishment, exhibits bistability for a wide range of parameters, consistent with values derived from biological literature. The AMPAR model we propose, hence, is a candidate for memory storage and switching behavior at a molecular-microscopic level. Furthermore, the stochastic formulation of the deterministic model leads to a mesoscopic interpretation by considering the effect of enzymatic fluctuations on the Michelis–Menten average dynamics. Under suitable hypotheses, this leads to a stochastic dynamical system with multiplicative noise whose probability density evolves according to a Fokker–Planck equation in the Stratonovich sense. In this approach, the probability density associated with each AMPAR phosphorylation state allows one to compute the probability of any concentration value, whereas the Michaelis–Menten equations consider the average concentration dynamics. We show that bistable dynamics are robust for multiplicative stochastic perturbations and that the presence of both noise and bistability simulates LTP and long-term depression (LTD) behavior. Interestingly, the LTP part of this model has been experimentally verified as a result of in vivo, one-trial inhibitory avoidance learning protocol in rats, that produced the same changes in hippocampal AMPARs phosphorylation state as observed with in vitro induction of LTP with high-frequency stimulation (HFS). A consequence of this model is the possibility of characterizing a molecular switch with a defined biochemical set of reactions showing bistability and bidirectionality. Thus, this 3-enzymes-based biophysical model can predict LTP as well as LTD and their transition rates. The theoretical results can be, in principle, validated by in vitro and in vivo experiments, such as fluorescence measurements and electrophysiological recordings at multiple scales, from molecules to neurons. A further consequence is that the bistable regime occurs only within certain parametric windows, which may simulate a “history-dependent threshold”. This effect might be related to the Bienenstock–Cooper–Munro theory of synaptic plasticity. PMID:19666550

Large-Scale Reactive Atomistic Simulation of Shock-induced Initiation Processes in Energetic Materials

NASA Astrophysics Data System (ADS)

Thompson, Aidan

2013-06-01

Initiation in energetic materials is fundamentally dependent on the interaction between a host of complex chemical and mechanical processes, occurring on scales ranging from intramolecular vibrations through molecular crystal plasticity up to hydrodynamic phenomena at the mesoscale. A variety of methods (e.g. quantum electronic structure methods (QM), non-reactive classical molecular dynamics (MD), mesoscopic continuum mechanics) exist to study processes occurring on each of these scales in isolation, but cannot describe how these processes interact with each other. In contrast, the ReaxFF reactive force field, implemented in the LAMMPS parallel MD code, allows us to routinely perform multimillion-atom reactive MD simulations of shock-induced initiation in a variety of energetic materials. This is done either by explicitly driving a shock-wave through the structure (NEMD) or by imposing thermodynamic constraints on the collective dynamics of the simulation cell e.g. using the Multiscale Shock Technique (MSST). These MD simulations allow us to directly observe how energy is transferred from the shockwave into other processes, including intramolecular vibrational modes, plastic deformation of the crystal, and hydrodynamic jetting at interfaces. These processes in turn cause thermal excitation of chemical bonds leading to initial chemical reactions, and ultimately to exothermic formation of product species. Results will be presented on the application of this approach to several important energetic materials, including pentaerythritol tetranitrate (PETN) and ammonium nitrate/fuel oil (ANFO). In both cases, we validate the ReaxFF parameterizations against QM and experimental data. For PETN, we observe initiation occurring via different chemical pathways, depending on the shock direction. For PETN containing spherical voids, we observe enhanced sensitivity due to jetting, void collapse, and hotspot formation, with sensitivity increasing with void size. For ANFO, we examine the effect of reaction rates on shock direction, fuel oil fraction, and crystal/fuel oil/void microstructural arrangement. 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. Dept. of Energy's National Nuclear Security Admin. under contract DEAC0494AL85000.

Steepest entropy ascent model for far-nonequilibrium thermodynamics: Unified implementation of the maximum entropy production principle

NASA Astrophysics Data System (ADS)

Beretta, Gian Paolo

2014-10-01

By suitable reformulations, we cast the mathematical frameworks of several well-known different approaches to the description of nonequilibrium dynamics into a unified formulation valid in all these contexts, which extends to such frameworks the concept of steepest entropy ascent (SEA) dynamics introduced by the present author in previous works on quantum thermodynamics. Actually, the present formulation constitutes a generalization also for the quantum thermodynamics framework. The analysis emphasizes that in the SEA modeling principle a key role is played by the geometrical metric with respect to which to measure the length of a trajectory in state space. In the near-thermodynamic-equilibrium limit, the metric tensor is directly related to the Onsager's generalized resistivity tensor. Therefore, through the identification of a suitable metric field which generalizes the Onsager generalized resistance to the arbitrarily far-nonequilibrium domain, most of the existing theories of nonequilibrium thermodynamics can be cast in such a way that the state exhibits the spontaneous tendency to evolve in state space along the path of SEA compatible with the conservation constraints and the boundary conditions. The resulting unified family of SEA dynamical models is intrinsically and strongly consistent with the second law of thermodynamics. The non-negativity of the entropy production is a general and readily proved feature of SEA dynamics. In several of the different approaches to nonequilibrium description we consider here, the SEA concept has not been investigated before. We believe it defines the precise meaning and the domain of general validity of the so-called maximum entropy production principle. Therefore, it is hoped that the present unifying approach may prove useful in providing a fresh basis for effective, thermodynamically consistent, numerical models and theoretical treatments of irreversible conservative relaxation towards equilibrium from far nonequilibrium states. The mathematical frameworks we consider are the following: (A) statistical or information-theoretic models of relaxation; (B) small-scale and rarefied gas dynamics (i.e., kinetic models for the Boltzmann equation); (C) rational extended thermodynamics, macroscopic nonequilibrium thermodynamics, and chemical kinetics; (D) mesoscopic nonequilibrium thermodynamics, continuum mechanics with fluctuations; and (E) quantum statistical mechanics, quantum thermodynamics, mesoscopic nonequilibrium quantum thermodynamics, and intrinsic quantum thermodynamics.

Mesoscopic structure of neuronal tracts from time-dependent diffusion

PubMed Central

Burcaw, Lauren M.; Fieremans, Els; Novikov, Dmitry S.

2015-01-01

Interpreting brain diffusion MRI measurements in terms of neuronal structure at a micrometer level is an exciting unresolved problem. Here we consider diffusion transverse to a bundle of fibers, and show theoretically, as well as using Monte Carlo simulations and measurements in a phantom made of parallel fibers mimicking axons, that the time dependent diffusion coefficient approaches its macroscopic limit slowly, in a (lnt)/t fashion. The logarithmic singularity arises due to short range disorder in the fiber packing. We identify short range disorder in axonal fibers based on histological data from the splenium, and argue that the time dependent contribution to the overall diffusion coefficient from the extra-axonal water dominates that of the intra-axonal water. This dominance may explain the bias in measuring axon diameters in clinical settings. The short range disorder is also reflected in the linear frequency dependence of the diffusion coefficient measured with oscillating gradients, in agreement with recent experiments. Our results relate the measured diffusion to the mesoscopic structure of neuronal tissue, uncovering the sensitivity of diffusion metrics to axonal arrangement within a fiber tract, and providing an alternative interpretation of axonal diameter mapping techniques. PMID:25837598

Mesoscopic structure of neuronal tracts from time-dependent diffusion.

PubMed

Burcaw, Lauren M; Fieremans, Els; Novikov, Dmitry S

2015-07-01

Interpreting brain diffusion MRI measurements in terms of neuronal structure at a micrometer level is an exciting unresolved problem. Here we consider diffusion transverse to a bundle of fibers, and show theoretically, as well as using Monte Carlo simulations and measurements in a phantom made of parallel fibers mimicking axons, that the time dependent diffusion coefficient approaches its macroscopic limit slowly, in a (ln t)/t fashion. The logarithmic singularity arises due to short range disorder in the fiber packing. We identify short range disorder in axonal fibers based on histological data from the splenium, and argue that the time dependent contribution to the overall diffusion coefficient from the extra-axonal water dominates that of the intra-axonal water. This dominance may explain the bias in measuring axon diameters in clinical settings. The short range disorder is also reflected in the asymptotically linear frequency dependence of the diffusion coefficient measured with oscillating gradients, in agreement with recent experiments. Our results relate the measured diffusion to the mesoscopic structure of neuronal tissue, uncovering the sensitivity of diffusion metrics to axonal arrangement within a fiber tract, and providing an alternative interpretation of axonal diameter mapping techniques. Copyright © 2015 Elsevier Inc. All rights reserved.

Taylor dispersion of colloidal particles in narrow channels

NASA Astrophysics Data System (ADS)

Sané, Jimaan; Padding, Johan T.; Louis, Ard A.

2015-09-01

We use a mesoscopic particle-based simulation technique to study the classic convection-diffusion problem of Taylor dispersion for colloidal discs in confined flow. When the disc diameter becomes non-negligible compared to the diameter of the pipe, there are important corrections to the original Taylor picture. For example, the colloids can flow more rapidly than the underlying fluid, and their Taylor dispersion coefficient is decreased. For narrow pipes, there are also further hydrodynamic wall effects. The long-time tails in the velocity autocorrelation functions are altered by the Poiseuille flow.

Developing mesoscopic models for the before and after study of the inter-county connector : phase-one.

DOT National Transportation Integrated Search

2013-03-01

This study developed a mesoscopic model for the before and after study of MD 200, the Inter-County Connector. It is in line with : recent efforts by the Maryland State Highway Administration (SHA) in developing effective modeling tools for traffic an...

Mesoscopic Rings with Spin-Orbit Interactions

ERIC Educational Resources Information Center

Berche, Bertrand; Chatelain, Christophe; Medina, Ernesto

2010-01-01

A didactic description of charge and spin equilibrium currents on mesoscopic rings in the presence of spin-orbit interaction is presented. Emphasis is made on the non-trivial construction of the correct Hamiltonian in polar coordinates, the calculation of eigenvalues and eigenfunctions and the symmetries of the ground-state properties. Spin…

Two-Scale Simulation of Drop-Induced Failure of Polysilicon MEMS Sensors

PubMed Central

Mariani, Stefano; Ghisi, Aldo; Corigliano, Alberto; Martini, Roberto; Simoni, Barbara

2011-01-01

In this paper, an industrially-oriented two-scale approach is provided to model the drop-induced brittle failure of polysilicon MEMS sensors. The two length-scales here investigated are the package (macroscopic) and the sensor (mesoscopic) ones. Issues related to the polysilicon morphology at the micro-scale are disregarded; an upscaled homogenized constitutive law, able to describe the brittle cracking of silicon, is instead adopted at the meso-scale. The two-scale approach is validated against full three-scale Monte-Carlo simulations, which allow for stochastic effects linked to the microstructural properties of polysilicon. Focusing on inertial MEMS sensors exposed to drops, it is shown that the offered approach matches well the experimentally observed failure mechanisms. PMID:22163885

Wide-range simulation of elastoplastic wave fronts and failure of solids under high-speed loading

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

Saveleva, Natalia, E-mail: saveleva@icmm.ru; Bayandin, Yuriy, E-mail: buv@icmm.ru; Naimark, Oleg, E-mail: naimark@icmm.ru

2015-10-27

The aim of this paper is numerical study of deformation processes and failure of vanadium under shock-wave loading. According developed statistical theory of solid with mesoscopic defects the constitutive equations were proposed in terms of two structural variables characterizing behavior of defects ensembles: defect density tensor and structural scaling parameter. On the basis of wide-range constitutive equations the mathematical model of deformation behavior and failure of vanadium was developed taking into account the bond relaxation mechanisms, multistage of fracture and nonlinearity kinetic of defects. Results of numerical simulation allow the description of the major effects of shock wave propagation (elasticmore » precursor decay, grow of spall strength under grow strain rate)« less

Physics-based statistical learning approach to mesoscopic model selection.

PubMed

Taverniers, Søren; Haut, Terry S; Barros, Kipton; Alexander, Francis J; Lookman, Turab

2015-11-01

In materials science and many other research areas, models are frequently inferred without considering their generalization to unseen data. We apply statistical learning using cross-validation to obtain an optimally predictive coarse-grained description of a two-dimensional kinetic nearest-neighbor Ising model with Glauber dynamics (GD) based on the stochastic Ginzburg-Landau equation (sGLE). The latter is learned from GD "training" data using a log-likelihood analysis, and its predictive ability for various complexities of the model is tested on GD "test" data independent of the data used to train the model on. Using two different error metrics, we perform a detailed analysis of the error between magnetization time trajectories simulated using the learned sGLE coarse-grained description and those obtained using the GD model. We show that both for equilibrium and out-of-equilibrium GD training trajectories, the standard phenomenological description using a quartic free energy does not always yield the most predictive coarse-grained model. Moreover, increasing the amount of training data can shift the optimal model complexity to higher values. Our results are promising in that they pave the way for the use of statistical learning as a general tool for materials modeling and discovery.

Role of oxygen diffusion at Ni/Cr2O3 interface in intergranular oxidation of Ni-Cr alloy

NASA Astrophysics Data System (ADS)

Medasani, Bharat; Sushko, Maria; Schreiber, Daniel; Rosso, Kevin; Bruemmer, Stephen

Certain Ni-Cr alloys used in nuclear systems experience intergranular oxidation and stress corrosion cracking when exposed to high-temperature water leading to their degradation and unexpected failure. To develop a mechanistic understanding of grain boundary oxidation processes, we proposed a mesoscale metal alloy oxidation model that combines quantum Density Functional Theory (DFT) with mesoscopic Poisson-Nernst-Planck/classical DFT. This framework encompasses the chemical specificity of elementary diffusion processes and mesoscale reactive dynamics, and allows modeling oxidation processes on experimentally relevant length scales from first principles. As a proof of concept, a preliminary model was previously employed that limited oxygen diffusion pathways to those through the oxide phase and did not allow oxygen diffusion in the alloy or across oxide/alloy interfaces. In this work, we expand the model to include oxygen diffusion pathways along Ni/Cr2O3 interfaces and demonstrate the increasing importance of such pathways for intergranular oxidation of Ni-Cr alloys with high Cr content. This work is supported by the U.S. Dept. of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division. Simulations are performed using PNNL Institutional Computing facility.

Nanoscale organization in the fluorinated room temperature ionic liquid: Tetraethyl ammonium (trifluoromethanesulfonyl)(nonafluorobutylsulfonyl)imide

NASA Astrophysics Data System (ADS)

Lo Celso, F.; Appetecchi, G. B.; Jafta, C. J.; Gontrani, L.; Canongia Lopes, J. N.; Triolo, A.; Russina, O.

2018-05-01

Fluorinated Room Temperature Ionic Liquids (FRTILs) are a branch of ionic liquids that is the object of growing interest for a wide range of potential applications, due to the synergic combination of specifically ionic features and those properties that stem from fluorous tails. So far limited experimental work exists on the micro- and mesoscopic structural organization in this class of compounds. Such a work is however necessary to fully understand morphological details at atomistic level that would have strong implications in terms of bulk properties. Here we use the synergy between X-ray and neutron scattering together with molecular dynamics simulations to access structural details of a technologically relevant FRTIL that is characterised by an anion bearing a long enough fluorinated tail to develop specific morphological features. In particular, we find the first experimental evidence that in FRTILs bearing an asymmetric bis(perfluoroalkyl)sulfonyl-imide anion, fluorous side chains tend to be spatially segregated into nm-scale spatial heterogeneities. This feature together with the well-established micro-segregation of side alkyl chains in conventional RTILs leads to the concept of triphilic ILs, whose technological applications are yet to be fully developed.

Revealing the fast atomic motion of network glasses.

PubMed

Ruta, B; Baldi, G; Chushkin, Y; Rufflé, B; Cristofolini, L; Fontana, A; Zanatta, M; Nazzani, F

2014-05-19

Still very little is known on the relaxation dynamics of glasses at the microscopic level due to the lack of experiments and theories. It is commonly believed that glasses are in a dynamical arrested state, with relaxation times too large to be observed on human time scales. Here we provide the experimental evidence that glasses display fast atomic rearrangements within a few minutes, even in the deep glassy state. Following the evolution of the structural relaxation in a sodium silicate glass, we find that this fast dynamics is accompanied by the absence of any detectable aging, suggesting a decoupling of the relaxation time and the viscosity in the glass. The relaxation time is strongly affected by the network structure with a marked increase at the mesoscopic scale associated with the ion-conducting pathways. Our results modify the conception of the glassy state and asks for a new microscopic theory.

Pattern Transitions in Bacterial Oscillating System under Nanofluidic Confinement

NASA Astrophysics Data System (ADS)

Shen, Jie-Pan; Chou, Chia-Fu

2011-03-01

Successful binary fission in E. coli relies on remarkable oscillatory behavior of the MinCDE protein system to determine the exact division site. The most favorable models to explain this fascinating spatiotemporal regulation on dynamic MinDE pattern formation in cells are based on reaction-diffusion scenario. Although not fully understood, geometric factors caused by bacterial morphology play a crucial role in MinDE dynamics. In the present study, bacteria were cultured, confined and reshaped in various micro/nanofluidic devices, to mimic either curvature changes of cell peripherals. Fluorescence imaging was utilized to detail the mode transitions in multiple MinDE patterns. The understanding of the physics in multiple pattern formations is further complemented via in silico modeling. The study synergizes the join merits of in vivo, in vitro and in silico approaches, to grasp the insight of stochastic dynamics inherited from the noisy mesoscopic biophysics. We acknowledge support from the Foresight Project, Academia Sinica.

Statistics of the quantized microwave electromagnetic field in mesoscopic elements at low temperature

NASA Astrophysics Data System (ADS)

Virally, Stéphane; Olivier Simoneau, Jean; Lupien, Christian; Reulet, Bertrand

2018-03-01

The quantum behavior of the electromagnetic field in mesoscopic elements is intimately linked to the quantization of the charge. In order to probe nonclassical aspects of the field in those elements, it is essential that thermal noise be reduced to the quantum level, i.e. to scales where kT ≲ hν. This is easily achieved in dilution refrigerators for frequencies of a few GHz, i.e. in the microwave domain. Several recent experiments have highlighted the link between discrete charge transport and discrete photon emission in simple mesoscopic elements such as a tunnel junction. Photocount statistics are inferred from the measurement of continuous variables such as the quadratures of the field.

Mesoscopic Magnetic Resonance Spectroscopy with a Remote Spin Sensor

NASA Astrophysics Data System (ADS)

Xie, Tianyu; Shi, Fazhan; Chen, Sanyou; Guo, Maosen; Chen, Yisheng; Zhang, Yixing; Yang, Yu; Gao, Xingyu; Kong, Xi; Wang, Pengfei; Tateishi, Kenichiro; Uesaka, Tomohiro; Wang, Ya; Zhang, Bo; Du, Jiangfeng

2018-06-01

Quantum sensing based on nitrogen-vacancy (N -V ) centers in diamond has been developed as a powerful tool for microscopic magnetic resonance. However, the reported sensor-to-sample distance is limited within tens of nanometers resulting from the cubic decrease of the signal of spin fluctuation with the increasing distance. Here we extend the sensing distance to tens of micrometers by detecting spin polarization rather than spin fluctuation. We detect the mesoscopic magnetic resonance spectra of polarized electrons of a pentacene-doped crystal, measure its two typical decay times, and observe the optically enhanced spin polarization. This work paves the way for the N -V -based mesoscopic magnetic resonance spectroscopy and imaging at ambient conditions.

Derivation of the Boltzmann Equation for Financial Brownian Motion: Direct Observation of the Collective Motion of High-Frequency Traders.

PubMed

Kanazawa, Kiyoshi; Sueshige, Takumi; Takayasu, Hideki; Takayasu, Misako

2018-03-30

A microscopic model is established for financial Brownian motion from the direct observation of the dynamics of high-frequency traders (HFTs) in a foreign exchange market. Furthermore, a theoretical framework parallel to molecular kinetic theory is developed for the systematic description of the financial market from microscopic dynamics of HFTs. We report first on a microscopic empirical law of traders' trend-following behavior by tracking the trajectories of all individuals, which quantifies the collective motion of HFTs but has not been captured in conventional order-book models. We next introduce the corresponding microscopic model of HFTs and present its theoretical solution paralleling molecular kinetic theory: Boltzmann-like and Langevin-like equations are derived from the microscopic dynamics via the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy. Our model is the first microscopic model that has been directly validated through data analysis of the microscopic dynamics, exhibiting quantitative agreements with mesoscopic and macroscopic empirical results.

Derivation of the Boltzmann Equation for Financial Brownian Motion: Direct Observation of the Collective Motion of High-Frequency Traders

NASA Astrophysics Data System (ADS)

Kanazawa, Kiyoshi; Sueshige, Takumi; Takayasu, Hideki; Takayasu, Misako

2018-03-01

A microscopic model is established for financial Brownian motion from the direct observation of the dynamics of high-frequency traders (HFTs) in a foreign exchange market. Furthermore, a theoretical framework parallel to molecular kinetic theory is developed for the systematic description of the financial market from microscopic dynamics of HFTs. We report first on a microscopic empirical law of traders' trend-following behavior by tracking the trajectories of all individuals, which quantifies the collective motion of HFTs but has not been captured in conventional order-book models. We next introduce the corresponding microscopic model of HFTs and present its theoretical solution paralleling molecular kinetic theory: Boltzmann-like and Langevin-like equations are derived from the microscopic dynamics via the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy. Our model is the first microscopic model that has been directly validated through data analysis of the microscopic dynamics, exhibiting quantitative agreements with mesoscopic and macroscopic empirical results.

Periodic order and defects in Ni-based inverse opal-like crystals on the mesoscopic and atomic scale

NASA Astrophysics Data System (ADS)

Chumakova, A. V.; Valkovskiy, G. A.; Mistonov, A. A.; Dyadkin, V. A.; Grigoryeva, N. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Petukhov, A. V.; Grigoriev, S. V.

2014-10-01

The structure of inverse opal crystals based on nickel was probed on the mesoscopic and atomic levels by a set of complementary techniques such as scanning electron microscopy and synchrotron microradian and wide-angle diffraction. The microradian diffraction revealed the mesoscopic-scale face-centered-cubic (fcc) ordering of spherical voids in the inverse opal-like structure with unit cell dimension of 750±10nm. The diffuse scattering data were used to map defects in the fcc structure as a function of the number of layers in the Ni inverse opal-like structure. The average lateral size of mesoscopic domains is found to be independent of the number of layers. 3D reconstruction of the reciprocal space for the inverse opal crystals with different thickness provided an indirect study of original opal templates in a depth-resolved way. The microstructure and thermal response of the framework of the porous inverse opal crystal was examined using wide-angle powder x-ray diffraction. This artificial porous structure is built from nickel crystallites possessing stacking faults and dislocations peculiar for the nickel thin films.

An asymmetric mesoscopic model for single bulges in RNA

NASA Astrophysics Data System (ADS)

de Oliveira Martins, Erik; Weber, Gerald

2017-10-01

Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.

Modeling mesoscopic cortical dynamics using a mean-field model of conductance-based networks of adaptive exponential integrate-and-fire neurons.

PubMed

Zerlaut, Yann; Chemla, Sandrine; Chavane, Frederic; Destexhe, Alain

2018-02-01

Voltage-sensitive dye imaging (VSDi) has revealed fundamental properties of neocortical processing at macroscopic scales. Since for each pixel VSDi signals report the average membrane potential over hundreds of neurons, it seems natural to use a mean-field formalism to model such signals. Here, we present a mean-field model of networks of Adaptive Exponential (AdEx) integrate-and-fire neurons, with conductance-based synaptic interactions. We study a network of regular-spiking (RS) excitatory neurons and fast-spiking (FS) inhibitory neurons. We use a Master Equation formalism, together with a semi-analytic approach to the transfer function of AdEx neurons to describe the average dynamics of the coupled populations. We compare the predictions of this mean-field model to simulated networks of RS-FS cells, first at the level of the spontaneous activity of the network, which is well predicted by the analytical description. Second, we investigate the response of the network to time-varying external input, and show that the mean-field model predicts the response time course of the population. Finally, to model VSDi signals, we consider a one-dimensional ring model made of interconnected RS-FS mean-field units. We found that this model can reproduce the spatio-temporal patterns seen in VSDi of awake monkey visual cortex as a response to local and transient visual stimuli. Conversely, we show that the model allows one to infer physiological parameters from the experimentally-recorded spatio-temporal patterns.

Microscopic molecular dynamics characterization of the second-order non-Navier-Fourier constitutive laws in the Poiseuille gas flow

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

Rana, A.; Ravichandran, R.; Park, J. H.

The second-order non-Navier-Fourier constitutive laws, expressed in a compact algebraic mathematical form, were validated for the force-driven Poiseuille gas flow by the deterministic atomic-level microscopic molecular dynamics (MD). Emphasis is placed on how completely different methods (a second-order continuum macroscopic theory based on the kinetic Boltzmann equation, the probabilistic mesoscopic direct simulation Monte Carlo, and, in particular, the deterministic microscopic MD) describe the non-classical physics, and whether the second-order non-Navier-Fourier constitutive laws derived from the continuum theory can be validated using MD solutions for the viscous stress and heat flux calculated directly from the molecular data using the statistical method.more » Peculiar behaviors (non-uniform tangent pressure profile and exotic instantaneous heat conduction from cold to hot [R. S. Myong, “A full analytical solution for the force-driven compressible Poiseuille gas flow based on a nonlinear coupled constitutive relation,” Phys. Fluids 23(1), 012002 (2011)]) were re-examined using atomic-level MD results. It was shown that all three results were in strong qualitative agreement with each other, implying that the second-order non-Navier-Fourier laws are indeed physically legitimate in the transition regime. Furthermore, it was shown that the non-Navier-Fourier constitutive laws are essential for describing non-zero normal stress and tangential heat flux, while the classical and non-classical laws remain similar for shear stress and normal heat flux.« less

Visualization of the collective vortex-like motions in liquid argon and water: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Anikeenko, A. V.; Malenkov, G. G.; Naberukhin, Yu. I.

