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