Nonlinear Dynamics and Pattern Formation on the Growth Interfaces of Protein Crystals
No abstract available
Vekilov, P. G.↗
SEARCH · Search NASA
Results for “Nonlinear Dynamics and Pattern Formation”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Surface Engineering by Simultaneous Action of Multiple External Fields (Final Technical Report)
This research project aims at enabling surface engineering strategies based on the fundamental understanding and predictive modeling of the surface morphological response of solid materials subjected to the combined action of multiple external forces. Surface morphological response to mismatch strain in strained-layer heterostructures also is analyzed. Our research focuses on the surface morphological evolution and stability of electrically conducting (metallic, such as Cu) and semiconducting (such as Si) solids under the simultaneous application of mechanical stresses, electric fields, and temperature gradients. We emphasize on identifying the conditions under which the multiply driven surface morphology is stable and on exploring the complexity of the corresponding various morphologically stable surface patterns. We also emphasize on the driven evolution of nanoscale features aiming at stabilizing and controlling nanoscale patterns on surfaces by their manipulation through simultaneously applied multiple external forces. Specifically, we address systematically the morphological response to the combined action of multiple external forces of bulk solid surfaces, surfaces of thin films grown epitaxially on thick or thin substrates, as well as nanoscale surface features such as coherently strained islands grown epitaxially on substrate surfaces. The research is based on a modeling approach that combines theoretical analyses of surface morphological stability with self-consistent dynamical simulations of surface evolution based on properly parameterized continuum and multiscale surface transport models.
36 MATERIALS SCIENCE↗
Black and gray box learning of amplitude equations: Application to phase field systems
Here, we present a data-driven approach to learning surrogate models for amplitude equations and illustrate its application to interfacial dynamics of phase field systems. In particular, we demonstrate learning effective partial differential equations describing the evolution of phase field interfaces from full phase field data. We illustrate this on a model phase field system, where analytical approximate equations for the dynamics of the phase field interface (a higher-order eikonal equation and its approximation, the Kardar-Parisi-Zhang equation) are known. For this system, we discuss data-driven approaches for the identification of equations that accurately describe the front interface dynamics. When the analytical approximate models mentioned above become inaccurate, as we move beyond the region of validity of the underlying assumptions, the data-driven equations outperform them. In these regimes, going beyond black box identification, we explore different approaches to learning data-driven corrections to the analytically approximate models, leading to effective gray box partial differential equations.
42 ENGINEERING↗
Exploring regular and turbulent flow states in active nematic channel flow via Exact Coherent Structures and their invariant manifolds
This work is a unified study of stable and unstable steady states of 2D active nematic channel flow using the framework of Exact Coherent Structures (ECS). ECS are stationary, periodic, quasiperiodic, or traveling wave solutions of the governing equations that, together with their invariant manifolds, organize the dynamics of nonlinear continuum systems. We extend our earlier work on ECS in the preturbulent regime by performing a comprehensive study of stable and unstable ECS for a wide range of activity values spanning the preturbulent and turbulent regimes. In the weakly turbulent regime, we compute more than 200 unstable ECS that co-exist at a single set of parameters, and uncover the role of symmetries in organizing the phase space geometry. We provide conclusive numerical evidence that in the preturbulent regime, generic trajectories shadow a series of unstable ECS before settling onto an attractor. Lastly, our studies hint at shadowing of quasiperiodic type ECS in the turbulent regime.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Dynamics of dendritic pattern formation
This paper is a brief review of recent and ongoing developments in the theory of dendritic pattern formation. A marginal stability hypothesis has achieved some success in predicting dendritic growth rates, but a fully nonlinear dynamic theory of the dendritic growth mechanism has yet to be developed. A possible clue for the construction of such a theory is the existence of a class of one-dimensional models in which a pattern is found to spread into an unstable region by propagating at the slowest stable speed. This mathematical realization of the marginal stability mechanism has led to the development of a boundary layer model which describes localized dynamics of fully two- or three-dimensional solidification fronts and which retains some of the mathematical features of the propagating systems. Preliminary results of numerical calculations using the boundary layer model indicate that it is capable of probing fully nonlinear features of dendritic pattern formation.
Langer, J. S.↗
Selection principles and pattern formation in fluid mechanics and nonlinear shell theory
Wave theories of vortex breakdown were studied. A setting which involved dynamical systems and bifurcations of homoclinic and heteroclinic orbits in infinite-dimensional spaces was investigated. The determination of axisymmetric inviscid flows bifurcating from the primary flow lead to the study of a system of ordinary differential equations. The problem of rotating plane Couette flow was solved by means of the structure parameter approach.
