STRATIGRAPHY, PALEOGEOGRAPHY AND GENETIC MODEL OF LATE CARNIAN CARBONATE BRECCIAS (CASTRO FORMATION, LOMBARDY, ITALY)

The stratigraphic and paleogeographic analysis of the Carnian-Norian boundary succession in central Lombardy allows the recognition of a new unit, the Castro Formation. This unit, 100-250 m thick, is represented by carbonatic intraformational breccias and associated limestones. Two lithozones have been recognized in the Castro Fm.: the lower one, heteropic with the S.Giovanni Bianco Fm., with dark dolomitic limestones and breccias intercalations, and the upper lithozone, massive, with amalgamated calcareous breccias. Microfacies, recrystallized and often tectonized, consist of mudstones, wackestones and fine packstones, locally rich in ostracods. Geochemical analyses show differences between the Castro Fm. and the overlying and underlying units, possibly because of early diagenetic meteoric imprint. The Castro Fm. depositional setting is represented by coastal ephemeral lakes with periodic emersions and erosional, tectonically controlled phenomena in a monsoonal regime

A high-order spectral element unified boussinesq model for floating point absorbers

International audienceNonlinear wave-body problems are important in renewable energy, especially in case of wave energy converters operating in the near-shore region. In this paper we simulate nonlinear interaction between waves and truncated bodies using an efficient spectral/hp element depth-integrated unified Boussinesq model. The unified Boussinesq model treats also the fluid below the body in a depth-integrated approach. We illustrate the versatility of the model by predicting the reflection and transmission of solitary waves passing truncated bodies. We also use the model to simulate the motion of a latched heaving box. In both cases the unified Boussinesq model show acceptable agreement with CFD results-if applied within the underlying assumptions of dispersion and nonlinearity-but with a significant reduction in computational effort

Runge-Kutta residual distribution schemes

We are concerned with the solution of time-dependent non-linear hyperbolic partial differential equations. We investigate the combination of residual distribution methods with a consistent mass matrix (discretisation in space) and a Runge–Kutta-type time-stepping (discretisation in time). The introduced non-linear blending procedure allows us to retain the explicit character of the time-stepping procedure. The resulting methods are second order accurate provided that both spatial and temporal approximations are. The proposed approach results in a global linear system that has to be solved at each time-step. An efficient way of solving this system is also proposed. To test and validate this new framework, we perform extensive numerical experiments on a wide variety of classical problems. An extensive numerical comparison of our approach with other multi-stage residual distribution schemes is also given

QM/MM MD and Free Energy Simulations of G9a-Like Protein (GLP) and Its Mutants: Understanding the Factors that Determine the Product Specificity

Certain lysine residues on histone tails could be methylated by protein lysine methyltransferases (PKMTs) using S-adenosyl-L-methionine (AdoMet) as the methyl donor. Since the methylation states of the target lysines play a fundamental role in the regulation of chromatin structure and gene expression, it is important to study the property of PKMTs that allows a specific number of methyl groups (one, two or three) to be added (termed as product specificity). It has been shown that the product specificity of PKMTs may be controlled in part by the existence of specific residues at the active site. One of the best examples is a Phe/Tyr switch found in many PKMTs. Here quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations are performed on wild type G9a-like protein (GLP) and its F1209Y and Y1124F mutants for understanding the energetic origin of the product specificity and the reasons for the change of product specificity as a result of single-residue mutations at the Phe/Tyr switch as well as other positions. The free energy barriers of the methyl transfer processes calculated from our simulations are consistent with experimental data, supporting the suggestion that the relative free energy barriers may determine, at least in part, the product specificity of PKMTs. The changes of the free energy barriers as a result of the mutations are also discussed based on the structural information obtained from the simulations. The results suggest that the space and active-site interactions around the ε-amino group of the target lysine available for methyl addition appear to among the key structural factors in controlling the product specificity and activity of PKMTs

Insights from Modeling the 3D Structure of New Delhi Metallo-β-Lactamse and Its Binding Interactions with Antibiotic Drugs

