Publications by authors named "Tartakovsky A"

For a multiple-fluid system, CG models capable of accurately predicting the interfacial properties as a function of curvature are still lacking. In this work, we propose a new probabilistic machine learning (ML) model for learning CG potentials for binary fluids. The water-hexane mixture is selected as a typical immiscible binary liquid-liquid system.

View Article and Find Full Text PDF

Motivation: Signaling pathways capable of switching between two states are ubiquitous within living organisms. They provide the cells with the means to produce reversible or irreversible decisions. Switch-like behavior of biological systems is realized through biochemical reaction networks capable of having two or more distinct steady states, which are dependent on initial conditions.

View Article and Find Full Text PDF

This work presents a method of model reduction that leads to models with three solutions of increasing fidelity (multifidelity models) for solute transport in a bounded layered porous media with random permeability. The model generalizes the Taylor-Aris dispersion theory to stochastic transport in random layered porous media with a known velocity covariance function. In the reduced model, we represent (random) concentration in terms of its cross-sectional average and a variation function.

View Article and Find Full Text PDF

We employ a pairwise force smoothed particle hydrodynamics (PF-SPH) model to simulate sessile and transient droplets on rough hydrophobic and hydrophilic surfaces. PF-SPH allows modeling of free-surface flows without discretizing the air phase, which is achieved by imposing the surface tension and dynamic contact angles with pairwise interaction forces. We use the PF-SPH model to study the effect of surface roughness and microscopic contact angle on the effective contact angle and droplet dynamics.

View Article and Find Full Text PDF

Thermal fluctuations cause perturbations of fluid-fluid interfaces and highly nonlinear hydrodynamics in multiphase flows. In this work, we develop a multiphase smoothed dissipative particle dynamics (SDPD) model. This model accounts for both bulk hydrodynamics and interfacial fluctuations.

View Article and Find Full Text PDF

We present a probability density function (PDF) method for a system of nonlinear stochastic ordinary differential equations driven by colored noise. The method provides an integrodifferential equation for the temporal evolution of the joint PDF of the system's state, which we close by means of a modified large-eddy-diffusivity (LED) closure. In contrast to the classical LED closure, the proposed closure accounts for advective transport of the PDF in the approximate temporal deconvolution of the integrodifferential equation.

View Article and Find Full Text PDF

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles.

View Article and Find Full Text PDF

We propose a novel smoothed particle hydrodynamics (SPH) discretization of the fully coupled Landau-Lifshitz-Navier-Stokes (LLNS) and stochastic advection-diffusion equations. The accuracy of the SPH solution of the LLNS equations is demonstrated by comparing the scaling of velocity variance and the self-diffusion coefficient with kinetic temperature and particle mass obtained from the SPH simulations and analytical solutions. The spatial covariance of pressure and velocity fluctuations is found to be in a good agreement with theoretical models.

View Article and Find Full Text PDF

One of the most significant challenges faced by hydrogeologic modelers is the disparity between the spatial and temporal scales at which fundamental flow, transport, and reaction processes can best be understood and quantified (e.g., microscopic to pore scales and seconds to days) and at which practical model predictions are needed (e.

View Article and Find Full Text PDF

We study the intermittency of fluid velocities in porous media and its relation to anomalous dispersion. Lagrangian velocities measured at equidistant points along streamlines are shown to form a spatial Markov process. As a consequence of this remarkable property, the dispersion of fluid particles can be described by a continuous time random walk with correlated temporal increments.

View Article and Find Full Text PDF

Understanding the mesoscopic behavior of dynamical systems described by Langevin equations with colored noise is a fundamental challenge in a variety of fields. We propose a new approach to derive closed-form equations for joint and marginal probability density functions of state variables. This approach is based on a so-called large-eddy-diffusivity closure and can be used to model a wide class of non-Markovian processes described by the noise with an arbitrary correlation function.

View Article and Find Full Text PDF

Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a kinetic Monte Carlo (KMC) model for a surface to a finite-difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition-dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution.

View Article and Find Full Text PDF

We present a discrete-element method (DEM) model to simulate the mechanical behavior of sea ice in response to ocean waves. The interaction of ocean waves and sea ice potentially can lead to the fracture and fragmentation of sea ice depending on the wave amplitude and period. The fracture behavior of sea ice explicitly is modeled by a DEM method where sea ice is modeled by densely packed spherical particles with finite sizes.

View Article and Find Full Text PDF

This paper presents a hybrid model for transport in connected macro-pores in porous media. A pore-scale model is used to parameterize the hybrid model. The hybrid model explicitly models the advection and diffusion of species in the connected macro-pores and treats the porous media around the connected macro-pores as a continuum with effective transport properties.