Sather, Duane P.↗
Beyond Ohm's law: Bernoulli effect and streaming in electron hydrodynamics
Recent observations of nonlocal transport in ultraclean two-dimensional materials raised the tantalizing possibility of accessing hydrodynamic correlated transport of a many-electron state. However, it has been pointed out that nonlocal transport can also arise from impurity scattering rather than interaction. At the crux of the ambiguity is the focus on linear effects, i.e., Ohm's law, which cannot easily differentiate among different modes of transport. Furthermore we propose experiments that can reveal rich hydrodynamic features in the system by tapping into the nonlinearity of the Navier-Stokes equation. Three experiments we propose will each manifest a unique phenomenon that is well known in classical fluids: the Bernoulli effect, Eckart streaming, and Rayleigh streaming. Analysis of known parameters confirms that the proposed experiments are feasible and the hydrodynamic signatures are within reach of graphene-based devices. Experimental realization of any one of the three phenomena will provide a stepping stone to formulating and exploring the notions of nonlinear electron fluid dynamics with an eye to celebrated examples from classical nonlaminar flows, e.g., pattern formation and turbulence.
2-dimensional systems↗
In Situ Observation of Growth Dynamics in DECLIC Directional Solidification Insert Onboard ISS: DSI-R Flight Campaign
The study of solidification microstructure formation is of utmost importance for materials design and processing, as solid-liquid interface patterns largely govern mechanical and physical properties. Pattern selection occurs under dynamic conditions of growth in which the initial morphological instability evolves nonlinearly and undergoes a reorganization process. The dynamic and nonlinear nature of this instability renders in situ observation of the interface an invaluable tool to gain knowledge on the time-evolution of the interface pattern. Transparent organic analogs, which solidify like metallic alloys, allow direct visualization of interface dynamics. Extensive ground-based studies of both metallic and organic bulk samples have established the presence of significant convection during solidification processes that alters the formation of interfacial microstructures. A reduced-gravity environment is therefore mandatory for fluid flow elimination in bulk samples. In the framework of the CNES project MISOL3D (MIcrostrutures de SOLidification 3D) and the NASA projects DSIP (Dynamical Selection of 3D Interface Patterns), SPADES (SPAtiotemporal Evolution of three-dimensional DEndritic array Structures) and CAMUS (ComputAtional Studies of MicrostrUcture Formation During Alloy Solidification in Microgravity), we participated in the development of the Directional Solidification Insert (DSI) of the DEvice for the study of Critical Liquids and Crystallization (DECLIC). The DECLIC-DSI is dedicated to in situ and real-time characterization of solid-liquid interface patterns during directional solidification of transparent alloys in diffusive transport regime. Between April 2010 and March 2011, the first ISS campaign (DSI) explored the entire range of microstructures resulting in unprecedented observations. A second campaign (DSI-R), performed between October 2017 and December 2018, in which the insert contained an alloy of higher solute concentration, allowed to complete the benchmark database. The increase of solute concentration resulted in well-developed dendritic patterns at lower velocities (lower interface curvature and larger tip radius). The microstructure resulting from dendritic growth is dominant in metallurgy so that it is fundamental to understand the mechanisms of its formation. The main aims of this experimental campaign are to understand: the mechanisms of the cell to dendrite transition, the fundamental mechanisms of sidebranching formation, the dependence of dendrite tip shapes on growth conditions, the interaction of primary array and secondary sidebranches, and the influence of subgrain boundaries on the spatiotemporal organization of the array structure. Preparation, analysis and interpretation of the experiments performed onboard ISS are considerably enhanced by experiments performed on ground using thin-samples (Pr. Trivedi’s group) and phase-field simulations of microstructure formation in a diffuse growth regime (Pr. Karma’s group). In this summary, we will present an initial assessment of the results obtained during the DSI-R campaign. Nomenclature Vp: pulling velocity G: thermal gradient L: solidified length rtip: tip curvature radius Acronyms/Abbreviations CADMOS: Centre d'Aide au Développement des activités en Micro-pesanteur et des Opérations Spatiales CNES: Centre National d’Études Spatiales DECLIC: Device for the study of Critical LIquids and Crystallization DSI: Directional Solidification Insert DSI-R: Directional Solidification Insert - Refurbish ISS: International Space Station NASA: National Aeronautics and Space Administration PF: phase-field SCN: Succinonitrile 3D: three-dimensional
Mota, F.L.↗
Emergence of complex-regular eutectic patterns in Al–Ge: Observations from correlative nano-imaging
Eutectic solidification exemplifies nonequilibrium pattern formation, making it a well-studied moving boundary problem. Yet the mechanisms behind the formation of complex-regular microstructures – particularly in highly anisotropic systems with a significant volume fraction of a faceted phase – remain poorly understood. Our understanding of such systems is made complicated by the nonlinear interface kinetics and unique growth dynamics characteristic of faceted phases. To address these challenges, we investigate a model Al–Ge eutectic system, where the faceted Ge phase constitutes a substantial volume fraction (~0.35) and where the two solid phases arrange into so-called “fishbone” or “feather” complex-regular patterns. Using synchrotron-based x-ray nano-imaging and nanotomography with high spatial resolution (22 nm per pixel), we capture in real-time the evolution of the solid–liquid interfaces and the resulting three-dimensional microstructures in this faceted/non-faceted eutectic system. By integrating these observations with electron backscattered diffraction, we elucidate the crystallographic biases on the solidification process and the mechanisms driving the formation of such complex-regular microstructures. These findings inform a new growth model for irregular eutectics in (near-)symmetrical phase diagrams, offering insight on advanced microstructural design and processing strategies. More broadly, we demonstrate how interfacial curvature is generated in irregular eutectic alloys and how it depends on the volume fraction of the faceted phase.
