48 research outputs found

    Markov models of biomolecular systems

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    Transient Cavity Dynamics and Divergence from the Stokes-Einstein Equation in Organic Aerosol

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    The diffusion of small molecules through viscous matrices formed by large organic molecules is important across a range of domains, including pharmaceutical science, materials chemistry, and atmospheric science, impacting on, for example, the formation of amorphous and crystalline phases. Here we report significant breakdowns in the Stokes–Einstein (SE) equation from measurements of the diffusion of water (spanning 5 decades) and viscosity (spanning 12 decades) in saccharide aerosol droplets. Molecular dynamics simulations show water diffusion is not continuous, but proceeds by discrete hops between transient cavities that arise and dissipate as a result of dynamical fluctuations within the saccharide lattice. The ratio of transient cavity volume to solvent volume increases with size of molecules making up the lattice, increasing divergence from SE predictions. This improved mechanistic understanding of diffusion in viscous matrices explains, for example, why organic compounds equilibrate according to SE predictions and water equilibrates more rapidly in aerosols

    Aerosol mass and size‑resolved metal content in urban Bangkok, Thailand

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    Inhalable particulate matter (PM) is a health concern, and people living in large cities such as Bangkok are exposed to high concentrations. This exposure has been linked to respiratory and cardiac diseases and cancers of the lung and brain. Throughout 2018, PM was measured in northern Bangkok near a toll road (13.87°N, 100.58°E) covering all three seasons (cool, hot and rainy). PM(10) was measured in 24- and 72-h samples. On selected dates aerodynamic size and mass distribution were measured as 3-day samples from a fixed 5th floor inlet. Particle number concentration was measured from the 5th floor inlet and in roadside survey measurements. There was a large fraction of particle number concentration in the sub-micron range, which showed the greatest variability compared with larger fractions. Metals associated with combustion sources were most found on the smaller size fraction of particles, which may have implications for associated adverse health outcomes because of the likely location of aerosol deposition in the distal airways of the lung. PM(10) samples varied between 30 and 100 μg m(−3), with highest concentrations in the cool season. The largest metal fractions present in the PM(10) measurements were calcium, iron and magnesium during the hot season with average airborne concentrations of 13.2, 3.6 and 2.0 μg m(−3), respectively. Copper, zinc, arsenic, selenium, molybdenum, cadmium, antimony and lead had large non-crustal sources. Principal component analysis (PCA) identified likely sources of the metals as crustal minerals, tailpipe exhaust and non-combustion traffic. A health risk analysis showed a higher risk of both carcinogenic and non-carcinogenic health effects in the drier seasons than the wet season due to ingestion of nickel, arsenic, cadmium and lead. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11356-022-20806-w

    Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

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    © 2019 Author(s). As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures
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