2018-03-01

We propose a new measure of collectivity of molecular motion in the liquid: the average vector of displacement of the particles, ⟨ΔR⟩, which initially have been localized within a sphere of radius Rsph and then have executed the diffusive motion during a time interval Δt. The more correlated the motion of the particles is, the longer will be the vector ⟨ΔR⟩. We visualize the picture of collective motions in molecular dynamics (MD) models of liquids by constructing the ⟨ΔR⟩ vectors and pinning them to the sites of the uniform grid which divides each of the edges of the model box into equal parts. MD models of liquid argon and water have been studied by this method. Qualitatively, the patterns of ⟨ΔR⟩ vectors are similar for these two liquids but differ in minor details. The most important result of our research is the revealing of the aggregates of ⟨ΔR⟩ vectors which have the form of extended flows which sometimes look like the parts of vortices. These vortex-like clusters of ⟨ΔR⟩ vectors have the mesoscopic size (of the order of 10 nm) and persist for tens of picoseconds. Dependence of the ⟨ΔR⟩ vector field on parameters Rsph, Δt, and on the model size has been investigated. This field in the models of liquids differs essentially from that in a random-walk model.

Simulation of laminate composites degradation using mesoscopic non-local damage model and non-local layered shell element

NASA Astrophysics Data System (ADS)

Germain, Norbert; Besson, Jacques; Feyel, Frédéric

2007-07-01

Simulating damage and failure of laminate composites structures often fails when using the standard finite element procedure. The difficulties arise from an uncontrolled mesh dependence caused by damage localization and an increase in computational costs. One of the solutions to the first problem, widely used to predict the failure of metallic materials, consists of using non-local damage constitutive equations. The second difficulty can then be solved using specific finite element formulations, such as shell element, which decrease the number of degrees of freedom. The main contribution of this paper consists of extending these techniques to layered materials such as polymer matrix composites. An extension of the non-local implicit gradient formulation, accounting for anisotropy and stratification, and an original layered shell element, based on a new partition of the unity, are proposed. Finally the efficiency of the resulting numerical scheme is studied by comparing simulation with experimental results.

Simulation of stochastic diffusion via first exit times

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

Lötstedt, Per, E-mail: perl@it.uu.se; Meinecke, Lina, E-mail: lina.meinecke@it.uu.se

2015-11-01

In molecular biology it is of interest to simulate diffusion stochastically. In the mesoscopic model we partition a biological cell into unstructured subvolumes. In each subvolume the number of molecules is recorded at each time step and molecules can jump between neighboring subvolumes to model diffusion. The jump rates can be computed by discretizing the diffusion equation on that unstructured mesh. If the mesh is of poor quality, due to a complicated cell geometry, standard discretization methods can generate negative jump coefficients, which no longer allows the interpretation as the probability to jump between the subvolumes. We propose a methodmore » based on the mean first exit time of a molecule from a subvolume, which guarantees positive jump coefficients. Two approaches to exit times, a global and a local one, are presented and tested in simulations on meshes of different quality in two and three dimensions.« less

Simulation of stochastic diffusion via first exit times

PubMed Central

Lötstedt, Per; Meinecke, Lina

2015-01-01

In molecular biology it is of interest to simulate diffusion stochastically. In the mesoscopic model we partition a biological cell into unstructured subvolumes. In each subvolume the number of molecules is recorded at each time step and molecules can jump between neighboring subvolumes to model diffusion. The jump rates can be computed by discretizing the diffusion equation on that unstructured mesh. If the mesh is of poor quality, due to a complicated cell geometry, standard discretization methods can generate negative jump coefficients, which no longer allows the interpretation as the probability to jump between the subvolumes. We propose a method based on the mean first exit time of a molecule from a subvolume, which guarantees positive jump coefficients. Two approaches to exit times, a global and a local one, are presented and tested in simulations on meshes of different quality in two and three dimensions. PMID:26600600

Waltzing route toward double-helix formation in cholesteric shells

NASA Astrophysics Data System (ADS)

Darmon, Alexandre; Benzaquen, Michael; Seč, David; Čopar, Simon; Dauchot, Olivier; Lopez-Leon, Teresa

2016-08-01

Liquid crystals, when confined to a spherical shell, offer fascinating possibilities for producing artificial mesoscopic atoms, which could then self-assemble into materials structured at a nanoscale, such as photonic crystals or metamaterials. The spherical curvature of the shell imposes topological constraints in the molecular ordering of the liquid crystal, resulting in the formation of defects. Controlling the number of defects, that is, the shell valency, and their positions, is a key success factor for the realization of those materials. Liquid crystals with helical cholesteric order offer a promising, yet unexplored way of controlling the shell defect configuration. In this paper, we study cholesteric shells with monovalent and bivalent defect configurations. By bringing together experiments and numerical simulations, we show that the defects appearing in these two configurations have a complex inner structure, as recently reported for simulated droplets. Bivalent shells possess two highly structured defects, which are composed of a number of smaller defect rings that pile up through the shell. Monovalent shells have a single radial defect, which is composed of two nonsingular defect lines that wind around each other in a double-helix structure. The stability of the bivalent configuration against the monovalent one is controlled by c = h/p, where h is the shell thickness and p the cholesteric helical pitch. By playing with the shell geometry, we can trigger the transition between the two configurations. This transition involves a fascinating waltz dynamics, where the two defects come closer while turning around each other.

Regular oscillations and random motion of glass microspheres levitated by a single optical beam in air

DOE PAGES

Moore, Jeremy; Martin, Leopoldo L.; Maayani, Shai; ...

2016-02-03

We experimentally reporton optical binding of many glass particles in air that levitate in a single optical beam. A diversity of particle sizes and shapes interact at long range in a single Gaussian beam. Our system dynamics span from oscillatory to random and dimensionality ranges from 1 to 3D. In conclusion, the low loss for the center of mass motion of the beads could allow this system to serve as a standard many body testbed, similar to what is done today with atoms, but at the mesoscopic scale.

Signature of phase singularities in diffusive regimes in disordered waveguide lattices: interplay and qualitative analysis.

PubMed

Ghosh, Somnath

2018-05-10

Coexistence and interplay between mesoscopic light dynamics with singular optics in spatially disordered waveguide lattices are reported. Two CW light beams of a 1.55 μm operating wavelength are launched as inputs to 1D waveguide lattices with controllable weak disorder in a complex refractive index profile. Direct observation of phase singularities in the speckle pattern along the length is numerically demonstrated. Quantitative analysis of the onset of such singular behavior and diffusive wave propagation is analyzed for the first time, to the best of our knowledge.

Mesoscale Modeling of Chromatin Folding

NASA Astrophysics Data System (ADS)

Schlick, Tamar

2009-03-01

Eukaryotic chromatin is the fundamental protein/nucleic acid unit that stores the genetic material. Understanding how chromatin fibers fold and unfold in physiological conditions is important for interpreting fundamental biological processes like DNA replication and transcription regulation. Using a mesoscopic model of oligonucleosome chains and tailored sampling protocols, we elucidate the energetics of oligonucleosome folding/unfolding and the role of each histone tail, linker histones, and divalent ions in regulating chromatin structure. The resulting compact topologies reconcile features of the zigzag model with straight linker DNAs with the solenoid model with bent linker DNAs for optimal fiber organization and reveal dynamic and energetic aspects involved.

Leggett-Garg tests of macrorealism for bosonic systems including double-well Bose-Einstein condensates and atom interferometers

NASA Astrophysics Data System (ADS)

Rosales-Zárate, L.; Opanchuk, B.; He, Q. Y.; Reid, M. D.

2018-04-01

We construct quantifiable generalizations of Leggett-Garg tests for macro- and mesoscopic realism and noninvasive measurability that apply when not all outcomes of measurement can be identified as arising from one of two macroscopically distinguishable states. We show how quantum mechanics predicts a negation of the Leggett-Garg premises for strategies involving ideal negative-result, weak, and minimally invasive ("nonclumsy") projective measurements on dynamical entangled systems, as might be realized with Bose-Einstein condensates in a double-well potential, path-entangled NOON states, and atom interferometers. Potential loopholes associated with each strategy are discussed.

Mesoscopic simulation of a micellar poly(N-isopropyl acrylamide)-b-(polyethylene oxide) copolymer system

NASA Astrophysics Data System (ADS)

Bautista-Reyes, Rubén; Soto-Figueroa, César; Vicente, Luis

2016-05-01

In this article we studied the micellar formation of poly(N-isopropyl acrylamide)-b-polyethylene oxide (PNIPAM-b-PEO) copolymers in an aqueous system. From molecular simulations the dependence on temperature of the Flory-Huggins interaction parameter χ for PNIPAM and PEO in water is obtained and compared with available experimental results and values from other theoretical calculations. By means of dissipative particle dynamics (DPD) we then simulated the coil-globule transition for PNIPAM chains in water with a transition temperature of around 305 K. The simulations for PNIPAM-b-PEO copolymers showed that at room temperature the chains are miscible in an aqueous phase but with a temperature increase the system turns into micelles at T  =  305 K. The change in micelle anisotropy due to a different ratio PNIPAM/PEO of chains is also analyzed. What is observed is that for large PEO the large number of dissolved PEO chains gives a large corona size and the micelle is not spherical but obloide and as the number of PNIPAM is increased the micelle acquires a spherical shape. As an important application we considered the system micelle-water/anionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate [BMIM]+[PF6]-). By increasing the temperature of the system from 306 K it is shown that at T  =  345 K there is a transfer of the micelle from water to the ionic liquid phase and this was due to the change in the relative affinity of PEO to water and ionic liquid expressed by the change in χ. All the simulation outcomes are qualitatively consistent with experimental results and thus to our knowledge we give the first set of χ values for the interaction between PNIPAM and water in a wide range of temperature values.

Many-Worlds Interpretation of Quantum Theory and Mesoscopic Anthropic Principle

NASA Astrophysics Data System (ADS)

Kamenshchik, A. Yu.; Teryaev, O. V.

2008-10-01

We suggest to combine the Anthropic Principle with Many-Worlds Interpretation of Quantum Theory. Realizing the multiplicity of worlds it provides an opportunity of explanation of some important events which are assumed to be extremely improbable. The Mesoscopic Anthropic Principle suggested here is aimed to explain appearance of such events which are necessary for emergence of Life and Mind. It is complementary to Cosmological Anthropic Principle explaining the fine tuning of fundamental constants. We briefly discuss various possible applications of Mesoscopic Anthropic Principle including the Solar Eclipses and assembling of complex molecules. Besides, we address the problem of Time's Arrow in the framework of Many-World Interpretation. We suggest the recipe for disentangling of quantities defined by fundamental physical laws and by an anthropic selection.

Mesoscopic fluctuations of the population of a qubit in a strong alternating field

NASA Astrophysics Data System (ADS)

Denisenko, M. V.; Satanin, A. M.

2016-12-01

Fluctuations of the population of a Josephson qubit in an alternating field, which is a superposition of electromagnetic pulses with large amplitudes, are studied. It is shown that the relative phase of pulses is responsible for the rate of Landau-Zener transitions and, correspondingly, for the frequency of transitions between adiabatic states. The durations of pulses incident on the qubit are controlled with an accuracy of the field period, which results in strong mesoscopic fluctuations of the population of the qubit. Similar to the magnetic field in mesoscopic physics, the relative phase of pulses can destroy the interference pattern of the population of the qubit. The influence of the duration of the pulse and noise on the revealed fluctuation effects is studied.

Computer modelling of the surface tension of the gas-liquid and liquid-liquid interface.

PubMed

Ghoufi, Aziz; Malfreyt, Patrice; Tildesley, Dominic J

2016-03-07

This review presents the state of the art in molecular simulations of interfacial systems and of the calculation of the surface tension from the underlying intermolecular potential. We provide a short account of different methodological factors (size-effects, truncation procedures, long-range corrections and potential models) that can affect the results of the simulations. Accurate calculations are presented for the calculation of the surface tension as a function of the temperature, pressure and composition by considering the planar gas-liquid interface of a range of molecular fluids. In particular, we consider the challenging problems of reproducing the interfacial tension of salt solutions as a function of the salt molality; the simulations of spherical interfaces including the calculation of the sign and size of the Tolman length for a spherical droplet; the use of coarse-grained models in the calculation of the interfacial tension of liquid-liquid surfaces and the mesoscopic simulations of oil-water-surfactant interfacial systems.

Community Detection for Correlation Matrices

NASA Astrophysics Data System (ADS)

MacMahon, Mel; Garlaschelli, Diego

2015-04-01

A challenging problem in the study of complex systems is that of resolving, without prior information, the emergent, mesoscopic organization determined by groups of units whose dynamical activity is more strongly correlated internally than with the rest of the system. The existing techniques to filter correlations are not explicitly oriented towards identifying such modules and can suffer from an unavoidable information loss. A promising alternative is that of employing community detection techniques developed in network theory. Unfortunately, this approach has focused predominantly on replacing network data with correlation matrices, a procedure that we show to be intrinsically biased because of its inconsistency with the null hypotheses underlying the existing algorithms. Here, we introduce, via a consistent redefinition of null models based on random matrix theory, the appropriate correlation-based counterparts of the most popular community detection techniques. Our methods can filter out both unit-specific noise and system-wide dependencies, and the resulting communities are internally correlated and mutually anticorrelated. We also implement multiresolution and multifrequency approaches revealing hierarchically nested subcommunities with "hard" cores and "soft" peripheries. We apply our techniques to several financial time series and identify mesoscopic groups of stocks which are irreducible to a standard, sectorial taxonomy; detect "soft stocks" that alternate between communities; and discuss implications for portfolio optimization and risk management.

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

Zhu, Yi; Cai, Zhonghou; Chen, Pice

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase seperated regions. The ability to simultanousely track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of- the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO 2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation ismore » initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO 2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, which is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO 2. Lastly, the direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.« less

Traffic and Driving Simulator Based on Architecture of Interactive Motion.

PubMed

Paz, Alexander; Veeramisti, Naveen; Khaddar, Romesh; de la Fuente-Mella, Hanns; Modorcea, Luiza

2015-01-01

This study proposes an architecture for an interactive motion-based traffic simulation environment. In order to enhance modeling realism involving actual human beings, the proposed architecture integrates multiple types of simulation, including: (i) motion-based driving simulation, (ii) pedestrian simulation, (iii) motorcycling and bicycling simulation, and (iv) traffic flow simulation. The architecture has been designed to enable the simulation of the entire network; as a result, the actual driver, pedestrian, and bike rider can navigate anywhere in the system. In addition, the background traffic interacts with the actual human beings. This is accomplished by using a hybrid mesomicroscopic traffic flow simulation modeling approach. The mesoscopic traffic flow simulation model loads the results of a user equilibrium traffic assignment solution and propagates the corresponding traffic through the entire system. The microscopic traffic flow simulation model provides background traffic around the vicinities where actual human beings are navigating the system. The two traffic flow simulation models interact continuously to update system conditions based on the interactions between actual humans and the fully simulated entities. Implementation efforts are currently in progress and some preliminary tests of individual components have been conducted. The implementation of the proposed architecture faces significant challenges ranging from multiplatform and multilanguage integration to multievent communication and coordination.

Traffic and Driving Simulator Based on Architecture of Interactive Motion

PubMed Central

Paz, Alexander; Veeramisti, Naveen; Khaddar, Romesh; de la Fuente-Mella, Hanns; Modorcea, Luiza

2015-01-01

This study proposes an architecture for an interactive motion-based traffic simulation environment. In order to enhance modeling realism involving actual human beings, the proposed architecture integrates multiple types of simulation, including: (i) motion-based driving simulation, (ii) pedestrian simulation, (iii) motorcycling and bicycling simulation, and (iv) traffic flow simulation. The architecture has been designed to enable the simulation of the entire network; as a result, the actual driver, pedestrian, and bike rider can navigate anywhere in the system. In addition, the background traffic interacts with the actual human beings. This is accomplished by using a hybrid mesomicroscopic traffic flow simulation modeling approach. The mesoscopic traffic flow simulation model loads the results of a user equilibrium traffic assignment solution and propagates the corresponding traffic through the entire system. The microscopic traffic flow simulation model provides background traffic around the vicinities where actual human beings are navigating the system. The two traffic flow simulation models interact continuously to update system conditions based on the interactions between actual humans and the fully simulated entities. Implementation efforts are currently in progress and some preliminary tests of individual components have been conducted. The implementation of the proposed architecture faces significant challenges ranging from multiplatform and multilanguage integration to multievent communication and coordination. PMID:26491711

Fractals, Coherence and Brain Dynamics

NASA Astrophysics Data System (ADS)

Vitiello, Giuseppe

2010-11-01

I show that the self-similarity property of deterministic fractals provides a direct connection with the space of the entire analytical functions. Fractals are thus described in terms of coherent states in the Fock-Bargmann representation. Conversely, my discussion also provides insights on the geometrical properties of coherent states: it allows to recognize, in some specific sense, fractal properties of coherent states. In particular, the relation is exhibited between fractals and q-deformed coherent states. The connection with the squeezed coherent states is also displayed. In this connection, the non-commutative geometry arising from the fractal relation with squeezed coherent states is discussed and the fractal spectral properties are identified. I also briefly discuss the description of neuro-phenomenological data in terms of squeezed coherent states provided by the dissipative model of brain and consider the fact that laboratory observations have shown evidence that self-similarity characterizes the brain background activity. This suggests that a connection can be established between brain dynamics and the fractal self-similarity properties on the basis of the relation discussed in this report between fractals and squeezed coherent states. Finally, I do not consider in this paper the so-called random fractals, namely those fractals obtained by randomization processes introduced in their iterative generation. Since self-similarity is still a characterizing property in many of such random fractals, my conjecture is that also in such cases there must exist a connection with the coherent state algebraic structure. In condensed matter physics, in many cases the generation by the microscopic dynamics of some kind of coherent states is involved in the process of the emergence of mesoscopic/macroscopic patterns. The discussion presented in this paper suggests that also fractal generation may provide an example of emergence of global features, namely long range correlation at mesoscopic/macroscopic level, from microscopic local deformation processes. In view of the wide spectrum of application of both, fractal studies and coherent state physics, spanning from solid state physics to laser physics, quantum optics, complex dynamical systems and biological systems, the results presented in the present report may lead to interesting practical developments in many research sectors.

Mesoscopic model for filament orientation in growing actin networks: the role of obstacle geometry

NASA Astrophysics Data System (ADS)

Weichsel, Julian; Schwarz, Ulrich S.

2013-03-01

Propulsion by growing actin networks is a universal mechanism used in many different biological systems, ranging from the sheet-like lamellipodium of crawling animal cells to the actin comet tails induced by certain bacteria and viruses in order to move within their host cells. Although the core molecular machinery for actin network growth is well preserved in all of these cases, the geometry of the propelled obstacle varies considerably. During recent years, filament orientation distribution has emerged as an important observable characterizing the structure and dynamical state of the growing network. Here we derive several continuum equations for the orientation distribution of filaments growing behind stiff obstacles of various shapes and validate the predicted steady state orientation patterns by stochastic computer simulations based on discrete filaments. We use an ordinary differential equation approach to demonstrate that for flat obstacles of finite size, two fundamentally different orientation patterns peaked at either ±35° or +70°/0°/ - 70° exhibit mutually exclusive stability, in agreement with earlier results for flat obstacles of very large lateral extension. We calculate and validate phase diagrams as a function of model parameters and show how this approach can be extended to obstacles with piecewise straight contours. For curved obstacles, we arrive at a partial differential equation in the continuum limit, which again is in good agreement with the computer simulations. In all cases, we can identify the same two fundamentally different orientation patterns, but only within an appropriate reference frame, which is adjusted to the local orientation of the obstacle contour. Our results suggest that two fundamentally different network architectures compete with each other in growing actin networks, irrespective of obstacle geometry, and clarify how simulated and electron tomography data have to be analyzed for non-flat obstacle geometries.

Final Report

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

Stinis, Panos

2016-08-07

This is the final report for the work conducted at the University of Minnesota (during the period 12/01/12-09/18/14) by PI Panos Stinis as part of the "Collaboratory on Mathematics for Mesoscopic Modeling of Materials" (CM4). CM4 is a multi-institution DOE-funded project whose aim is to conduct basic and applied research in the emerging field of mesoscopic modeling of materials.

Lead iodide perovskite sensitized all-solid-state submicron thin film mesoscopic solar cell with efficiency exceeding 9%.

PubMed

Kim, Hui-Seon; Lee, Chang-Ryul; Im, Jeong-Hyeok; Lee, Ki-Beom; Moehl, Thomas; Marchioro, Arianna; Moon, Soo-Jin; Humphry-Baker, Robin; Yum, Jun-Ho; Moser, Jacques E; Grätzel, Michael; Park, Nam-Gyu

2012-01-01

We report on solid-state mesoscopic heterojunction solar cells employing nanoparticles (NPs) of methyl ammonium lead iodide (CH(3)NH(3))PbI(3) as light harvesters. The perovskite NPs were produced by reaction of methylammonium iodide with PbI(2) and deposited onto a submicron-thick mesoscopic TiO(2) film, whose pores were infiltrated with the hole-conductor spiro-MeOTAD. Illumination with standard AM-1.5 sunlight generated large photocurrents (J(SC)) exceeding 17 mA/cm(2), an open circuit photovoltage (V(OC)) of 0.888 V and a fill factor (FF) of 0.62 yielding a power conversion efficiency (PCE) of 9.7%, the highest reported to date for such cells. Femto second laser studies combined with photo-induced absorption measurements showed charge separation to proceed via hole injection from the excited (CH(3)NH(3))PbI(3) NPs into the spiro-MeOTAD followed by electron transfer to the mesoscopic TiO(2) film. The use of a solid hole conductor dramatically improved the device stability compared to (CH(3)NH(3))PbI(3) -sensitized liquid junction cells.

Lead Iodide Perovskite Sensitized All-Solid-State Submicron Thin Film Mesoscopic Solar Cell with Efficiency Exceeding 9%

PubMed Central

Kim, Hui-Seon; Lee, Chang-Ryul; Im, Jeong-Hyeok; Lee, Ki-Beom; Moehl, Thomas; Marchioro, Arianna; Moon, Soo-Jin; Humphry-Baker, Robin; Yum, Jun-Ho; Moser, Jacques E.; Grätzel, Michael; Park, Nam-Gyu

2012-01-01

We report on solid-state mesoscopic heterojunction solar cells employing nanoparticles (NPs) of methyl ammonium lead iodide (CH3NH3)PbI3 as light harvesters. The perovskite NPs were produced by reaction of methylammonium iodide with PbI2 and deposited onto a submicron-thick mesoscopic TiO2 film, whose pores were infiltrated with the hole-conductor spiro-MeOTAD. Illumination with standard AM-1.5 sunlight generated large photocurrents (JSC) exceeding 17 mA/cm2, an open circuit photovoltage (VOC) of 0.888 V and a fill factor (FF) of 0.62 yielding a power conversion efficiency (PCE) of 9.7%, the highest reported to date for such cells. Femto second laser studies combined with photo-induced absorption measurements showed charge separation to proceed via hole injection from the excited (CH3NH3)PbI3 NPs into the spiro-MeOTAD followed by electron transfer to the mesoscopic TiO2 film. The use of a solid hole conductor dramatically improved the device stability compared to (CH3NH3)PbI3 -sensitized liquid junction cells. PMID:22912919

The development of a 3D mesoscopic model of metallic foam based on an improved watershed algorithm

NASA Astrophysics Data System (ADS)

Zhang, Jinhua; Zhang, Yadong; Wang, Guikun; Fang, Qin

2018-06-01

The watershed algorithm has been used widely in the x-ray computed tomography (XCT) image segmentation. It provides a transformation defined on a grayscale image and finds the lines that separate adjacent images. However, distortion occurs in developing a mesoscopic model of metallic foam based on XCT image data. The cells are oversegmented at some events when the traditional watershed algorithm is used. The improved watershed algorithm presented in this paper can avoid oversegmentation and is composed of three steps. Firstly, it finds all of the connected cells and identifies the junctions of the corresponding cell walls. Secondly, the image segmentation is conducted to separate the adjacent cells. It generates the lost cell walls between the adjacent cells. Optimization is then performed on the segmentation image. Thirdly, this improved algorithm is validated when it is compared with the image of the metallic foam, which shows that it can avoid the image segmentation distortion. A mesoscopic model of metallic foam is thus formed based on the improved algorithm, and the mesoscopic characteristics of the metallic foam, such as cell size, volume and shape, are identified and analyzed.

Microscopic theory of linear light scattering from mesoscopic media and in near-field optics.

PubMed

Keller, Ole

2005-08-01

On the basis of quantum mechanical response theory a microscopic propagator theory of linear light scattering from mesoscopic systems is presented. The central integral equation problem is transferred to a matrix equation problem by discretization in transitions between pairs of (many-body) energy eigenstates. The local-field calculation which appears from this approach is valid down to the microscopic region. Previous theories based on the (macroscopic) dielectric constant concept make use of spatial (geometrical) discretization and cannot in general be trusted on the mesoscopic length scale. The present theory can be applied to light scattering studies in near-field optics. After a brief discussion of the macroscopic integral equation problem a microscopic potential description of the scattering process is established. In combination with the use of microscopic electromagnetic propagators the formalism allows one to make contact to the macroscopic theory of light scattering and to the spatial photon localization problem. The quantum structure of the microscopic conductivity response tensor enables one to establish a clear physical picture of the origin of local-field phenomena in mesoscopic and near-field optics. The Huygens scalar propagator formalism is revisited and its generality in microscopic physics pointed out.

The Generalized Hellmann-Feynman Theorem Approach to Quantum Effects of Mesoscopic Complicated Coupling Circuit at Finite Temperature

NASA Astrophysics Data System (ADS)

Wang, Xiu-Xia

2016-02-01

By employing the generalized Hellmann-Feynman theorem, the quantization of mesoscopic complicated coupling circuit is proposed. The ensemble average energy, the energy fluctuation and the energy distribution are investigated at finite temperature. It is shown that the generalized Hellmann-Feynman theorem plays the key role in quantizing a mesoscopic complicated coupling circuit at finite temperature, and when the temperature is lower than the specific temperature, the value of (\\vartriangle {hat {H}})2 is almost zero and the values of e and (\\vartriangle hat {{H}})2are basically constant, but while the temperature rises to the specific temperature, both of them move upward rapidly. The energy fluctuation of the system becomes larger when the coupling inductance is larger or the coupling capacitance is smaller.