36 MATERIALS SCIENCE↗
Statistical mechanics of neocortical interactions - Dynamics of synaptic modification
A recent study has demonstrated that several scales of neocortical interactions can be consistently analyzed with the use of methods of modern nonlinear nonequilibrium statistical mechanics. The formation, stability, and interaction of spatial-temporal patterns of columnar firings are explicitly calculated, to test hypothesized mechanisms relating to information processing. In this context, most probable patterns of columnar firings are associated with chemical and electrical synaptic modifications. It is stressed that synaptic modifications and shifts in most-probable firing patterns are highly nonlinear and interactive sets of phenomena. A detailed scenario of information processing is calculated of columnar coding of external stimuli, short-term storage via hysteresis, and long-term storage via synaptic modification.
Ingber, L.↗
Dynamical Signatures of Living Systems
One of the main challenges in modeling living systems is to distinguish a random walk of physical origin (for instance, Brownian motions) from those of biological origin and that will constitute the starting point of the proposed approach. As conjectured, the biological random walk must be nonlinear. Indeed, any stochastic Markov process can be described by linear Fokker-Planck equation (or its discretized version), only that type of process has been observed in the inanimate world. However, all such processes always converge to a stable (ergodic or periodic) state, i.e., to the states of a lower complexity and high entropy. At the same time, the evolution of living systems directed toward a higher level of complexity if complexity is associated with a number of structural variations. The simplest way to mimic such a tendency is to incorporate a nonlinearity into the random walk; then the probability evolution will attain the features of diffusion equation: the formation and dissipation of shock waves initiated by small shallow wave disturbances. As a result, the evolution never "dies:" it produces new different configurations which are accompanied by an increase or decrease of entropy (the decrease takes place during formation of shock waves, the increase-during their dissipation). In other words, the evolution can be directed "against the second law of thermodynamics" by forming patterns outside of equilibrium in the probability space. Due to that, a specie is not locked up in a certain pattern of behavior: it still can perform a variety of motions, and only the statistics of these motions is constrained by this pattern. It should be emphasized that such a "twist" is based upon the concept of reflection, i.e., the existence of the self-image (adopted from psychology). The model consists of a generator of stochastic processes which represents the motor dynamics in the form of nonlinear random walks, and a simulator of the nonlinear version of the diffusion equation which represents the mental dynamics. It has been demonstrated that coupled mental-motor dynamics can simulate emerging self-organization, prey-predator games, collaboration and competition, "collective brain," etc.
