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44 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Large Deviations for Gaussian Diffusions with Delay

Dynamical systems driven by nonlinear delay SDEs with small noise can exhibit important rare events on long timescales. When there is no delay, classical large deviations theory quantifies rare events such as escapes from metastable fixed points. Near such fixed points, one can approximate nonlinear delay SDEs by linear delay SDEs. Here, we develop a fully explicit large deviations framework for (necessarily Gaussian) processes X{sub t} driven by linear delay SDEs with small diffusion coefficients. Our approach enables fast numerical computation of the action functional controlling rare events for X{sub t} and of the most likely paths transiting from X{sub 0}=p to X{sub T}=q. Via linear noise local approximations, we can then compute most likely routes of escape from metastable states for nonlinear delay SDEs. We apply our methodology to the detailed dynamics of a genetic regulatory circuit, namely the co-repressive toggle switch, which may be described by a nonlinear chemical Langevin SDE with delay.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1994

On the Behavior of Three-dimensional Wave Packets in Viscously Spreading Mixing Layers

We consider analytically the evolution of a three-dimensional wave packet generated by an impulsive source in a mixing layer. The base flow is assumed to be spreading due to viscous diffusion. The analysis is restricted to small disturbances (linearized theory). A suitable high-frequency ansatz is used to describe the packet; the key elements of this description are a complex phase and a wave action density. It is found that the product of this density and an infinitesimal material volume convecting at the local group velocity is not conserved: there is a continuous interaction between the base flow and the wave action. This interaction is determined by suitable mode-weighted averages of the second and fourth derivatives of the base-flow velocity profile. Although there is some tendency for the dominant wave number in the packet to shift from the most unstable value toward the neutral value, this shift is quite moderate. In practice, wave packets do not become locally neutral in a diverging base flow (as do instability modes), therefore, they are expected to grow more suddenly than pure instability modes and do not develop critical layers. The group velocity is complex; the full significance of this is realized by analytically continuing the equations for the phase and wave action into a complex domain. The implications of this analytic continuation are discussed vis-a-vis the secondary instabilities of the packet: very small scale perturbations on the phase can grow very rapidly initially, but saturate later because most of the energy in these perturbations is convected away by the group velocity. This remark, as well as the one regarding critical layers, has consequences for the nonlinear theories.

Balsa, Thomas F.↗
NASA NTRS2002

Development of a New Membrane Casting Apparatus for Studying Macrovoid Defects in Low-G

A new membrane-casting apparatus is developed for studying macrovoid defects in polymeric membranes made by the wet- and dry-casting process in low-gravity. Macrovoids are large (10-50 micron), open cavities interspersed among the smaller pores in the substructure under the gelled skin surface layer of the cast membrane. Although their occurrence is considered endemic to the wet- and dry-casting process since they can lead to compaction or skin rupture in the membrane process, recent studies suggest several useful applications such as transdermal and osmotic drug delivery systems, miniature bioreactors, etc. However, lack of knowledge about the macrovoid formation mechanism is an obstacle to further development of applications using them. An on-going debate is the role of the surface-tension-driven solutocapillary convection during macrovoid formation. The rapid growth of macrovoids within 1-5 seconds and the high polymer concentration in and near macrovoids make it difficult to explain the mechanism of macrovoid growth by diffusion alone, which is the widely accepted hypothesis proposed by Reuvers et al. The hypothesis advanced by our research group can explain this rapid growth via a mechanism that involves diffusion from the casting solution in the meta-stable region to the macrovoid enhanced by solutocapillary convection induced by the steep nonsolvent concentration gradient in the vicinity of the macrovoid. Since macrovoid growth is hypothesized to be the interplay of a solutocapillary-induced driving force counteracted by viscous drag and buoyancy, eliminate the latter provides a means for testing this hypothesis. Moreover, free convection mass transfer in the nonsolvent immersion bath used to cause phase-separation in membrane casting complicates developing a model for both the wet-casting process and macrovoid growth. The low-g environment minimizes gravitationally induced free convection thereby permitting a tractable solution to the ternary diffusion equations that characterize membrane formation. NASA's Parabolic Flight Research Aircraft provides a small window of low-g (approximately 25 s) that can be used to study macrovoid development in both wet- and dry-cast membranes if an appropriate casting apparatus is used. This casting apparatus should be able to cast the membrane in both low- and high-g in a manner so that essential one-dimensional mass transfer conditions are achieved to insure lateral uniformity in the membrane. The apparatus used in previous research on membrane casting in low-gravity was operated with the plunger driven mechanism. The spring-loaded plunger pushes the bottom block containing the polymer casting solution well directly under the absorbent chamber located in the upper stationary block. However, membranes made via this casting apparatus often displayed lateral nonuniformities that precluded obtaining quantitative information on the macrovoid growth process. Thus, it was necessary to determine the reason for these structural irregularities observed in the low-g casting apparatus. Both experimental as well as computer simulation studies of the low-g casting apparatus established that the impulsive action of the plunger caused the undesired structural nonuniformities. The simulation results showed that the width-to-depth aspect ratio of the shallow well that contains the casting solution in this apparatus was not an important factor in minimizing this problem. Even for a 40:1 (width : depth) aspect ratio, any convection induced by the horizontal motion of the interface of the casting solution will be damped out within 6.25x10(exp 4) seconds. However, the experimental studies revealed that the impulsive motion of the plunger caused a 'sloshing' of the casting solution that had to be eliminated. Therefore, the plungerdriven mechanism was changed to a cam-driven mechanism that did not cause any impulsive motion of the casting solution. Other refinements to this new membrane-casting apparatus include provision for removing the membranes from the casting wells in a less destructive manner. This was accomplished by using a slit geometry for the casting well that permitted disassembly for removal of the cast membrane. The materials used in the construction of this casting apparatus were chosen to insure wetting at the side walls and to maintain precise control of the thickness of the polymer solution in the casting well. An additional provision in this new casting apparatus is the ability to carry out both wet- as well as dry-casting. As such, this apparatus permitted the first studies of the wet-casting of polymeric membranes in low-g. Both wet- and dry-casting experiments on NASA's KC-135 research aircraft employing this new membrane-casting apparatus are scheduled in July 2002. The morphology of the resulting membranes will be characterized using an environmental scanning electron microscope (ESEM). The results of these low-g studies will be reported later.