Mesoscopic fluctuations of the population of a qubit in a strong alternating field

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

Denisenko, M. V., E-mail: mar.denisenko@gmail.com; Satanin, A. M.

Fluctuations of the population of a Josephson qubit in an alternating field, which is a superposition of electromagnetic pulses with large amplitudes, are studied. It is shown that the relative phase of pulses is responsible for the rate of Landau–Zener transitions and, correspondingly, for the frequency of transitions between adiabatic states. The durations of pulses incident on the qubit are controlled with an accuracy of the field period, which results in strong mesoscopic fluctuations of the population of the qubit. Similar to the magnetic field in mesoscopic physics, the relative phase of pulses can destroy the interference pattern of themore » population of the qubit. The influence of the duration of the pulse and noise on the revealed fluctuation effects is studied.« less

Harvesting dissipated energy with a mesoscopic ratchet

NASA Astrophysics Data System (ADS)

Roche, B.; Roulleau, P.; Jullien, T.; Jompol, Y.; Farrer, I.; Ritchie, D. A.; Glattli, D. C.

2015-04-01

The search for new efficient thermoelectric devices converting waste heat into electrical energy is of major importance. The physics of mesoscopic electronic transport offers the possibility to develop a new generation of nanoengines with high efficiency. Here we describe an all-electrical heat engine harvesting and converting dissipated power into an electrical current. Two capacitively coupled mesoscopic conductors realized in a two-dimensional conductor form the hot source and the cold converter of our device. In the former, controlled Joule heating generated by a voltage-biased quantum point contact results in thermal voltage fluctuations. By capacitive coupling the latter creates electric potential fluctuations in a cold chaotic cavity connected to external leads by two quantum point contacts. For unequal quantum point contact transmissions, a net electrical current is observed proportional to the heat produced.

Macroscopic and mesoscopic approach to the alkali-silica reaction in concrete

NASA Astrophysics Data System (ADS)

Grymin, Witold; Koniorczyk, Marcin; Pesavento, Francesco; Gawin, Dariusz

2018-01-01

A model of the alkali-silica reaction, which takes into account couplings between thermal, hygral, mechanical and chemical phenomena in concrete, has been discussed. The ASR may be considered at macroscopic or mesoscopic scale. The main features of each approach have been summarized and development of the model for both scales has been briefly described. Application of the model to experimental results for both scales has been presented. Even though good accordance of the model has been obtained for both approaches, consideration of the model at the mesoscopic scale allows to model different mortar mixes, prepared with the same aggregate, but of different grain size, using the same set of parameters. It enables also to predict reaction development assuming different alkali sources, such as de-icing salts or alkali leaching.

Solvent Electrostatic Response: From Simple Solutes to Proteins

NASA Astrophysics Data System (ADS)

Dinpajooh, Mohammadhasan

How water behaves at interfaces is relevant to many scientific and technological applications; however, many subtle phenomena are unknown in aqueous solutions. In this work, interfacial structural transition in hydration shells of a polarizable solute at critical polarizabilities is discovered. The transition is manifested in maximum water response, the reorientation of the water dipoles at the interface, and an increase in the density of dangling OH bonds. This work also addresses the role of polarizability of the active site of proteins in biological catalytic reactions. For proteins, the hydration shell becomes very heterogeneous and involves a relatively large number of water molecules. The molecular dynamics simulations show that the polarizability, along with the atomic charge distribution, needs to be a part of the picture describing how enzymes work. Non Gaussian dynamics in time-resolved linear and nonlinear (correlation) 2D spectra are also analyzed. Additionally, a theoretical formalism is presented to show that when preferential orientations of water dipoles exist at the interface, electrophoretic charges can be produced without free charge carriers, i.e., neutral solutes can move in a constant electric field due to the divergence of polarization at the interface. Furthermore, the concept of interface susceptibility is introduced. It involves the fluctuations of the surface charge density caused by thermal motion and its correlation over the characteristic correlation length with the fluctuations of the solvent charge density. Solvation free energy and interface dielectric constant are formulated accordingly. Unlike previous approaches, the solvation free energy scales quite well in a broad range of ion sizes, namely in the range of 2-14 A. Interface dielectric constant is defined such that the boundary conditions in the Laplace equation describing a micro- or mesoscopic interface are satisfied. The effective dielectric constant of interfacial water is found to be significantly lower than its bulk value. Molecular dynamics simulation results show that the interface dielectric constant for a TIP3P water model changes from nine to four when the effective solute radius is increased from 5 Ato 18 A. The small value of the interface dielectric constant of water has potentially dramatic consequences for hydration.

Predictive Simulation of Process Windows for Powder Bed Fusion Additive Manufacturing: Influence of the Powder Bulk Density.

PubMed

Rausch, Alexander M; Küng, Vera E; Pobel, Christoph; Markl, Matthias; Körner, Carolin

2017-09-22

The resulting properties of parts fabricated by powder bed fusion additive manufacturing processes are determined by their porosity, local composition, and microstructure. The objective of this work is to examine the influence of the stochastic powder bed on the process window for dense parts by means of numerical simulation. The investigations demonstrate the unique capability of simulating macroscopic domains in the range of millimeters with a mesoscopic approach, which resolves the powder bed and the hydrodynamics of the melt pool. A simulated process window reveals the influence of the stochastic powder layer. The numerical results are verified with an experimental process window for selective electron beam-melted Ti-6Al-4V. Furthermore, the influence of the powder bulk density is investigated numerically. The simulations predict an increase in porosity and surface roughness for samples produced with lower powder bulk densities. Due to its higher probability for unfavorable powder arrangements, the process stability is also decreased. This shrinks the actual parameter range in a process window for producing dense parts.

Predictive Simulation of Process Windows for Powder Bed Fusion Additive Manufacturing: Influence of the Powder Bulk Density

PubMed Central

Rausch, Alexander M.; Küng, Vera E.; Pobel, Christoph; Körner, Carolin

2017-01-01

The resulting properties of parts fabricated by powder bed fusion additive manufacturing processes are determined by their porosity, local composition, and microstructure. The objective of this work is to examine the influence of the stochastic powder bed on the process window for dense parts by means of numerical simulation. The investigations demonstrate the unique capability of simulating macroscopic domains in the range of millimeters with a mesoscopic approach, which resolves the powder bed and the hydrodynamics of the melt pool. A simulated process window reveals the influence of the stochastic powder layer. The numerical results are verified with an experimental process window for selective electron beam-melted Ti-6Al-4V. Furthermore, the influence of the powder bulk density is investigated numerically. The simulations predict an increase in porosity and surface roughness for samples produced with lower powder bulk densities. Due to its higher probability for unfavorable powder arrangements, the process stability is also decreased. This shrinks the actual parameter range in a process window for producing dense parts. PMID:28937633

A simplified model for dynamics of cell rolling and cell-surface adhesion

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

Cimrák, Ivan, E-mail: ivan.cimrak@fri.uniza.sk

2015-03-10

We propose a three dimensional model for the adhesion and rolling of biological cells on surfaces. We study cells moving in shear flow above a wall to which they can adhere via specific receptor-ligand bonds based on receptors from selectin as well as integrin family. The computational fluid dynamics are governed by the lattice-Boltzmann method. The movement and the deformation of the cells is described by the immersed boundary method. Both methods are fully coupled by implementing a two-way fluid-structure interaction. The adhesion mechanism is modelled by adhesive bonds including stochastic rules for their creation and rupture. We explore amore » simplified model with dissociation rate independent of the length of the bonds. We demonstrate that this model is able to resemble the mesoscopic properties, such as velocity of rolling cells.« less

Development of atomic force microscope with wide-band magnetic excitation for study of soft matter dynamics

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Chikamoto, Takuma; Ogawa, Tatsuya; Hirata, Yoshiki; Inoue, Takahito; Naitoh, Yoshitaka; Li, Yan Jun; Sugawara, Yasuhiro

2009-02-01

In order to probe dynamical properties of mesoscopic soft matter systems such as polymers, structured liquid, etc., a new atomic force microscopy apparatus with a wide-band magnetic cantilever excitation system was developed. Constant-current driving of an electromagnet up to 1 MHz was implemented with a closed-loop driver circuit. Transfer function of a commercial cantilever attached with a magnetic particle was measured in a frequency range of 1-1000 kHz in distilled water. Effects of the laser spot position, distribution of the force exerted on the cantilever, and difference in the detection scheme on the obtained transfer function are discussed in comparison with theoretical predictions by other research groups. A preliminary result of viscoelasticity spectrum measurement of a single dextran chain is shown and is compared with a recent theoretical calculation.

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.

Non-Linear Meissner Effect in Mesoscopic Superconductors

DTIC Science & Technology

1998-06-01

6525 ED Nijmegen, the Netherlands Abstract. Magnetization measurements on superconducting bulk samples and large radius cylinders had resulted in the...Phenomenological London’s theory that is found to be violated in recent magnetization measurements in superconducting mesoscopic discs that exhibit a...quantity. Recently Geim et al [1] used sub-micron Hall probes to detect the magnetization of thin (thickness down to d - 0.07 pm) single superconducting

Using Models at the Mesoscopic Scale in Teaching Physics: Two Experimental Interventions in Solid Friction and Fluid Statics

ERIC Educational Resources Information Center

Besson, Ugo; Viennot, Laurence

2004-01-01

This article examines the didactic suitability of introducing models at an intermediate (i.e. mesoscopic) scale in teaching certain subjects, at an early stage. The design and evaluation of two short sequences based on this rationale will be outlined: one bears on propulsion by solid friction, the other on fluid statics in the presence of gravity.…

Fabrication methods for mesoscopic flying vehicle

NASA Astrophysics Data System (ADS)

Cheng, Yih-Lin

2001-10-01

Small-scale flying vehicles are attractive tools for atmospheric science research. A centimeter-size mesoscopic electric helicopter, the mesicopter, has been developed at Stanford University for these applications. The mesoscopic scale implies a design with critical features between tens of microns and several millimeters. Three major parts in the mesicopter are challenging to manufacture. Rotors require smooth 3D surfaces and a blade thickness of less than 100 mum. Components in the DC micro-motor must be made of engineering materials, which is difficult on the mesoscopic scale. Airframe fabrication has to integrate complex 3D geometry into one single structure at this scale. In this research, material selection and manufacturing approaches have been investigated and implemented. In rotor fabrication, high-strength polymers manufactured by the Shape Deposition Manufacturing (SDM) technique were the top choice. Aluminum alloys were only considered as the second choice because the fabrication process is more involved. Lift tests showed that the 4-blade polymer and aluminum rotors could deliver about 90% of the expected lift (4g). To explain the rotor performance, structural analyses of spinning rotors were performed and the fabricated geometry was investigated. The bending deflections and the torsional twists were found to be too small to degrade aerodynamic performance. The rotor geometry was verified by laser scanning and by cross-section observations. Commercially available motors are used in the prototypes but a smaller DC micro-motor was designed for future use. Components of the DC micro-motors were fabricated by the Mesoscopic Additive/Subtractive Material Processing technique, which is capable of shaping engineering materials on the mesoscopic scale. The approaches are described in this thesis. The airframe was manufactured using the SDM process, which is capable of building complex parts without assembly. Castable polymers were chosen and mixed with glass microspheres to reduce their density. The finished airframe (65.5 mm x 65.5 mm) weighed only 1.5g. Two mesicopter prototypes, weighing 3g and 17g, have illustrated that powered flight at this scale is feasible. This research provides solutions to manufacture the challenging parts for the mesicopter. The manufacturing approaches discussed here are applicable to other small flying vehicles in similar and even smaller size regimes.

Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions

NASA Astrophysics Data System (ADS)

Biswas, Rajib; Bagchi, Biman

2018-01-01

In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.

Application of Lattice Boltzmann Methods in Complex Mass Transfer Systems

NASA Astrophysics Data System (ADS)

Sun, Ning

Lattice Boltzmann Method (LBM) is a novel computational fluid dynamics method that can easily handle complex and dynamic boundaries, couple local or interfacial interactions/reactions, and be easily parallelized allowing for simulation of large systems. While most of the current studies in LBM mainly focus on fluid dynamics, however, the inherent power of this method makes it an ideal candidate for the study of mass transfer systems involving complex/dynamic microstructures and local reactions. In this thesis, LBM is introduced to be an alternative computational method for the study of electrochemical energy storage systems (Li-ion batteries (LIBs) and electric double layer capacitors (EDLCs)) and transdermal drug design on mesoscopic scale. Based on traditional LBM, the following in-depth studies have been carried out: (1) For EDLCs, the simulation of diffuse charge dynamics is carried out for both the charge and the discharge processes on 2D systems of complex random electrode geometries (pure random, random spheres and random fibers). Steric effect of concentrated solutions is considered by using modified Poisson-Nernst-Plank (MPNP) equations and compared with regular Poisson-Nernst-Plank (PNP) systems. The effects of electrode microstructures (electrode density, electrode filler morphology, filler size, etc.) on the net charge distribution and charge/discharge time are studied in detail. The influence of applied potential during discharging process is also discussed. (2) For the study of dendrite formation on the anode of LIBs, it is shown that the Lattice Boltzmann model can capture all the experimentally observed features of microstructure evolution at the anode, from smooth to mossy to dendritic. The mechanism of dendrite formation process in mesoscopic scale is discussed in detail and compared with the traditional Sand's time theories. It shows that dendrite formation is closely related to the inhomogeneous reactively at the electrode-electrolyte interface. When the inhomogeneity is small, dendrites form mainly under high current densities, in which the mass transfer is dominated by electromigration; when the inhomogeneity is very large, dendrites may form under both high and low current densities, which is dominated by electromigration in high current density and by surface reactivity in low current density. We show that the critical current density for dendrite formation is sensitive to surface inhomogeneous reactivity and the onset time of dendrite formation is sensitive to the initial roughness of electrode. A new analysis method is introduced, which can predict the formation of dendrites in batteries at a very early stage even before large dendrites form. Charge/discharge cyclic properties of the system are also studied, which shows that electrode roughness will increase during cycles and the break-off of dendritic structures is inevitable once big dendrites form; however, it is possible to minimize the amount of break-off materials by optimizing the rate of discharge. (3) The LBM is also used to simulate intercalation reactions in a Li-Ion battery with graphite as anode and pure Li metal as counter electrode. Both galvanostatic and potentiostatic conditions were studied. The relation between operation parameters (current and potential) and electrode parameters (porosity, thickness and diffusivity) and plating times were discussed. Different equilibrium potentials forms (empirical fitting, fitting of SONY 18650 cell, and staged profiles) were also compared. By modifying the morphology of electrode with a density gradient, it was shown that much better electrode performance can be obtained, which can be helpful for the designing and manufacturing of better batteries. (4) The transdermal drug delivery system is also simulated by using LBM. Two kinds of transdermal structures are discussed: "brick and mortar" structure and a simple homogenized structure. It is demonstrated that the homogenized system is able to obtain similar steady state flux as the "brick and mortar" structure; however, in the early transient region, their flux value can be different. The influence of different system parameters (amount of drug in patch, patch thickness, partition coefficient at patch/ Stratum Corneum (SC) interface, and the diffusion coefficient of drug in each component) is discussed in details. It turns out that in this system, the rate-determine step for mass transfer should be the partition between patch and SC layers and the diffusion in the SC layer. The influence of enhancer is also tested. It is shown that by adding enhancers, the drug flux can be significantly increased. However, the peak time of drug does not necessarily match the peak flux time of enhancer. The peak time of drug could be adjusted (pushed earlier or dragged later) by using different kinds of enhancers, which has higher/smaller diffusivity than drug in the SC layer.

Corticonic models of brain mechanisms underlying cognition and intelligence

NASA Astrophysics Data System (ADS)

Farhat, Nabil H.

The concern of this review is brain theory or more specifically, in its first part, a model of the cerebral cortex and the way it: (a) interacts with subcortical regions like the thalamus and the hippocampus to provide higher-level-brain functions that underlie cognition and intelligence, (b) handles and represents dynamical sensory patterns imposed by a constantly changing environment, (c) copes with the enormous number of such patterns encountered in a lifetime by means of dynamic memory that offers an immense number of stimulus-specific attractors for input patterns (stimuli) to select from, (d) selects an attractor through a process of “conjugation” of the input pattern with the dynamics of the thalamo-cortical loop, (e) distinguishes between redundant (structured) and non-redundant (random) inputs that are void of information, (f) can do categorical perception when there is access to vast associative memory laid out in the association cortex with the help of the hippocampus, and (g) makes use of “computation” at the edge of chaos and information driven annealing to achieve all this. Other features and implications of the concepts presented for the design of computational algorithms and machines with brain-like intelligence are also discussed. The material and results presented suggest, that a Parametrically Coupled Logistic Map network (PCLMN) is a minimal model of the thalamo-cortical complex and that marrying such a network to a suitable associative memory with re-entry or feedback forms a useful, albeit, abstract model of a cortical module of the brain that could facilitate building a simple artificial brain. In the second part of the review, the results of numerical simulations and drawn conclusions in the first part are linked to the most directly relevant works and views of other workers. What emerges is a picture of brain dynamics on the mesoscopic and macroscopic scales that gives a glimpse of the nature of the long sought after brain code underlying intelligence and other higher level brain functions.

Electrodynamic soil plate oscillator: Modeling nonlinear mesoscopic elastic behavior and hysteresis in nonlinear acoustic landmine detection

NASA Astrophysics Data System (ADS)

Korman, M. S.; Duong, D. V.; Kalsbeck, A. E.

2015-10-01

An apparatus (SPO), designed to study flexural vibrations of a soil loaded plate, consists of a thin circular elastic clamped plate (and cylindrical wall) supporting a vertical soil column. A small magnet attached to the center of the plate is driven by a rigid AC coil (located coaxially below the plate) to complete the electrodynamic soil plate oscillator SPO design. The frequency dependent mechanical impedance Zmech (force / particle velocity, at the plate's center) is inversely proportional to the electrical motional impedance Zmot. Measurements of Zmot are made using the complex output to input response of a Wheatstone bridge that has an identical coil element in one of its legs. Near resonance, measurements of Zmot (with no soil) before and after a slight point mass loading at the center help determine effective mass, spring, damping and coupling constant parameters of the system. "Tuning curve" behavior of real{ Zmot } and imaginary{ Zmot } at successively higher vibration amplitudes of dry sifted masonry sand are measured. They exhibit a decrease "softening" in resonance frequency along with a decrease in the quality Q factor. In soil surface vibration measurements a bilinear hysteresis model predicts the tuning curve shape for this nonlinear mesoscopic elastic SPO behavior - which also models the soil vibration over an actual plastic "inert" VS 1.6 buried landmine. Experiments are performed where a buried 1m cube concrete block supports a 12 inch deep by 30 inch by 30 inch concrete soil box for burying a VS 1.6 in dry sifted masonry sand for on-the-mine and off-the-mine soil vibration experiments. The backbone curve (a plot of the peak amplitude vs. corresponding resonant frequency from a family of tuning curves) exhibits mostly linear behavior for "on target" soil surface vibration measurements of the buried VS 1.6 or drum-like mine simulants for relatively low particle velocities of the soil. Backbone curves for "on target" measurements exhibit significant curvature when the soil particle velocity is relatively higher. An oscillator with hysteresis modeled by a distribution of parallel spring elements each with a different threshold slip condition seems to describe fairly linear backbone curve behavior [W. D. Iwan, Transactions of the ASME, J. of Applied Mech., 33,(1966), 893-900], while a single bilinear hysteresis element describes the backbone curvature results in the experiments reported here [T. K. Caughey, Transactions of the ASME, J. of Applied Mech., 27, (1960), 640-643]. When "off target" resonances have a different backbone curvature than "on the mine" backbone curves, then false alarms may be eliminated due to resonances from the natural soil layering. See [R. A. Guyer, J. TenCate, and P. Johnson, "Hysteresis and the Dynamic Elasticity of Consolidated Granular Materials," Phys. Rev. Lett., 82, 16 (1999), 3280-3283] for recent models of nonlinear mesoscopic behavior.

Disentangling α and β relaxation in orientationally disordered crystals with theory and experiments

NASA Astrophysics Data System (ADS)

Cui, Bingyu; Gebbia, Jonathan F.; Tamarit, Josep-Lluis; Zaccone, Alessio

2018-05-01

We use a microscopically motivated generalized Langevin equation (GLE) approach to link the vibrational density of states (VDOS) to the dielectric response of orientational glasses (OGs). The dielectric function calculated based on the GLE is compared with experimental data for the paradigmatic case of two OGs: freon-112 and freon-113, around and just above Tg. The memory function is related to the integral of the VDOS times a spectral coupling function γ (ωp) , which tells the degree of dynamical coupling between molecular degrees of freedom at different eigenfrequencies. The comparative analysis of the two freons reveals that the appearance of a secondary β relaxation in freon-112 is due to cooperative dynamical coupling in the regime of mesoscopic motions caused by stronger anharmonicity (absent in freon-113) and is associated with the comparatively lower boson peak in the VDOS. The proposed framework brings together all the key aspects of glassy physics (VDOS with the boson peak, dynamical heterogeneity, dissipation, and anharmonicity) into a single model.

Numerical studies from quantum to macroscopic scales of carbon nanoparticules in hydrogen plasma

NASA Astrophysics Data System (ADS)

Lombardi, Guillaume; Ngandjong, Alain; Mezei, Zsolt; Mougenot, Jonathan; Michau, Armelle; Hassouni, Khaled; Seydou, Mahamadou; Maurel, François

2016-09-01

Dusty plasmas take part in large scientific domains from Universe Science to nanomaterial synthesis processes. They are often generated by growth from molecular precursor. This growth leads to the formation of larger clusters which induce solid germs nucleation. Particle formed are described by an aerosol dynamic taking into account coagulation, molecular deposition and transport processes. These processes are controlled by the elementary particle. So there is a strong coupling between particle dynamics and plasma discharge equilibrium. This study is focused on the development of a multiscale physic and numeric model of hydrogen plasmas and carbon particles around three essential coupled axes to describe the various physical phenomena: (i) Macro/mesoscopic fluid modeling describing in an auto-coherent way, characteristics of the plasma, molecular clusters and aerosol behavior; (ii) the classic molecular dynamics offering a description to the scale molecular of the chains of chemical reactions and the phenomena of aggregation; (iii) the quantum chemistry to establish the activation barriers of the different processes driving the nanopoarticule formation.

Nonequilibrium self-organization of colloidal particles on substrates: adsorption, relaxation, and annealing.

PubMed

Araújo, Nuno A M; Dias, Cristóvão S; Telo da Gama, Margarida M

2017-01-11

Colloidal particles are considered ideal building blocks to produce materials with enhanced physical properties. The state-of-the-art techniques for synthesizing these particles provide control over shape, size, and directionality of the interactions. In spite of these advances, there is still a huge gap between the synthesis of individual components and the management of their spontaneous organization towards the desired structures. The main challenge is the control over the dynamics of self-organization. In their kinetic route towards thermodynamically stable structures, colloidal particles self-organize into intermediate (mesoscopic) structures that are much larger than the individual particles and become the relevant units for the dynamics. To follow the dynamics and identify kinetically trapped structures, one needs to develop new theoretical and numerical tools. Here we discuss the self-organization of functionalized colloids (also known as patchy colloids) on attractive substrates. We review our recent results on the adsorption and relaxation and explore the use of annealing cycles to overcome kinetic barriers and drive the relaxation towards the targeted structures.

Anomalous diffusion with linear reaction dynamics: from continuous time random walks to fractional reaction-diffusion equations.

PubMed

Henry, B I; Langlands, T A M; Wearne, S L

2006-09-01

We have revisited the problem of anomalously diffusing species, modeled at the mesoscopic level using continuous time random walks, to include linear reaction dynamics. If a constant proportion of walkers are added or removed instantaneously at the start of each step then the long time asymptotic limit yields a fractional reaction-diffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term. If the walkers are added or removed at a constant per capita rate during the waiting time between steps then the long time asymptotic limit has a standard linear reaction kinetics term but a fractional order temporal derivative operating on a nonstandard diffusion term. Results from the above two models are compared with a phenomenological model with standard linear reaction kinetics and a fractional order temporal derivative operating on a standard diffusion term. We have also developed further extensions of the CTRW model to include more general reaction dynamics.

Modeling Stochastic Complexity in Complex Adaptive Systems: Non-Kolmogorov Probability and the Process Algebra Approach.

PubMed

Sulis, William H

2017-10-01

Walter Freeman III pioneered the application of nonlinear dynamical systems theories and methodologies in his work on mesoscopic brain dynamics.Sadly, mainstream psychology and psychiatry still cling to linear correlation based data analysis techniques, which threaten to subvert the process of experimentation and theory building. In order to progress, it is necessary to develop tools capable of managing the stochastic complexity of complex biopsychosocial systems, which includes multilevel feedback relationships, nonlinear interactions, chaotic dynamics and adaptability. In addition, however, these systems exhibit intrinsic randomness, non-Gaussian probability distributions, non-stationarity, contextuality, and non-Kolmogorov probabilities, as well as the absence of mean and/or variance and conditional probabilities. These properties and their implications for statistical analysis are discussed. An alternative approach, the Process Algebra approach, is described. It is a generative model, capable of generating non-Kolmogorov probabilities. It has proven useful in addressing fundamental problems in quantum mechanics and in the modeling of developing psychosocial systems.

