We have developed a simulation technique of multiscale Lagrangian fluid dynamics to tackle hierarchical problems relating to historical dependency of polymeric fluid. We investigate flow dynamics of dilute polymeric fluid by using the multiscale simulation approach incorporating Lagrangian particle fluid dynamics technique (the modified smoothed particle hydrodynamics) with stochastic coarse-gr...

The directional change of a fluid particle can be measured by the angle between two subsequent particle displacement increments. At small values of the time-increment the so-defined angle is proportional to the curvature of the trajectory. At large values this coarse-grained curvature should be affected by the presence of solid no-slip walls around the flow domain. We compare homogeneous and co...

[1] Bed surface coarsening was found to be an important effect for the formation of ripples and the dynamics of the boundary layer above a predominantly silt-sized sediment bed (median particle size equal to 26 mm; 20% fine sand, 70% silt, 10% clay) under oscillatory flow (with orbital velocities of 0.32–0.52 m/s) in a laboratory wave duct. Following bed liquefaction, substantial winnowing of t...

Many theoretical works have attempted to coarse grain gene expression at the level of transcription and translation via frameworks based on exclusion processes. Usually in these models the threedimensional conformation of the substrates (DNA and mRNA) is neglected, and particles move on a static unidimensional lattice in contact to an infinite reservoir. In this work we generalise the paradigma...

We present a molecular-dynamics study of force patterns, tensile strength, and crack formation in a cohesive granular model where the particles are subjected to swelling or shrinkage gradients. Nonuniform particle size change generates self-equilibrated forces that lead to crack initiation as soon as the strongest tensile contacts begin to fail. We find that the tensile strength is well below t...

Subcutaneous implantation of coarse powders (74-420 micron) of demineralized diaphyseal bone matrix resulted in the local differentiation of endochondral bone. However, implantation of matrix with particle size of 44-74 micron (Fine matrix) did not induce bone. We have recently reported that the dissociative extraction of coarse matrix with 4 M guanidine HCl resulted in a complete loss of the a...

The size effect on mechanical properties of glassy polyethylene (PE) nanoscale particles has been investigated by extensive coarse-grained molecular dynamics simulations. The diameter of the PE particles varies in the range of 5-40 nm, we confirm that the particle's behaviour under compressive stress strongly depends on its size-the smaller the particle diameter is, the stiffer the particle beh...

Distributions of heavy particles suspended in incompressible turbulent flows are investigated by means of high-resolution direct numerical simulations. It is shown that particles form fractal clusters in the dissipative range, with properties independent of the Reynolds number. Conversely, in the inertial range, the particle distribution is not scale-invariant. It is however shown that deviatio...

We have investigated protein stability in an environment of Escherichia coli cytoplasm using coarse-grained computer simulations. To coarse-grain a small slide of E. coli's cytoplasm consisting of over 16 million atoms, we have developed a self-assembled clustering algorithm (CGCYTO). CGCYTO uses the shape parameter and asphericity as well as a parameter λ (ranging from 0 to 1) that measures th...

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e.,...