Water-peptide dynamics during conformational transitions

Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that the water molecules represent an integral part of the molecular system during the conformational changes, in contrast to the metastable periods when water and peptide dynamics are essentially decoupled

The nut-and-bolt motion of a bacteriophage sliding along a bacterial flagellum: a complete hydrodynamics model

Abstract The ‘nut-and-bolt’ mechanism of a bacteriophage-bacteria flagellum translocation motion is modelled by numerically integrating the 3D Stokes equations using a Finite-Element Method (FEM). Following the works by Katsamba and Lauga (Phys Rev Fluids 4(1): 013101, 2019), two mechanical models of the flagellum-phage complex are considered. In the first model, the phage fiber wraps around the smooth flagellum surface separated by some distance. In the second model, the phage fiber is partly immersed in the flagellum volume via a helical groove imprinted in the flagellum and replicating the fiber shape. In both cases, the results of the Stokes solution for the translocation speed are compared with the Resistive Force Theory (RFT) solutions (obtained in Katsamba and Lauga Phys Rev Fluids 4(1): 013101, 2019) and the asymptotic theory in a limiting case. The previous RFT solutions of the same mechanical models of the flagellum-phage complex showed opposite trends for how the phage translocation speed depends on the phage tail length. The current work uses complete hydrodynamics solutions, which are free from the RFT assumptions to understand the divergence of the two mechanical models of the same biological system. A parametric investigation is performed by changing pertinent geometrical parameters of the flagellum-phage complex and computing the resulting phage translocation speed. The FEM solutions are compared with the RFT results using insights provided from the velocity field visualisation in the fluid domain

Zonal jets in the Southern Ocean: A semi-analytical model based on scale separation

A reduced-order semi-analytic model of multiple zonal jets in the Southern Ocean is proposed based on the statistical approach and scale decomposition. By introducing two dominant scales in the vorticity equation, the model describes the large-scale and mesoscale dynamics using the explicit momentum dissipation in the horizontal and vertical directions. For validation and physical insights, the results of the reduced-order model are compared with solutions of two eddy-resolving ocean models: (i) a realistic primitive-equation HYCOM (HYbrid Coordinate Ocean Model) simulation of the Southern Ocean and (ii) an idealized quasi-geostrophic model of a shear-driven channel flow. •There is a scale separation in vorticity spectrum of the Southern Ocean.•The large- and small-scale components are described by a semi-analytical model.•The large-scale flow is derived by wind and dissipated via bottom friction.•Zonal jets result from balance of beta term, vertical stretching and dissipation.•Zonal jets are coupled to the background flow through eddy viscosity

Lateral migration of peptides in transversely sheared flows in water: an atomistic-scale-resolving simulation

For atomistic scale-resolving simulations of peptide diffusion, which are representative of molecular sorting in micro-fluidic device, a hybrid Fluctuating Hydrodynamics - Molecular Dynamics (FH/MD) model is implemented based on the two-phase flow analogy framework. Thanks to the used framework, in comparison with existing simulations in the literature, the suggested model captures inter-atomic forces between the peptides and the surrounding shell of water atoms at atomistic resolution while concurrently taking into account the non-uniform flow effect. In comparison with previous applications of the hybrid two-phase flow analogy method, multiple moving atomic-resolution zones are implemented for the first time here. The moving zones comprise one and two peptides solvated in water with a Poiseuille flow applied, where each diffusing peptide and the surrounding water shell are dynamically resolved. The models are validated in comparison with the pure all-atom molecular dynamics simulations for the no flow case and then used to investigate how the flow rate and the starting location of peptides in the parabolic flow profile affect their lateral migration over a range of flow Reynolds numbers. It is estimated that for the Poiseuille flows considered, the FH/MD model is 2–20 times faster in comparison with the conventional all-atom non-equilibrium molecular dynamics simulations.</p

Flow and noise predictions of the isolated subsonic jets from the Doak Laboratory experiment

Flow and noise solutions using Large Eddy Simulation (LES) are evaluated for two jets at acoustic Mach numbers 0.6 and 0.8. The jets correspond to Doak Laboratory Experiment performed at the University of Southampton. LES method is based on the Compact Accurately Boundary-Adjusting High-Resolution Technique (CABARET) scheme and is implemented on Graphics Processing Units. In comparison with many other jet noise benchmarks, the Doak jet cases include well-defined boundary conditions corresponding to the meanflow velocity and turbulent intensity profiles measured just downstream of the nozzle exit. The far-field noise predictions are obtained using two approaches. First, the LES solutions are coupled with the penetrable surface formation of the Ffowcs Williams–Hawkings method. The second approach is based on the reduced-order implementation of the Generalised Acoustic Analogy model for which time averaged quantities are obtained from the LES solutions. All numerical solutions are compared with the flow and acoustic microphone measurements from the Doak experiment. The results are cross-validated using the sJet code, which corresponds to an empirical model obtained from interpolations over a large set of NASA jet noise data

A novel computational method for modelling stochastic advection in heterogeneous media

The paper is devoted to a new computational method for problems of transport in highly non-uniform media. In particular, the method is applied to the problem of anomalous contaminant transport in a field with a randomly distributed permeability, which was modelled as a stochastic advection process governed by a stochastic advection model. The stochastic advection model is used to generate different realisations of micro-dispersion parameters required for direct numerical simulations. The new numerical method combines the merits of finite-volume and finite-difference approaches and is demonstrated to be efficient and robust in several benchmark advection tests. For the stochastic advection problem considered the results of the new computational method are in a good agreement with analytical predictions available for different stochastic advection regimes.</p

Jet flow and noise predictions for the Doak laboratory experiment

Large-eddy simulations (LESs) are performed for two isolated unheated jet flows corresponding to a Doak Laboratory experiment performed at the University of Southampton. The jet speeds studied correspond to acoustic Mach numbers of 0.6 and 0.8 as well as Reynolds numbers based on the nozzle exit diameter of about one million. The LES method is based on the compact accurately boundary-adjusting high-resolution technique (CABARET) and is implemented on graphics processing units (GPUs) to obtain 1000–1100 convective time units for statistical averaging with reasonable run times. In comparison with the previous jet LES calculations with the GPU CABARET method, the mean-flow velocity and turbulent intensity profiles are matched with the hot-wire measurements just downstream of the nozzle exit. The far-field noise spectra of the Doak jets are evaluated using two methods: the Ffowcs Williams–Hawkings approach and a reduced-order implementation of the Goldstein generalized acoustic analogy. The flow and noise results are compared with hot-wire and acoustic microphone measurements of the Doak Laboratory and critically analyzed in comparison with the NASA small hot jet acoustic rig database