Long-range viscosity of the plasma membrane of a living cell measured by a shear-driven flow method.

The viscosity of the plasma membrane in living cells is a crucial biophysical parameter that regulates cellular functions. We categorize the plasma membrane viscosity into short-range and long-range viscosities based on the spatial scale of the cellular processes they influence. Short-range viscosity originates from the Brownian motion of membrane molecules, i.

Self-reinforcement in filled rubber via strain-induced crystallisation.

Strain-induced crystallisation in elastomers markedly increases their elastic moduli and rupture resistance. However, the mechanisms underlying this self-reinforcement in filled elastomers remain unclear owing to the nanoscale nature of the involved processes. Herein, isoprene rubber with/without silica nanoparticles is stretched to strains of >5 and concomitantly imaged via in situ transmission electron microscopy.

Dynamics of an Ellipsoidal Active Particle Wrapping by a Giant Unilamellar Vesicle.

Engulfment of self-propelled particles by biological membranes is ubiquitous in cellular life. The particles can be very small organisms such as rod-shaped pathogenic bacteria that have the capacity to cause diseases in humans or artificially made active particles such as Janus colloids. In this article, we investigate the wrapping dynamics of an ellipsoidal self-propelled particle by a giant unilamellar vesicle (GUV).

GPU Accelerated Hybrid Particle-Field Molecular Dynamics: Multi-Node/Multi-GPU Implementation and Large-Scale Benchmarks of the OCCAM Code.

A parallelization strategy for hybrid particle-field molecular dynamics (hPF-MD) simulations on multi-node multi-GPU architectures is proposed. Two design principles have been followed to achieve a massively parallel version of the OCCAM code for distributed GPU computing: performing all the computations only on GPUs, minimizing data exchange between CPU and GPUs, and among GPUs. The hPF-MD scheme is particularly suitable to develop a GPU-resident and low data exchange code.

Effects of grafted polymers on the lipid membrane fluidity.

Since the membrane fluidity controls the cellular functions, it is important to identify the factors that determine the cell membrane viscosity. Cell membranes are composed of not only lipids and proteins but also polysaccharide chain-anchored molecules, such as glycolipids. To reveal the effects of grafted polymers on the membrane fluidity, in this study, we measured the membrane viscosity of polymer-grafted giant unilamellar vesicles (GUVs), which were prepared by introducing the poly (ethylene glycol) (PEG)-anchored lipids to the ternary GUVs composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol.

Reaction-induced morphological transitions in a blend of diblock copolymers and reactive monomers: dissipative particle dynamics simulation.

The dissipative particle dynamics (DPD) method is applied to the morphological transitions of microphase-separated domains in a mixture of symmetric AB-diblock copolymers and reactive C-monomers, where polymerization and cross-linking reactions take place among C-monomers. The initial structure for the DPD simulation is an equilibrated cylindrical domain structure prepared by the density-biased Monte Carlo method with density profiles obtained from the self-consistent field theory. By introducing a cross-linking reaction among reactive C-monomers, we confirmed that the DPD simulation reproduces the morphological transitions observed in experiments, where the domain morphology changes due to segregation between A-blocks of diblock copolymers and cross-linking networks of C-monomers.

Synthesising a minimal cell with artificial metabolic pathways.

A "synthetic minimal cell" is considered here as a cell-like artificial vesicle reproduction system in which a chemical and physico-chemical transformation network is regulated by information polymers. Here we synthesise such a minimal cell consisting of three units: energy production, information polymer synthesis, and vesicle reproduction. Supplied ingredients are converted to energy currencies which trigger the synthesis of an information polymer, where the vesicle membrane plays the role of a template.

Efficient compressed database of equilibrated configurations of ring-linear polymer blends for MD simulations.

