A mathematical and numerical study of nonlinear waves arising in a one-dimensional model of a fluidized bed. Final report

In sections 2-4 the authors present the fundamental mathematical model and the important features they have discovered during the last three years. The model presented in section 2 is typical of the set of equations studied by researchers in the past. However, a novel approach is taken here by the introduction of a stream function for the total mass flux. This is done because the differences and similarities between the one-dimensional and two-dimensional models emerge very clearly in this setting. The mathematical model is a quasilinear hyperbolic-elliptic system of partial differential equations. In one dimension the hyperbolic and elliptic parts decouple and in two dimensions they do not. As shocks and free boundaries are expected to play an important part, the authors also develop the jump conditions for the model in section 2

Strain and rupture of HIV-1 capsids during uncoating

Viral replication in HIV-1 relies on a fullerene-shaped capsid to transport genetic material deep into the nucleus of an infected cell. Capsid stability is linked to the presence of cofactors, including inositol hexakisphosphates (IP6) that bind to pores found in the capsid. Using extensive all-atom molecular dynamics simulations of HIV-1 cores imaged from cryo-electron tomography (cryoET) in intact virions, which contain IP6 and a ribonucleoprotein complex, we find markedly striated patterns of strain on capsid lattices. The presence of these cofactors also increases rigidity of the capsid. Conformational analysis of capsid proteins (CA) show CA accommodates strain by locally flexing away from structures resolved using X-ray crystallography and cryo-ET. Then, cryo-ET of HIV-1 cores undergoing endogenous reverse transcription demonstrates that lattice strain increases in the capsid prior to mechanical failure and that the capsid ruptures by crack propagation along regions of high strain. These results uncover HIV-1 capsid properties involved in their critical disassembly process

Sociocultural Competence Training in Higher Engineering Education: The Role of Gaming Simulation

The present study focuses on competency-based approach in higher engineering education. Today engineers are required to be socially, culturally and communicatively skilled and able to act in constantly changing sociocultural environment. Presently the development of engineers’ sociocultural competency is of great importance, which is seen from the criteria for accrediting engineering programs of numerous international organizations, e.g. ABET. The paper presents some methods of sociocultural competency training based on the techniques of gaming simulation. Here we describe the educational games “Intercultural communication” and “The art of presentation” for the students of Elite Education Department of National Research Tomsk Polytechnic University. The results of incorporating the gaming technologies in education contribute to the effectiveness of engineers’ sociocultural competency training. The paper ends by pointing out gaming simulation which is a cutting-edge pedagogical approach which allows students to participate in realistic scenarios and develop sociocultural competency

Rhesus TRIM5α disrupts the HIV-1 capsid at the inter-hexamer interfaces

TRIM proteins play important roles in the innate immune defense against retroviral infection, including human immunodeficiency virus type-1 (HIV-1). Rhesus macaque TRIM5α (TRIM5αrh) targets the HIV-1 capsid and blocks infection at an early post-entry stage, prior to reverse transcription. Studies have shown that binding of TRIM5α to the assembled capsid is essential for restriction and requires the coiled-coil and B30.2/SPRY domains, but the molecular mechanism of restriction is not fully understood. In this study, we investigated, by cryoEM combined with mutagenesis and chemical cross-linking, the direct interactions between HIV-1 capsid protein (CA) assemblies and purified TRIM5αrh containing coiled-coil and SPRY domains (CC-SPRYrh). Concentration-dependent binding of CC-SPRYrh to CA assemblies was observed, while under equivalent conditions the human protein did not bind. Importantly, CC-SPRYrh, but not its human counterpart, disrupted CA tubes in a non-random fashion, releasing fragments of protofilaments consisting of CA hexamers without dissociation into monomers. Furthermore, such structural destruction was prevented by inter-hexamer crosslinking using P207C/T216C mutant CA with disulfide bonds at the CTD-CTD trimer interface of capsid assemblies, but not by intra-hexamer crosslinking via A14C/E45C at the NTD-NTD interface. The same disruption effect by TRIM5αrh on the inter-hexamer interfaces also occurred with purified intact HIV-1 cores. These results provide insights concerning how TRIM5α disrupts the virion core and demonstrate that structural damage of the viral capsid by TRIM5α is likely one of the important components of the mechanism of TRIM5α-mediated HIV-1 restriction. © 2011 Zhao et al