Lee, Hanyong↗
DOE OSTI2021

Fractional Modeling in Action: A Survey of Nonlocal Models for Subsurface Transport, Turbulent Flows, and Anomalous Materials

Modeling of phenomena such as anomalous transport via fractional-order differential equations has been established as an effective alternative to partial differential equations, due to the inherent ability to describe large-scale behavior with greater efficiency than fully-resolved classical models. In this review article, we first provide a broad overview of fractional-order derivatives with a clear emphasis on the stochastic processes that underlie their use. We then survey three exemplary application areas – subsurface transport, turbulence, and anomalous materials – in which fractional-order differential equations provide accurate and predictive models. For each area, we report on the evidence of anomalous behavior that justifies the use of fractional-order models, and survey both foundational models as well as more expressive state-of-the-art models. We also propose avenues for future research, including more advanced and physically sound models, as well as tools for calibration and discovery of fractional-order models.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

A Prediction of Uranium(VI) Diffusion in Montmorillonite at Various Chemical Solution Conditions

Most nuclear waste disposal options include compacted bentonite, predominately consisting of montmorillonite clay, as part of a barrier system to minimize contaminant mobility. Uranium (U) is the primary element in spent nuclear fuel, and a potential contaminant of water resources. Uranium sorption onto clay and its slow diffusive transport away from waste canisters are expected to limit U(VI) mobility, and possibly also control nuclear fuel degradation rates based on mass action considerations. A prediction of U(VI) diffusion in these systems is complicated by two main factors: (1) the complex mineralogical structure of montmorillonite clay, leading to two types of clay porosities and surface sites, and (2) the dependence of U(VI) sorption on U(VI) solution speciation and the specific chemical system conditions. For instance, depending on pH and ionic strength, U(VI) may sorb onto montmorillonite due to weak ion exchange reactions or the formation of stable surface complexes. Furthermore, in contrast to conventional porous media, U(VI) diffusion in montmorillonite is not only limited by contaminant sorption, but also by a (potential) lack of access to the full clay porosity for some U(VI) solution species. For instance, at the high degrees of clay compaction expected in future barrier systems, the partial or full exclusion of U(VI) from negatively-charged clay interlayer spaces may substantially decrease U(VI) fluxes. In this modeling study, we specifically investigated how the charge of U(VI) solution species affects U(VI) sorption and diffusion behavior. For this purpose, we first simplified complex chemical solution speciation diagrams to charge speciation diagrams. Then, we coupled an existing U(VI) surface complexation model (Tournassat et al., Geochim. Cosmochim. Acta, 2018) with an analytical solution of the diffusion equation to simulate U(VI) mobility in lab-scale through-diffusion experiments for various chemical conditions. Our results suggest that there are two important parameters that govern U(VI) diffusion in these systems. First, U(VI) surface complexation on clay edge surfaces leads to contaminant retardation. On the field scale, this will determine how early a plume may cross site boundaries and pose risks to drinking water resources. Second, the degree of access of U(VI) solution species to diffuse layers in clay interlayer spaces largely controls U(VI) diffusive fluxes. In the field, this parameter will govern the level of U(VI) concentrations that can be expected in contaminated waters.

