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The Natural History of a Patient Along with COVID-19 Pneumonia along with Muted Hypoxemia.
Our results suggest that VR enables the intelligent curation of high-quality data, which accelerates the learning process.Ebola virus (EBOV) is a human pathogen with the ability to cause hemorrhagic fever and bleeding diathesis in hosts. The life cycle of EBOV depends on its nucleocapsid. The Ebola nucleocapsid consists of a helical assembly of nucleoproteins (NPs) encapsidating single-stranded viral RNA (ssRNA). Knowledge of the molecular determinants of Ebola nucleocapsid stability is essential for the development of therapeutics against EBOV. However, large degrees of freedom associated with the Ebola nucleocapsid helical assembly pose a computational challenge, thereby limiting the previous simulation studies to the level of monomers. check details In the present work, we have performed all atom molecular dynamics (MD) simulations of the helical assembly of EBOV nucleoproteins in the absence and presence of ssRNA. We found that ssRNA is essential for maintaining structural integrity of the nucleocapsid. Other molecular determinants observed to stabilize the nucleocapsid include NP-RNA and NP-NP interactions and ion distributions. Additionally, the structural and dynamical behavior of the nucleocapsid monomer depends on its position in the helical assembly. NP monomers present on the longitudinal edges of the helical tube are more exposed, flexible, and have weaker NP-NP interactions than those residing in the center. This work provides key structural features stabilizing the nucleocapsid that may serve as therapeutic targets.Even though the study of interfacial phenomena can be traced back to Laplace and was given a solid thermodynamic foundation by Gibbs, it appears that some concepts and relations among them are still causing some confusion and debates in the literature, particularly for interfaces involving solids. In particular, the definitions of the concepts of interfacial tension, free energy, and stress and the relationships between them sometimes lack clarity, and some authors even question their validity. So far, the debates about these relationships, in particular the Shuttleworth equation, have taken place within the framework of classical thermodynamics. In this work, we are offering to look at these concepts within the framework of statistical mechanics, which can be readily tested in Molecular Dynamics (MD) simulations. For a simple one component system of particles interacting via the Lennard-Jones potential, we calculate by the cleaving method the excess free energy of a solid-vacuum interface (solid surface) for systems in different states of tangential strain and compare the results to the calculation of surface stress via the difference of normal and tangential forces at the surface. As a result, we demonstrate consistency, within the statistical uncertainty, of the thermodynamic and statistical mechanical definitions of surface free energy and surface stress and how they are expressed via interaction-dependent quantities in MD simulations.Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is challenging to simulate both binding and unbinding of peptides and calculate peptide binding free energies through conventional molecular dynamics, due to long biological timescales and extremely high flexibility of the peptides. Based on the Gaussian accelerated molecular dynamics (GaMD) enhanced sampling technique, we have developed a new computational method "Pep-GaMD," which selectively boosts essential potential energy of the peptide in order to effectively model its high flexibility. In addition, another boost potential is applied to the remaining potential energy of the entire system in a dual-boost algorithm. Pep-GaMD has been demonstrated on binding of three model peptides to the SH3 domains. Independent 1 µs dual-boost Pep-GaMD simulations have captured repetitive peptide dissociation and binding events, which enable us to calculate peptide binding thermodynamics and kinetics. The calculated binding free energies and kinetic rate constants agreed very well with available experimental data. Furthermore, the all-atom Pep-GaMD simulations have provided important insights into the mechanism of peptide binding to proteins that involves long-range electrostatic interactions and mainly conformational selection. In summary, Pep-GaMD provides a highly efficient, easy-to-use approach for unconstrained enhanced sampling and calculations of peptide binding free energies and kinetics.This paper is focused on the experimental and theoretical study of the phase separation of a magnetic nanoparticle suspension under rotating magnetic fields in a frequency range, 5 Hz ≤ ν ≤ 25 Hz, relevant for several biomedical applications. The phase separation is manifested through the appearance of needle-like dense particle aggregates synchronously rotating with the field. Their size progressively increases with time due to the absorption of individual nanoparticles (aggregate growth) and coalescence with neighboring aggregates. The aggregate growth is enhanced by the convection of nanoparticles toward rotating aggregates. The maximal aggregate length, Lmax ∝ ν-2, is limited by fragmentation arising as a result of their collisions. Experimentally, the aggregate growth and coalescence occur at a similar timescale, ∼1 min, weakly dependent on the field frequency. The proposed theoretical model provides a semi-quantitative agreement with the experiments on the average aggregate size, aggregation timescale, and size distribution function without any adjustable parameter.An explicit expression relating the magnitude of the fifth-order off-diagonal cusp in the real part of the one-electron reduced density matrix to the "on-top" two-electron density is derived in a rigorous manner from the behavior of the underlying electronic wavefunction at the electron-electron coalescence. The implications of the presence of this cusp upon electronic structure calculations of quantum chemistry and solid-state physics, including the limits imposed upon their accuracy, are elucidated. In particular, the power-law decay of the occupation numbers of the natural orbitals is demonstrated for 1S states of systems composed of arbitrary even numbers of electrons. The practical importance of analogous off-diagonal cusps in many-electron reduced density matrices is briefly discussed.
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