Recently, it was demonstrated that implicit solvent models were capable of generating stable B-form DNA structures. Specifically, generalized Born (GB) implicit solvent models have improved regarding the solvation of conformational sampling of DNA [1,2]. Here, we examine the performance of the GBSW and GBMV models in CHARMM for characterizing base flipping free energy profiles of undamaged and damaged DNA bases. Umbrella sampling of the base flipping process was performed for the bases cytosine, uracil and xanthine. The umbrella sampling simulations were carried-out with both explicit (TIP3P) and implicit (GB) solvent in order to establish the impact of the solvent model on base flipping. Overall, base flipping potential of mean force (PMF) profiles generated with GB solvent resulted in a greater free energy difference of flipping than profiles generated with TIP3P. One of the significant differences between implicit and explicit solvent models is the approximation of solute-solvent interactions in implicit solvent models. We calculated electrostatic interaction energies between explicit water molecules and the base targeted for flipping. These interaction energies were calculated over the base flipping reaction coordinate to illustrate the stabilizing effect of the explicit water molecules on the flipped-out state. It is known that nucleic base pair hydrogen bonds also influenced the free energy of flipping since these favorable interactions must be broken in order for a base to flip-out of the helix. The Watson-Crick base pair hydrogen bond fractions were calculated over the umbrella sampling simulation windows in order to determine the effect of base pair interactions on the base flipping free energy. It is shown that interaction energies between the flipping base and explicit water molecules are responsible for the lower base flipping free energy difference in the explicit solvent PMF profiles.

A surface based lattice Boltzmann impedance boundary condition (BC) using Ozyoruk’s model [J. Comput. Phys., 146 (1998), pp. 29-57] is proposed and implemented in PowerFLOW. In Ozyoruk’s model, pressure fluctuation is directly linked to normal velocity on an impedance surface. In the present study, the relation between pressure and normal velocity is realized precisely by imposing a mass flux on the surface. This impedance BC is generalized and can handle complex geometry. Combined with the turbulence model in the lattice Boltzmann solver PowerFLOW, this BC can be used to model the effect of a liner in presence of a complex 3D turbulent flow. Preliminary simulations of the NASA Langley grazing flow tube and Kundt tube show satisfying agreement with experimental results.

The structural and functional description of protein-protein complexes and their comprehension is a key concept, not only to increase the scientific knowledge in basic terms but also for the application to the biomedical and pharmaceutical industry. The binding association between proteins is nowadays attribute to a few key residues at the interface – the hot-spots. The complex between the RNase inhibitor (RI) and RNaseA protein provides an excellent system to study the role of the functional epitope as it is essential in various molecular recognition processes and constitute one of the tightest complexes known. An energetic pattern of the interface is accomplished by computational alanine scanning mutagenesis and a dynamical characterization is accomplished by a detailed study of the molecular dynamical simulations. A special emphasis is given to the role of solvation across the interface and the shielding of warm-and hot-spots from water.

A diesel particulate filter (DPF) is a key technology to meet future emission standards of particulate matters (PM), mainly soot. It is generally consists of a wall-flow type filter positioned in the exhaust stream of a diesel vehicle. It is difficult to simulate the thermal flow in DPF, because we need to consider the soot deposition and combustion in the complex geometry of filter wall. In our previous study, we proposed an approach for the conjugate simulation of gas-solid flow. That is, the gas phase was simulated by the lattice Boltzmann method (LBM), coupled with the equation of heat conduction inside the solid filter substrate. However, its numerical procedure was slightly complex. In this study, to reduce numerical costs, we have tested a new boundary condition with chemical equilibrium in soot combustion at the surface of filter substrate. Based on the soot oxidation rate with catalysts evaluated in experiments, the lattice Boltzmann simulation of soot combustion in the catalyzed DPF is firstly presented to consider the process in the after-treatment of diesel exhaust gas. The heat and mass transfer is shown to discuss the effect of catalysts.

A new VMD plugin that interfaces with DelPhi to provide ensemble-averaged electrostatic calculations using the Poisson-Boltzmann equation is presented. The general theory and context of this approach are discussed, and examples of the plugin interface and calculations are presented. This new tool is applied to systems of current biological interest, obtaining the ensemble-averaged electrostatic properties of the two major influenza virus glycoproteins, hemagglutinin and neuraminidase, from explicitly solvated all-atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems.