Pistorino, Jonathan C.↗
DOE OSTI2017

Shrinking of core neoclassical tearing mode magnetic islands due to edge localized modes and the role of ion-scale turbulence in island recovery in DIII-D

Experimental signature of long-wavelength turbulence accelerating the recovery of Neoclassical Tearing Mode (NTM) magnetic islands after they have been transiently reduced in size due to inter- action with Edge Localized Modes (ELMs) is reported for the first time. This work shows that per- turbations associated with ELMs result in peaking of the electron temperature (Te) in the O-point region of saturated core m/n 1/4 2/1 islands (m/n being the poloidal/toroidal mode numbers). In syn- chronization with this Te peak, the island width shrinks by as much as 30% suggesting a key role of the Te peak in NTM stability due to modified pressure gradient (rp) and perturbed bootstrap cur- rent (djBS) at the O-point. Next, this Te peak relaxes via anomalous transport (i.e., the diffusivity is 2 orders of magnitude larger than the neoclassical value) and the island recovers. Long-wavelength turbulent density fluctuations (n~) are reduced at the O-point of flat islands but these fluctuations are increased when Te is peaked which offers an explanation for the observed anomalous transport that is responsible for the relaxation of the Te peak. Linear gyrokinetic simulations indicate that n~ inside the peaked island is dominantly driven by the Ion Temperature Gradient instability. These measure- ments suggest that n~ accelerates NTM recovery after an ELM crash via accelerating the relaxation of rp at the O-point. These observations are qualitatively replicated by coupled predator-prey equations and modified Rutherford equation. In this simple model, turbulence accelerates NTM recovery via relaxing rp and therefore restoring djBS at the O-point. The key physics of the rela- tionship between the Te peak and NTM stability has potentially far-reaching consequences, such as NTM control via pellet injection in high-b tokamak plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Weakly dynamic dark energy via metric-scalar couplings with torsion

We study the dynamical aspects of dark energy in the context of a non-minimally coupled scalar field with curvature and torsion. Whereas the scalar field acts as the source of the trace mode of torsion, a suitable constraint on the torsion pseudo-trace provides a mass term for the scalar field in the effective action. In the equivalent scalar-tensor framework, we find explicit cosmological solutions representing dark energy in both Einstein and Jordan frames. We demand the dynamical evolution of the dark energy to be weak enough, so that the present-day values of the cosmological parameters could be estimated keeping them within the confidence limits set for the standard LCDM model from recent observations. For such estimates, we examine the variations of the effective matter density and the dark energy equation of state parameters over different redshift ranges. In spite of being weakly dynamic, the dark energy component differs significantly from the cosmological constant, both in characteristics and features, for e.g. it interacts with the cosmological (dust) fluid in the Einstein frame, and crosses the phantom barrier in the Jordan frame. We also obtain the upper bounds on the torsion mode parameters and the lower bound on the effective Brans-Dicke parameter. The latter turns out to be fairly large, and in agreement with the local gravity constraints, which therefore come in support of our analysis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS2015

Free-Energy Calculations. A Mathematical Perspective

Ion channels are pore-forming assemblies of transmembrane proteins that mediate and regulate ion transport through cell walls. They are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses. They are also essential to cardiac processes, muscle contraction and epithelial transport. Ion channels from lower organisms can act as toxins or antimicrobial agents, and in a number of cases are involved in infectious diseases. Because of their important and diverse biological functions they are frequent targets of drug action. Also, simple natural or synthetic channels find numerous applications in biotechnology. For these reasons, studies of ion channels are at the forefront of biophysics, structural biology and cellular biology. In the last decade, the increased availability of X-ray structures has greatly advanced our understanding of ion channels. However, their mechanism of action remains elusive. This is because, in order to assist controlled ion transport, ion channels are dynamic by nature, but X-ray crystallography captures the channel in a single, sometimes non-native state. To explain how ion channels work, X-ray structures have to be supplemented with dynamic information. In principle, molecular dynamics (MD) simulations can aid in providing this information, as this is precisely what MD has been designed to do. However, MD simulations suffer from their own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. To assess the reliability of MD simulations it is only natural to turn to the main function of channels - conducting ions - and compare calculated ionic conductance with electrophysiological data, mainly single channel recordings, obtained under similar conditions. If this comparison is satisfactory it would greatly increase our confidence that both the structures and our computational methodologies are sufficiently accurate. Channel conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

free energy↗