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We present TTCF4LAMMPS, a toolkit for performing non-equilibrium molecular dynamics (NEMD) simulations to study the fluid behaviour at low shear rates using the LAMMPS software. By combining direct NEMD simulations and the transient-time correlation function (TTCF) technique, we study the fluid response to shear rates spanning 15 orders of magnitude. We present two examples for simple monatomic systems: one consisting of a bulk liquid and another with a liquid layer confined between two solid walls. The small bulk system is suitable for testing on personal computers, while the larger confined system requires high-performance computing (HPC) resources. We demonstrate that the TTCF formalism can successfully detect the system response for arbitrarily weak external fields. We provide a brief mathematical explanation for this feature. Although we showcase the method for simple monatomic systems, TTCF can be readily extended to study more complex molecular fluids. Moreover, in addition to shear flows, the method can be extended to investigate elongational or mixed flows as well as thermal or electric fields. The high computational cost needed for the method is offset by the two following benefits: i) the cost is independent of the magnitude of the external field, and ii) the simulations can be made highly efficient on HPC architectures by exploiting the parallel design of the algorithm. We expect the toolkit to be useful for computational researchers striving to study the nonequilibrium behaviour of fluids under experimentally-accessible conditions. Program title: TTCF4LAMMPS CPC Library link to program files: https://doi.org/10.17632/hh2rkcxbrf.1 Developer's repository link: https://github.com/edwardsmith999/TTCF4LAMMPS Licensing provisions: GNU General Public License 3 Programming language: Python 3 Nature of problem: Measuring the nonequilibrium behaviour of bulk and confined fluids under experimentally accessible strain rates in non-equilibrium molecular dynamics (NEMD) simulations. Solution method: Creating a Python-based code that utilises the transient-time correlation function method and the LAMMPS software to enable the bulk fluid properties (e.g. viscosity) and confined fluid interfacial properties (e.g. shear stress and slip velocity) to be computed at low shear rates with NEMD. [ABSTRACT FROM AUTHOR]

Adhesion between cells and blood vessel wall plays an essential role in many biological processes such as immune response and cancer metastasis. Unlike the other adhesion processes taking place in relatively quiescent milieu, cells in blood vessel tend to be subjected to hydrodynamic impact from the blood flow. Understanding the kinetic response of cells to the blood flow helps in shedding light on the related biological processes. In this paper, a theoretical model is established to depict the kinetic behavior of a cell in shear flow by equating cell adhesion, which is mediated by ligand-receptor reactions, as speed-dependent inter-surface interaction in combination with the kinetics of a rolling object. Our results indicate that the steady state of the cell depends on the shear rate of the flow. In a flow with relatively low shear rate, the cell would finally rest on the vessel wall. If the shear rate is sufficiently high, the cell would be rolling at a steady speed on the wall. In a flow with intermediate shear rate, the cell would either rest or roll at a steady speed on the vessel, depending on its initial status. These predictions are verified by Monte Carlo simulations and are also consistent with the ‘bistability’ phenomenon of the rolling cell as reported in literature. Our findings not only shed light on the mechanics of adhesive rolling of cells on vessel wall but also have potential applications in the design of biomedical systems such as microscopic carriers for drug delivery in blood circulation. [ABSTRACT FROM AUTHOR]

In this paper, the flow-induced vibrations of an elastically mounted circular cylinder subjected to the planar shear flow with the 1-DOF (only transverse direction) and 2-DOF (in-line and cross-flow directions) movements are studied numerically in the laminar flow (Re = 150). Based on a characteristic-based-split (CBS) finite element method, the numerical simulation is conducted, and is verified through the benchmark problem of the uniform flow past an elastically mounted circular cylinder. The computation is carried out for lower reduced mass of M r = 2.0 and the structural damping ratio is set to zero to maximize the vortex-induced response of the cylinder. The effects of some key parameters, such as shear rate ( k = 0.0–0.1), reduced velocity ( U r = 3.0–12.0) and natural frequency ratio ( r = 1.0–2.0), on the characteristics of vortex-induced vibration (VIV) responses are studied. The results show that, in the 1-DOF system, the frequency synchronization region extends with the increasing of k . The shear rate greatly affects the phase portraits, which shift from the double-valued type to the single-valued one. On the other hand, in the 2-DOF system, the increasing of k causes the extension of the single-resonant region and dual-resonant one at the lower natural frequency ratios. While at the higher natural frequency ratios, the change of k only expands the single-resonant region in the transverse direction. The predominant vortex shedding patterns are 2S and P + S modes. Finally, the interaction between vortex and cylinder as well as the mechanism of flow-induced vibration in planar shear flow are revealed. The phase between the force and its corresponding displacement changes from out-of-phase to in-phase and the higher harmonic forces appear with the increasing of shear rate, resulting in the energy transferring from the fluid to the structure and then the dynamic response of the cylinder intensifying. [ABSTRACT FROM AUTHOR]