A finite difference scheme with ghost cell technique is used to study viscous fluid sloshing in 2D and 3D tanks with internal structures. The Navier-Stokes equations in a moving coordinate system are derived and they are mapped onto a time-independent and stretched domain. The staggered grid is used and the revised SIMPLEC iteration algorithm is performed. The developed numerical model is rigorously validated by extensive comparisons with reported analytical, numerical and experimental results. The present numerical results were also validated through an experiment setup with a tank excited by an inclined horizontal excitation or a tank mounted by a vertical baffle. The method is then applied to a number of problems including sloshing fluid in a 2D tank with a bottom-mounted baffle and in a 3D tank with a vertical plate. The phenomena of diagonal sloshing waves affected by a vertical plate are investigated in detail in this work. The effects of internal structures on the resonant frequency of a tank with liquid are discussed and the present developed numerical method can successfully analyze the sloshing phenomenon in 2D or 3D tanks with internal structures.

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

We employ the lattice Boltzmann method and random walk particle tracking to simulate the time evolution of hydrodynamic dispersion in bulk, random, monodisperse, hard-sphere packings with bed porosities (interparticle void volume fractions) between the random-close and the random-loose packing limit. Using Jodrey-Tory and Monte Carlo-based algorithms and a systematic variation of the packing protocols we generate a portfolio of packings, whose microstructures differ in their degree of heterogeneity (DoH). Because the DoH quantifies the heterogeneity of the void space distribution in a packing, the asymptotic longitudinal dispersion coefficient calculated for the packings increases with the packings’ DoH. We investigate the influence of packing length (up to 150 dp, where dp is the sphere diameter) and grid resolution (up to 90 nodes per dp) on the simulated hydrodynamic dispersion coefficient, and demonstrate that the chosen packing dimensions of 10 dpx 10 dpx 70 dp and the employed grid resolution of 60 nodes per dp are sufficient to observe asymptotic behavior of the dispersion coefficient and to minimize finite size effects. Asymptotic values of the dispersion coefficients calculated for the generated packings are compared with simulated as well as experimental data from the literature and yield good to excellent agreement.

This work is concerned with the modelling of the interaction of fluid flow with flexibly supported rigid bodies. The fluid flow is modelled by Lattice-Boltzmann Method, coupled to a set of ordinary differential equations describing the dynamics of the solid body in terms its elastic and damping properties. The time discretization of the body dynamics is performed via the Time Discontinuous Galerkin Method. Several numerical examples are presented and highlight the robustness and efficiency of the proposed methodology, by means of comparisons with previously published results. The examples show that the present fluid-structure method is able to capture vortex- induced oscillations of flexibly-supported rigid body.

Proton transport is one of the most important and interesting phenomena in living cells. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins. We describe proton dynamics quantum mechanically via a density functional approach while implicitly model other solvent ions as a dielectric continuum to reduce the number of degrees of freedom. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic level. We formulate a total free energy functional to put proton kinetic and potential energies as well as electrostatic energy of all ions on an equal footing. The variational principle is employed to derive nonlinear governing equations for the proton transport system. Generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained from the variational framework. Theoretical formulations for the proton density and proton conductance are constructed based on fundamental principles. The molecular surface of the channel protein is utilized to split the discrete protein domain and the continuum solvent domain, and facilitate the multiscale discrete/continuum/quantum descriptions. A number of mathematical algorithms, including the Dirichlet to Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to demonstrate the performance of the proposed proton transport model and validate the efficiency of proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. The proton conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and validates the proposed model.

Previous works on impinging streams mainly focused on the structures of flow field, but paid less attention to the structures of temperature field, which are very important in practical applications. In this paper, the influences of the Reynolds number (Re) and Prandtl number (Pr) on the structures of flow and temperature fields of non-isothermal laminar impinging streams are both studied numerically with the lattice Boltzmann method, and two cases with and without buoyancy effect are considered. Numerical results show that the structures are quite different in these cases. Moreover, in the case with buoyancy effect, some new deflection and periodic structures are found, and their independence on the outlet boundary condition is also verified. These findings may help to understand the flow and temperature structures of non-isothermal impinging streams further.