Zak, M.↗
Pattern formation in a coupled membrane-bulk reaction-diffusion model for intracellular polarization and oscillations
Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity molecules. Here we study the distribution of the polarity protein Cdc42 in a mass-conserved membrane-bulk model, and explore the effects of diffusion and spatial dimensionality on spatio-temporal pattern formation. We first analyze a one-dimensional (1-D) model for Cdc42 oscillations in fission yeast, consisting of two diffusion equations in the bulk domain coupled to nonlinear ODEs for binding kinetics at each end of the cell. In 1-D, our analysis reveals the existence of symmetric and asymmetric steady states, as well as anti-phase relaxation oscillations typical of slow-fast systems. We then extend our analysis to a two-dimensional (2-D) model with circular bulk geometry, for which species can either diffuse inside the cell or become bound to the membrane and undergo a nonlinear reaction-diffusion process. We also consider a nonlocal system of PDEs approximating the dynamics of the 2-D membrane-bulk model in the limit of fast bulk diffusion. In all three model variants we find that mass conservation selects perturbations of spatial modes that simply redistribute mass. In 1-D, only anti-phase oscillations between the two ends of the cell can occur, and in-phase oscillations are excluded. In higher dimensions, no radially symmetric oscillations are observed. Instead, the only instabilities are symmetry-breaking, either corresponding to stationary Turing instabilities, leading to the formation of stationary patterns, or to oscillatory Turing instabilities, leading to traveling and standing waves. Codimension-two Bogdanov—Takens bifurcations occur when the two distinct instabilities coincide, causing traveling waves to slow down and to eventually become stationary patterns. Our work clarifies the effect of geometry and dimensionality on behaviors observed in ma.ss-conserved cell polarity models.
97 MATHEMATICS AND COMPUTING↗
The Effect of Surface Topography on the Nonlinear Dynamics of Rossby Waves
Boussinesq convection in rotating systems attracts a sustained attention of the fluid dynamics community, because it has intricate non-linear dynamics (Cross & Hohenberg 1993) and plays an important role in geophysical and astrophysical applications, such as the motion of the liquid outer core of Earth, the Red Spot in Jupiter, the giant cells in the Sun etc. (Alridge et al. 1990). A fundamental distinction between the real geo- and astrophysical problems and the idealized laboratory studies is that natural systems are inhomogeneous (Alridge et al. 1990). Heterogeneities modulate the flow and influence significantly the dynamics of convective patterns (Alridge et al. 1990; Hide 1971). The effect of modulations on pattern formation and transition to turbulence in Boussinesq convection is far from being completely understood (Cross & Hohenberg 1993; Aranson & Kramer 2002). It is generally accepted that in the liquid outer core of the Earth the transport of the angular momentum and internal heat occurs via thermal Rossby waves (Zhang et al. 2001; Kuang & Bloxham 1999). These waves been visualized in laboratory experiments in rotating liquid-filled spheres and concentric spherical shells (Zhang et al. 2001; Kuang & Bloxham 1999). The basic dynamical features of Rossby waves have been reproduced in a cylindrical annulus, a system much simpler than the spherical ones (Busse & Or 1986; Or & Busse 1987). For convection in a cylindrical annulus, the fluid motion is two-dimensional, and gravity is replaced by a centrifugal force, (Busse & Or 1986; Or & Busse 1987). Hide (1971) has suggested that the momentum and heat transport in the core might be influenced significantly by so-called bumps, which are heterogeneities on the mantle-core boundary. To model the effect of surface topography on the transport of momentum and energy in the liquid outer core of the Earth, Bell & Soward (1996), Herrmann & Busse (1998) and Westerburg & Busse (2001) have studied the nonlinear dynamics of thermal Rossby waves in a cylindrical annulus with azimuthally modulated height.
Abarzhi, S. I.↗
Observational and numerical studies of extreme frontal scale contraction
The general objective of this effort is to increase understanding of how frontal scale contraction processes may create and sustain intense mesoscale precipitation along intensifying cold fronts. The five-part project (an expansion of the originally proposed two-part project) employed conventional meteorological data, special mesoscale data, remote sensing measurements, and various numerical models. First an idealized hydrostatic modeling study of the scale contraction effects of differential cloud cover on low-level frontal structure and dynamics was completed and published in a peer-reviewed journal. The second objective was to complete and publish the results from a three dimensional numerical model simulation of a cold front in which differential sensible heating related to cloud coverage patterns was apparently crucial in the formation of a severe frontal squall line. The third objective was to use a nonhydrostatic model to examine the nonlinear interactions between the transverse circulation arising from inhomogeneous cloud cover, the adiabatic frontal circulation related to semi-geostrophic forcing, and diabatic effects related to precipitation processes, in the development of a density current-like microstructure at the leading edge of cold fronts. Although the development of a frontal model that could be used to initialize such a primitive equation model was begun, we decided to focus our efforts instead on a project that could be successfully completed in this short time, due to the lack of prospects for continued NASA funding beyond this first year (our proposal was not accepted for future funding). Thus, a fourth task was added, which was to use the nonhydrostatic model to test tentative hypotheses developed from the most detailed observations ever obtained on a density current (primarily sodar and wind profiler data). These simulations were successfully completed, the findings were reported at a scientific conference, and the results have recently been submitted to a peer-reviewed journal. The fifth objective was to complete the analysis of data collected during the Cooperative Oklahoma Profiler Studies (COPS-91) field project, which was supported by NASA. The analysis of the mesoscale surface and sounding data, Doppler radar imagery, and other remote sensing data from multi frequency wind profiler, microwave radiometer, and the Radio Acoustic Sounding System has been completed. This study is a unique investigation of processes that caused the contraction of a cold front to a microscale zone exhibiting an undular bore-like structure. Results were reported at a scientific conference and are being prepared for publication. In summary, considerable progress has been achieved under NASA funding in furthering our understanding of frontal scale contraction and density current - gravity wave interaction processes, and in utilizing models and remotely sensed data in such studies.