Smoothed dissipative particle dynamics model for mesoscopic multiphase flows in the presence of thermal fluctuations

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

Lei, Huan; Baker, Nathan A.; Wu, Lei

2016-08-05

Thermal fluctuations cause perturbations of fluid-fluid interfaces and highly nonlinear hydrodynamics in multiphase flows. In this work, we develop a novel multiphase smoothed dissipative particle dynamics model. This model accounts for both bulk hydrodynamics and interfacial fluctuations. Interfacial surface tension is modeled by imposing a pairwise force between SDPD particles. We show that the relationship between the model parameters and surface tension, previously derived under the assumption of zero thermal fluctuation, is accurate for fluid systems at low temperature but overestimates the surface tension for intermediate and large thermal fluctuations. To analyze the effect of thermal fluctuations on surface tension,more » we construct a coarse-grained Euler lattice model based on the mean field theory and derive a semi-analytical formula to directly relate the surface tension to model parameters for a wide range of temperatures and model resolutions. We demonstrate that the present method correctly models the dynamic processes, such as bubble coalescence and capillary spectra across the interface.« less

Magnetic disorder in superconductors: Enhancement by mesoscopic fluctuations

NASA Astrophysics Data System (ADS)

Burmistrov, I. S.; Skvortsov, M. A.

2018-01-01

We study the density of states (DOS) and the transition temperature Tc in a dirty superconducting film with rare classical magnetic impurities of an arbitrary strength described by the Poissonian statistics. We take into account that the potential disorder is a source of mesoscopic fluctuations of the local DOS, and, consequently, of the effective strength of magnetic impurities. We find that these mesoscopic fluctuations result in a nonzero DOS for all energies in the region of the phase diagram where without this effect the DOS is zero within the standard mean-field theory. This mechanism can be more efficient in filling the mean-field superconducting gap than rare fluctuations of the potential disorder (instantons). Depending on the magnetic impurity strength, the suppression of Tc by spin-flip scattering can be faster or slower than in the standard mean-field theory.

Hilbert's sixth problem and the failure of the Boltzmann to Euler limit

NASA Astrophysics Data System (ADS)

Slemrod, Marshall

2018-04-01

This paper addresses the main issue of Hilbert's sixth problem, namely the rigorous passage of solutions to the mesoscopic Boltzmann equation to macroscopic solutions of the Euler equations of compressible gas dynamics. The results of the paper are that (i) in general Hilbert's program will fail because of the appearance of van der Waals-Korteweg capillarity terms in a macroscopic description of motion of a gas, and (ii) the van der Waals-Korteweg theory itself might satisfy Hilbert's quest for a map from the `atomistic view' to the laws of motion of continua. This article is part of the theme issue `Hilbert's sixth problem'.

Non-Gaussianity in a quasiclassical electronic circuit

NASA Astrophysics Data System (ADS)

Suzuki, Takafumi J.; Hayakawa, Hisao

2017-05-01

We study the non-Gaussian dynamics of a quasiclassical electronic circuit coupled to a mesoscopic conductor. Non-Gaussian noise accompanying the nonequilibrium transport through the conductor significantly modifies the stationary probability density function (PDF) of the flux in the dissipative circuit. We incorporate weak quantum fluctuation of the dissipative LC circuit with a stochastic method and evaluate the quantum correction of the stationary PDF. Furthermore, an inverse formula to infer the statistical properties of the non-Gaussian noise from the stationary PDF is derived in the classical-quantum crossover regime. The quantum correction is indispensable to correctly estimate the microscopic transfer events in the QPC with the quasiclassical inverse formula.

On scattered waves and lipid domains: detecting membrane rafts with X-rays and neutrons

DOE PAGES

Marquardt, Drew; Heberle, Frederick A.; Nickels, Jonathan D.; ...

2015-09-21

In order to understand the biological role of lipids in cell membranes, it is necessary to determine the mesoscopic structure of well-defined model membrane systems. Neutron and X-ray scattering are non-invasive, probe-free techniques that have been used extensively in such systems to probe length scales ranging from angstroms to microns, and dynamics occurring over picosecond to millisecond time scales. Finally, recent developments in the area of phase separated lipid systems mimicking membrane rafts will be presented, and the underlying concepts of the different scattering techniques used to study them will be discussed in detail.

Neuronal synchrony: Peculiarity and generality

PubMed Central

Nowotny, Thomas; Huerta, Ramon; Rabinovich, Mikhail I.

2008-01-01

Synchronization in neuronal systems is a new and intriguing application of dynamical systems theory. Why are neuronal systems different as a subject for synchronization? (1) Neurons in themselves are multidimensional nonlinear systems that are able to exhibit a wide variety of different activity patterns. Their “dynamical repertoire” includes regular or chaotic spiking, regular or chaotic bursting, multistability, and complex transient regimes. (2) Usually, neuronal oscillations are the result of the cooperative activity of many synaptically connected neurons (a neuronal circuit). Thus, it is necessary to consider synchronization between different neuronal circuits as well. (3) The synapses that implement the coupling between neurons are also dynamical elements and their intrinsic dynamics influences the process of synchronization or entrainment significantly. In this review we will focus on four new problems: (i) the synchronization in minimal neuronal networks with plastic synapses (synchronization with activity dependent coupling), (ii) synchronization of bursts that are generated by a group of nonsymmetrically coupled inhibitory neurons (heteroclinic synchronization), (iii) the coordination of activities of two coupled neuronal networks (partial synchronization of small composite structures), and (iv) coarse grained synchronization in larger systems (synchronization on a mesoscopic scale). PMID:19045493

Waiting time distribution revealing the internal spin dynamics in a double quantum dot

NASA Astrophysics Data System (ADS)

Ptaszyński, Krzysztof

2017-07-01

Waiting time distribution and the zero-frequency full counting statistics of unidirectional electron transport through a double quantum dot molecule attached to spin-polarized leads are analyzed using the quantum master equation. The waiting time distribution exhibits a nontrivial dependence on the value of the exchange coupling between the dots and the gradient of the applied magnetic field, which reveals the oscillations between the spin states of the molecule. The zero-frequency full counting statistics, on the other hand, is independent of the aforementioned quantities, thus giving no insight into the internal dynamics. The fact that the waiting time distribution and the zero-frequency full counting statistics give a nonequivalent information is associated with two factors. Firstly, it can be explained by the sensitivity to different timescales of the dynamics of the system. Secondly, it is associated with the presence of the correlation between subsequent waiting times, which makes the renewal theory, relating the full counting statistics and the waiting time distribution, no longer applicable. The study highlights the particular usefulness of the waiting time distribution for the analysis of the internal dynamics of mesoscopic systems.

Shockwave dynamics: a comparison between stochastic and periodic porous architectures

NASA Astrophysics Data System (ADS)

Branch, Brittany; Ionite, Axinte; Clements, Bradford; Montgomery, David; Schmalzer, Andrew; Patterson, Brian; Mueller, Alexander; Jensen, Brian; Dattelbaum, Dana

Polymeric foams are used extensively as structural supports and load mitigating materials in which they are subjected to compressive loading at a range of strain rates, up to the high strain rates encountered in blast and shockwave loading. To date, there have been few insights into compaction phenomena in porous structures at the mesoscale, and the influence of structure on shockwave localization. Of particular interest is when the properties of the inherent mesoscopic, periodic structure begin to emerge, versus the discrete behavior of the individual cell. Here, we illustrate, for the first time, modulation of shockwave dynamics controlled at micron-length scales in additively manufactured periodic porous structures measured using in situ, time-resolved x-ray phase contrast imaging at the Advanced Photon Source. Further, we demonstrate how the shockwave dynamics in periodic structures differ from stochastic foams of similar density and we conclude that microstructural control in elastomer foams has a dramatic effect on shockwave dynamics and can be tailored towards a variety of applications. Laboratory Directed Research and Development (LDRD) program at Los Alamos National Laboratory (project# 20160103DR) and DOE/NNSA Campaign 2.

A discrete mesoscopic particle model of the mechanics of a multi-constituent arterial wall.

PubMed

Witthoft, Alexandra; Yazdani, Alireza; Peng, Zhangli; Bellini, Chiara; Humphrey, Jay D; Karniadakis, George Em

2016-01-01

Blood vessels have unique properties that allow them to function together within a complex, self-regulating network. The contractile capacity of the wall combined with complex mechanical properties of the extracellular matrix enables vessels to adapt to changes in haemodynamic loading. Homogenized phenomenological and multi-constituent, structurally motivated continuum models have successfully captured these mechanical properties, but truly describing intricate microstructural details of the arterial wall may require a discrete framework. Such an approach would facilitate modelling interactions between or the separation of layers of the wall and would offer the advantage of seamless integration with discrete models of complex blood flow. We present a discrete particle model of a multi-constituent, nonlinearly elastic, anisotropic arterial wall, which we develop using the dissipative particle dynamics method. Mimicking basic features of the microstructure of the arterial wall, the model comprises an elastin matrix having isotropic nonlinear elastic properties plus anisotropic fibre reinforcement that represents the stiffer collagen fibres of the wall. These collagen fibres are distributed evenly and are oriented in four directions, symmetric to the vessel axis. Experimental results from biaxial mechanical tests of an artery are used for model validation, and a delamination test is simulated to demonstrate the new capabilities of the model. © 2016 The Author(s).

Estimation of effective connectivity via data-driven neural modeling

PubMed Central

Freestone, Dean R.; Karoly, Philippa J.; Nešić, Dragan; Aram, Parham; Cook, Mark J.; Grayden, David B.

2014-01-01

This research introduces a new method for functional brain imaging via a process of model inversion. By estimating parameters of a computational model, we are able to track effective connectivity and mean membrane potential dynamics that cannot be directly measured using electrophysiological measurements alone. The ability to track the hidden aspects of neurophysiology will have a profound impact on the way we understand and treat epilepsy. For example, under the assumption the model captures the key features of the cortical circuits of interest, the framework will provide insights into seizure initiation and termination on a patient-specific basis. It will enable investigation into the effect a particular drug has on specific neural populations and connectivity structures using minimally invasive measurements. The method is based on approximating brain networks using an interconnected neural population model. The neural population model is based on a neural mass model that describes the functional activity of the brain, capturing the mesoscopic biophysics and anatomical structure. The model is made subject-specific by estimating the strength of intra-cortical connections within a region and inter-cortical connections between regions using a novel Kalman filtering method. We demonstrate through simulation how the framework can be used to track the mechanisms involved in seizure initiation and termination. PMID:25506315

Serial sectioning of grain microstructures under junction control: An old problem in a new guise

NASA Astrophysics Data System (ADS)

Zöllner, D.; Streitenberger, P.

2015-04-01

In the present work the importance of 3D and 4D microstructure analyses are shown. To that aim, we study polycrystalline grain microstructures obtained by grain growth under grain boundary, triple line and quadruple point control. The microstructures themselves are obtained by mesoscopic computer simulations, which enjoy a far greater control over the kinetic and thermodynamic parameters affecting grain growth than can be realized experimentally. In extensive simulation studies we find by 3D respectively 4D microstructure analyses that metrical and topological properties of the microstructures depend strongly on the microstructural feature controlling the growth kinetics. However, the differences between the growth kinetics vanish when we look at classical 2D sections of the 3D ensembles making a differentiation of the controlling grain feature near impossible.

Simulation of loss mechanisms in organic solar cells: A description of the mesoscopic Monte Carlo technique and an evaluation of the first reaction method.

PubMed

Groves, Chris; Kimber, Robin G E; Walker, Alison B

2010-10-14

In this letter we evaluate the accuracy of the first reaction method (FRM) as commonly used to reduce the computational complexity of mesoscale Monte Carlo simulations of geminate recombination and the performance of organic photovoltaic devices. A wide range of carrier mobilities, degrees of energetic disorder, and applied electric field are considered. For the ranges of energetic disorder relevant for most polyfluorene, polythiophene, and alkoxy poly(phenylene vinylene) materials used in organic photovoltaics, the geminate separation efficiency predicted by the FRM agrees with the exact model to better than 2%. We additionally comment on the effects of equilibration on low-field geminate separation efficiency, and in doing so emphasize the importance of the energy at which geminate carriers are created upon their subsequent behavior.

Quantum gambling using mesoscopic ring qubits

NASA Astrophysics Data System (ADS)

Pakuła, Ireneusz

2007-07-01

Quantum Game Theory provides us with new tools for practising games and some other risk related enterprices like, for example, gambling. The two party gambling protocol presented by Goldenberg {\\it et al} is one of the simplest yet still hard to implement applications of Quantum Game Theory. We propose potential physical realisation of the quantum gambling protocol with use of three mesoscopic ring qubits. We point out problems in implementation of such game.

Intrinsic behavior of face-centered-cubic supra-crystals of nanocrystals self-organized on mesoscopic scale

NASA Astrophysics Data System (ADS)

Pileni, M. P.

2005-12-01

We describe intrinsic behavior due to the high ordering of nanocrystals at the mesoscopic scale. The first example shows well-defined columns in the formation of cobalt nanocrystals when an applied magnetic field is applied during the evaporation process. Collective breathing properties between nanocrystals are demonstrated. In both cases, these features are observed when the nanocrystals are highly ordered in fcc supra-crystals.

1997 Technical Digest Series. Volume 9: Quantum Optoelectronics

DTIC Science & Technology

1997-03-01

Program Co-Chair Shigehisa Arai, Tokyo Institute of Technology, Japan Yasuhiko Arakawa, University of Tokyo, Japan Israel Bar-Joseph, Weizmann...assembly formed quantum dot active layers, (p. 3) 2:30pm (Invited) QWA3 • Optical probing of mesoscopic and nano-structures, Yasuhiko Arakawa, Univ...80, 3466 (1996). 6/QWA3-1 Optical Probing of Mesoscopic and Nano-Structures Yasuhiko Arakawa University of Tokyo, Japan We investigate the

Polymorphism of Lysozyme Condensates.

PubMed

Safari, Mohammad S; Byington, Michael C; Conrad, Jacinta C; Vekilov, Peter G

2017-10-05

Protein condensates play essential roles in physiological processes and pathological conditions. Recently discovered mesoscopic protein-rich clusters may act as crucial precursors for the nucleation of ordered protein solids, such as crystals, sickle hemoglobin polymers, and amyloid fibrils. These clusters challenge settled paradigms of protein condensation as the constituent protein molecules present features characteristic of both partially misfolded and native proteins. Here we employ the antimicrobial enzyme lysozyme and examine the similarities between mesoscopic clusters, amyloid structures, and disordered aggregates consisting of chemically modified protein. We show that the mesoscopic clusters are distinct from the other two classes of aggregates. Whereas cluster formation and amyloid oligomerization are both reversible, aggregation triggered by reduction of the intramolecular S-S bonds is permanent. In contrast to the amyloid structures, protein molecules in the clusters retain their enzymatic activity. Furthermore, an essential feature of the mesoscopic clusters is their constant radius of less than 50 nm. The amyloid and disordered aggregates are significantly larger and rapidly grow. These findings demonstrate that the clusters are a product of limited protein structural flexibility. In view of the role of the clusters in the nucleation of ordered protein solids, our results suggest that fine-tuning the degree of protein conformational stability is a powerful tool to control and direct the pathways of protein condensation.

Mesoscopic Framework Enables Facile Ionic Transport in Solid Electrolytes for Li Batteries

DOE PAGES

Ma, Cheng; Cheng, Yongqiang; Chen, Kai; ...

2016-03-29

In Li-ion-conducting solid electrolytes can simultaneously overcome two grand challenges for Li-ion batteries: the severe safety concerns that limit the large-scale application and the poor electrolyte stability that forbids the use of high-voltage cathodes. Nevertheless, the ionic conductivity of solid electrolytes is typically low, compromising the battery performances. Precisely determining the ionic transport mechanism(s) is a prerequisite for the rational design of highly conductive solid electrolytes. For decades, the research on this subject has primarily focused on the atomic and microscopic scales, where the main features of interest are unit cells and microstructures, respectively. We show that the largely overlookedmore » mesoscopic scale lying between these extremes could be the key to fast ionic conduction. In a prototype system, (Li 0.33La 0.56)TiO 3, a mesoscopic framework is revealed for the first time by state-of-the-art scanning transmission electron microscopy. Corroborated by theoretical calculations and impedance measurements, it is demonstrated that such a unique configuration maximizes the number of percolation directions and thus most effectively improves the ionic conductivity. Finally, this discovery reconciles the long-standing structure–property inconsistency in (Li 0.33La 0.56)TiO 3 and also identifies mesoscopic ordering as a promising general strategy for optimizing Li+ conduction.« less

Transforming Mesoscopic (Bio)materials with Holographic Optical Tweezers

NASA Astrophysics Data System (ADS)

Grier, David

2004-03-01

An optical tweezer uses the forces exerted by a strongly focused beam of light to trap and move objects ranging in size from tens of nanometers to tens of micrometers. Since their introduction in 1986, optical tweezers have become a mainstay of research in biology, physical chemistry, and soft condensed matter physics. This talk highlights recent advances made possible by new classes of optical traps created with computer-designed holograms, a technique we call holographic optical trapping. Holographic optical tweezers can trap hundreds of mesoscopic objects simultaneously and move them independently in three dimensions. Arrays of optical traps can be used to continuously sort heterogeneous samples into selected fractions, a process we call optical fractionation. The same holograms can transform optical traps into optical scalpels and scissors that photochemically transform mesoscopic samples with exquisite spatial resolution. They also can impose arbitrary phase profiles onto the trapping beams, thereby creating optical vortices and related optical machines capable of actuating MEMS devices and driving mesoscale pumps and mixers. These new applications for laser light promise to take optical tweezers out of the laboratory and into real-world applications including manufacturing, diagnostics, and even consumer products. The unprecedented access to the mesoscopic world provided by holographic optical tweezers also offers revolutionary new opportunities for fundamental and applied research.

Signal enhancement in optical projection tomography via virtual high dynamic range imaging of single exposure

NASA Astrophysics Data System (ADS)

Yang, Yujie; Dong, Di; Shi, Liangliang; Wang, Jun; Yang, Xin; Tian, Jie

2015-03-01

Optical projection tomography (OPT) is a mesoscopic scale optical imaging technique for specimens between 1mm and 10mm. OPT has been proven to be immensely useful in a wide variety of biological applications, such as developmental biology and pathology, but its shortcomings in imaging specimens containing widely differing contrast elements are obvious. The longer exposure for high intensity tissues may lead to over saturation of other areas, whereas a relatively short exposure may cause similarity with surrounding background. In this paper, we propose an approach to make a trade-off between capturing weak signals and revealing more details for OPT imaging. This approach consists of three steps. Firstly, the specimens are merely scanned in 360 degrees above a normal exposure but non-overexposure to acquire the projection data. This reduces the photo bleaching and pre-registration computation compared with multiple different exposures in conventional high dynamic range (HDR) imaging method. Secondly, three virtual channels are produced for each projection image based on the histogram distribution to simulate the low, normal and high exposure images used in the traditional HDR technology in photography. Finally, each virtual channel is normalized to the full gray scale range and three channels are recombined into one image using weighting coefficients optimized by a standard eigen-decomposition method. After applying our approach on the projection data, filtered back projection (FBP) algorithm is carried out for 3-dimentional reconstruction. The neonatal wild-type mouse paw has been scanned to verify this approach. Results demonstrated the effectiveness of the proposed approach.

Directed motion of a Brownian motor in a temperature gradient

NASA Astrophysics Data System (ADS)

Liu, Yibing; Nie, Wenjie; Lan, Yueheng

2017-05-01

Directed motion of mesoscopic systems in a non-equilibrium environment is of great interest to both scientists and engineers. Here, the translation and rotation of a Brownian motor is investigated under non-equilibrium conditions. An anomalous directed translation is found if the two heads of the Brownian motor are immersed in baths with different particle masses, which is hinted in the analytic computation and confirmed by the numerical simulation. Similar consideration is also used to find the directed movement in the single rotational and translational degree of freedom of the Brownian motor when residing in one thermal bath with a temperature gradient.

Macroscale superlubricity enabled by graphene nanoscroll formation

NASA Astrophysics Data System (ADS)

Berman, Diana; Deshmukh, Sanket A.; Sankaranarayanan, Subramanian K. R. S.; Erdemir, Ali; Sumant, Anirudha V.

2015-06-01

Friction and wear remain as the primary modes of mechanical energy dissipation in moving mechanical assemblies; thus, it is desirable to minimize friction in a number of applications. We demonstrate that superlubricity can be realized at engineering scale when graphene is used in combination with nanodiamond particles and diamondlike carbon (DLC). Macroscopic superlubricity originates because graphene patches at a sliding interface wrap around nanodiamonds to form nanoscrolls with reduced contact area that slide against the DLC surface, achieving an incommensurate contact and substantially reduced coefficient of friction (~0.004). Atomistic simulations elucidate the overall mechanism and mesoscopic link bridging the nanoscale mechanics and macroscopic experimental observations.

A Discrete Velocity Kinetic Model with Food Metric: Chemotaxis Traveling Waves.

PubMed

Choi, Sun-Ho; Kim, Yong-Jung

2017-02-01

We introduce a mesoscopic scale chemotaxis model for traveling wave phenomena which is induced by food metric. The organisms of this simplified kinetic model have two discrete velocity modes, [Formula: see text] and a constant tumbling rate. The main feature of the model is that the speed of organisms is constant [Formula: see text] with respect to the food metric, not the Euclidean metric. The uniqueness and the existence of the traveling wave solution of the model are obtained. Unlike the classical logarithmic model case there exist traveling waves under super-linear consumption rates and infinite population pulse-type traveling waves are obtained. Numerical simulations are also provided.

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

Spontaneous cortical activity is transiently poised close to criticality

PubMed Central

Monier, Cyril; Kumar, Arvind; Deco, Gustavo; Frégnac, Yves

2017-01-01

Brain activity displays a large repertoire of dynamics across the sleep-wake cycle and even during anesthesia. It was suggested that criticality could serve as a unifying principle underlying the diversity of dynamics. This view has been supported by the observation of spontaneous bursts of cortical activity with scale-invariant sizes and durations, known as neuronal avalanches, in recordings of mesoscopic cortical signals. However, the existence of neuronal avalanches in spiking activity has been equivocal with studies reporting both its presence and absence. Here, we show that signs of criticality in spiking activity can change between synchronized and desynchronized cortical states. We analyzed the spontaneous activity in the primary visual cortex of the anesthetized cat and the awake monkey, and found that neuronal avalanches and thermodynamic indicators of criticality strongly depend on collective synchrony among neurons, LFP fluctuations, and behavioral state. We found that synchronized states are associated to criticality, large dynamical repertoire and prolonged epochs of eye closure, while desynchronized states are associated to sub-criticality, reduced dynamical repertoire, and eyes open conditions. Our results show that criticality in cortical dynamics is not stationary, but fluctuates during anesthesia and between different vigilance states. PMID:28542191

Spontaneous cortical activity is transiently poised close to criticality.

PubMed

Hahn, Gerald; Ponce-Alvarez, Adrian; Monier, Cyril; Benvenuti, Giacomo; Kumar, Arvind; Chavane, Frédéric; Deco, Gustavo; Frégnac, Yves

2017-05-01

Brain activity displays a large repertoire of dynamics across the sleep-wake cycle and even during anesthesia. It was suggested that criticality could serve as a unifying principle underlying the diversity of dynamics. This view has been supported by the observation of spontaneous bursts of cortical activity with scale-invariant sizes and durations, known as neuronal avalanches, in recordings of mesoscopic cortical signals. However, the existence of neuronal avalanches in spiking activity has been equivocal with studies reporting both its presence and absence. Here, we show that signs of criticality in spiking activity can change between synchronized and desynchronized cortical states. We analyzed the spontaneous activity in the primary visual cortex of the anesthetized cat and the awake monkey, and found that neuronal avalanches and thermodynamic indicators of criticality strongly depend on collective synchrony among neurons, LFP fluctuations, and behavioral state. We found that synchronized states are associated to criticality, large dynamical repertoire and prolonged epochs of eye closure, while desynchronized states are associated to sub-criticality, reduced dynamical repertoire, and eyes open conditions. Our results show that criticality in cortical dynamics is not stationary, but fluctuates during anesthesia and between different vigilance states.

A Lattice Boltzmann Fictitious Domain Method for Modeling Red Blood Cell Deformation and Multiple-Cell Hydrodynamic Interactions in Flow

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

Shi, Xing; Lin, Guang; Zou, Jianfeng

To model red blood cell (RBC) deformation in flow, the recently developed LBM-DLM/FD method ([Shi and Lim, 2007)29], derived from the lattice Boltzmann method and the distributed Lagrange multiplier/fictitious domain methodthe fictitious domain method, is extended to employ the mesoscopic network model for simulations of red blood cell deformation. The flow is simulated by the lattice Boltzmann method with an external force, while the network model is used for modeling red blood cell deformation and the fluid-RBC interaction is enforced by the Lagrange multiplier. To validate parameters of the RBC network model, sThe stretching numerical tests on both coarse andmore » fine meshes are performed and compared with the corresponding experimental data to validate the parameters of the RBC network model. In addition, RBC deformation in pipe flow and in shear flow is simulated, revealing the capacity of the current method for modeling RBC deformation in various flows.« less

Mesoscopic monodisperse ferromagnetic colloids enable magnetically controlled photonic crystals.

PubMed

Xu, Xiangling; Majetich, Sara A; Asher, Sanford A

2002-11-20

We report here the first synthesis of mesoscopic, monodisperse particles which contain nanoscopic inclusions of ferromagnetic cobalt ferrites. These monodisperse ferromagnetic composite particles readily self-assemble into magnetically responsive photonic crystals that efficiently Bragg diffract incident light. Magnetic fields can be used to control the photonic crystal orientation and, thus, the diffracted wavelength. We demonstrate the use of these ferromagnetic particles to fabricate magneto-optical diffracting fluids and magnetically switchable diffracting mirrors.

