Biological membranes are essential for cell life and hydration. Water provides the driving force for the assembly and stability of many cell components. Here, we study the structural properties of ...water in a phospholipid membrane. We characterize the local structures, inspecting the intermediate range order （IRO） and adopting a sensitive local order metric recently proposed by Martelli et al. that measures and grades the degree of overlap of the local environment with the structures of perfect ice. Close to the membrane, water acquires a high IRO and changes its dynamical properties; i.e., its translational and rotational degrees of freedom slow in a region that extends over - 1 nm from the membrane interface. Surprisingly, we show that at distances as far as -~ 2.5 mn from the interface, although the bulk-like dynamics are recovered, the IRO of water is still slightly higher than that in the bulk under the same thermodynamic conditions. Therefore, the water-membrane interface has a structural effect at ambient conditions that propagates further than the often-invoked 1-nm length scale. Consequently, this should be considered when analyzing experimental data of water confined by membranes and could help us to understand the role of water in biological systems.
Metal cations are ubiquitous components in biological environments and play an important role in regulating cellular functions and membrane properties. By applying metadynamics simulations, we have ...performed systematic free energy calculations of Na+, K+, Ca2+, and Mg2+ bound to phospholipid membrane surfaces for the first time. The free energy landscapes unveil specific binding behaviors of metal cations on phospholipid membranes. Na+ and K+ are more likely to stay in the aqueous solution and can bind easily to a few lipid oxygens by overcoming low free energy barriers. Ca2+ is most stable when it is bound to four lipid oxygens of the membrane rather than being hydrated in the aqueous solution. Mg2+ is tightly hydrated, and it shows hardly any loss of a hydration water or binding directly to the membrane. When bound to the membrane, the cations’ most favorable total coordination numbers with water and lipid oxygens are the same as their corresponding hydration numbers in aqueous solution, indicating a competition between ion binding to water and lipids. The binding specificity of metal cations on membranes is highly correlated with the hydration free energy and the size of the hydration shell.
The separation of liquid mixture components is relevant to many applications-ranging from water purification to biofuel production-and is a growing concern related to the UN Sustainable Development ...Goals (SDGs), such as "Clean water and Sanitation" and "Affordable and clean energy". One promising technique is using graphene slit-pores as filters, or sponges, because the confinement potentially affects the properties of the mixture components in different ways, favoring their separation. However, no systematic study has shown how the size of a pore changes the thermodynamics of the surrounding mixture. Here, we focus on water-methanol mixtures and explore, using Molecular Dynamics simulations, the effects of a graphene pore, with size ranging from 6.5 to 13 Å, for three compositions: pure water, 90%-10%, and 75%-25% water-methanol. We show that tuning the pore size can change the mixture pressure, density and composition in bulk due to the size-dependent methanol sequestration within the pore. Our results can help in optimizing the graphene pore size for filtering applications.
In this article, using numerical simulations we investigate the self-assembly of rod-like particles in suspension due to depletion forces which naturally emerge due to the presence of smaller ...spherical depletant particles. We characterize the type of clusters that are formed and the evolution of aggregation departing from a random initial configuration. We show that eventually the system reaches a thermodynamic equilibrium state in which the aggregates break and reform dynamically. We investigate the equilibrium state of aggregation, which exhibits a strong dependence on depletant concentration. In addition, we provide a simple thermodynamic model inspired on the theory of self-assembly of amphiphilic molecules which allows us to understand qualitatively the equilibrium aggregate size distributions that we obtain in simulation.
Saturated phospholipids, unsaturated phospholipids, and cholesterol are essential components of cell membranes, making the understanding of their mutual interactions of great significance. We have ...performed microsecond molecular dynamics simulations on the ternary mixtures of DPPC/POPC/cholesterol to systematically examine lipid-lipid and cholesterol-lipid interactions in the liquid-ordered and the liquid-disordered phases. The results show that there exists a competition between the tighter packing of cholesterol-lipid and the looser packing of lipid-lipid as the membrane changes from the liquid-disordered phase to the liquid-ordered phase. Depending on the lipid saturation, the favor of lipid-lipid interactions is in the order of saturated-saturated > monounsaturated-monounsaturated > saturated-monounsaturated. Cholesterol-saturated lipid interactions are more favorable than cholesterol-monounsaturated lipid ones. The results are consistent with the push-pull forces derived from experiments and give general insights into the interactions among membrane components.
Cell membranes separate the interior of cells and the exterior environment, providing protection, controlling the passage of substances, and governing the interaction with other biomolecules and ...signalling processes ...
Field-driven direct assembly of nanoscale matter has impact in disparate fields of science. In microscale systems, such concept has been recently exploited to optimize propulsion in viscous fluids. ...Despite the great potential offered by miniaturization, using self-assembly to achieve transport at the nanoscale remains an elusive task. Here we show that a hybrid propeller, composed by a ferromagnetic nanorod and a paramagnetic microsphere, can be steered in a fluid in a variety of modes, from pusher to puller, when the pair is dynamically actuated by a simple oscillating magnetic field. We exploit this unique design to build more complex structures capable of carrying several colloidal cargos as microscopic trains that quickly disassemble at will under magnetic command. In addition, our prototype can be extended to smaller nanorods below the diffraction limit, but still dynamically reconfigurable by the applied magnetic field.
We report on a quantum mechanics popularisation software,
Eigengame
, developed to get general audiences to play with key concepts in quantum mechanics, i.e., the wave function, the quantization of ...energy, the probability density and, to some extent, the measurement problem. The software is developed in python and is available online at github.
This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and ...biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid’s structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.
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