13 research outputs found
On the Suppression and Distortion of Non-Equilibrium Fluctuations by Transpiration
A fluid in a non-equilibrium state exhibits long-ranged correlations of its
hydrodynamic fluctuations. In this article, we examine the effect of a
transpiration interface on these correlations -- specifically, we consider a
dilute gas in a domain bisected by the interface. The system is held in a
non-equilibrium steady state by using isothermal walls to impose a temperature
gradient. The gas is simulated using both direct simulation Monte Carlo (DSMC)
and fluctuating hydrodynamics (FHD). For the FHD simulations two models are
developed for the interface based on master equation and Langevin approaches.
For appropriate simulation parameters, good agreement is observed between DSMC
and FHD results with the latter showing a significant advantage in
computational speed. For each approach we quantify the effects of transpiration
on long-ranged correlations in the hydrodynamic variables
A Staggered Scheme for the Compressible Fluctuating Hydrodynamics of Multispecies Fluid Mixtures
We present a numerical formulation for the solution of non-isothermal,
compressible, Navier-Stokes equations with thermal fluctuations to describe
mesoscale transport phenomena in multispecies fluid mixtures. The novelty of
our numerical method is the use of staggered grid momenta along with a finite
volume discretization of the thermodynamic variables to solve the resulting
stochastic partial differential equations. The key advantages of the numerical
scheme are significantly simplified and compact discretization of the diffusive
and stochastic momentum fluxes, and an unambiguous prescription of boundary
conditions involving pressure. The staggered grid scheme more accurately
reproduces the equilibrium static structure factor of hydrodynamic fluctuations
in gas mixtures compared to a collocated scheme described previously in
Balakrishnan et al., Phys. Rev. E 89:013017, 2014. The numerical method is
tested for ideal noble gases mixtures under various nonequilibrium conditions,
such as applied thermal and concentration gradients, to assess the role of
cross-diffusion effects, such as Soret and Dufour, on the long-ranged
correlations of hydrodynamic fluctuations, which are also more accurately
reproduced compared to the collocated scheme. We numerically study giant
nonequilibrium fluctuations driven by concentration gradients, and
fluctuation-driven Rayleigh-Taylor instability in gas mixtures. Wherever
applicable, excellent agreement is observed with theory and measurements from
the direct simulation Monte Carlo (DSMC) method.Comment: 20 pages, 9 figures, 9 pages supplementary materia
A Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm for Modeling Electrolytes
In this paper we develop a methodology for the mesoscale simulation of strong
electrolytes. The methodology is an extension of the Fluctuating Immersed
Boundary (FIB) approach that treats a solute as discrete Lagrangian particles
that interact with Eulerian hydrodynamic and electrostatic fields. In both
cases the Immersed Boundary (IB) method of Peskin is used for particle-field
coupling. Hydrodynamic interactions are taken to be overdamped, with thermal
noise incorporated using the fluctuating Stokes equation, including a "dry
diffusion" Brownian motion to account for scales not resolved by the
coarse-grained model of the solvent. Long range electrostatic interactions are
computed by solving the Poisson equation, with short range corrections included
using a novel immersed-boundary variant of the classical Particle-Particle
Particle-Mesh (P3M) technique. Also included is a short range repulsive force
based on the Weeks-Chandler-Andersen (WCA) potential. The new methodology is
validated by comparison to Debye-H{\"u}ckel theory for ion-ion pair correlation
functions, and Debye-H{\"u}ckel-Onsager theory for conductivity, including the
Wein effect for strong electric fields. In each case good agreement is
observed, provided that hydrodynamic interactions at the typical ion-ion
separation are resolved by the fluid grid.Comment: 30 pages, 12 figures, 2 table
Modeling Electrokinetic Flows with the Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm
In this article we develop an algorithm for the efficient simulation of
electrolytes in the presence of physical boundaries. In previous work the
Discrete Ion Stochastic Continuum Overdamped Solvent (DISCOS) algorithm was
derived for triply periodic domains, and was validated through ion-ion pair
correlation functions and Debye-H{\"u}ckel-Onsager theory for conductivity,
including the Wien effect for strong electric fields. In extending this
approach to include an accurate treatment of physical boundaries we must
address several important issues. First, the modifications to the spreading and
interpolation operators necessary to incorporate interactions of the ions with
the boundary are described. Next we discuss the modifications to the
electrostatic solver to handle the influence of charges near either a fixed
potential or dielectric boundary. An additional short-ranged potential is also
introduced to represent interaction of the ions with a solid wall. Finally, the
dry diffusion term is modified to account for the reduced mobility of ions near
a boundary, which introduces an additional stochastic drift correction. Several
validation tests are presented confirming the correct equilibrium distribution
of ions in a channel. Additionally, the methodology is demonstrated using
electro-osmosis and induced charge electro-osmosis, with comparison made to
theory and other numerical methods. Notably, the DISCOS approach achieves
greater accuracy than a continuum electrostatic simulation method. We also
examine the effect of under-resolving hydrodynamic effects using a `dry