Mesoscopic Fluctuations for the Thinned Circular Unitary Ensemble

NASA Astrophysics Data System (ADS)

Berggren, Tomas; Duits, Maurice

2017-09-01

In this paper we study the asymptotic behavior of mesoscopic fluctuations for the thinned Circular Unitary Ensemble. The effect of thinning is that the eigenvalues start to decorrelate. The decorrelation is stronger on the larger scales than on the smaller scales. We investigate this behavior by studying mesoscopic linear statistics. There are two regimes depending on the scale parameter and the thinning parameter. In one regime we obtain a CLT of a classical type and in the other regime we retrieve the CLT for CUE. The two regimes are separated by a critical line. On the critical line the limiting fluctuations are no longer Gaussian, but described by infinitely divisible laws. We argue that this transition phenomenon is universal by showing that the same transition and their laws appear for fluctuations of the thinned sine process in a growing box. The proofs are based on a Riemann-Hilbert problem for integrable operators.

Miniaturized integration of a fluorescence microscope

PubMed Central

Ghosh, Kunal K.; Burns, Laurie D.; Cocker, Eric D.; Nimmerjahn, Axel; Ziv, Yaniv; Gamal, Abbas El; Schnitzer, Mark J.

2013-01-01

The light microscope is traditionally an instrument of substantial size and expense. Its miniaturized integration would enable many new applications based on mass-producible, tiny microscopes. Key prospective usages include brain imaging in behaving animals towards relating cellular dynamics to animal behavior. Here we introduce a miniature (1.9 g) integrated fluorescence microscope made from mass-producible parts, including semiconductor light source and sensor. This device enables high-speed cellular-level imaging across ∼0.5 mm2 areas in active mice. This capability allowed concurrent tracking of Ca2+ spiking in >200 Purkinje neurons across nine cerebellar microzones. During mouse locomotion, individual microzones exhibited large-scale, synchronized Ca2+ spiking. This is a mesoscopic neural dynamic missed by prior techniques for studying the brain at other length scales. Overall, the integrated microscope is a potentially transformative technology that permits distribution to many animals and enables diverse usages, such as portable diagnostics or microscope arrays for large-scale screens. PMID:21909102

Jamming and Localization of Interacting Run-and-Tumble Particles

NASA Astrophysics Data System (ADS)

Blythe, Richard; Evans, Martin; Slowman, Alexander

Certain species of bacteria, notably Escherichia coli, exhibit a characteristic run-and-tumble motion comprising a sequence of straight-line runs at constant velocity interspersed with tumble events that randomize the direction of motion. In a many-body setting, this nonequilibrium dynamics can generate the phenomenon of motility-induced phase separation, which is also seen for a wide variety of self-propelled particles more generally. Whilst the propensity of self-propelled particles to phase separate is understood at a mesoscopic level, the origin of this behaviour in the inelastic collisions between particles implied by the microscopic dynamics is not. Here we present exact results for run-and-tumble particles in one dimension that reveal a richly-structured stationary state that comprises a superposition of three distinct physical states whose relative weights vary with the run and tumble rates, namely a jammed state, a localized state and a delocalized state.

Quantum Synchronization of Two Ensembles of Atoms

NASA Astrophysics Data System (ADS)

Xu, Minghui; Tieri, David; Fine, Effie; Thompson, James; Holland, Murray

2014-05-01

We present a system that exhibits quantum synchronization as a modern analogue of the Huygens experiment which is implemented using state-of-the-art neutral atom lattice clocks of the highest precision. In particular, we study the correlated phase dynamics of two mesoscopic ensembles of atoms through their collective coupling to an optical cavity. We find a dynamical quantum phase transition induced by pump noise and cavity output-coupling. The spectral properties of the superradiant light emitted from the cavity show that at a critical pump rate the system undergoes a transition from the independent behavior of two disparate oscillators to the phase-locking that is the signature of quantum synchronization. Besides being of fundamental importance in nonequilibrium quantum many-body physics, this work could have broad implications for many practical applications of ultrastable lasers and precision measurements. This work was supported by the DARPA QuASAR program, the NSF, and NIST.

Overbias light emission due to higher-order quantum noise in a tunnel junction.

PubMed

Xu, F; Holmqvist, C; Belzig, W

2014-08-08

Understanding tunneling from an atomically sharp tip to a metallic surface requires us to account for interactions on a nanoscopic scale. Inelastic tunneling of electrons generates emission of photons, whose energies intuitively should be limited by the applied bias voltage. However, experiments [G. Schull et al., Phys. Rev. Lett. 102, 057401 (2009) indicate that more complex processes involving the interaction of electrons with plasmon polaritons lead to photon emission characterized by overbias energies. We propose a model of this observation in analogy to the dynamical Coulomb blockade, originally developed for treating the electronic environment in mesoscopic circuits. We explain the experimental finding quantitatively by the correlated tunneling of two electrons interacting with a LRC circuit modeling the local plasmon-polariton mode. To explain the overbias emission, the non-Gaussian statistics of the tunneling dynamics of the electrons is essential.

Miniaturized integration of a fluorescence microscope.

PubMed

Ghosh, Kunal K; Burns, Laurie D; Cocker, Eric D; Nimmerjahn, Axel; Ziv, Yaniv; Gamal, Abbas El; Schnitzer, Mark J

2011-09-11

The light microscope is traditionally an instrument of substantial size and expense. Its miniaturized integration would enable many new applications based on mass-producible, tiny microscopes. Key prospective usages include brain imaging in behaving animals for relating cellular dynamics to animal behavior. Here we introduce a miniature (1.9 g) integrated fluorescence microscope made from mass-producible parts, including a semiconductor light source and sensor. This device enables high-speed cellular imaging across ∼0.5 mm2 areas in active mice. This capability allowed concurrent tracking of Ca2+ spiking in >200 Purkinje neurons across nine cerebellar microzones. During mouse locomotion, individual microzones exhibited large-scale, synchronized Ca2+ spiking. This is a mesoscopic neural dynamic missed by prior techniques for studying the brain at other length scales. Overall, the integrated microscope is a potentially transformative technology that permits distribution to many animals and enables diverse usages, such as portable diagnostics or microscope arrays for large-scale screens.

Tomonaga-Luttinger physics in electronic quantum circuits.

PubMed

Jezouin, S; Albert, M; Parmentier, F D; Anthore, A; Gennser, U; Cavanna, A; Safi, I; Pierre, F

2013-01-01

In one-dimensional conductors, interactions result in correlated electronic systems. At low energy, a hallmark signature of the so-called Tomonaga-Luttinger liquids is the universal conductance curve predicted in presence of an impurity. A seemingly different topic is the quantum laws of electricity, when distinct quantum conductors are assembled in a circuit. In particular, the conductances are suppressed at low energy, a phenomenon called dynamical Coulomb blockade. Here we investigate the conductance of mesoscopic circuits constituted by a short single-channel quantum conductor in series with a resistance, and demonstrate a proposed link to Tomonaga-Luttinger physics. We reformulate and establish experimentally a recently derived phenomenological expression for the conductance using a wide range of circuits, including carbon nanotube data obtained elsewhere. By confronting both conductance data and phenomenological expression with the universal Tomonaga-Luttinger conductance curve, we demonstrate experimentally the predicted mapping between dynamical Coulomb blockade and the transport across a Tomonaga-Luttinger liquid with an impurity.

Mesoscopic model of actin-based propulsion.

PubMed

Zhu, Jie; Mogilner, Alex

2012-01-01

Two theoretical models dominate current understanding of actin-based propulsion: microscopic polymerization ratchet model predicts that growing and writhing actin filaments generate forces and movements, while macroscopic elastic propulsion model suggests that deformation and stress of growing actin gel are responsible for the propulsion. We examine both experimentally and computationally the 2D movement of ellipsoidal beads propelled by actin tails and show that neither of the two models can explain the observed bistability of the orientation of the beads. To explain the data, we develop a 2D hybrid mesoscopic model by reconciling these two models such that individual actin filaments undergoing nucleation, elongation, attachment, detachment and capping are embedded into the boundary of a node-spring viscoelastic network representing the macroscopic actin gel. Stochastic simulations of this 'in silico' actin network show that the combined effects of the macroscopic elastic deformation and microscopic ratchets can explain the observed bistable orientation of the actin-propelled ellipsoidal beads. To test the theory further, we analyze observed distribution of the curvatures of the trajectories and show that the hybrid model's predictions fit the data. Finally, we demonstrate that the model can explain both concave-up and concave-down force-velocity relations for growing actin networks depending on the characteristic time scale and network recoil. To summarize, we propose that both microscopic polymerization ratchets and macroscopic stresses of the deformable actin network are responsible for the force and movement generation.

The Stability Analysis Method of the Cohesive Granular Slope on the Basis of Graph Theory.

PubMed

Guan, Yanpeng; Liu, Xiaoli; Wang, Enzhi; Wang, Sijing

2017-02-27

This paper attempted to provide a method to calculate progressive failure of the cohesivefrictional granular geomaterial and the spatial distribution of the stability of the cohesive granular slope. The methodology can be divided into two parts: the characterization method of macro-contact and the analysis of the slope stability. Based on the graph theory, the vertexes, the edges and the edge sequences are abstracted out to characterize the voids, the particle contact and the macro-contact, respectively, bridging the gap between the mesoscopic and macro scales of granular materials. This paper adopts this characterization method to extract a graph from a granular slope and characterize the macro sliding surface, then the weighted graph is analyzed to calculate the slope safety factor. Each edge has three weights representing the sliding moment, the anti-sliding moment and the braking index of contact-bond, respectively, . The safety factor of the slope is calculated by presupposing a certain number of sliding routes and reducing Weight repeatedly and counting the mesoscopic failure of the edge. It is a kind of slope analysis method from mesoscopic perspective so it can present more detail of the mesoscopic property of the granular slope. In the respect of macro scale, the spatial distribution of the stability of the granular slope is in agreement with the theoretical solution.

Different Scalable Implementations of Collision and Streaming for Optimal Computational Performance of Lattice Boltzmann Simulations

NASA Astrophysics Data System (ADS)

Geneva, Nicholas; Wang, Lian-Ping

2015-11-01

In the past 25 years, the mesoscopic lattice Boltzmann method (LBM) has become an increasingly popular approach to simulate incompressible flows including turbulent flows. While LBM solves more solution variables compared to the conventional CFD approach based on the macroscopic Navier-Stokes equation, it also offers opportunities for more efficient parallelization. In this talk we will describe several different algorithms that have been developed over the past 10 plus years, which can be used to represent the two core steps of LBM, collision and streaming, more effectively than standard approaches. The application of these algorithms spans LBM simulations ranging from basic channel to particle laden flows. We will cover the essential detail on the implementation of each algorithm for simple 2D flows, to the challenges one faces when using a given algorithm for more complex simulations. The key is to explore the best use of data structure and cache memory. Two basic data structures will be discussed and the importance of effective data storage to maximize a CPU's cache will be addressed. The performance of a 3D turbulent channel flow simulation using these different algorithms and data structures will be compared along with important hardware related issues.

Coherence-enhanced phase-dependent dissipation in long SNS Josephson junctions: Revealing Andreev bound state dynamics

NASA Astrophysics Data System (ADS)

Dassonneville, B.; Murani, A.; Ferrier, M.; Guéron, S.; Bouchiat, H.

2018-05-01

One of the best known causes of dissipation in ac-driven quantum systems stems from photon absorption causing transitions between levels. Dissipation can also be caused by the retarded response to the time-dependent excitation, and in general gives insight into the system's relaxation times and mechanisms. Here we address the dissipation in a mesoscopic normal wire with superconducting contacts, that sustains a dissipationless supercurrent at zero frequency and that may therefore naively be expected to remain dissipationless at a frequency lower than the superconducting gap. We probe the high-frequency linear response of such a normal metal/superconductor (NS) ring to a time-dependent flux by coupling it to a highly sensitive multimode microwave resonator. Far from being the simple, dissipationless derivative of the supercurrent-versus-phase relation, the ring's ac susceptibility also displays a dissipative component whose phase dependence is a signature of the dynamical processes occurring within the Andreev spectrum. We show how dissipation is driven by the competition between two mechanisms. The first is the relaxation of the Andreev level distribution function, while the second corresponds to microwave-induced transitions within the spectrum. Depending on the relative strength of those contributions, dissipation can be maximal at π , a phase at which the proximity-induced minigap closes, or can be maximal near π /2 , a phase at which the dc supercurrent is maximal. We also find that the dissipative response paradoxically increases at low temperature and can even exceed the normal-state conductance. The results are successfully confronted with theoretical predictions of the Kubo linear response and time-dependent Usadel equations, derived from the Bogoliubov-de Gennes Hamiltonian describing the SNS junction. These experiments thus demonstrate the power of the ac susceptibility measurement of individual hybrid mesoscopic systems in probing in a controlled way the quantum dynamics of Andreev bound states. By spanning different physical regimes, our experiments provide unique access to inelastic scattering and spectroscopy of an isolated quantum coherent system, and reveal the associated relaxation times. This technique should be a tool of choice to investigate topological superconductivity and detect the topological protection of edge states.

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

Lingerfelt, Eric J; Endeve, Eirik; Hui, Yawei

Improvements in scientific instrumentation allow imaging at mesoscopic to atomic length scales, many spectroscopic modes, and now--with the rise of multimodal acquisition systems and the associated processing capability--the era of multidimensional, informationally dense data sets has arrived. Technical issues in these combinatorial scientific fields are exacerbated by computational challenges best summarized as a necessity for drastic improvement in the capability to transfer, store, and analyze large volumes of data. The Bellerophon Environment for Analysis of Materials (BEAM) platform provides material scientists the capability to directly leverage the integrated computational and analytical power of High Performance Computing (HPC) to perform scalablemore » data analysis and simulation and manage uploaded data files via an intuitive, cross-platform client user interface. This framework delivers authenticated, "push-button" execution of complex user workflows that deploy data analysis algorithms and computational simulations utilizing compute-and-data cloud infrastructures and HPC environments like Titan at the Oak Ridge Leadershp Computing Facility (OLCF).« less

Coupling microscopic and mesoscopic scales to simulate chemical equilibrium between a nanometric carbon cluster and detonation products fluid.

PubMed

Bourasseau, Emeric; Maillet, Jean-Bernard

2011-04-21

This paper presents a new method to obtain chemical equilibrium properties of detonation products mixtures including a solid carbon phase. In this work, the solid phase is modelled through a mesoparticle immersed in the fluid, such that the heterogeneous character of the mixture is explicitly taken into account. Inner properties of the clusters are taken from an equation of state obtained in a previous work, and interaction potential between the nanocluster and the fluid particles is derived from all-atoms simulations using the LCBOPII potential (Long range Carbon Bond Order Potential II). It appears that differences in chemical equilibrium results obtained with this method and the "composite ensemble method" (A. Hervouet et al., J. Phys. Chem. B, 2008, 112.), where fluid and solid phases are considered as non-interacting, are not significant, underlining the fact that considering the inhomogeneity of such system is crucial.

mm_par2.0: An object-oriented molecular dynamics simulation program parallelized using a hierarchical scheme with MPI and OPENMP

NASA Astrophysics Data System (ADS)

Oh, Kwang Jin; Kang, Ji Hoon; Myung, Hun Joo

2012-02-01

We have revised a general purpose parallel molecular dynamics simulation program mm_par using the object-oriented programming. We parallelized the revised version using a hierarchical scheme in order to utilize more processors for a given system size. The benchmark result will be presented here. New version program summaryProgram title: mm_par2.0 Catalogue identifier: ADXP_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXP_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2 390 858 No. of bytes in distributed program, including test data, etc.: 25 068 310 Distribution format: tar.gz Programming language: C++ Computer: Any system operated by Linux or Unix Operating system: Linux Classification: 7.7 External routines: We provide wrappers for FFTW [1], Intel MKL library [2] FFT routine, and Numerical recipes [3] FFT, random number generator, and eigenvalue solver routines, SPRNG [4] random number generator, Mersenne Twister [5] random number generator, space filling curve routine. Catalogue identifier of previous version: ADXP_v1_0 Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 560 Does the new version supersede the previous version?: Yes Nature of problem: Structural, thermodynamic, and dynamical properties of fluids and solids from microscopic scales to mesoscopic scales. Solution method: Molecular dynamics simulation in NVE, NVT, and NPT ensemble, Langevin dynamics simulation, dissipative particle dynamics simulation. Reasons for new version: First, object-oriented programming has been used, which is known to be open for extension and closed for modification. It is also known to be better for maintenance. Second, version 1.0 was based on atom decomposition and domain decomposition scheme [6] for parallelization. However, atom decomposition is not popular due to its poor scalability. On the other hand, domain decomposition scheme is better for scalability. It still has a limitation in utilizing a large number of cores on recent petascale computers due to the requirement that the domain size is larger than the potential cutoff distance. To go beyond such a limitation, a hierarchical parallelization scheme has been adopted in this new version and implemented using MPI [7] and OPENMP [8]. Summary of revisions: (1) Object-oriented programming has been used. (2) A hierarchical parallelization scheme has been adopted. (3) SPME routine has been fully parallelized with parallel 3D FFT using volumetric decomposition scheme [9]. K.J.O. thanks Mr. Seung Min Lee for useful discussion on programming and debugging. Running time: Running time depends on system size and methods used. For test system containing a protein (PDB id: 5DHFR) with CHARMM22 force field [10] and 7023 TIP3P [11] waters in simulation box having dimension 62.23 Å×62.23 Å×62.23 Å, the benchmark results are given in Fig. 1. Here the potential cutoff distance was set to 12 Å and the switching function was applied from 10 Å for the force calculation in real space. For the SPME [12] calculation, K, K, and K were set to 64 and the interpolation order was set to 4. To do the fast Fourier transform, we used Intel MKL library. All bonds including hydrogen atoms were constrained using SHAKE/RATTLE algorithms [13,14]. The code was compiled using Intel compiler version 11.1 and mvapich2 version 1.5. Fig. 2 shows performance gains from using CUDA-enabled version [15] of mm_par for 5DHFR simulation in water on Intel Core2Quad 2.83 GHz and GeForce GTX 580. Even though mm_par2.0 is not ported yet for GPU, its performance data would be useful to expect mm_par2.0 performance on GPU. Timing results for 1000 MD steps. 1, 2, 4, and 8 in the figure mean the number of OPENMP threads. Timing results for 1000 MD steps from double precision simulation on CPU, single precision simulation on GPU, and double precision simulation on GPU.

Spatially coupled catalytic ignition of CO oxidation on Pt: mesoscopic versus nano-scale

PubMed Central

Spiel, C.; Vogel, D.; Schlögl, R.; Rupprechter, G.; Suchorski, Y.

2015-01-01

Spatial coupling during catalytic ignition of CO oxidation on μm-sized Pt(hkl) domains of a polycrystalline Pt foil has been studied in situ by PEEM (photoemission electron microscopy) in the 10−5 mbar pressure range. The same reaction has been examined under similar conditions by FIM (field ion microscopy) on nm-sized Pt(hkl) facets of a Pt nanotip. Proper orthogonal decomposition (POD) of the digitized FIM images has been employed to analyze spatiotemporal dynamics of catalytic ignition. The results show the essential role of the sample size and of the morphology of the domain (facet) boundary in the spatial coupling in CO oxidation. PMID:26021411

Physics at the FQMT'11 conference

NASA Astrophysics Data System (ADS)

Špička, V.; Nieuwenhuizen, Th M.; Keefe, P. D.

2012-11-01

This paper deals with the recent state of the art of the following topics presented at the FQMT'11 conference: foundations of quantum physics, quantum measurement; nonequilibrium quantum statistical physics; quantum thermodynamics; quantum measurement, entanglement and coherence; dissipation, dephasing, noise, and decoherence; quantum optics; macroscopic quantum behavior; e.g. cold atoms; Bose-Einstein condensates; physics of quantum computing and quantum information; mesoscopic, nano-electro-mechanical systems and nano-optical systems; spin systems and their dynamics; biological systems and molecular motors; and cosmology, gravitation and astrophysics. The lectures and discussions at the FQMT'11 conference, as well as the contributions to the related topical issue, reveal important themes for future development. The recent literature is included.

Interpreting neurodynamics: concepts and facts

PubMed Central

Rotter, Stefan

2008-01-01

The dynamics of neuronal systems, briefly neurodynamics, has developed into an attractive and influential research branch within neuroscience. In this paper, we discuss a number of conceptual issues in neurodynamics that are important for an appropriate interpretation and evaluation of its results. We demonstrate their relevance for selected topics of theoretical and empirical work. In particular, we refer to the notions of determinacy and stochasticity in neurodynamics across levels of microscopic, mesoscopic and macroscopic descriptions. The issue of correlations between neural, mental and behavioral states is also addressed in some detail. We propose an informed discussion of conceptual foundations with respect to neurobiological results as a viable step to a fruitful future philosophy of neuroscience. PMID:19003452

Mesoscopic entanglement induced by spontaneous emission in solid-state quantum optics.

PubMed

González-Tudela, Alejandro; Porras, Diego

2013-02-22

Implementations of solid-state quantum optics provide us with devices where qubits are placed at fixed positions in photonic or plasmonic one-dimensional waveguides. We show that solely by controlling the position of the qubits and with the help of a coherent driving, collective spontaneous decay may be engineered to yield an entangled mesoscopic steady state. Our scheme relies on the realization of pure superradiant Dicke models by a destructive interference that cancels dipole-dipole interactions in one dimension.

Modeling off-resonant nonlinear-optical cascading in mesoscopic thin films and guest-host molecular systems

NASA Astrophysics Data System (ADS)

Dawson, Nathan J.; Andrews, James H.; Crescimanno, Michael

2013-12-01

A model for off-resonant microscopic cascading of (hyper)polarizabilities is developed using a self-consistent field approach to study mesoscopic systems of nonlinear polarizable atoms and molecules. We find enhancements in the higher-order susceptibilities resulting from geometrical and boundary orientation effects. We include an example of the dependence on excitation beam cross sectional structure and a simplified derivation of the microscopic cascading of the nonlinear-optical response in guest-host systems.

Mesoscopic Vortex–Meissner currents in ring ladders

NASA Astrophysics Data System (ADS)

Haug, Tobias; Amico, Luigi; Dumke, Rainer; Kwek, Leong-Chuan

2018-07-01

Recent experimental progress have revealed Meissner and Vortex phases in low-dimensional ultracold atoms systems. Atomtronic setups can realize ring ladders, while explicitly taking the finite size of the system into account. This enables the engineering of quantized chiral currents and phase slips in between them. We find that the mesoscopic scale modifies the current. Full control of the lattice configuration reveals a reentrant behavior of Vortex and Meissner phases. Our approach allows a feasible diagnostic of the currents’ configuration through time-of-flight measurements.

Fractal Tomlinson model for mesoscopic friction: from microscopic velocity-dependent damping to macroscopic Coulomb friction.

PubMed

Filippov, A E; Popov, V L

2007-02-01

A modified Tomlinson equation with fractal potential is studied. The effective potential is numerically generated and its mesoscopic structure is gradually adjusted to different scales by a number of Fourier modes. It is shown that with the change of scale the intensity of velocity-dependent damping in an effective Langevin equation can be gradually substituted by an equivalent constant "dry friction." For smooth macrosopic surfaces the effective equation completely reduces to the well known Coulomb law.

Quantum Device Applications of Mesoscopic Superconductivity

NASA Astrophysics Data System (ADS)

Hakonen, P. J.

2006-08-01

A brief account is given on the possibilities of mesoscopic superconductivity in low-noise amplifier and detector applications. In particular, three devices will be described: 1) Bloch oscillating transistor (BOT), 2) Inductively-read superconducting Cooper pair transistor (L-SET), and 3) Quantum capacitive phase detector (C-SET). The BOT is a low-noise current amplifier while the L-SET and C-SET act as ultra-sensitive charge and phase detectors, respectively. The basic operating principles and the main characteristics of these devices will be reviewed and discussed.

Superconductivity in disordered thin films: giant mesoscopic fluctuations.

PubMed

Skvortsov, M A; Feigel'man, M V

2005-07-29

We discuss the intrinsic inhomogeneities of superconductive properties of uniformly disordered thin films with a large dimensionless conductance g. It is shown that mesoscopic fluctuations, which usually contain a small factor 1/g, are crucially enhanced near the critical conductance g(cF) > 1 where superconductivity is destroyed at T = 0 due to Coulomb suppression of the Cooper attraction. This leads to strong spatial fluctuations of the local transition temperature and thus to the percolative nature of the thermal superconductive transition.

Universal broadening of the Bardeen-Cooper-Schrieffer coherence peak of disordered superconducting films.

PubMed

Feigel'man, M V; Skvortsov, M A

2012-10-05

In disordered superconductors, the local pairing field fluctuates in space, leading to the smearing of the BCS peak in the density of states and the appearance of the subgap tail states. We analyze the universal mesoscopic contributions to these effects and show that they are enhanced by the Coulomb repulsion. In the vicinity of the quantum critical point, where superconductivity is suppressed by the "fermionic mechanism," strong smearing of the peak due to mesoscopic fluctuations is predicted.

Disorder-Enhanced Dielectric Response of Nanoscale and Mesoscopic Insulators

NASA Astrophysics Data System (ADS)

Onoda, Shigeki; Chern, Chyh-Hong; Murakami, Shuichi; Ogimoto, Yasushi; Nagaosa, Naoto

2006-12-01

Enhancement of the dielectric response of insulators by disorder is theoretically proposed, where the quantum interference of electronic waves through the nanoscale or mesoscopic system and its change due to external perturbations control the polarization. In the disordered case with all the states being localized, the resonant tunneling, which is topologically protected, plays a crucial role, and enhances the dielectric response by a factor 30 40 compared with the pure case. The realization of this idea with accessible materials or structures is also discussed.

Exact solution for the energy spectrum of Kelvin-wave turbulence in superfluids

NASA Astrophysics Data System (ADS)

Boué, Laurent; Dasgupta, Ratul; Laurie, Jason; L'Vov, Victor; Nazarenko, Sergey; Procaccia, Itamar

2011-08-01

We study the statistical and dynamical behavior of turbulent Kelvin waves propagating on quantized vortices in superfluids and address the controversy concerning the energy spectrum that is associated with these excitations. Finding the correct energy spectrum is important because Kelvin waves play a major role in the dissipation of energy in superfluid turbulence at near-zero temperatures. In this paper, we show analytically that the solution proposed by [L’vov and Nazarenko, JETP Lett.JTPLA20021-364010.1134/S002136401008014X 91, 428 (2010)] enjoys existence, uniqueness, and regularity of the prefactor. Furthermore, we present numerical results of the dynamical equation that describes to leading order the nonlocal regime of the Kelvin-wave dynamics. We compare our findings with the analytical results from the proposed local and nonlocal theories for Kelvin-wave dynamics and show an agreement with the nonlocal predictions. Accordingly, the spectrum proposed by L’vov and Nazarenko should be used in future theories of quantum turbulence. Finally, for weaker wave forcing we observe an intermittent behavior of the wave spectrum with a fluctuating dissipative scale, which we interpreted as a finite-size effect characteristic of mesoscopic wave turbulence.

