A consistency study of coarse-grained dynamical chains through a Nonlinear wave equation of mixed type

A dynamical atomistic chain to simulate mechanical properties of a one-dimensional material with zero temperature may be modelled by the molecular dynamics (MD) model. Because the number of particles (atoms) is huge for a MD model, in practice one often takes a much smaller number of particles to formulate a coarse-grained approximation. We shall mainly consider the consistency of the coarse-grained model with respect to the grain (mesh) size to provide a justification to the goodness of such an approximation. In order to reduce the characteristic oscillations with very different frequencies in such a model, we either add a viscous term to the coarse-grained MD model or apply a space average to the coarse-grained MD solutions for the consistency study. The coarse-grained solution is also compared with the solution of the (macroscopic) continuum model (a nonlinear wave equation of mixed type) to show how well the coarse-grained model can approximate the macroscopic behavior of the material. We also briefly study the instability of the dynamical atomistic chain and the solution of the Riemann problem of the continuum model which may be related to the defect of the atomistic chain under a large deformation in certain locations.Comment: 25 pages, 15 figure

Lithofacies paleogeography mapping and reservoir prediction in tight sandstone strata: A case study from central Sichuan Basin, China

AbstractSand-rich tight sandstone reservoirs are potential areas for oil and gas exploration. However, the high ratio of sandstone thickness to that of the strata in the formation poses many challenges and uncertainties to traditional lithofacies paleogeography mapping. Therefore, the prediction of reservoir sweet spots has remained problematic in the field of petroleum exploration. This study provides new insight into resolving this problem, based on the analyses of depositional characteristics of a typical modern sand-rich formation in a shallow braided river delta of the central Sichuan Basin, China. The varieties of sand-rich strata in the braided river delta environment include primary braided channels, secondary distributary channels and the distribution of sediments is controlled by the successive superposed strata deposited in paleogeomorphic valleys. The primary distributary channels have stronger hydrodynamic forces with higher proportions of coarse sand deposits than the secondary distributary channels. Therefore, lithofacies paleogeography mapping is controlled by the geomorphology, valley locations, and the migration of channels. We reconstructed the paleogeomorphology and valley systems that existed prior to the deposition of the Xujiahe Formation. Following this, rock-electro identification model for coarse skeletal sand bodies was constructed based on coring data. The results suggest that skeletal sand bodies in primary distributary channels occur mainly in the valleys and low-lying areas, whereas secondary distributary channels and fine deposits generally occur in the highland areas. The thickness distribution of skeletal sand bodies and lithofacies paleogeography map indicate a positive correlation in primary distributary channels and reservoir thickness. A significant correlation exists between different sedimentary facies and petrophysical properties. In addition, the degree of reservoir development in different sedimentary facies indicates that the mapping method reliably predicts the distribution of sweet spots. The application and understanding of the mapping method provide a reference for exploring tight sandstone reservoirs on a regional basis

Prediction and Identification of Potential Immunodominant Epitopes in Glycoproteins B, C, E, G, and I of Herpes Simplex Virus Type 2

Twenty B candidate epitopes of glycoproteins B (gB2), C (gC2), E (gE2), G (gG2), and I (gI2) of herpes simplex virus type 2 (HSV-2) were predicted using DNAstar, Biosun, and Antheprot methods combined with the polynomial method. Subsequently, the biological functions of the peptides were tested via experiments in vitro. Among the 20 epitope peptides, 17 could react with the antisera to the corresponding parent proteins in the EIA tests. In particular, five peptides, namely, gB2466–473 (EQDRKPRN), gC2216–223 (GRTDRPSA), gE2483–491 (DPPERPDSP), gG2572–579 (EPPDDDDS), and gI2286-295 (CRRRYRRPRG) had strong reaction with the antisera. All conjugates of the five peptides with the carrier protein BSA could stimulate mice into producing antibodies. The antisera to these peptides reacted strongly with the corresponding parent glycoproteins during the Western Blot tests, and the peptides reacted strongly with the antibodies against the parent glycoproteins during the EIA tests. The antisera against the five peptides could neutralize HSV-2 infection in vitro, which has not been reported until now. These results suggest that the immunodominant epitopes screened using software algorithms may be used for virus diagnosis and vaccine design against HSV-2