A 3D lattice Boltzmann (LB) model with twenty-seven discrete velocities is presented and used for the simulation of three-dimensional porous media flows. Its accuracy in combination with the half-way bounce back boundary condition is assessed. Characteristic properties of the gas diffusion layers that are used in polymer electrolyte fuel cells can be determined with this model. Simulation in samples that have been obtained via X-ray tomographic microscopy, allows to estimate the values of permeability and relative effective diffusivity. Furthermore, the computational LB results are compared with the results of other numerical tools, as well as with experimental values.

Lattice-Boltzmann methods are versatile numerical modeling techniques capable of reproducing a wide variety of fluid-mechanical behavior. These methods are well suited to parallel implementation, particularly on the single-instruction multiple data (SIMD) parallel processing environments found in computer graphics processing units (GPUs).

Although recent programming tools dramatically improve the ease with which GPUbased applications can be written, the programming environment still lacks the flexibility available to more traditional CPU programs. In particular, it may be difficult to develop modular and extensible programs that require variable on-device functionality with current GPU architectures.

This paper describes a process of automatic code generation that overcomes these difficulties for lattice-Boltzmann simulations. It details the development of GPU-based modules for an extensible lattice-Boltzmann simulation package – LBHydra. The performance of the automatically generated code is compared to equivalent purposewritten codes for both single-phase,multiphase, andmulticomponent flows. The flexibility of the new method is demonstrated by simulating a rising, dissolving droplet moving through a porous medium with user generated lattice-Boltzmann models and subroutines.

Fresh water is one of the most significant resources for human activities and survival, and irrigation is among the most important uses of water. The sustainibility and performance of irrigation canals can be greatly affected by sediment transport and deposition. In our previous works, we proposed a Lattice Boltzmann model for simulating a free surface flow in an irrigation canal, as an alternative to more traditional models mainly based on shallow water equations. Here we introduce the sedimentation phenomenon into our model by adding a new algorithm, based on the earlier work by B. Chopard, A. Dupuis and A. Masselot [9,11,12,27]. Transport, erosion, deposition and toppling of sediments are taken into account and enable the global sedimentation algorithm to simulate different transport modes such as bed load and suspended load. In the present work, we study both the behaviour of a sediment deposit located at an underflow submerged gate (depending on the gate opening and the flow discharge) and the influence of the presence of such a deposit on the flow. Both numerical and experimental validations have been performed. The experiments were realized on the micro-canal of the LCIS laboratory at Valence, France. The comparisons between simulations and experiments give good qualitative agreement.

We investigate the hydrodynamic interactions of spherical colloidal nano particles and nano tetrahedra near a planar wall by means of molecular dynamics (MD) simulations of rigid particles within an all-atom solvent. For both spherical and nano-tetrahedral particles, we find that the parallel and perpendicular components of the local diffusion coefficient and viscosity, show good agreement with hydrodynamic theory of Faxén and Brenner. This provides further evidence that low perturbations from sphericality of a nanoparticle’s shape has little influence on its local diffusive behaviour, and that for this particular case, the continuum theory fluid dynamics is valid even down to molecular scales.

Stent placement is considered as a promising and minimally invasive technique to prevent rupture of aneurysm and favor coagulation mechanism inside the aneurysm. Many scholars study the effect of the stent on blood flow in cerebral aneurysm by numerical simulations, and usually regard blood as the Newtonian fluid, blood, however, is a kind of non-Newtonian fluid in practice. The main purpose of the present paper is to investigate the effect of non-Newtonian behavior on the hemodynamic characteristics of blood flow in stented cerebral aneurysm with lattice Boltzmann method. The Casson model is used to describe the blood non-Newtonian character, which is one of the most popular models in depicting blood fluid. In particular, hemodynamic characteristics derived with Newtonian and non-Newtonian models are studied, and compared in detail. The results show that the non-Newtonian effect gives a great influence on hemodynamic characteristics of blood flow in stented cerebral aneurysm, especially in small necked ones.