To effectively archive configuration data during molecular dynamics (MD) simulations of polymer systems, we present an efficient compression method with good numerical accuracy that preserves the topology of ring-linear polymer blends. To compress the fraction of floating-point data, we used the Jointed Hierarchical Precision Compression Number - Data Format (JHPCN-DF) method to apply zero padding for the tailing fraction bits, which did not affect the numerical accuracy, then compressed the data with Huffman coding. We also provided a dataset of well-equilibrated configurations of MD simulations for ring-linear polymer blends with various lengths of linear and ring polymers, including ring complexes composed of multiple rings such as polycatenane.

Modeling of chemically active particles at an air-liquid interface.

The collective motion of chemically active particles at an air-liquid interface is studied theoretically as a dynamic self-organization problem. Based on a physical consideration, we propose a minimal model for self-propelled particles by combining hydrodynamic interaction, capillary interaction, driving force by Marangoni effect, and Marangoni flow. Our model has successfully captured the features of chemically active particles, that represent dynamic self-organized states such as crystalline, chain, liquid-like and spreading states.

Hybrid particle-field molecular dynamics under constant pressure.

Hybrid particle-field methods are computationally efficient approaches for modeling soft matter systems. So far, applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field interactions to represent systems coupled to constant external pressure.

Viscosity Landscape of Phase-Separated Lipid Membrane Estimated from Fluid Velocity Field.

In cell membranes, the functional constituents such as peptides, proteins, and polysaccharides diffuse in a sea of lipids as single molecules and molecular aggregates. Thus, the fluidity of the heterogeneous multicomponent membrane is important for understanding the roles of the membrane in cell functionality. Recently, Henle and Levine described the hydrodynamics of molecular diffusion in a spherical membrane.

Mesoscale Electrostatics Driving Particle Dynamics in Nonhomogeneous Dielectrics.

We introduce a density functional-based formalism to compute the electrostatic energy and forces for a mesoscopic system in the condensed phase, described with molecular resolution. The dielectric permittivity is variable in space, and it is dependent on the density fields of the individual particles present in the system. The electrostatic potential is obtained from standard numerical solutions of the generalized Poisson equation.

Time-Resolved Structured Illumination Microscopy for Phase Separation Dynamics of Water and 2-Butoxyethanol Mixtures: Interpretation of "Early Stage" Involving Micelle-Like Structures.

Phase separation dynamics of a water/2-butoxyethanol (2BE) mixture was studied with newly developed time-resolved structured illumination microscopy (SIM). Interestingly, an employed hydrophobic fluorescent probe for SIM showed spectral shifts up to 500 ns after a laser-induced temperature jump, which suggests 2BE micellar-like aggregates become more hydrophobic at the initial stage of phase separation. This hydrophobic environment in 2BE aggregates, probably due to the ejection of water molecules, continued up to at least 10 μs.

Molecular structure and multi-body potential of mean force in silica-polystyrene nanocomposites.

We perform a systematic application of the hybrid particle-field molecular dynamics technique [Milano, et al., J. Chem.

Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment.

We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayer and sodium dodecyl sulfate (SDS) surfactant in an aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolytes. According to the hybrid approach, the intramolecular interactions are treated by a standard molecular Hamiltonian, and the nonelectrostatic intermolecular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure, as recently proposed [Zhu et al.

Translocation of a vesicle through a narrow hole across a membrane.

We study the translocation process of a vesicle through a hole in a solid membrane separating two chambers by using the Onsager principle. By considering the stretching energy of the vesicle and the driving force due to pressure difference, we derive a free energy that shows clearly a decrease in the energy barrier as the pressure difference between two sides of the membrane increases. The difference between the reaction path obtained from the string method and the actual kinetic paths obtained from the Onsager principle is discussed when the friction parameter changes.

Onsager's variational principle for the dynamics of a vesicle in a Poiseuille flow.

We propose a systematic formulation of the migration behaviors of a vesicle in a Poiseuille flow based on Onsager's variational principle, which can be used to determine the most stable steady state. Our model is described by a combination of the phase field theory for the vesicle and the hydrodynamics for the flow field. The dynamics is governed by the bending elastic energy and the dissipation functional, the latter being composed of viscous dissipation of the flow field, dissipation of the bending energy of the vesicle, and the friction between the vesicle and the flow field.

pH sensing by lipids in membranes: The fundamentals of pH-driven migration, polarization and deformations of lipid bilayer assemblies.