New Delhi metallo-beta-lactamase (NDM-1) is an enzyme that makes bacteria resistant to a broad range of beta-lactam antibiotic drugs. This is because it can inactivate most beta-lactam antibiotic drugs by hydrolyzing them. For in-depth understanding of the hydrolysis mechanism, the three-dimensional structure of NDM-1 was developed. With such a structural frame, two enzyme-ligand complexes were derived by respectively docking Imipenem and Meropenem (two typical beta-lactam antibiotic drugs) to the NDM-1 receptor. It was revealed from the NDM-1/Imipenem complex that the antibiotic drug was hydrolyzed while sitting in a binding pocket of NDM-1 formed by nine residues. And for the case of NDM-1/Meropenem complex, the antibiotic drug was hydrolyzed in a binding pocket formed by twelve residues. All these constituent residues of the two binding pockets were explicitly defined and graphically labeled. It is anticipated that the findings reported here may provide useful insights for developing new antibiotic drugs to overcome the resistance problem

A Comparative Study on the Nonlinear Interaction Between a Focusing Wave and Cylinder Using State-of-the-art Solvers: Part A

This paper presents ISOPE’s 2020 comparative study on the interaction between focused waves and a fixed cylinder. The paper discusses the qualitative and quantitative comparisons between 20 different numerical solvers from various universities across the world for a fixed cylinder. The moving cylinder cases are reported in a companion paper as part B (Agarwal, Saincher, et al., 2021). The numerical solvers presented in this paper are the recent state of the art in the field, mostly developed in-house by various academic institutes. The majority of the participants used hybrid modeling (i.e., a combination of potential flow and Navier–Stokes solvers). The qualitative comparisons based on the wave probe and pressure probe time histories and spectral components between laminar, turbulent, and potential flow solvers are presented in this paper. Furthermore, the quantitative error analyses based on the overall relative error in peak and phase shifts in the wave probe and pressure probe of all the 20 different solvers are reported. The quantitative errors with respect to different spectral component energy levels (i.e., in primary, sub-, and superharmonic regions) capturing capability are reported. Thus, the paper discusses the maximum, minimum, and median relative errors present in recent solvers as regards application to industrial problems rather than attempting to find the best solver. Furthermore, recommendations are drawn based on the analysis

Analysing extremely small sized ratio datasets

10.1504/IJBRA.2015.069225International Journal of Bioinformatics Research and Applications113268-28

Communication: Conformation state diagram of polypeptides: A chain length induced α - β transition

By using a generic coarse grained polypeptide model, we perform multicanonical molecular dynamics simulations for determining the equilibrium conformation state diagram of a single homopolypeptide chain as a function of the chain length and temperature. The state diagram highlights the thermal regimes of stability for various conformational patterns in polypeptides, including swollen, random and collapsed coils, globular structures, extended and bended helices, and compact bundles. Remarkably, at low temperatures we observe a sharp transition from extended helix to compact bundles as the chain length increases. This finding indicates that the chain length is one of the intrisic factors that can trigger - transformations in a broad class of polypeptides. © 2011 American Institute of Physics

Thermoreflectance studies of yttrium-iron garnet crystals

The thermoreflectance of YIG single crystals was measured in the visible energy range. Spectra of this compound support a model that incorporates both localised and one-electron band states. All structures of the thermoreflectance spectra exhibit temperature dependence. Those at low energies, which occur at 16390, 17220, 19321, 20350, 21450, 22410, 23609 and 24271 cm-1 and exhibit a small temperature shift and broadening, were assigned to crystal-field-split localised interionic transitions between the 3d states of Fe3+. The other structures, occurring at 25775, 27367, 30453, 32500, 35248, 39514 and 44202 cm-1 with a considerable temperature shift (between 2*10-3 and 8*10-4 eV K-1) and broadening were ascribed to pair transitions between the 3d states of iron and/or to charge-transfer transitions involving delocalised valence-band oxygen states and iron d-like bands