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The thermostats in molecular dynamics (MD) simulations of highly confined channel flow may have significant influences on the fidelity of transport phenomena. In this study, we exploit non-equilibrium MD simulations to generate Couette flows with different combinations of thermostat algorithms and strategies. We provide a comprehensive analysis on the effectiveness of three thermostat algorithms Nosé-Hoover chain (NHC), Langevin (LGV) and dissipative particle dynamics (DPD) when applied in three thermostat strategies, thermostating either walls (TW) or fluid (TF), and thermostating both the wall and fluid (TWTF). Our results of thermal and mechanical properties show that the TW strategy more closely resembles experimental conditions. The TF and TWTF systems also produce considerably similar behaviors in weakly sheared systems, but deviate the dynamics in strongly sheared systems due to the isothermal condition. The LGV and DPD thermostats used in the TF and TWTF systems provide vital ways to yield correct dynamics in coarse-grained systems by tuning the fluid transport coefficients. Using conventional NHC thermostat to thermostat fluid only produces correct thermal behaviors in weakly sheared systems, and breaks down due to significant thermal inhomogeneity in strongly sheared systems. [ABSTRACT FROM AUTHOR]

The effectiveness of five temperature control algorithms for dual control volume grand canonical molecular dynamics is investigated in the study of hydrogen atom diffusion in a palladium bulk. The five algorithms, namely, Gaussian, generalized Gaussian moment thermostat (GGMT), velocity scaling, Nosé-Hoover (NH), and its enhanced version Nosé-Hoover chain (NHC) are examined in both equilibrium and nonequilibrium simulation studies. Our numerical results show that Gaussian yields the most inaccurate solutions for the hydrogen-palladium system due to the high friction coefficient generated from the large velocity fluctuation of hydrogen, while NHC, NH, and GGMT produce the most accurate temperature and density profiles in both equilibrium and nonequilibrium cases with their feedback control mechanisms. However, this feedback control also overestimates the self-diffusion coefficients in equilibrium systems and the diffusion coefficient in nonequilibrium systems. Velocity scaling thermostat produces slight inhomogeneities in the temperature and density profiles, but due to the dissipated heat accumulated in the control volumes it still yields accurate self-diffusion coefficients that are in good agreement with the experimental data at a wide range of temperatures while others tend to deviate. [ABSTRACT FROM AUTHOR]

We present a high performance modularly-built open-source software - OpenIFEM. OpenIFEM is a C++ implementation of the modified immersed finite element method (mIFEM) to solve fluid-structure interaction (FSI) problems. This software is modularly built to perform multiple tasks including fluid dynamics (incompressible and slightly compressible fluid models), linear and nonlinear solid mechanics, and fully coupled fluid-structure interactions. Most of open-source software packages are restricted to certain discretization methods; some are under-tested, under-documented, and lack modularity as well as extensibility. OpenIFEM is designed and built to include a set of generic classes for users to adapt so that any fluid and solid solvers can be coupled through the FSI algorithm. In addition, the package utilizes well-developed and tested libraries. It also comes with standard test cases that serve as software and algorithm validation. The software can be built on cross-platform, i.e., Linux, Windows, and Mac OS, using CMake. Efficient parallelization is also implemented for high-performance computing for large-sized problems. OpenIFEM is documented using Doxygen and publicly available to download on GitHub. It is expected to benefit the future development of FSI algorithms and be applied to a variety of FSI applications. [ABSTRACT FROM AUTHOR]

We present a numerical procedure to model the artery wall remodeling stimulated by stenting considering varying degree of residual stresses. This framework sets up biological remodeling with the existence of residual stress. Previous studies suggest that the residual stress originates from the growth and remodeling of the premature tissue. Meanwhile, it is known that tissue remodeling can happen under mechanical loading. However, none of the existing research studies the impact of residual stress on the mechanical-driven growth of biomaterials. To fill this gap, we build a numerical framework that couples the residual stress with a growth model, and examine its impact on tissue remodeling. The proposed approach is applied to in-stent restenosis, where the tissue remodeling process is modeled with finite element method, and the residual stress is generated geometrically using open angle method. The result shows that residual stress reverses the radial distribution of stress concentration, which is ameliorated by tissue remodeling. The thickening of vessel wall tends to increase with residual stress, which links to more severe in-stent restenosis. The results demonstrate the important interplay between residual stress and tissue remodeling. The findings suggest that residual stress should be considered in the future simulation of tissue remodeling. [ABSTRACT FROM AUTHOR]

An introduction to this issue is presented in which the editors discuss topics including fluid-structure interaction (FSI) modeling, Stokes interface problem, and finite element method.