Close-up view of the modifications of fluid membranes due to phospholipase A(2)

Modeling temperature-dependent transport properties in dissipative particle dynamics: A top-down coarse-graining toward realistic dynamics at the mesoscale

Dissipative particle dynamics (DPD) is a widespread computational tool to simulate the behavior of soft matter and liquids in and out of equilibrium. Although there are many applications in which the effect of temperature is relevant, most of the DPD studies have been carried out at a fixed system temperature. Therefore, this work investigates how to incorporate the effect of system temperature variation within the DPD model to capture realistic temperature-dependent system properties. In particular, this work focuses on the relationship between temperature and transport properties, and therefore, an extended DPD model for transport properties prediction is employed. Transport properties, unlike the equilibrium properties, are often overlooked despite their significant influence on the flow dynamics of non-isothermal mesoscopic systems. Moreover, before simulating the response of the system induced by a temperature change, it is important to first estimate transport properties at a certain temperature. Thus here, the same fluid is simulated across different temperature conditions using isothermal DPD with the aim to identify a temperature-dependent parametrization methodology, capable of ensuring the correctness of both equilibrium and dynamical properties. Liquid water is used as a model system for these analyses. This work proposes a temperature-dependent form of the extended DPD model where both conservative and non-conservative interaction parameters incorporate the variation of the temperature. The predictions provided by our simulations are in excellent agreement with experimental data.

DPD Modelling of the Self- and Co-Assembly of Polymers and Polyelectrolytes in Aqueous Media: Impact on Polymer Science

This review article is addressed to a broad community of polymer scientists. We outline and analyse the fundamentals of the dissipative particle dynamics (DPD) simulation method from the point of view of polymer physics and review the articles on polymer systems published in approximately the last two decades, focusing on their impact on macromolecular science. Special attention is devoted to polymer and polyelectrolyte self- and co-assembly and self-organisation and to the problems connected with the implementation of explicit electrostatics in DPD numerical machinery. Critical analysis of the results of a number of successful DPD studies of complex polymer systems published recently documents the importance and suitability of this coarse-grained method for studying polymer systems.

Metabolomic, behavioral, and reproductive effects of the aromatase inhibitor fadrozole hydrochloride on the unionid mussel Lampsilis fasciola

Androgen-induced masculinization of female aquatic biota poses concerns for natural population stability. This research evaluated the effects of a twelve day exposure of fadrozole hydrochloride on the metabolism and reproductive status of the unionid mussel Lampsilis fasciola. Although this compound is not considered to be widespread in the aquatic environment, it was selected as a model aromatase (enzyme that converts testosterone to estradiol) inhibitor. Adult mussels were exposed to a control and 3 concentrations of fadrozole (2μg/L, 20μg/L, and 50μg/L), and samples of gill tissue were taken on days 4 and 12 for metabolomics analysis. Gills were used because of the variety of critical processes they mediate, such as feeding, ion exchange, and siphoning. Daily observed mussel behavior included female mantle display, foot protrusion, siphoning, and larval (glochidia) releases. Glochidia mortality was significantly higher in the 20μg/L treatment. Fewer conglutinate (packets of glochidia) releases were observed in the 50μg/L treatment, and mortality was highly correlated to release numbers. Foot protrusion was significantly higher in females in nearly all treatments, including the control, during the first 4days of observations. However, this sex difference was observed only in the 50μg/L treatment during the last 8days. Generally, metabolites were significantly altered in female gill tissue in the 2μg/L treatment whereas males were mostly affected only at the highest (50μg/L) treatment. Both sexes also revealed significant reductions in fadrozole-induced metabolic effects in gill tissue sampled after 12days compared to tissue sampled after 4days, indicating time-dependent mechanisms of disruptions in metabolic pathways and homeostatic processes to compensate for such disruptions.

Spatially resolved simulations of membrane reactions and dynamics: multipolar reaction DPD

Biophysical chemistry of mesoscale systems and quantitative modeling in systems biology now require a simulation methodology unifying chemical reaction kinetics with essential collective physics. This will enable the study of the collective dynamics of complex chemical and structural systems in a spatially resolved manner with a combinatorially complex variety of different system constituents. In order to allow a direct link-up with experimental data (e.g. high-throughput fluorescence images) the simulations must be constructed locally, i.e. mesoscale phenomena have to emerge from local composition and interactions that can be extracted from experimental data. Under suitable conditions, the simulation of such local interactions must lead to processes such as vesicle budding, transport of membrane-bounded compartments and protein sorting, all of which result from a sophisticated interplay between chemical and mechanical processes and require the link-up of different length scales. In this work, we show that introducing multipolar interactions between particles in dissipative particle dynamics (DPD) leads to extended membrane structures emerging in a self-organized manner and exhibiting the necessary mechanical stability for transport, correct scaling behavior, and membrane fluidity so as to provide a two-dimensional self-organizing dynamic reaction environment for kinetic studies in the context of cell biology.

Cluster formation of transmembrane proteins due to hydrophobic mismatching

Membranes are the defining envelopes of living cells. At this boundary a multitude of transmembrane proteins mediate signal and mass transfer between cells and their environment. Clustering of these proteins is a frequent and often vital phenomenon that relies at least in part on membrane-mediated interactions. Indeed, the mismatch between proteins' hydrophobic transmembrane domains and the surrounding lipid bilayer has been predicted to facilitate clustering, yet unequivocal quantitative data in support of these predictions have been lacking. Here, we have used coarse-grained membrane simulations to thoroughly address the clustering of transmembrane proteins in detail. Our results emphasize the universal nature of membrane-mediated attraction which relaxes the need for a plethora of fine-tuned interactions between membrane proteins.

Activation of interfacial enzymes at membrane surfaces

A host of water-soluble enzymes are active at membrane surfaces and in association with membranes. Some of these enzymes are involved in signalling and in modification and remodelling of the membranes. A special class of enzymes, the phospholipases, and in particular secretory phospholipase A(2) (sPLA(2)), are only activated at the interface between water and membrane surfaces, where they lead to a break-down of the lipid molecules into lysolipids and free fatty acids. The activation is critically dependent on the physical properties of the lipid-membrane substrate. A topical review is given of our current understanding of the physical mechanisms responsible for activation of sPLA(2) as derived from a range of different experimental and theoretical investigations.

Size-dependent diffusion of membrane inclusions

Experimentally determined diffusion constants are often used to elucidate the size and oligomeric state of membrane proteins and domains. This approach critically relies on the knowledge of the size-dependence of diffusion. We have used mesoscopic simulations to thoroughly quantify the size-dependent diffusion properties of membrane inclusions. For small radii R, we find that the lateral diffusion coefficient D is well described by the Saffman-Delbrück relation, which predicts a logarithmic decrease of D with R. However, beyond a critical radius Rc approximately hetam/(2etac) (h, bilayer thickness; etam/c, viscosity of the membrane/surrounding solvent) we observe significant deviations and the emergence of an asymptotic scaling D approximately 1/R2. The latter originates from the asymptotic hydrodynamics and the inclusion's internal degrees of freedom that become particularly relevant on short timescales. In contrast to the lateral diffusion, the size dependence of the rotational diffusion constant Dr follows the predicted hydrodynamic scaling Dr approximately 1/R2 over the entire range of sizes studied here.