Noise, chaos, and (ɛ, τ)-entropy per unit time

NASA Astrophysics Data System (ADS)

Gaspard, Pierre; Wang, Xiao-Jing

1993-12-01

The degree of dynamical randomness of different time processes is characterized in terms of the (ε, τ)-entropy per unit time. The (ε, τ)-entropy is the amount of information generated per unit time, at different scales τ of time and ε of the observables. This quantity generalizes the Kolmogorov-Sinai entropy per unit time from deterministic chaotic processes, to stochastic processes such as fluctuations in mesoscopic physico-chemical phenomena or strong turbulence in macroscopic spacetime dynamics. The random processes that are characterized include chaotic systems, Bernoulli and Markov chains, Poisson and birth-and-death processes, Ornstein-Uhlenbeck and Yaglom noises, fractional Brownian motions, different regimes of hydrodynamical turbulence, and the Lorentz-Boltzmann process of nonequilibrium statistical mechanics. We also extend the (ε, τ)-entropy to spacetime processes like cellular automata, Conway's game of life, lattice gas automata, coupled maps, spacetime chaos in partial differential equations, as well as the ideal, the Lorentz, and the hard sphere gases. Through these examples it is demonstrated that the (ε, τ)-entropy provides a unified quantitative measure of dynamical randomness to both chaos and noises, and a method to detect transitions between dynamical states of different degrees of randomness as a parameter of the system is varied.

Friction. Macroscale superlubricity enabled by graphene nanoscroll formation.

PubMed

Berman, Diana; Deshmukh, Sanket A; Sankaranarayanan, Subramanian K R S; Erdemir, Ali; Sumant, Anirudha V

2015-06-05

Friction and wear remain as the primary modes of mechanical energy dissipation in moving mechanical assemblies; thus, it is desirable to minimize friction in a number of applications. We demonstrate that superlubricity can be realized at engineering scale when graphene is used in combination with nanodiamond particles and diamondlike carbon (DLC). Macroscopic superlubricity originates because graphene patches at a sliding interface wrap around nanodiamonds to form nanoscrolls with reduced contact area that slide against the DLC surface, achieving an incommensurate contact and substantially reduced coefficient of friction (~0.004). Atomistic simulations elucidate the overall mechanism and mesoscopic link bridging the nanoscale mechanics and macroscopic experimental observations. Copyright © 2015, American Association for the Advancement of Science.

Wireless Sensors for Wind Turbine Blades Monitoring

NASA Astrophysics Data System (ADS)

Iftimie, N.; Steigmann, R.; Danila, N. A.; Rosu, D.; Barsanescu, P. D.; Savin, A.

2017-06-01

The most common defects in turbine blades may be faulty microscopic and mesoscopic appeared in matrix, no detected by classical nondestructive testing (i.e. using phased array sensors), broken fibers can also appear and develop under moderated loads, or cracks and delaminations due to low energy impacts, etc. The paper propose to present the results obtained from testing of glass fiber reinforced plastic used in the construction of the wind turbine blades as well as the monitoring of the entire scalable blade using wireless sensors placed on critical location on blade. In order to monitories the strain/stress during the tests, the determination of the location and the nature of defects have been simulated using FEM.

Mesoscopic description of random walks on combs

NASA Astrophysics Data System (ADS)

Méndez, Vicenç; Iomin, Alexander; Campos, Daniel; Horsthemke, Werner

2015-12-01

Combs are a simple caricature of various types of natural branched structures, which belong to the category of loopless graphs and consist of a backbone and branches. We study continuous time random walks on combs and present a generic method to obtain their transport properties. The random walk along the branches may be biased, and we account for the effect of the branches by renormalizing the waiting time probability distribution function for the motion along the backbone. We analyze the overall diffusion properties along the backbone and find normal diffusion, anomalous diffusion, and stochastic localization (diffusion failure), respectively, depending on the characteristics of the continuous time random walk along the branches, and compare our analytical results with stochastic simulations.

Quantitative measurements of nanoscale permittivity and conductivity using tuning-fork-based microwave impedance microscopy

NASA Astrophysics Data System (ADS)

Wu, Xiaoyu; Hao, Zhenqi; Wu, Di; Zheng, Lu; Jiang, Zhanzhi; Ganesan, Vishal; Wang, Yayu; Lai, Keji

2018-04-01

We report quantitative measurements of nanoscale permittivity and conductivity using tuning-fork (TF) based microwave impedance microscopy (MIM). The system is operated under the driving amplitude modulation mode, which ensures satisfactory feedback stability on samples with rough surfaces. The demodulated MIM signals on a series of bulk dielectrics are in good agreement with results simulated by finite-element analysis. Using the TF-MIM, we have visualized the evolution of nanoscale conductance on back-gated MoS2 field effect transistors, and the results are consistent with the transport data. Our work suggests that quantitative analysis of mesoscopic electrical properties can be achieved by near-field microwave imaging with small distance modulation.

Influence of surface modification of halloysite nanotubes on their dispersion in epoxy matrix: Mesoscopic DPD simulation

NASA Astrophysics Data System (ADS)

Komarov, P.; Markina, A.; Ivanov, V.

2016-06-01

The problems of constructing of a meso-scale model of composites based on polymers and aluminosilicate nanotubes for prediction of the filler's spatial distribution at early stages of material formation have been considered. As a test system for the polymer matrix, the mixture of 3,4-epoxycyclohexylmethyl-3,4-epoxycyclohexanecarboxylate as epoxy resin monomers and 4-methylhexahydrophthalic anhydride as curing agent has been used. It is shown that the structure of a mixture of uncured epoxy resin and nanotubes is (mainly) determined by the surface functionalization of nanotubes. The results indicate that only nanotubes with maximum functionalization can preserve a uniform distribution in space.

Elastic properties of magnetorheological elastomer: description with the two-particle mesoscopic model

NASA Astrophysics Data System (ADS)

Biller, A. M.; Stolbov, O. V.; Raikher, Yu L.

2017-06-01

A pair of magnetizable solid particles embedded in a cylinder made of high-elasticity material is considered as a model of a mesoscopic structure element of a magnetorheological elastomer. An applied magnetic field induces ponderomotive interaction of the particles making them to move relative to one another so as to balance the counteracting magnetic and elastic forces. In a certain parameter range, the system exhibits bistability due to which under the increase / decrease of the field, the interparticle distance changes in a hysteretic manner. This behavior has a significant effect on the ability of the mesoscopic element to resist external load. Using the developed two-particle model prone to the magnetomechanical hysteresis, we extend it to the case of a virtually macroscopic sample presenting the latter as a superposition of such elements with distributed interparticle distances. In spite of its simplicity, this scheme in a generally correct way describes the field-induced changes of the internal structure and elastic modulus of the magnetorheological composites.

Mesohysteresis model for ferromagnetic materials by minimization of the micromagnetic free energy

NASA Astrophysics Data System (ADS)

van den Berg, A.; Dupré, L.; Van de Wiele, B.; Crevecoeur, G.

2009-04-01

To study the connection between macroscopic hysteretic behavior and the microstructural properties, this paper presents and validates a new material dependent three-dimensional mesoscopic magnetic hysteresis model. In the presented mesoscopic description, the different micromagnetic energy terms are reformulated on the space scale of the magnetic domains. The sample is discretized in cubic cells, each with a local stress state, local bcc crystallographic axes, etc. The magnetization is assumed to align with one of the three crystallographic axes, in positive or negative sense, defining six volume fractions within each cell. The micromagnetic Gibbs free energy is described in terms of these volume fractions. Hysteresis loops are computed by minimizing the mesoscopic Gibbs free energy using a modified gradient search for a sequence of external applied fields. To validate the mesohysteresis model, we studied the magnetic memory properties. Numerical experiments reveal that (1) minor hysteresis loops are indeed closed and (2) the closed minor loops are erased from the memory.

Interface Engineering Based on Liquid Metal for Compact-Layer-free, Fully Printable Mesoscopic Perovskite Solar Cells.

PubMed

Zhang, Yumin; Zhao, Jianhong; Zhang, Jin; Jiang, Xixi; Zhu, Zhongqi; Liu, Qingju

2018-05-09

A printing process for the fabrication of perovskite solar cells (PSCs) exhibits promising future application in the photovoltaic industry due to its low-cost and eco-friendly preparation. In mesoscopic carbon-based PSCs, however, compared to conventional ones, the hole-transport-layer-free PSCs often lead to inefficient hole extraction. Here, we used liquid metal (LM, Galinstan) as an interface modifier material in combination with a carbon electrode. Considering the high conductivity and room-temperature fluidity, it is found that LMs are superior in improving hole extraction and, more importantly, LMs tend to be reserved at the interface between ZrO 2 and carbon for enhancing the contact property. Correspondingly, the carrier transfer resistance was decreased at the carbon/perovskite interface. As optimized content, the triple mesoscopic PSCs based on mixed-cation perovskite with a power conversion efficiency of 13.51% was achieved, involving a 26% increase compared to those without LMs. This work opens new techniques for LMs in optoelectronics and printing.

Quantum mechanics and the second law of thermodynamics: an insight gleaned from magnetic hysteresis in the first order phase transition of an isolated mesoscopic-size type I superconductor

NASA Astrophysics Data System (ADS)

Keefe, Peter D.

2012-11-01

J Bardeen proposed that the adiabatic phase transition of mesoscopic-size type I superconductors must be accompanied by magnetic hysteresis in the critical magnetic field of sufficient magnitude to satisfy the second law of thermodynamics, herein referred to as ‘Bardeen Hysteresis’. Bardeen Hysteresis remains speculative in that it has not been reported in the literature. This paper investigates Bardeen Hysteresis as a possible accompaniment to the adiabatic phase transition of isolated mesoscopic-size type I superconductors and its implications with respect to the second law of thermodynamics. A causal mechanism for Bardeen Hysteresis is discussed which contrasts with the long accepted causal mechanism of magnetic hysteresis, as first summarized by Pippard, herein referred to as ‘Pippard Hysteresis’. The paper offers guidance for an experimental verification and comments on how the existence of Bardeen Hysteresis has relation to a quantum mechanical basis for the second law of thermodynamics.

Mesoscopic superconductivity and high spin polarization coexisting at metallic point contacts on Weyl semimetal TaAs

PubMed Central

Aggarwal, Leena; Gayen, Sirshendu; Das, Shekhar; Kumar, Ritesh; Süß, Vicky; Felser, Claudia; Shekhar, Chandra; Sheet, Goutam

2017-01-01

A Weyl semimetal is a topologically non-trivial phase of matter that hosts mass-less Weyl fermions, the particles that remained elusive for more than 80 years since their theoretical discovery. The Weyl semimetals exhibit unique transport properties and remarkably high surface spin polarization. Here we show that a mesoscopic superconducting phase with critical temperature Tc=7 K can be realized by forming metallic point contacts with silver (Ag) on single crystals of TaAs, while neither Ag nor TaAs are superconductors. Andreev reflection spectroscopy of such point contacts reveals a superconducting gap of 1.2 meV that coexists with a high transport spin polarization of 60% indicating a highly spin-polarized supercurrent flowing through the point contacts on TaAs. Therefore, apart from the discovery of a novel mesoscopic superconducting phase, our results also show that the point contacts on Weyl semimetals are potentially important for applications in spintronics. PMID:28071685

The Stability Analysis Method of the Cohesive Granular Slope on the Basis of Graph Theory

PubMed Central

Guan, Yanpeng; Liu, Xiaoli; Wang, Enzhi; Wang, Sijing

2017-01-01

This paper attempted to provide a method to calculate progressive failure of the cohesive-frictional granular geomaterial and the spatial distribution of the stability of the cohesive granular slope. The methodology can be divided into two parts: the characterization method of macro-contact and the analysis of the slope stability. Based on the graph theory, the vertexes, the edges and the edge sequences are abstracted out to characterize the voids, the particle contact and the macro-contact, respectively, bridging the gap between the mesoscopic and macro scales of granular materials. This paper adopts this characterization method to extract a graph from a granular slope and characterize the macro sliding surface, then the weighted graph is analyzed to calculate the slope safety factor. Each edge has three weights representing the sliding moment, the anti-sliding moment and the braking index of contact-bond, respectively, E1E2E3E1E2E3. The safety factor of the slope is calculated by presupposing a certain number of sliding routes and reducing Weight E3 repeatedly and counting the mesoscopic failure of the edge. It is a kind of slope analysis method from mesoscopic perspective so it can present more detail of the mesoscopic property of the granular slope. In the respect of macro scale, the spatial distribution of the stability of the granular slope is in agreement with the theoretical solution. PMID:28772596

The effects of distributed life cycles on the dynamics of viral infections.

PubMed

Campos, Daniel; Méndez, Vicenç; Fedotov, Sergei

2008-09-21

We explore the role of cellular life cycles for viruses and host cells in an infection process. For this purpose, we derive a generalized version of the basic model of virus dynamics (Nowak, M.A., Bangham, C.R.M., 1996. Population dynamics of immune responses to persistent viruses. Science 272, 74-79) from a mesoscopic description. In its final form the model can be written as a set of Volterra integrodifferential equations. We consider the role of distributed lifespans and a intracellular (eclipse) phase. These processes are implemented by means of probability distribution functions. The basic reproductive ratio R(0) of the infection is properly defined in terms of such distributions by using an analysis of the equilibrium states and their stability. It is concluded that the introduction of distributed delays can strongly modify both the value of R(0) and the predictions for the virus loads, so the effects on the infection dynamics are of major importance. We also show how the model presented here can be applied to some simple situations where direct comparison with experiments is possible. Specifically, phage-bacteria interactions are analyzed. The dynamics of the eclipse phase for phages is characterized analytically, which allows us to compare the performance of three different fittings proposed before for the one-step growth curve.

Growth of monodisperse mesoscopic metal-oxide colloids under constant monomer supply

NASA Astrophysics Data System (ADS)

Nozawa, Koh; Delville, Marie-Hélène; Ushiki, Hideharu; Panizza, Pascal; Delville, Jean-Pierre

2005-07-01

In closed systems, control over the size of monodisperse metal-oxide colloids is generally limited to submicrometric dimensions. To overcome this difficulty, we explore the formation and growth of silica particles under constant monomer supply. The monomer source is externally driven by the progressive addition into the system of one of the precursors. Monodisperse spherical particles are produced up to a mesoscopic size. We analyze their growth versus the monomer addition rate at different temperatures. Our results show that in the presence of a continuous monomer addition, growth is limited by diffusion over the investigated temporal window. Using the temperature variation of the growth rate, we prove that rescaling leads to a data reduction onto a single master curve. Contrary to the growth process, the final particle’s size reached after the end of the reagent supply strongly depends on the addition rate. The variation of the final particle size versus addition rate can be deduced from an analogy with crystal formation in jet precipitation. Within this framework, and using the temperature dependences of both the particle growth law and the final size, we determine the value of the molecular heat of dissolution associated to the silica solubility. These observations support the fact that classical theories of phase-ordering dynamics can be extended to the synthesis of inorganic particles. The emergence of a master behavior in the presence of continuous monomer addition also suggests the extension of these theories to open systems.

In silico assembly and nanomechanical characterization of carbon nanotube buckypaper.

PubMed

Cranford, Steven W; Buehler, Markus J

2010-07-02

Carbon nanotube sheets or films, also known as 'buckypaper', have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young's modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2-3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures.

In silico assembly and nanomechanical characterization of carbon nanotube buckypaper

NASA Astrophysics Data System (ADS)

Cranford, Steven W.; Buehler, Markus J.

2010-07-01

Carbon nanotube sheets or films, also known as 'buckypaper', have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young's modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2-3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures.

On the macroscopic modeling of dilute emulsions under flow in the presence of particle inertia

NASA Astrophysics Data System (ADS)

Mwasame, Paul M.; Wagner, Norman J.; Beris, Antony N.

2018-03-01

Recently, Mwasame et al. ["On the macroscopic modeling of dilute emulsions under flow," J. Fluid Mech. 831, 433 (2017)] developed a macroscopic model for the dynamics and rheology of a dilute emulsion with droplet morphology in the limit of negligible particle inertia using the bracket formulation of non-equilibrium thermodynamics of Beris and Edwards [Thermodynamics of Flowing Systems: With Internal Microstructure (Oxford University Press on Demand, 1994)]. Here, we improve upon that work to also account for particle inertia effects. This advance is facilitated by using the bracket formalism in its inertial form that allows for the natural incorporation of particle inertia effects into macroscopic level constitutive equations, while preserving consistency to the previous inertialess approximation in the limit of zero inertia. The parameters in the resultant Particle Inertia Thermodynamically Consistent Ellipsoidal Emulsion (PITCEE) model are selected by utilizing literature-available mesoscopic theory for the rheology at small capillary and particle Reynolds numbers. At steady state, the lowest level particle inertia effects can be described by including an additional non-affine inertial term into the evolution equation for the conformation tensor, thereby generalizing the Gordon-Schowalter time derivative. This additional term couples the conformation and vorticity tensors and is a function of the Ohnesorge number. The rheological and microstructural predictions arising from the PITCEE model are compared against steady-shear simulation results from the literature. They show a change in the signs of the normal stress differences that is accompanied by a change in the orientation of the major axis of the emulsion droplet toward the velocity gradient direction with increasing Reynolds number, capturing the two main signatures of particle inertia reported in simulations.

Numerical simulation of wave-induced fluid flow seismic attenuation based on the Cole-Cole model.

PubMed

Picotti, Stefano; Carcione, José M

2017-07-01

The acoustic behavior of porous media can be simulated more realistically using a stress-strain relation based on the Cole-Cole model. In particular, seismic velocity dispersion and attenuation in porous rocks is well described by mesoscopic-loss models. Using the Zener model to simulate wave propagation is a rough approximation, while the Cole-Cole model provides an optimal description of the physics. Here, a time-domain algorithm is proposed based on the Grünwald-Letnikov numerical approximation of the fractional derivative involved in the time-domain representation of the Cole-Cole model, while the spatial derivatives are computed with the Fourier pseudospectral method. The numerical solution is successfully tested against an analytical solution. The methodology is applied to a model of saline aquifer, where carbon dioxide (CO 2 ) is injected. To follow the migration of the gas and detect possible leakages, seismic monitoring surveys should be carried out periodically. To this aim, the sensitivity of the seismic method must be carefully assessed for the specific case. The simulated test considers a possible leakage in the overburden, above the caprock, where the sandstone is partially saturated with gas and brine. The numerical examples illustrate the implementation of the theory.

2D Lattice Boltzmann Simulation Of Chemical Reactions Within Rayleigh-Bénard And Poiseuille-Bénard Convection Systems

NASA Astrophysics Data System (ADS)

Amaya-Ventura, Gilberto; Rodríguez-Romo, Suemi

2011-09-01

This paper deals with the computational simulation of the reaction-diffusion-advection phenomena emerging in Rayleigh-Bénard (RB) and Poiseuille-Bénard reactive convection systems. We use the Boussinesq's approximation for buoyancy forces and the Lattice Boltzmann method (LBM). The first kinetic mesoscopic model proposed here is based on the discrete Boltzmann equation needed to solve the momentum balance coupled with buoyancy forces. Then, a second lattice Boltzmann algorithm is applied to solve the reaction-diffusion-advection equation to calculate the evolution of the chemical species concentration. We use a reactive system composed by nitrous oxide (so call laughing gas) in air as an example; its spatio-temporal decomposition is calculated. Two cases are considered, a rectangular enclosed cavity and an open channel. The simulations are performed at low Reynolds numbers and in a steady state between the first and second thermo-hydrodynamic instabilities. The results presented here, for the thermo-hydrodynamic behavior, are in good agreement with experimental data; while our| chemical kinetics simulation yields expected results. Some applications of our approach are related to chemical reactors and atmospheric phenomena, among others.

Interactive, graphical processing unitbased evaluation of evacuation scenarios at the state scale

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

Perumalla, Kalyan S; Aaby, Brandon G; Yoginath, Srikanth B

2011-01-01

In large-scale scenarios, transportation modeling and simulation is severely constrained by simulation time. For example, few real- time simulators scale to evacuation traffic scenarios at the level of an entire state, such as Louisiana (approximately 1 million links) or Florida (2.5 million links). New simulation approaches are needed to overcome severe computational demands of conventional (microscopic or mesoscopic) modeling techniques. Here, a new modeling and execution methodology is explored that holds the potential to provide a tradeoff among the level of behavioral detail, the scale of transportation network, and real-time execution capabilities. A novel, field-based modeling technique and its implementationmore » on graphical processing units are presented. Although additional research with input from domain experts is needed for refining and validating the models, the techniques reported here afford interactive experience at very large scales of multi-million road segments. Illustrative experiments on a few state-scale net- works are described based on an implementation of this approach in a software system called GARFIELD. Current modeling cap- abilities and implementation limitations are described, along with possible use cases and future research.« less

Breakdown of the independent electron picture in mesoscopic samples at low temperatures: The hunt for the Unicorn

NASA Astrophysics Data System (ADS)

Webb, R. A.

1998-03-01

A variety of experiments are discussed where, at low temperatures, it appears that the non-interacting picture of electrons in a Fermi liquid description of a mesoscopic sample is breaking down. Specifically, experiments on the temperature dependence of the phase-coherence time, energy relaxation rate, spin-flip scattering time, persistent currents in normal metals and transmission through a barrier in the fractional quantum Hall regime all display low-temperature properties which can not be accounted for in the independent electron picture.

Spintronics: spin accumulation in mesoscopic systems.

PubMed

Johnson, Mark

2002-04-25

In spintronics, in which use is made of the spin degree of freedom of the electron, issues concerning electrical spin injection and detection of electron spin diffusion are fundamentally important. Jedema et al. describe a magneto-resistance study in which they claim to have observed spin accumulation in a mesoscopic copper wire, but their one-dimensional model ignores two-dimensional spin-diffusion effects, which casts doubt on their analysis. A two-dimensional vector formalism of spin transport is called for to model spin-injection experiments, and the identification of spurious background resistance effects is crucial.

Mesoscopic Free Path of Nonthermalized Photogenerated Carriers in a Ferroelectric Insulator.

PubMed

Gu, Zongquan; Imbrenda, Dominic; Bennett-Jackson, Andrew L; Falmbigl, Matthias; Podpirka, Adrian; Parker, Thomas C; Shreiber, Daniel; Ivill, Mathew P; Fridkin, Vladimir M; Spanier, Jonathan E

2017-03-03

We show how finite-size scaling of a bulk photovoltaic effect-generated electric field in epitaxial ferroelectric insulating BaTiO_{3}(001) films and a photo-Hall response involving the bulk photovoltaic current reveal a large room-temperature mean free path of photogenerated nonthermalized electrons. Experimental determination of mesoscopic ballistic optically generated carrier transport opens a new paradigm for hot electron-based solar energy conversion, and for facile control of ballistic transport distinct from existing low-dimensional semiconductor interfaces, surfaces, layers, or other structures.

Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation.

PubMed

Erban, Radek; Kevrekidis, Ioannis G; Adalsteinsson, David; Elston, Timothy C

2006-02-28

We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately initialized short bursts of stochastic simulations; the results of these are processed to estimate coarse-grained quantities of interest, such as mesoscopic transport coefficients. In particular, using a simple model of a genetic toggle switch, we illustrate the computation of an effective free energy Phi and of a state-dependent effective diffusion coefficient D that characterize an unavailable effective Fokker-Planck equation. Additionally we illustrate the linking of equation-free techniques with continuation methods for performing a form of stochastic "bifurcation analysis"; estimation of mean switching times in the case of a bistable switch is also implemented in this equation-free context. The accuracy of our methods is tested by direct comparison with long-time stochastic simulations. This type of equation-free analysis appears to be a promising approach to computing features of the long-time, coarse-grained behavior of certain classes of complex stochastic models of gene regulatory networks, circumventing the need for long Monte Carlo simulations.

Partial spin absorption induced magnetization switching and its voltage-assisted improvement in an asymmetrical all spin logic device at the mesoscopic scale

NASA Astrophysics Data System (ADS)

Zhang, Yue; Zhang, Zhizhong; Wang, Lezhi; Nan, Jiang; Zheng, Zhenyi; Li, Xiang; Wong, Kin; Wang, Yu; Klein, Jacques-Olivier; Khalili Amiri, Pedram; Zhang, Youguang; Wang, Kang L.; Zhao, Weisheng

2017-07-01

Beyond memory and storage, future logic applications put forward higher requirements for electronic devices. All spin logic devices (ASLDs) have drawn exceptional interest as they utilize pure spin current instead of charge current, which could promise ultra-low power consumption. However, relatively low efficiencies of spin injection, transport, and detection actually impede high-speed magnetization switching and challenge perspectives of ASLD. In this work, we study partial spin absorption induced magnetization switching in asymmetrical ASLD at the mesoscopic scale, in which the injector and detector have the nano-fabrication compatible device size (>100 nm) and their contact areas are different. The enlarged contact area of the detector is conducive to the spin current absorption, and the contact resistance difference between the injector and the detector can decrease the spin current backflow. Rigorous spin circuit modeling and micromagnetic simulations have been carried out to analyze the electrical and magnetic features. The results show that, at the fabrication-oriented technology scale, the ferromagnetic layer can hardly be switched by geometrically partial spin current absorption. The voltage-controlled magnetic anisotropy (VCMA) effect has been applied on the detector to accelerate the magnetization switching by modulating magnetic anisotropy of the ferromagnetic layer. With a relatively high VCMA coefficient measured experimentally, a voltage of 1.68 V can assist the whole magnetization switching within 2.8 ns. This analysis and improving approach will be of significance for future low-power, high-speed logic applications.