diffusion' approach, and find that considerable computational speedup can be
achieved with a negligible impact on accuracy.Comment: 27 pages, 15 figure
XRCC1 haploinsufficiency in mice has little effect on aging, but adversely modifies exposure-dependent susceptibility
Oxidative DNA damage plays a role in disease development and the aging process. A prominent participant in orchestrating the repair of oxidative DNA damage, particularly single-strand breaks, is the scaffold protein XRCC1. A series of chronological and biological aging parameters in XRCC1 heterozygous (HZ) mice were examined. HZ and wild-type (WT) C57BL/6 mice exhibit a similar median lifespan of ~26 months and a nearly identical maximal life expectancy of ~37 months. However, a number of HZ animals (7 of 92) showed a propensity for abdominal organ rupture, which may stem from developmental abnormalities given the prominent role of XRCC1 in endoderm and mesoderm formation. For other end-points evaluated—weight, fat composition, blood chemistries, condition of major organs, tissues and relevant cell types, behavior, brain volume and function, and chromosome and telomere integrity—HZ mice exhibited by-and-large a normal phenotype. Treatment of animals with the alkylating agent azoxymethane resulted in both liver toxicity and an increased incidence of precancerous lesions in the colon of HZ mice. Our study indicates that XRCC1 haploinsufficiency in mammals has little effect on chronological longevity and many key biological markers of aging in the absence of environmental challenges, but may adversely affect normal animal development or increase disease susceptibility to a relevant genotoxic exposure
XRCC1 haploinsufficiency in mice has little effect on aging, but adversely modifies exposure-dependent susceptibility
Oxidative DNA damage plays a role in disease development and the aging process. A prominent participant in orchestrating the repair of oxidative DNA damage, particularly single-strand breaks, is the scaffold protein XRCC1. A series of chronological and biological aging parameters in XRCC1 heterozygous (HZ) mice were examined. HZ and wild-type (WT) C57BL/6 mice exhibit a similar median lifespan of ~26 months and a nearly identical maximal life expectancy of ~37 months. However, a number of HZ animals (7 of 92) showed a propensity for abdominal organ rupture, which may stem from developmental abnormalities given the prominent role of XRCC1 in endoderm and mesoderm formation. For other end-points evaluated—weight, fat composition, blood chemistries, condition of major organs, tissues and relevant cell types, behavior, brain volume and function, and chromosome and telomere integrity—HZ mice exhibited by-and-large a normal phenotype. Treatment of animals with the alkylating agent azoxymethane resulted in both liver toxicity and an increased incidence of precancerous lesions in the colon of HZ mice. Our study indicates that XRCC1 haploinsufficiency in mammals has little effect on chronological longevity and many key biological markers of aging in the absence of environmental challenges, but may adversely affect normal animal development or increase disease susceptibility to a relevant genotoxic exposure
Cross species application of quantitative neuropathology assays developed for clinical Alzheimer’s disease samples
A major obstacle for preclinical testing of Alzheimer's disease (AD) therapies is the availability of translationally relevant AD models. Critical for the validation of such models is the application of the same approaches and techniques used for the neuropathological characterization of AD. Deposition of amyloid-β 42 (Aβ42) plaques and neurofibrillary tangles containing phospho-Tau (pTau) are the pathognomonic features of AD. In the neuropathologic evaluation of AD, immunohistochemistry (IHC) is the current standard method for detection of Aβ42 and pTau. Although IHC is indispensable for determining the distribution of AD pathology, it is of rather limited use for assessment of the quantity of AD pathology. We have recently developed Luminex-based assays for the quantitative assessment of Aβ42 and pTau in AD brains. These assays are based on the same antibodies that are used for the IHC-based diagnosis of AD neuropathologic change. Here we report the application and extension of such quantitative AD neuropathology assays to commonly used genetically engineered AD models and to animals that develop AD neuropathologic change as they age naturally. We believe that identifying AD models that have Aβ42 or pTau levels comparable to those observed in AD will greatly improve the ability to develop AD therapies. Abbreviations: Alzheimer's disease (AD); amyloid β 42 (Aβ42); phospho-Tau (pTau); immunohistochemistry (IHC)
Squeeze-Film Effect on Atomically Thin Resonators in the High-Pressure Limit
The resonance frequency of membranes depends on the gas pressure due to the squeeze-film effect, induced by the compression of a thin gas film that is trapped underneath the resonator by the high-frequency motion. This effect is particularly large in low-mass graphene membranes, which makes them promising candidates for pressure-sensing applications. Here, we study the squeeze-film effect in single-layer graphene resonators and find that their resonance frequency is lower than expected from models assuming ideal compression. To understand this deviation, we perform Boltzmann and continuum finite-element simulations and propose an improved model that includes the effects of gas leakage and can account for the observed pressure dependence of the resonance frequency. Thus, this work provides further understanding of the squeeze-film effect and provides further directions into optimizing the design of squeeze-film pressure sensors from 2D materials. QN/Steeneken LabQN/van der Zant LabDynamics of Micro and Nano System