Most biological molecules contain acido-basic groups that modulate their structure and interactions. A consequence is that pH gradients, local heterogeneities and dynamic variations are used by cells and organisms to drive or regulate specific biological functions including energetic metabolism, vesicular traffic, migration and spatial patterning of tissues in development. While the direct or regulatory role of pH in protein function is well documented, the role of hydrogen and hydroxyl ions in modulating the properties of lipid assemblies such as bilayer membranes is only beginning to be understood.

Coarse-Grained Molecular Simulation Model for Gecko Feet Keratin.

The mechanical properties of gecko setae and spatulae are investigated with a coarse-grained model having two bead types. The two-bead model is based on both experimental information of the internal structure of setae and the chemical amino acid composition. Because the seta is composed of a stiff fibril region and a soft matrix region, we model each of the regions separately.

Orientation-shape coupling between liquid crystal and membrane through the anchoring effect.

We perform a series of Monte Carlo simulations on an interface between a liquid crystal (LC) material in isotropic phase in its bulk and a surfactant membrane. These two objects are simulated using coarse-grained molecular models. We estimate physical properties of the membrane such as the interfacial tension and the bending rigidity, focusing on the anchoring effects of the membrane on the LC.

Biomembrane solubilization mechanism by Triton X-100: a computational study of the three stage model.

The solubilization mechanism of lipid membranes in the presence of Triton X-100 (TX-100) is investigated at molecular resolution using molecular dynamics (MD) simulations. Thanks to the large time and length scales accessible by the hybrid particle-field formulation of the models employed here, the complex process of membrane solubilization has been studied, with the goal of verifying the three stage model reported in the literature. DPPC lipid bilayers and vesicles have been studied at different concentrations of the TX-100 detergent employing coarse grained (CG) models.

Migration of Phospholipid Vesicles Can Be Selectively Driven by Concentration Gradients of Metal Chloride Solutions.

We have investigated the migrations of phospholipid vesicles under the concentration gradients of metal ions. We microinjected metal chloride solutions, monovalent (NaCl and KCl), divalent (CaCl and MgCl), and trivalent (LaCl) salts, toward phospholipid giant vesicles (GVs) composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). For NaCl, CaCl, and MgCl solutions, the GVs migrated straight toward the tip of the micropipette in response to the concentration gradients, whereas for KCl and LaCl, GVs moved to the opposite direction.

Phase behavior of a binary fluid mixture of quadrupolar molecules.

We propose a model molecule to investigate microscopic properties of a binary mixture with a closed-loop coexistence region. The molecule is comprised of a Lennard-Jones particle and a uniaxial quadrupole. Gibbs ensemble Monte Carlo simulations demonstrate that the high-density binary fluid of the molecules with the quadrupoles of the same magnitude but of the opposite signs can show closed-loop immiscibility.

Self-assembly of carbon nanotubes in polymer melts: simulation of structural and electrical behaviour by hybrid particle-field molecular dynamics.

Self-assembly processes of carbon nanotubes (CNTs) dispersed in different polymer phases have been investigated using a hybrid particle-field molecular dynamics technique (MD-SCF). This efficient computational method allowed simulations of large-scale systems (up to ∼1 500 000 particles) of flexible rod-like particles in different matrices made of bead spring chains on the millisecond time scale. The equilibrium morphologies obtained for longer CNTs are in good agreement with those proposed by several experimental studies that hypothesized a two level "multiscale" organization of CNT assemblies.

Migration of phospholipid vesicles in response to OH(-) stimuli.

We demonstrate migration of phospholipid vesicles in response to a pH gradient. Upon simple micro-injection of a NaOH solution, the vesicles linearly moved to the tip of the micro-pipette and the migration velocity was proportional to the gradient of OH(-) concentration. Vesicle migration was characteristic of OH(-) ions and no migration was observed for monovalent salts or nonionic sucrose solutions.