Koch, Steven E.↗
An evolving MHD vortex street model for quasi-periodic solar wind fluctuations
Magnetohydrodynamic (MHD) simulation are used to provide a dynamical basis for the 'vortex street' model of the quasi-periodic meridional flow observed by Voyager 2 in the outer heliosphere. Various observations suggest the existence near the current sheet at solar minimum, of a vorticity distribution of two opposite shear layers with an antisymmetric staggered velocity pattern due to structured high-speed wind surrounding low-speed equatorial flow. It is shown that this flow pattern leads to the formation of a highly stable vortex street through the nonlinear interaction of the two shear layers. Spatial profiles of various simulated parameters (velocity, density, meridional flow angle and the location of magnetic sector boundaries) and their relative locations in the quasi-steady vortex street are generally in good agreement with the observations.
Siregar, Edouard↗
Solidification Furnace for In Situ Observation of Bulk Transparent Systems and Image Analysis Methods
This paper aims to describe the experimental framework of the Directional Solidification Insert (DSI), installed onboard the International Space Station (ISS), dedicated to the in situ and real-time characterization of the dynamic selection of the solid-liquid interface morphology in bulk samples of transparent materials under diffusive growth conditions. The in situ observation of the solid-liquid interface is an invaluable tool for gaining knowledge on the time-evolution of the interface pattern because the initial morphological instability evolves nonlinearly and undergoes a reorganization process. The result of each experiment, characterized by the sample concentration, a thermal gradient and a pulling rate, is a large number of images. Interpretation of these images necessitates a robust identification of each cell/dendrite position and size during the entire solidification. Several image analysis methods have been developed to achieve this goal reliably despite varying contrast and noise levels, and are described in details. Typical solidification experiments are presented and the dynamics of the pattern formation are analyzed to illustrate the application of the image analysis methods.
Programming languages↗
Possible fluid dynamical interpretation of some reported features in the Jovian atmosphere
A fluid dynamical interpretation is presented of the two major types of disturbance found in the southern hemisphere of Jupiter by the Voyager 1 imaging data. The observed features always occur together, and consist of a compact elliptically shaped formation having an anticyclonic flow which is poleward of a pair of more elongated cyclonic structures, as in the Great Red Spot and the white ovals. It is noted that the anticyclonic features at 41 deg S may be described by the cnoidal wave solutions to the appropriate nonlinear evolution equation, and that flow patterns derived in the vicinity of the Great Red Spot and white ovals are strikingly similar to those obtained for the flow around a solitary wave of the type than can exist in a zonal flow such as that found in the Jupiter atmosphere. Results of computations in terms of solitary wave theory of flow fields in the atmospheric structure and zonal velocity profiles determined from Voyager infrared spectroscopy and radiometry data are then presented which show that the pattern must be a singular solitary wave mode, the east-west structure of which is best described by the Korteweg-de-Vries equation
Maxworthy, T.↗
Newton-Euler Dynamic Equations of Motion for a Multi-body Spacecraft
The Magnetospheric MultiScale (MMS) mission employs a formation of spinning spacecraft with several flexible appendages and thruster-based control. To understand the complex dynamic interaction of thruster actuation, appendage motion, and spin dynamics, each spacecraft is modeled as a tree of rigid bodies connected by spherical or gimballed joints. The method presented facilitates assembling by inspection the exact, nonlinear dynamic equations of motion for a multibody spacecraft suitable for solution by numerical integration. The building block equations are derived by applying Newton's and Euler's equations of motion to an "element" consisting of two bodies and one joint (spherical and gimballed joints are considered separately). Patterns in the "mass" and L'force" matrices guide assembly by inspection of a general N-body tree-topology system. Straightforward linear algebra operations are employed to eliminate extraneous constraint equations, resulting in a minimum-dimension system of equations to solve. This method thus combines a straightforward, easily-extendable, easily-mechanized formulation with an efficient computer implementation.
Stoneking, Eric↗