Modification and optimization of the united-residue (UNRES) potential-energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins

PubMed Central

Liwo, Adam; Khalili, Mey; Czaplewski, Cezary; Kalinowski, Sebastian; Ołdziej, Stanisław; Wachucik, Katarzyna; Scheraga, Harold A.

2011-01-01

We report the modification and parameterization of the united-residue (UNRES) force field for energy-based protein-structure prediction and protein-folding simulations. We tested the approach on three training proteins separately: 1E0L (β), 1GAB (α), and 1E0G (α + β). Heretofore, the UNRES force field had been designed and parameterized to locate native-like structures of proteins as global minima of their effective potential-energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES, and applied it with success to simulate protein folding pathways. How ever, the force field turned out to be largely biased towards α-helical structures in canonical simulations because the conformational entropy had been neglected in the parameterization. We applied the hierarchical optimization method developed in our earlier work to optimize the force field, in which the conformational space of a training protein is divided into levels each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy-function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a predominance of folded or unfolded structures, as well as to structures at the putative folding-transition temperature, changing the sign of the gaps at the transition temperature. This enabled us to obtain force fields characterized by a single peak in the heat capacity at the transition temperature. Furthermore, we introduced temperature dependence to the UNRES force field; this is consistent with the fact that it is a free-energy and not a potential-energy function. PMID:17201450

Note: A simple picture of subdiffusive polymer motion from stochastic simulations

NASA Astrophysics Data System (ADS)

Gniewek, Pawel; Kolinski, Andrzej

2011-02-01

Entangled polymer solutions and melts exhibit unusual frictional properties. In the entanglement limit self-diffusion coefficient of long flexible polymers decays with the second power of chain length and viscosity increases with 3-3.5 power of chain length.1 It is very difficult to provide detailed molecular-level explanation of the entanglement effect.2 Perhaps, the problem of many entangled polymer chains is the most complex multibody issue of classical physics. There are different approaches to polymer melt dynamics. Some of these recognize hydrodynamic interactions as a dominant term, while topological constraints for polymer chains are assumed as a secondary factor. Other theories consider the topological constraints as the most important factors controlling polymer dynamics. Herman and co-workers describe polymer dynamics in melts, as a lateral sliding of a chain along other chains until complete mutual disentanglement. Despite the success in explaining the power-laws for viscosity, the model has some limitations. First of all, memory effects are ignored, that is, polymer segments are treated independently. Also, each entanglement/obstacle is treated as a separate entity, which is certainly a simplification of the memory effect problem. In addition to that, correlated motions of segments are addressed within the framework of renormalized Rouse-chain theory,7 without calling any topological entanglements in advance. This approach leads to the generalized Langevin equation characterized by distinct memory kernels describing local and nonlocal segment correlations or to the Smoluchowski equation in which the segments' mobility is treated as a stochastic variable.11 Both models describe the polymer segments motion at a microscopic level. An interesting alternative is to solve the integrodifferential equation for the chain relaxation with a sophisticated kernel function.12 The design of the kernel function is based on a mesoscopic description of the polymer melt. These theories explain some experimental data, although the description of the crossover between the Rouse and non-Rouse behavior is not satisfactory. Obviously, within the scope of a short note we cannot review all theoretical concepts of the polymer melt dynamics. Here we focus just on the interpretation of the observed single segment autocorrelation function.

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

PubMed

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

2018-06-27

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

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Correlation between hierarchical structure of crystal networks and macroscopic performance of mesoscopic soft materials and engineering principles.

PubMed

Lin, Naibo; Liu, Xiang Yang

2015-11-07

This review examines how the concepts and ideas of crystallization can be extended further and applied to the field of mesoscopic soft materials. It concerns the structural characteristics vs. the macroscopic performance, and the formation mechanism of crystal networks. Although this subject can be discussed in a broad sense across the area of mesoscopic soft materials, our main focus is on supramolecular materials, spider and silkworm silks, and biominerals. First, the occurrence of a hierarchical structure, i.e. crystal network and domain network structures, will facilitate the formation kinetics of mesoscopic phases and boost up the macroscopic performance of materials in some cases (i.e. spider silk fibres). Second, the structure and performance of materials can be correlated in some way by the four factors: topology, correlation length, symmetry/ordering, and strength of association of crystal networks. Moreover, four different kinetic paths of crystal network formation are identified, namely, one-step process of assembly, two-step process of assembly, mixed mode of assembly and foreign molecule mediated assembly. Based on the basic mechanisms of crystal nucleation and growth, the formation of crystal networks, such as crystallographic mismatch (or noncrystallographic) branching (tip branching and fibre side branching) and fibre/polymeric side merging, are reviewed. This facilitates the rational design and construction of crystal networks in supramolecular materials. In this context, the (re-)construction of a hierarchical crystal network structure can be implemented by thermal, precipitate, chemical, and sonication stimuli. As another important class of soft materials, the unusual mechanical performance of spider and silkworm silk fibres are reviewed in comparison with the regenerated silk protein derivatives. It follows that the considerably larger breaking stress and unusual breaking strain of spider silk fibres vs. silkworm silk fibres can be interpreted according to the synergistically correlated hierarchical structures of the domain and crystal networks, which can be quantified by the hierarchical structural correlation and the four structural parameters. Based on the concept of crystal networks, the new understanding acquired will transfer the research and engineering of mesoscopic materials, particularly, soft functional materials, to a new phase.

Generic features of the primary relaxation in glass-forming materials (Review Article)

NASA Astrophysics Data System (ADS)

Kokshenev, Valery B.

2017-08-01

We discuss structural relaxation in molecular and polymeric supercooled liquids, metallic alloys and orientational glass crystals. The study stresses especially the relationships between observables raised from underlying constraints imposed on degrees of freedom of vitrification systems. A self-consistent parametrization of the α-timescale on macroscopic level results in the material-and-model independent universal equation, relating three fundamental temperatures, characteristic of the primary relaxation, that is numerically proven in all studied glass formers. During the primary relaxation, the corresponding small and large mesoscopic clusters modify their size and structure in a self-similar way, regardless of underlying microscopic realizations. We show that cluster-shape similarity, instead of cluster-size fictive divergence, gives rise to universal features observed in primary relaxation. In all glass formers with structural disorder, including orientational-glass materials (with the exception of plastic crystals), structural relaxation is shown to be driven by local random fields. Within the dynamic stochastic approach, the universal subdiffusive dynamics corresponds to random walks on small and large fractals.

In situ dynamic observations of perovskite crystallisation and microstructure evolution intermediated from [PbI6]4- cage nanoparticles

NASA Astrophysics Data System (ADS)

Hu, Qin; Zhao, Lichen; Wu, Jiang; Gao, Ke; Luo, Deying; Jiang, Yufeng; Zhang, Ziyi; Zhu, Chenhui; Schaible, Eric; Hexemer, Alexander; Wang, Cheng; Liu, Yi; Zhang, Wei; Grätzel, Michael; Liu, Feng; Russell, Thomas P.; Zhu, Rui; Gong, Qihuang

2017-06-01

Hybrid lead halide perovskites have emerged as high-performance photovoltaic materials with their extraordinary optoelectronic properties. In particular, the remarkable device efficiency is strongly influenced by the perovskite crystallinity and the film morphology. Here, we investigate the perovskites crystallisation kinetics and growth mechanism in real time from liquid precursor continually to the final uniform film. We utilize some advanced in situ characterisation techniques including synchrotron-based grazing incident X-ray diffraction to observe crystal structure and chemical transition of perovskites. The nano-assemble model from perovskite intermediated [PbI6]4- cage nanoparticles to bulk polycrystals is proposed to understand perovskites formation at a molecular- or nano-level. A crystallisation-depletion mechanism is developed to elucidate the periodic crystallisation and the kinetically trapped morphology at a mesoscopic level. Based on these in situ dynamics studies, the whole process of the perovskites formation and transformation from the molecular to the microstructure over relevant temperature and time scales is successfully demonstrated.

Tomonaga–Luttinger physics in electronic quantum circuits

PubMed Central

Jezouin, S.; Albert, M.; Parmentier, F. D.; Anthore, A.; Gennser, U.; Cavanna, A.; Safi, I.; Pierre, F.

2013-01-01

In one-dimensional conductors, interactions result in correlated electronic systems. At low energy, a hallmark signature of the so-called Tomonaga–Luttinger liquids is the universal conductance curve predicted in presence of an impurity. A seemingly different topic is the quantum laws of electricity, when distinct quantum conductors are assembled in a circuit. In particular, the conductances are suppressed at low energy, a phenomenon called dynamical Coulomb blockade. Here we investigate the conductance of mesoscopic circuits constituted by a short single-channel quantum conductor in series with a resistance, and demonstrate a proposed link to Tomonaga–Luttinger physics. We reformulate and establish experimentally a recently derived phenomenological expression for the conductance using a wide range of circuits, including carbon nanotube data obtained elsewhere. By confronting both conductance data and phenomenological expression with the universal Tomonaga–Luttinger conductance curve, we demonstrate experimentally the predicted mapping between dynamical Coulomb blockade and the transport across a Tomonaga–Luttinger liquid with an impurity. PMID:23653214

In situ dynamic observations of perovskite crystallisation and microstructure evolution intermediated from [PbI6]4− cage nanoparticles

PubMed Central

Hu, Qin; Zhao, Lichen; Wu, Jiang; Gao, Ke; Luo, Deying; Jiang, Yufeng; Zhang, Ziyi; Zhu, Chenhui; Schaible, Eric; Hexemer, Alexander; Wang, Cheng; Liu, Yi; Zhang, Wei; Grätzel, Michael; Liu, Feng; Russell, Thomas P.; Zhu, Rui; Gong, Qihuang

2017-01-01

Hybrid lead halide perovskites have emerged as high-performance photovoltaic materials with their extraordinary optoelectronic properties. In particular, the remarkable device efficiency is strongly influenced by the perovskite crystallinity and the film morphology. Here, we investigate the perovskites crystallisation kinetics and growth mechanism in real time from liquid precursor continually to the final uniform film. We utilize some advanced in situ characterisation techniques including synchrotron-based grazing incident X-ray diffraction to observe crystal structure and chemical transition of perovskites. The nano-assemble model from perovskite intermediated [PbI6]4− cage nanoparticles to bulk polycrystals is proposed to understand perovskites formation at a molecular- or nano-level. A crystallisation-depletion mechanism is developed to elucidate the periodic crystallisation and the kinetically trapped morphology at a mesoscopic level. Based on these in situ dynamics studies, the whole process of the perovskites formation and transformation from the molecular to the microstructure over relevant temperature and time scales is successfully demonstrated. PMID:28635947

PREFACE: International Symposium on Non-Equilibrium Soft Matter 2010 International Symposium on Non-Equilibrium Soft Matter 2010

NASA Astrophysics Data System (ADS)

Kawakatsu, T.; Matsuyama, A.; Ohta, T.; Tanaka, H.; Tanaka, S.

2011-07-01

Soft matter is a rapidly growing interdisciplinary research field covering a range of subject areas including physics, chemistry, biology, mathematics and engineering. Some of the important universal features of these materials are their mesoscopic structures and their dynamics. Due to the existence of such large-scale structures, which nevertheless exhibit interactions of the order of the thermal energy, soft matter can readily be taken out of equilibrium by imposing a weak external field such as an electric field, a mechanical stress or a shear flow. The importance of the coexistence of microscopic molecular dynamics and the mesoscopic/macroscopic structures and flows requires us to develop hierarchical approaches to understand the nonlinear and nonequilibrium phenomena, which is one of the central issues of current soft matter research. This special section presents selected contributions from the 'International Symposium on Non-Equilibrium Soft Matter 2010' held from 17-20 August 2010 in Nara, Japan, which aimed to describe recent advances in soft matter research focusing especially on its nonequilibrium aspects. The topics discussed cover statics and dynamics of a wide variety of materials ranging from traditional soft matter like polymers, gels, emulsions, liquid crystals and colloids to biomaterials such as biopolymers and biomembranes. Among these studies, we highlighted the physics of biomembranes and vesicles, which has attracted great attention during the last decade; we organized a special session for this active field. The work presented in this issue deals with (1) structure formation in biomembranes and vesicles, (2) rheology of polymers and gels, (3) mesophases in block copolymers, (4) mesoscopic structures in liquid crystals and ionic liquids, and (5) nonequilibrium dynamics. This symposium was organized as part of a research project supported by the Grant-in-Aid for the priority area 'Soft Matter Physics' (2006-2010) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan. We thank those who contributed to this symposium as well as members of the 'Soft Matter Physics' project for their valuable discussions and collaborations. Non-equilibrium soft matter contents Insights on raft behavior from minimal phenomenological models G Garbès Putzel and M Schick Dynamical membrane curvature instability controlled by intermonolayer friction Anne-Florence Bitbol, Jean-Baptiste Fournier, Miglena I Angelova and Nicolas Puff Numerical investigations of the dynamics of two-component vesicles Takashi Taniguchi, Miho Yanagisawa and Masayuki Imai Asymmetric distribution of cone-shaped lipids in a highly curved bilayer revealed by a small angle neutron scattering technique Y Sakuma, N Urakami, T Taniguchi and M Imai Hydration, phase separation and nonlinear rheology of temperature-sensitive water-soluble polymers Fumihiko Tanaka, Tsuyoshi Koga, Isamu Kaneda and Françoise M Winnik Morphology and rheology of an immiscible polymer blend subjected to a step electric field under shear flow H Orihara, Y Nishimoto, K Aida, Y H Na, T Nagaya and S Ujiie Surfactant-induced friction reduction for hydrogels in the boundary lubrication regime Kosuke Kamada, Hidemitsu Furukawa, Takayuki Kurokawa, Tomohiro Tada, Taiki Tominaga, Yukihiro Nakano and Jian Ping Gong Fabrication and structural analysis of polyrotaxane fibers and films Yasuhiro Sakai, Kentaro Ueda, Naoya Katsuyama, Koji Shimizu, Shunya Sato, Jun Kuroiwa, Jun Araki, Akira Teramoto, Koji Abe, Hideaki Yokoyama and Kohzo Ito Micellization kinetics of diblock copolymers in a homopolymer matrix: a self-consistent field study Raghuram Thiagarajan and David C Morse Hierarchical self-assembly of two-length-scale multiblock copolymers Gerrit ten Brinke, Katja Loos, Ivana Vukovic and Gerrit Gobius du Sart Kaleidoscopic morphologies from ABC star-shaped terpolymers Yushu Matsushita, Kenichi Hayashida, Tomonari Dotera and Atsushi Takano Direct and inverted nematic dispersions for soft matter photonics I Muševič, M Škarabot and M Humar Solvation effects in phase transitions in soft matter Akira Onuki, Takeaki Araki and Ryuichi Okamoto Non-equilibrium dynamics of 2D liquid crystals driven by transmembrane gas flow Kazuyoshi Seki, Ken Ueda, Yu-ichi Okumura and Yuka Tabe Roles of bond orientational ordering in glass transition and crystallization Hajime Tanaka Shear banding in thixotropic and normal emulsions José Paredes, Noushine Shahidzadeh-Bonn and Daniel Bonn Effects of hydrodynamic interactions in binary colloidal mixtures driven oppositely by oscillatory external fields Adam Wysocki and Hartmut Löwen Onsager's variational principle in soft matter Masao Doi

Mesoscopic bar magnet based on ε-Fe2O3 hard ferrite.

PubMed

Ohkoshi, Shin-Ichi; Namai, Asuka; Yamaoka, Takehiro; Yoshikiyo, Marie; Imoto, Kenta; Nasu, Tomomichi; Anan, Shizuka; Umeta, Yoshikazu; Nakagawa, Kosuke; Tokoro, Hiroko

2016-06-07

Ferrite magnets have a long history. They are used in motors, magnetic fluids, drug delivery systems, etc. Herein we report a mesoscopic ferrite bar magnet based on rod-shaped ε-Fe2O3 with a large coercive field (>25 kOe). The ε-Fe2O3-based bar magnet is a single crystal with a single magnetic domain along the longitudinal direction. A wide frequency range spectroscopic study shows that the crystallographic a-axis of ε-Fe2O3, which corresponds to the longitudinal direction of the bar magnet, plays an important role in linear and non-linear magneto-optical transitions, phonon modes, and the magnon (Kittel mode). Due to its multiferroic property, a magnetic-responsive non-linear optical sheet is manufactured as an application using an ε-Fe2O3-based bar magnet, resin, and polyethylene terephthalate. Furthermore, from the viewpoint of the large coercive field property, we demonstrate that a mesoscopic ε-Fe2O3 bar magnet can be used as a magnetic force microscopy probe.

Mesoscopic bar magnet based on ɛ-Fe2O3 hard ferrite

NASA Astrophysics Data System (ADS)

Ohkoshi, Shin-Ichi; Namai, Asuka; Yamaoka, Takehiro; Yoshikiyo, Marie; Imoto, Kenta; Nasu, Tomomichi; Anan, Shizuka; Umeta, Yoshikazu; Nakagawa, Kosuke; Tokoro, Hiroko

2016-06-01

Ferrite magnets have a long history. They are used in motors, magnetic fluids, drug delivery systems, etc. Herein we report a mesoscopic ferrite bar magnet based on rod-shaped ɛ-Fe2O3 with a large coercive field (>25 kOe). The ɛ-Fe2O3-based bar magnet is a single crystal with a single magnetic domain along the longitudinal direction. A wide frequency range spectroscopic study shows that the crystallographic a-axis of ɛ-Fe2O3, which corresponds to the longitudinal direction of the bar magnet, plays an important role in linear and non-linear magneto-optical transitions, phonon modes, and the magnon (Kittel mode). Due to its multiferroic property, a magnetic-responsive non-linear optical sheet is manufactured as an application using an ɛ-Fe2O3-based bar magnet, resin, and polyethylene terephthalate. Furthermore, from the viewpoint of the large coercive field property, we demonstrate that a mesoscopic ɛ-Fe2O3 bar magnet can be used as a magnetic force microscopy probe.

Nonlocal electrical detection of spin accumulation generated by anomalous Hall effect in mesoscopic N i81F e19 films

NASA Astrophysics Data System (ADS)

Qin, Chuan; Chen, Shuhan; Cai, Yunjiao; Kandaz, Fatih; Ji, Yi

2017-10-01

Spin accumulation generated by the anomalous Hall effect (AHE) in mesoscopic ferromagnetic N i81F e19 (permalloy, Py) films is detected electrically by a nonlocal method. The reciprocal phenomenon, the inverse spin Hall effect (ISHE), can also be generated and detected all electrically in the same structure. For accurate quantitative analysis, a series of nonlocal AHE/ISHE structures and supplementary structures are fabricated on each sample substrate to account for statistical variations and to accurately determine all essential physical parameters in situ. By exploring Py thicknesses of 4, 8, and 12 nm, the Py spin diffusion length λPy is found to be much shorter than the film thicknesses. The product of λPy and the Py spin Hall angle αSH is determined to be independent of thickness and resistivity: αSHλPy=(0.066 ±0.009 ) nm at 5 K and (0.041 ±0.010 )nm at 295 K. These values are comparable to those obtained from mesoscopic Pt films.

Can mutation-mediated effects occurring early in development cause long-term seizure susceptibility in genetic generalized epilepsies?

PubMed

Reid, Christopher Alan; Rollo, Ben; Petrou, Steven; Berkovic, Samuel F

2018-05-01

Epilepsy has a strong genetic component, with an ever-increasing number of disease-causing genes being discovered. Most epilepsy-causing mutations are germ line and thus present from conception. These mutations are therefore well positioned to have a deleterious impact during early development. Here we review studies that investigate the role of genetic lesions within the early developmental window, specifically focusing on genetic generalized epilepsy (GGE). Literature on the potential pathogenic role of sub-mesoscopic structural changes in GGE is also reviewed. Evidence from rodent models of genetic epilepsy support the idea that functional and structural changes can occur in early development, leading to altered seizure susceptibility into adulthood. Both animal and human studies suggest that sub-mesoscopic structural changes occur in GGE. The existence of sub-mesoscopic structural changes prior to seizure onset may act as biomarkers of excitability in genetic epilepsies. We also propose that presymptomatic treatment may be essential for limiting the long-term consequences of disease-causing mutations in genetic epilepsies. Wiley Periodicals, Inc. © 2018 International League Against Epilepsy.

Mesoscopic structure conditions the emergence of cooperation on social networks

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

Lozano, S.; Arenas, A.; Sanchez, A.

We study the evolutionary Prisoner's Dilemma on two social networks substrates obtained from actual relational data. We find very different cooperation levels on each of them that cannot be easily understood in terms of global statistical properties of both networks. We claim that the result can be understood at the mesoscopic scale, by studying the community structure of the networks. We explain the dependence of the cooperation level on the temptation parameter in terms of the internal structure of the communities and their interconnections. We then test our results on community-structured, specifically designed artificial networks, finding a good agreement withmore » the observations in both real substrates. Our results support the conclusion that studies of evolutionary games on model networks and their interpretation in terms of global properties may not be sufficient to study specific, real social systems. Further, the study allows us to define new quantitative parameters that summarize the mesoscopic structure of any network. In addition, the community perspective may be helpful to interpret the origin and behavior of existing networks as well as to design structures that show resilient cooperative behavior.« less

Quantitative measurements of nanoscale permittivity and conductivity using tuning-fork-based microwave impedance microscopy

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

Wu, Xiaoyu; Hao, Zhenqi; Wu, Di

Here, we report quantitative measurements of nanoscale permittivity and conductivity using tuning-fork (TF) based microwave impedance microscopy (MIM). The system is operated under the driving amplitude modulation mode, which ensures satisfactory feedback stability on samples with rough surfaces. The demodulated MIM signals on a series of bulk dielectrics are in good agreement with results simulated by finite-element analysis. Using the TF-MIM, we have visualized the evolution of nanoscale conductance on back-gated MoS 2 field effect transistors, and the results are consistent with the transport data. Our work suggests that quantitative analysis of mesoscopic electrical properties can be achieved by near-fieldmore » microwave imaging with small distance modulation.« less

Quantitative measurements of nanoscale permittivity and conductivity using tuning-fork-based microwave impedance microscopy

DOE PAGES

Wu, Xiaoyu; Hao, Zhenqi; Wu, Di; ...

2018-04-01

Here, we report quantitative measurements of nanoscale permittivity and conductivity using tuning-fork (TF) based microwave impedance microscopy (MIM). The system is operated under the driving amplitude modulation mode, which ensures satisfactory feedback stability on samples with rough surfaces. The demodulated MIM signals on a series of bulk dielectrics are in good agreement with results simulated by finite-element analysis. Using the TF-MIM, we have visualized the evolution of nanoscale conductance on back-gated MoS 2 field effect transistors, and the results are consistent with the transport data. Our work suggests that quantitative analysis of mesoscopic electrical properties can be achieved by near-fieldmore » microwave imaging with small distance modulation.« less

Antiferromagnetic spinor condensates in a bichromatic superlattice

NASA Astrophysics Data System (ADS)

Tang, Tao; Zhao, Lichao; Chen, Zihe; Liu, Yingmei

2017-04-01

A spinor Bose-Einstein condensate in an optical supelattice has been considered as a good quantum simulator for understanding mesoscopic magnetism. We report an experimental study on an antiferromagnetic spinor condensate in a bichromatic superlattice constructed by a cubic red-detuned optical lattice and a one-dimensional blue-detuned optical lattice. Our data demonstrate a few advantages of this bichromatic superlattice over a monochromatic lattice. One distinct advantage is that the bichromatic superlattice enables realizing the first-order superfluid to Mott-insulator phase transitions within a much wider range of magnetic fields. In addition, we discuss an apparent discrepancy between our data and the mean-field theory. We thank the National Science Foundation and the Oklahoma Center for the Advancement of Science and Technology for financial support.

Molecular structure of bottlebrush polymers in melts

PubMed Central

Paturej, Jarosław; Sheiko, Sergei S.; Panyukov, Sergey; Rubinstein, Michael

2016-01-01

Bottlebrushes are fascinating macromolecules that display an intriguing combination of molecular and particulate features having vital implications in both living and synthetic systems, such as cartilage and ultrasoft elastomers. However, the progress in practical applications is impeded by the lack of knowledge about the hierarchic organization of both individual bottlebrushes and their assemblies. We delineate fundamental correlations between molecular architecture, mesoscopic conformation, and macroscopic properties of polymer melts. Numerical simulations corroborate theoretical predictions for the effect of grafting density and side-chain length on the dimensions and rigidity of bottlebrushes, which effectively behave as a melt of flexible filaments. These findings provide quantitative guidelines for the design of novel materials that allow architectural tuning of their properties in a broad range without changing chemical composition. PMID:28861466

Fano effect in the transport of an artificial molecule

NASA Astrophysics Data System (ADS)

Norimoto, Shota; Nakamura, Shuji; Okazaki, Yuma; Arakawa, Tomonori; Asano, Kenichi; Onomitsu, Koji; Kobayashi, Kensuke; Kaneko, Nobu-hisa

2018-05-01

The Fano effect is a ubiquitous phenomenon arising from interference between a discrete energy state and an energy continuum. We explore this effect in an artificial molecule, namely, two lateral quantum dots (QDs) fabricated from a two-dimensional electron gas system and coupled in series. When the coupling between the leads and QDs is small, the charge stability diagram of the system shows a honeycomb lattice structure that is characteristic of a double QD system. As the coupling increases, a honeycomb structure consisting of the Fano resonances emerges. A numerical simulation based on the T-matrix method can satisfactorily reproduce our experimental observation. This report constitutes a clear example of the ubiquitous nature of the Fano effect in mesoscopic transport.

Crystal plasticity investigation of the microstructural factors influencing dislocation channeling in a model irradiated bcc material

DOE PAGES

Patra, Anirban; McDowell, David L.