View Article and Find Full Text PDF

A dissipative-particle-dynamics model for the quantitative simulation of biofilm growth controlled by substrate (nutrient) consumption, advective and diffusive substrate transport, and hydrodynamic interactions with fluid flow (including fragmentation and reattachment) is described. The model was used to simulate biomass growth, decay, and spreading. It predicts how the biofilm morphology depends on flow conditions, biofilm growth kinetics, the rheomechanical properties of the biofilm, and adhesion to solid surfaces.

View Article and Find Full Text PDF
Multinomial diffusion equation.

Phys Rev E Stat Nonlin Soft Matter Phys

June 2011

We describe a new, microscopic model for diffusion that captures diffusion induced fluctuations at scales where the concept of concentration gives way to discrete particles. We show that in the limit as the number of particles N→∞, our model is equivalent to the classical stochastic diffusion equation (SDE). We test our new model and the SDE against Langevin dynamics in numerical simulations, and show that our model successfully reproduces the correct ensemble statistics, while the classical model fails.

View Article and Find Full Text PDF
Langevin model for reactive transport in porous media.

Phys Rev E Stat Nonlin Soft Matter Phys

August 2010

Existing continuum models for reactive transport in porous media tend to overestimate the extent of solute mixing and mixing-controlled reactions because the continuum models treat both the mechanical and diffusive mixings as an effective Fickian process. Recently, we have proposed a phenomenological Langevin model for flow and transport in porous media [A. M.

View Article and Find Full Text PDF

In this paper we present a smoothed particle hydrodynamics (SPH) pore-scale multicomponent reactive transport model with competitive adsorption. SPH is a Lagrangian, particle based modeling method which uses the particles as interpolation points to discretize and solve flow and transport equations. The theory and details of the SPH pore-scale model are presented along with a novel method for handling surface reactions, the continuum surface reaction (CSR) model.

View Article and Find Full Text PDF

Diffuse-interface theory provides a foundation for the modeling and simulation of microstructure evolution in a very wide range of materials, and for the tracking and capturing of dynamic interfaces between different materials on larger scales. Smoothed particle hydrodynamics (SPH) is also widely used to simulate fluids and solids that are subjected to large deformations and have complex dynamic boundaries and/or interfaces, but no explicit interface tracking or capturing is required, even when topological changes such as fragmentation and coalescence occur, because of its Lagrangian particle nature. Here we developed a SPH model for single-component two-phase fluids that is based on diffuse-interface theory.

View Article and Find Full Text PDF

We present a new model for fluid flow and solute transport in porous media, which employs smoothed particle hydrodynamics to solve a Langevin equation for flow and dispersion in porous media. This allows for effective separation of the advective and diffusive mixing mechanisms, which is absent in the classical dispersion theory that lumps both types of mixing into dispersion coefficient. The classical dispersion theory overestimates both mixing-induced effective reaction rates and the effective fractal dimension of the mixing fronts associated with miscible fluid Rayleigh-Taylor instabilities.

View Article and Find Full Text PDF

A two-dimensional numerical model based on smoothed particle hydrodynamics (SPH) was used to simulate unsaturated (multiphase) flow through fracture junctions. A combination of standard SPH equations with pairwise fluid-fluid and fluid-solid particle-particle interactions allowed surface tension and three-phase contact dynamics to be simulated. The model was validated by calculating the surface tension in four different ways: (i) from small-amplitude oscillations of fluid drops, (ii) from the dependence of the capillary pressure on drop radius, (iii) from capillary rise simulations, and (iv) from the behavior of a fluid drop confined between parallel walls under the influence of gravity.

View Article and Find Full Text PDF

A platform for specifically modulating kinase-dependent signaling using peptides derived from the catalytic domain of the kinase is presented. This technology, termed KinAce, utilizes the canonical structure of protein kinases. The targeted regions (subdomain V and subdomains IX and X) are analyzed and their sequence, three-dimensional structure, and involvement in protein-protein interaction are highlighted.

View Article and Find Full Text PDF

The adsorption of cationic and amphoteric copolymers onto controlled pore glass (CPG) powders has been studied by measurement of the powder particle zeta (zeta) potential, by determination of the adsorption isotherm, and by FT Raman measurements of the polymer-coated powder. The cationic polymers consisted chiefly of homopolymers of dimethyldiallylammonium chloride (DMDAAC) or copolymers of DMDAAC and acrylamide. The amphoteric polymers studied included copolymers of DMDAAC and acrylic acid.

View Article and Find Full Text PDF

The osteogenic growth peptide (OGP) is a 14mer mitogen of osteoblastic and fibroblastic cells. Physiologically, OGP is present in high abundance in human and other mammalian sera. Most of the serum OGP is complexed noncovalently to heat sensitive, high molecular weight OGP-binding proteins (OGPBPs).

View Article and Find Full Text PDF

The osteogenic growth peptide (OGP) was recently characterized in regenerating bone marrow. In experimental animals in increases osteogenesis and hemopoiesis. In stromal cell cultures OGP stimulates proliferation, alkaline phosphatase activity, and matrix mineralization.

View Article and Find Full Text PDF