Design and Synthesis of Novel Peptide Nucleic Acid Monomers

All of the four nucleobases in DNA have replaced the 4‐hydroxy group of N‐[2‐(tert‐butoxycarbonylaminomethyl)‐trans‐4‐hydroxy] tetrahydropyrrole acetic acid methyl ester with cis ‐stereochemistry. An efficient route for the synthesis of N‐[2‐(tert‐butoxycarbonylaminomethyl)‐trans‐4‐hydroxy]‐tetrahydropyrrole acetic acid methyl ester has been developed. Starting with this intermediate, the protected monomers were synthesized by the Mitsunobu reaction or via its tosylate.     

A hybrid FVM–LBM method for single and multi‐fluid compressible flow problems

The lattice Boltzmann method (LBM) has established itself as an alternative approach to solve the fluid flow equations. In this work we combine LBM with the conventional finite volume method (FVM), and propose a non‐iterative hybrid method for the simulation of compressible flows. LBM is used to calculate the inter‐cell face fluxes and FVM is used to calculate the node parameters. The hybrid method is benchmarked for several one‐dimensional and two‐dimensional test cases. The results obtained by the hybrid method show a steeper and more accurate shock profile as compared with the results obtained by the widely used Godunov scheme or by a representative flux vector splitting scheme. Additional features of the proposed scheme are that it can be implemented on a non‐uniform grid, study of multi‐fluid problems is possible, and it is easily extendable to multi‐dimensions. These features have been demonstrated in this work. The proposed method is therefore robust and can possibly be applied to a variety of compressible flow situations. Copyright © 2009 John Wiley & Sons, Ltd.     

Semi-discrete integrable nonlinear Schrödinger system with background-controlled inter-site resonant coupling

We summarize the most featured items characterizing the semi-discrete nonlinear Schrödinger system with background-controlled inter-site resonant coupling. The system is shown to be integrable in the Lax sense that make it possible to obtain its soliton solutions in the framework of properly parameterized dressing procedure based on the Darboux transformation. On the other hand the system integrability inspires an infinite hierarchy of local conservation laws some of which were found explicitly in the framework of generalized recursive approach. The system consists of two basic dynamic subsystems and one concomitant subsystem and it permits the Hamiltonian formulation accompanied by the highly nonstandard Poisson structure. The nonzero background level of concomitant fields mediates the appearance of an additional type of inter-site resonant coupling and as a consequence it establishes the triangular-lattice-ribbon spatial arrangement of location sites for the basic field excitations. Adjusting the background parameter we are able to switch over the system dynamics between two essentially different regimes separated by the critical point. The system criticality against the background parameter is manifested both indirectly by the auxiliary linear spectral problem and directly by the nonlinear dynamical equations themselves. The physical implications of system criticality become evident after the rather sophisticated canonization procedure of basic field variables. There are two variants of system standardization equal in their rights. Each variant is realizable in the form of two nonequivalent canonical subsystems. The broken symmetry between canonical subsystems gives rise to the crossover effect in the nature of excited states. Thus in the under-critical region the system support the bright excitations in both subsystems, while in the over-critical region one of subsystems converts into the subsystem of dark excitations.     

A lattice Boltzmann fictitious domain method for modeling red blood cell deformation and multiple‐cell hydrodynamic interactions in flow

To model red blood cell (RBC) deformation and multiple‐cell interactions in flow, the recently developed technique derived from the lattice Boltzmann method and the distributed Lagrange multiplier/fictitious domain method is extended to employ the mesoscopic network model for simulations of RBCs in flow. The flow is simulated by the lattice Boltzmann method with an external force, while the network model is used for modeling RBC deformation. The fluid–RBC interactions are enforced by the Lagrange multiplier. To validate parameters of the RBC network model, stretching tests on both coarse and fine meshes are performed and compared with the corresponding experimental data. Furthermore, RBC deformation in pipe and shear flows is simulated, revealing the capacity of the current method for modeling RBC deformation in various flows. Moreover, hydrodynamic interactions between two RBCs are studied in pipe flow. Numerical results illustrate that the leading cell always has a larger flow velocity and deformation, while the following cells move slower and deform less.Copyright © 2013 John Wiley & Sons, Ltd.     

Harmonics in the stress response of a WCA-Lennard-Jones liquid under oscillatory elongational flow

The WCA fluid shows a nonlinear behaviour toward a periodic elongational flow through the presence of higher harmonics in stress responses. At the same time the liquid remains purely viscous and isotropic. The absence of numerical artefacts is checked and the physical origin of the harmonics is discussed.