2016-03-25

We use a continuum crystal plasticity framework to study the effect of microstructure and mesoscopic factors on dislocation channeling and flow localization in an irradiated model bcc alloy. For simulated dislocation channeling characteristics we correlate the dislocation and defect densities in the substructure, local Schmid factor, and stress triaxiality, in terms of their temporal and spatial evolution. A metric is introduced to assess the propensity for localization and is correlated to the grain-level Schmid factor. We also found that localization generally takes place in grains with a local Schmid factor in the range 0.42 or higher. Surface slip step heightsmore » are computed at free surfaces and compared to relevant experiments.« less

Modeling cardiovascular hemodynamics using the lattice Boltzmann method on massively parallel supercomputers

NASA Astrophysics Data System (ADS)

Randles, Amanda Elizabeth

Accurate and reliable modeling of cardiovascular hemodynamics has the potential to improve understanding of the localization and progression of heart diseases, which are currently the most common cause of death in Western countries. However, building a detailed, realistic model of human blood flow is a formidable mathematical and computational challenge. The simulation must combine the motion of the fluid, the intricate geometry of the blood vessels, continual changes in flow and pressure driven by the heartbeat, and the behavior of suspended bodies such as red blood cells. Such simulations can provide insight into factors like endothelial shear stress that act as triggers for the complex biomechanical events that can lead to atherosclerotic pathologies. Currently, it is not possible to measure endothelial shear stress in vivo, making these simulations a crucial component to understanding and potentially predicting the progression of cardiovascular disease. In this thesis, an approach for efficiently modeling the fluid movement coupled to the cell dynamics in real-patient geometries while accounting for the additional force from the expansion and contraction of the heart will be presented and examined. First, a novel method to couple a mesoscopic lattice Boltzmann fluid model to the microscopic molecular dynamics model of cell movement is elucidated. A treatment of red blood cells as extended structures, a method to handle highly irregular geometries through topology driven graph partitioning, and an efficient molecular dynamics load balancing scheme are introduced. These result in a large-scale simulation of the cardiovascular system, with a realistic description of the complex human arterial geometry, from centimeters down to the spatial resolution of red-blood cells. The computational methods developed to enable scaling of the application to 294,912 processors are discussed, thus empowering the simulation of a full heartbeat. Second, further extensions to enable the modeling of fluids in vessels with smaller diameters and a method for introducing the deformational forces exerted on the arterial flows from the movement of the heart by borrowing concepts from cosmodynamics are presented. These additional forces have a great impact on the endothelial shear stress. Third, the fluid model is extended to not only recover Navier-Stokes hydrodynamics, but also a wider range of Knudsen numbers, which is especially important in micro- and nano-scale flows. The tradeoffs of many optimizations methods such as the use of deep halo level ghost cells that, alongside hybrid programming models, reduce the impact of such higher-order models and enable efficient modeling of extreme regimes of computational fluid dynamics are discussed. Fourth, the extension of these models to other research questions like clogging in microfluidic devices and determining the severity of co-arctation of the aorta is presented. Through this work, a validation of these methods by taking real patient data and the measured pressure value before the narrowing of the aorta and predicting the pressure drop across the co-arctation is shown. Comparison with the measured pressure drop in vivo highlights the accuracy and potential impact of such patient specific simulations. Finally, a method to enable the simulation of longer trajectories in time by discretizing both spatially and temporally is presented. In this method, a serial coarse iterator is used to initialize data at discrete time steps for a fine model that runs in parallel. This coarse solver is based on a larger time step and typically a coarser discretization in space. Iterative refinement enables the compute-intensive fine iterator to be modeled with temporal parallelization. The algorithm consists of a series of prediction-corrector iterations completing when the results have converged within a certain tolerance. Combined, these developments allow large fluid models to be simulated for longer time durations than previously possible.

Magnetic nanostructures.

PubMed

Bennemann, K

2010-06-23

Characteristic results of magnetism in small particles, thin films and tunnel junctions are presented. As a consequence of the reduced atomic coordination in small clusters and thin films the electronic states and density of states are modified. Thus, magnetic moments and magnetization are affected. Generally, in clusters and thin films magnetic anisotropy plays a special role. In tunnel junctions the interplay of magnetism, spin currents and superconductivity are of particular interest. In ring-like mesoscopic systems Aharonov-Bohm-induced currents are studied. Results are given for single transition metal clusters, cluster ensembles, thin films, mesoscopic structures and tunnel systems. © 2010 IOP Publishing Ltd

Nanoscale patterning of electronic devices at the amorphous LaAlO3/SrTiO3 oxide interface using an electron sensitive polymer mask

NASA Astrophysics Data System (ADS)

Bjørlig, Anders V.; von Soosten, Merlin; Erlandsen, Ricci; Dahm, Rasmus Tindal; Zhang, Yu; Gan, Yulin; Chen, Yunzhong; Pryds, Nini; Jespersen, Thomas S.

2018-04-01

A simple approach is presented for designing complex oxide mesoscopic electronic devices based on the conducting interfaces of room temperature grown LaAlO3/SrTiO3 heterostructures. The technique is based entirely on methods known from conventional semiconductor processing technology, and we demonstrate a lateral resolution of ˜100 nm. We study the low temperature transport properties of nanoscale wires and demonstrate the feasibility of the technique for defining in-plane gates allowing local control of the electrostatic environment in mesoscopic devices.

Research on discrete element simulation of anchor frame beam reinforcement in bedding shale slope

NASA Astrophysics Data System (ADS)

Zhang, Xiao yong; Xie, Xiao ting

2017-11-01

The anchor frame beam is a new type of composite support method, which is a kind of slope protection structure considering the interaction between the anchors and the slope. Based on the reinforcement project of a bedding shale slope in Chengzhang highway, the reinforced effect of anchor frame beam is studied by discrete element method. Firstly, the mesoscopic parameters of the rock mass are obtained by calibration while that of anchor frame beam are obtained by calculation. Then the slope model with the reinforcement of anchor frame beam is established by particle flow software PFC2D. Afterwards, the statement of slope can be analyzed and the reinforcement effect of anchor frame beam can be predicted. Results show that: there is no instability in the slope after reinforcement, and the sliding of slope can be effectively prevented by anchor frame beam. The simulation results can provide reference for the design and construction of the project.

An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems

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

Padgett, Jill M. A.; Ilie, Silvana, E-mail: silvana@ryerson.ca

2016-03-15

Stochastic modelling is critical for studying many biochemical processes in a cell, in particular when some reacting species have low population numbers. For many such cellular processes the spatial distribution of the molecular species plays a key role. The evolution of spatially heterogeneous biochemical systems with some species in low amounts is accurately described by the mesoscopic model of the Reaction-Diffusion Master Equation. The Inhomogeneous Stochastic Simulation Algorithm provides an exact strategy to numerically solve this model, but it is computationally very expensive on realistic applications. We propose a novel adaptive time-stepping scheme for the tau-leaping method for approximating themore » solution of the Reaction-Diffusion Master Equation. This technique combines effective strategies for variable time-stepping with path preservation to reduce the computational cost, while maintaining the desired accuracy. The numerical tests on various examples arising in applications show the improved efficiency achieved by the new adaptive method.« less

Fluctuations When Driving Between Nonequilibrium Steady States

NASA Astrophysics Data System (ADS)

Riechers, Paul M.; Crutchfield, James P.

2017-08-01

Maintained by environmental fluxes, biological systems are thermodynamic processes that operate far from equilibrium without detailed-balanced dynamics. Yet, they often exhibit well defined nonequilibrium steady states (NESSs). More importantly, critical thermodynamic functionality arises directly from transitions among their NESSs, driven by environmental switching. Here, we identify the constraints on excess heat and dissipated work necessary to control a system that is kept far from equilibrium by background, uncontrolled "housekeeping" forces. We do this by extending the Crooks fluctuation theorem to transitions among NESSs, without invoking an unphysical dual dynamics. This and corresponding integral fluctuation theorems determine how much work must be expended when controlling systems maintained far from equilibrium. This generalizes thermodynamic feedback control theory, showing that Maxwellian Demons can leverage mesoscopic-state information to take advantage of the excess energetics in NESS transitions. We also generalize an approach recently used to determine the work dissipated when driving between functionally relevant configurations of an active energy-consuming complex system. Altogether, these results highlight universal thermodynamic laws that apply to the accessible degrees of freedom within the effective dynamic at any emergent level of hierarchical organization. By way of illustration, we analyze a voltage-gated sodium ion channel whose molecular conformational dynamics play a critical functional role in propagating action potentials in mammalian neuronal membranes.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

NASA Astrophysics Data System (ADS)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-08-01

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes.

PubMed

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-08-28

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

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

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kineticsmore » resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.« less

Understanding the phase formation kinetics of nano-crystalline kesterite deposited on mesoscopic scaffolds via in situ multi-wavelength Raman-monitored annealing.

PubMed

Wang, Zhuoran; Elouatik, Samir; Demopoulos, George P

2016-10-26

Kesterite, a highly promising photo-absorbing crystalline form of Cu 2 ZnSnS 4 (CZTS), has been prepared via various routes. However, the lack of in-depth understanding of the dynamic phase formation process of kesterite leads to difficulties in optimizing its annealing conditions, hence its light harvesting performance. In this paper, in situ Raman monitored-annealing is applied to study the phase formation kinetics of nano-crystalline kesterite from a precursor deposited on a TiO 2 mesoscopic scaffold. By performing in situ Raman annealing under different experimental conditions and wavelengths, several facts have been discovered: kesterite crystallization starts at as low as 170 °C, but after short time annealing at 300 °C followed by cooling, the initially formed kesterite is found to decompose. Annealing at 400 °C or higher is proven to be sufficient for stabilizing the kesterite phase. Annealing at the higher temperature of 500 °C is necessary though to promote a complete reaction and thus eliminate the parasitic copper tin sulfide (CTS) impurity intermediates identified at lower annealing temperatures. More importantly, the real-time temperature dependence of Raman peak intensity enhancement, shift and broadening for CZTS is established experimentally at 500 °C for 1 h, providing a valuable reference in future CZTS research. This work demonstrates the significance of using in situ Raman spectroscopy in elucidating the kesterite phase formation kinetics, a critical step towards full crystal phase control - a prerequisite for developing fully functional CZTS-based optoelectronic devices.

Neocortical dynamics at multiple scales: EEG standing waves, statistical mechanics, and physical analogs.

PubMed

Ingber, Lester; Nunez, Paul L

2011-02-01

The dynamic behavior of scalp potentials (EEG) is apparently due to some combination of global and local processes with important top-down and bottom-up interactions across spatial scales. In treating global mechanisms, we stress the importance of myelinated axon propagation delays and periodic boundary conditions in the cortical-white matter system, which is topologically close to a spherical shell. By contrast, the proposed local mechanisms are multiscale interactions between cortical columns via short-ranged non-myelinated fibers. A mechanical model consisting of a stretched string with attached nonlinear springs demonstrates the general idea. The string produces standing waves analogous to large-scale coherent EEG observed in some brain states. The attached springs are analogous to the smaller (mesoscopic) scale columnar dynamics. Generally, we expect string displacement and EEG at all scales to result from both global and local phenomena. A statistical mechanics of neocortical interactions (SMNI) calculates oscillatory behavior consistent with typical EEG, within columns, between neighboring columns via short-ranged non-myelinated fibers, across cortical regions via myelinated fibers, and also derives a string equation consistent with the global EEG model. Copyright © 2010 Elsevier Inc. All rights reserved.

Mechanism of anisotropic surface self-diffusivity at the prismatic ice-vapor interface.

PubMed

Gladich, Ivan; Oswald, Amrei; Bowens, Natalie; Naatz, Sam; Rowe, Penny; Roeselova, Martina; Neshyba, Steven

2015-09-21

Predictive theoretical models for mesoscopic roughening of ice require improved understanding of attachment kinetics occurring at the ice-vapor interface. Here, we use classical molecular dynamics to explore the generality and mechanics of a transition from anisotropic to isotropic self-diffusivity on exposed prismatic surfaces. We find that self-diffusion parallel to the crystallographic a-axis is favored over the c-axis at sub-melt temperatures below about -35 °C, for three different representations of the water-water intermolecular potential. In the low-temperature anisotropic regime, diffusion results from interstitial admolecules encountering entropically distinct barriers to diffusion in the two in-plane directions. At higher temperatures, isotropic self-diffusion occurring deeper within the quasi-liquid layer becomes the dominant mechanism, owing to its larger energy of activation.

Torque-mixing magnetic resonance spectroscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Losby, Joseph; Fani Sani, Fatemeh; Grandmont, Dylan T.; Diao, Zhu; Belov, Miro; Burgess, Jacob A.; Compton, Shawn R.; Hiebert, Wayne K.; Vick, Doug; Mohammad, Kaveh; Salimi, Elham; Bridges, Gregory E.; Thomson, Douglas J.; Freeman, Mark R.

2016-10-01

An optomechanical platform for magnetic resonance spectroscopy will be presented. The method relies on frequency mixing of orthogonal RF fields to yield a torque amplitude (arising from the transverse component of a precessing dipole moment, in analogy to magnetic resonance detection by electromagnetic induction) on a miniaturized resonant mechanical torsion sensor. In contrast to induction, the method is fully broadband and allows for simultaneous observation of the equilibrium net magnetic moment alongside the associated magnetization dynamics. To illustrate the method, comprehensive electron spin resonance spectra of a mesoscopic, single-crystal YIG disk at room temperature will be presented, along with situations where torque spectroscopy can offer complimentary information to existing magnetic resonance detection techniques. The authors are very grateful for support from NSERC, CRC, AITF, and NINT. Reference: Science 350, 798 (2015).

Multifrequency acoustics as a probe of mesoscopic blood coagulation dynamics

NASA Astrophysics Data System (ADS)

Ganesan, Adarsh; Rajendran, Gokulnath; Ercole, Ari; Seshia, Ashwin

2016-08-01

Coagulation is a complex enzymatic polymerisation cascade. Disordered coagulation is common in medicine and may be life-threatening yet clinical assays are typically bulky and/or provide an incomplete picture of clot mechanical evolution. We present the adaptation of an in-plane acoustic wave device: quartz crystal microbalance with dissipation at multiple harmonics to determine the time-evolution of mesoscale mechanical properties of clot formation in vitro. This approach is sensitive to changes in surface and bulk clot structure in various models of induced coagulopathy. Furthermore, we are able to show that clot formation at surfaces has different kinetics and mechanical strength to that in the bulk, which may have implications for the design of bioprosthetic materials. The "Multifrequency acoustics" approach thus enables unique capability to portray biological processes concerning blood coagulation.

Self-organization and feedback effects in the shock compressed media

NASA Astrophysics Data System (ADS)

Khantuleva, Tatyana

2005-07-01

New theoretical approach to the transport in condensed matter far from equilibrium combines methods of statistical mechanics and cybernetic physics in order to construct closed mathematical model of a system with self-organization and self-regulation. Mesoscopic effects are considered as a result of the structure formation and the feedback effects in an open system under dynamic loading. Nonequilibrium state equations had been involved to incorporate the velocity dispersion. Integrodifferential balance equations describe both wave and dissipative transport properties. Boundary conditions determine the internal scale spectra. The model is completed by the feedback that introduces the structure evolution basing the methods of cybernetic physics. The obtained results open a wide prospective for the control methods in applications to new technologies, intellectual systems and prediction of catastrophic phenomena.

Rapid crystallization of externally produced ions in a Penning trap

NASA Astrophysics Data System (ADS)

Murböck, T.; Schmidt, S.; Birkl, G.; Nörtershäuser, W.; Thompson, R. C.; Vogel, M.

2016-10-01

We have studied the cooling dynamics, formation process, and geometric structure of mesoscopic crystals of externally produced magnesium ions in a Penning trap. We present a cooling model and measurements for a combination of buffer gas cooling and laser cooling which has been found to reduce the ion kinetic energy by eight orders of magnitude from several hundreds of eV to μ eV and below within seconds. With ion numbers of the order of 1 ×103 to 1 ×105 , such cooling leads to the formation of ion Coulomb crystals which display a characteristic shell structure in agreement with the theory of non-neutral plasmas. We show the production and characterization of two-species ion crystals as a means of sympathetic cooling of ions lacking a suitable laser-cooling transition.

Modeling slip system strength evolution in Ti-7Al informed by in-situ grain stress measurements

DOE PAGES

Pagan, Darren C.; Shade, Paul A; Barton, Nathan R.; ...

2017-02-17

Far-field high-energy X-ray diffraction microscopy is used to asses the evolution of slip system strengths in hexagonal close-packed (HCP) Ti-7A1 during tensile deformation in-situ. The following HCP slip system families are considered: basal < a >, prismatic < a >, pyramidal < a >, and first-order pyramidal < c + a >. A 1 mm length of the specimen's gauge section, marked with fiducials and comprised of an aggregate of over 500 grains, is tracked during continuous deformation. The response of each slip system family is quantified using 'slip system strength curves' that are calculated from the average stress tensorsmore » of each grain over the applied deformation history. These curves, which plot the average resolved shear stress for each slip system family versus macroscopic strain, represent a mesoscopic characterization of the aggregate response. A short time-scale transient softening is observed in the basal < a >, prismatic < a >, and pyramidal < a > slip systems, while a long time-scale transient hardening is observed in the pyramidal < c + a > slip systems. These results are used to develop a slip system strength model as part of an elasto-viscoplastic constitutive model for the single crystal behavior. A suite of finite element simulations is performed on a virtual polycrystal to demonstrate the relative effects of the different parameters in the slip system strength model. Finally, the model is shown to accurately capture the macroscopic stress-strain response using parameters that are chosen to capture the mesoscopic slip system responses.« less

Computing the full spectrum of large sparse palindromic quadratic eigenvalue problems arising from surface Green's function calculations

NASA Astrophysics Data System (ADS)

Huang, Tsung-Ming; Lin, Wen-Wei; Tian, Heng; Chen, Guan-Hua

2018-03-01

Full spectrum of a large sparse ⊤-palindromic quadratic eigenvalue problem (⊤-PQEP) is considered arguably for the first time in this article. Such a problem is posed by calculation of surface Green's functions (SGFs) of mesoscopic transistors with a tremendous non-periodic cross-section. For this problem, general purpose eigensolvers are not efficient, nor is advisable to resort to the decimation method etc. to obtain the Wiener-Hopf factorization. After reviewing some rigorous understanding of SGF calculation from the perspective of ⊤-PQEP and nonlinear matrix equation, we present our new approach to this problem. In a nutshell, the unit disk where the spectrum of interest lies is broken down adaptively into pieces small enough that they each can be locally tackled by the generalized ⊤-skew-Hamiltonian implicitly restarted shift-and-invert Arnoldi (G⊤SHIRA) algorithm with suitable shifts and other parameters, and the eigenvalues missed by this divide-and-conquer strategy can be recovered thanks to the accurate estimation provided by our newly developed scheme. Notably the novel non-equivalence deflation is proposed to avoid as much as possible duplication of nearby known eigenvalues when a new shift of G⊤SHIRA is determined. We demonstrate our new approach by calculating the SGF of a realistic nanowire whose unit cell is described by a matrix of size 4000 × 4000 at the density functional tight binding level, corresponding to a 8 × 8nm2 cross-section. We believe that quantum transport simulation of realistic nano-devices in the mesoscopic regime will greatly benefit from this work.

Inflow/outflow boundary conditions for particle-based blood flow simulations: Application to arterial bifurcations and trees

DOE PAGES

Lykov, Kirill; Li, Xuejin; Lei, Huan; ...

2015-08-28

When blood flows through a bifurcation, red blood cells (RBCs) travel into side branches at different hematocrit levels, and it is even possible that all RBCs enter into one branch only, leading to a complete separation of plasma and R- BCs. To quantify this phenomenon via particle-based mesoscopic simulations, we developed a general framework for open boundary conditions in multiphase flows that is effective even for high hematocrit levels. The inflow at the inlet is duplicated from a fully developed flow generated in a pilot simulation with periodic boundary conditions. The outflow is controlled by adaptive forces to maintain themore » flow rate and velocity gradient at fixed values, while the particles leaving the arteriole at the outlet are removed from the system. Upon valida- tion of this approach, we performed systematic 3D simulations to study plasma skimming in arterioles of diameters 20 to 32 microns. For a flow rate ratio 6:1 at the branches, we observed the \\all-or-nothing" phenomenon with plasma only entering the low flow rate branch. We then simulated blood-plasma separation in arteriolar bifurcations with different bifurcation angles and same diameter of the daughter branches. Our simulations predict a significant increase in RBC flux through the main daughter branch as the bifurcation angle is increased. Lastly, we demonstrated the new methodology for simulating blood flow in ves- sels with multiple inlets and outlets, constructed using an angiogenesis model.« less

Inflow/outflow boundary conditions for particle-based blood flow simulations: Application to arterial bifurcations and trees

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

Lykov, Kirill; Li, Xuejin; Lei, Huan

When blood flows through a bifurcation, red blood cells (RBCs) travel into side branches at different hematocrit levels, and it is even possible that all RBCs enter into one branch only, leading to a complete separation of plasma and R- BCs. To quantify this phenomenon via particle-based mesoscopic simulations, we developed a general framework for open boundary conditions in multiphase flows that is effective even for high hematocrit levels. The inflow at the inlet is duplicated from a fully developed flow generated in a pilot simulation with periodic boundary conditions. The outflow is controlled by adaptive forces to maintain themore » flow rate and velocity gradient at fixed values, while the particles leaving the arteriole at the outlet are removed from the system. Upon valida- tion of this approach, we performed systematic 3D simulations to study plasma skimming in arterioles of diameters 20 to 32 microns. For a flow rate ratio 6:1 at the branches, we observed the \\all-or-nothing" phenomenon with plasma only entering the low flow rate branch. We then simulated blood-plasma separation in arteriolar bifurcations with different bifurcation angles and same diameter of the daughter branches. Our simulations predict a significant increase in RBC flux through the main daughter branch as the bifurcation angle is increased. Lastly, we demonstrated the new methodology for simulating blood flow in ves- sels with multiple inlets and outlets, constructed using an angiogenesis model.« less

Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees.

PubMed

Lykov, Kirill; Li, Xuejin; Lei, Huan; Pivkin, Igor V; Karniadakis, George Em

2015-08-01

When blood flows through a bifurcation, red blood cells (RBCs) travel into side branches at different hematocrit levels, and it is even possible that all RBCs enter into one branch only, leading to a complete separation of plasma and RBCs. To quantify this phenomenon via particle-based mesoscopic simulations, we developed a general framework for open boundary conditions in multiphase flows that is effective even for high hematocrit levels. The inflow at the inlet is duplicated from a fully developed flow generated in a pilot simulation with periodic boundary conditions. The outflow is controlled by adaptive forces to maintain the flow rate and velocity gradient at fixed values, while the particles leaving the arteriole at the outlet are removed from the system. Upon validation of this approach, we performed systematic 3D simulations to study plasma skimming in arterioles of diameters 20 to 32 microns. For a flow rate ratio 6:1 at the branches, we observed the "all-or-nothing" phenomenon with plasma only entering the low flow rate branch. We then simulated blood-plasma separation in arteriolar bifurcations with different bifurcation angles and same diameter of the daughter branches. Our simulations predict a significant increase in RBC flux through the main daughter branch as the bifurcation angle is increased. Finally, we demonstrated the effectiveness of the new methodology in simulations of blood flow in vessels with multiple inlets and outlets, constructed using an angiogenesis model.

Observable consequences of zero-point energy

NASA Astrophysics Data System (ADS)

Sen, Siddhartha; Gupta, Kumar S.

2017-12-01

Spectral line widths, the Lamb shift and the Casimir effect are generally accepted to be observable consequences of the zero-point electromagnetic (ZPEM) fields. A new class of observable consequences of ZPEM field at the mesoscopic scale were recently proposed and observed. Here, we extend this class of observable effects and predict that mesoscopic water layers should have a high value for its solid-liquid phase transition temperature, as illustrated by water inside a single-walled carbon nanotube (CNT). For this case, our analysis predicts that the phase transition temperature scales inversely with the square of the effective radius available for the water flow within the CNT.

Equilibrium finite-frequency noise of an interacting mesoscopic capacitor studied in time-dependent density functional theory

NASA Astrophysics Data System (ADS)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-03-01

We calculate the frequency-dependent equilibrium noise of a mesoscopic capacitor in time-dependent density functional theory (TDDFT). The capacitor is modeled as a single-level quantum dot with on-site Coulomb interaction and tunnel coupling to a nearby reservoir. The noise spectra are derived from linear-response conductances via the fluctuation-dissipation theorem. Thereby, we analyze the performance of a recently derived exchange-correlation potential with time-nonlocal density dependence in the finite-frequency linear-response regime. We compare our TDDFT noise spectra with real-time perturbation theory and find excellent agreement for noise frequencies below the reservoir temperature.

Thermodynamics of the mesoscopic thermoelectric heat engine beyond the linear-response regime.

PubMed

Yamamoto, Kaoru; Hatano, Naomichi

2015-10-01

Mesoscopic thermoelectric heat engine is much anticipated as a device that allows us to utilize with high efficiency wasted heat inaccessible by conventional heat engines. However, the derivation of the heat current in this engine seems to be either not general or described too briefly, even inappropriately in some cases. In this paper, we give a clear-cut derivation of the heat current of the engine with suitable assumptions beyond the linear-response regime. It resolves the confusion in the definition of the heat current in the linear-response regime. After verifying that we can construct the same formalism as that of the cyclic engine, we find the following two interesting results within the Landauer-Büttiker formalism: the efficiency of the mesoscopic thermoelectric engine reaches the Carnot efficiency if and only if the transmission probability is finite at a specific energy and zero otherwise; the unitarity of the transmission probability guarantees the second law of thermodynamics, invalidating Benenti et al.'s argument in the linear-response regime that one could obtain a finite power with the Carnot efficiency under a broken time-reversal symmetry [Phys. Rev. Lett. 106, 230602 (2011)]. These results demonstrate how quantum mechanics constrains thermodynamics.