A variable time step self-consistent mean field DSMC model for three-dimensional environments

A self-consistent mean field direct simulation Monte Carlo (SCMFD) algorithm was recently proposed for simulating collision environments for a range of one-dimensional model systems. This work extends the one-dimensional SCMFD approach to three dimensions and introduces a variable time step (3D-vt-SCMFD), enabling the modeling of a considerably wider range of different collision environments. We demonstrate the performance of the augmented method by modeling a varied set of test systems: ideal gas mixtures, Poiseuille flow of argon, and expansion of gas into high vacuum. For the gas mixtures, the 3D-vt-SCMFD method reproduces the properties (mean free path, mean free time, collision frequency, and temperature) in excellent agreement with theoretical predictions. From the Poiseuille flow simulations, we extract flow profiles that agree with the solution to the Navier–Stokes equations in the high-density limit and resemble free molecular flow at low densities, as expected. The measured viscosity from 3D-vt-SCMF is ∼15% lower than the theoretical prediction from Chapman–Enskog theory. The expansion of gas into vacuum is examined in the effusive regime and at the hydrodynamic limit. In both cases, 3D-vt-SCMDF simulations produce gas beam density, velocity, and temperature profiles in excellent agreement with analytical models. In summary, our tests show that 3D-vt-SCMFD is robust and computationally efficient, while also illustrating the diversity of systems the SCMFD model can be successfully applied to

Nonspecific membrane-matrix interactions influence diffusivity of lipid vesicles in hydrogels

The diffusion of extracellular vesicles and liposomes in vivo is affected by different tissue environmental conditions and is of great interest in the development of liposome-based therapeutics and drug-delivery systems. Here, we use a bottom-up biomimetic approach to better isolate and study steric and electrostatic interactions and their influence on the diffusivity of synthetic large unilamellar vesicles in hydrogel environments. Single-particle tracking of these extracellular vesicle-like particles in agarose hydrogels as an extracellular matrix model shows that membrane deformability and surface charge affect the hydrogel pore spaces that vesicles have access to, which determines overall diffusivity. Moreover, we show that passivation of vesicles with PEGylated lipids, as often used in drug-delivery systems, enhances diffusivity, but that this effect cannot be fully explained with electrostatic interactions alone. Finally, we compare our experimental findings with existing computational and theoretical work in the field to help explain the nonspecific interactions between diffusing particles and gel matrix environments

Modeling Water Interactions with Graphene and Graphite via Force Fields Consistent with Experimental Contact Angles

Accurate simulation models for water interactions with graphene and graphite are important for nanofluidic applications, but existing force fields produce widely varying contact angles. Our extensive review of the experimental literature reveals extreme variation among reported values of graphene–water contact angles and a clustering of graphite–water contact angles into groups of freshly exfoliated (60° ± 13°) and not-freshly exfoliated graphite surfaces. The carbon–oxygen dispersion energy for a classical force field is optimized with respect to this 60° graphite–water contact angle in the infinite-force-cutoff limit, which in turn yields a contact angle for unsupported graphene of 80°, in agreement with the mean of the experimental results. Interaction force fields for finite cutoffs are also derived. A method for calculating contact angles from pressure tensors of planar equilibrium simulations that is ideally suited to graphite and graphene surfaces is introduced. Our methodology is widely applicable to any liquid-surface combination

Effects of surface rigidity and metallicity on dielectric properties and ion interactions at aqueous hydrophobic interfaces

Using classical molecular dynamics simulations, we investigate the dielectric properties at interfaces of water with graphene, graphite, hexane, and water vapor. For graphite, we compare metallic and nonmetallic versions. At the vapor–liquid water and hexane–water interfaces, the laterally averaged dielectric profiles are significantly broadened due to interfacial roughness and only slightly anisotropic. In contrast, at the rigid graphene surface, the dielectric profiles are strongly anisotropic and the perpendicular dielectric profile exhibits pronounced oscillations and sign changes. The interfacial dielectric excess, characterized by the shift of the dielectric dividing surface with respect to the Gibbs dividing surface, is positive for all surfaces, showing that water has an enhanced dielectric response at hydrophobic surfaces. The dielectric dividing surface positions vary significantly among the different surfaces, which points to pronounced surface-specific dielectric behavior. The interfacial repulsion of a chloride ion is shown to be dominated by electrostatic interactions for the soft fluid–fluid interfaces and by non-electrostatic Lennard-Jones interactions for the rigid graphene–water interface. A linear tensorial dielectric model for the ion–interface interaction with sharp dielectric interfaces located on the dielectric dividing surface positions works well for graphene but fails for vapor and hexane, because these interfaces are smeared out. The repulsion of chloride from the metallic and nonmetallic graphite versions differs very little, which reflects the almost identical interfacial water structure and can be understood based on linear continuum dielectric theory. Interface flexibility shows up mostly in the nonlinear Coulomb part of the ion–interface interaction, which changes significantly close to the interfaces and signals the breakdown of linear dielectric continuum theory

Observation of enhanced rate coefficients in the H2+_2^+ + H2_2 →\rightarrow H3+_3^+ + H reaction at low collision energies

The energy dependence of the rate coefficient of the H$_2^+\ + {\rm H}_2 \rightarrow {\rm H}_3^+ + {\rm H}$ reaction has been measured in the range of collision energies between $k_\mathrm{B}\cdot 10$ K and $k_\mathrm{B}\cdot 300$ mK. A clear deviation of the rate coefficient from the value expected on the basis of the classical Langevin-capture behavior has been observed at collision energies below $k_\mathrm{B}\cdot 1$ K, which is attributed to the joint effects of the ion-quadrupole and Coriolis interactions in collisions involving ortho-H$_2$ molecules in the $j = 1$ rotational level, which make up 75% of the population of the neutral H$_2$ molecules in the experiments. The experimental results are compared to very recent predictions by Dashevskaya, Litvin, Nikitin and Troe (J. Chem. Phys., in press), with which they are in agreement.Comment: 14 pages, 3 figure

Using a direct simulation Monte Carlo approach to model collisions in a buffer gas cell

A direct simulation Monte Carlo (DSMC) method is applied to model collisions between He buffer gas atoms and ammonia molecules within a buffer gas cell. State-tostate cross sections, calculated as a function of collision energy, enable the inelastic collisions between He and NH3 to be considered explicitly. The inclusion of rotationalstate-changing collisions affects the translational temperature of the beam, indicating that elastic and inelastic processes should not be considered in isolation. The properties of the cold molecular beam exiting the cell are examined as a function of the cell parameters and operating conditions; the rotational and translational energy distributions and are in accord with experimental measurements. The DSMC calculations show that thermalisation occurs well within the typical 10-20 mm length of many buffer gas cells, suggesting that shorter cells could be employed in many instances – yielding a higher flux of cold molecules

New method to study ion-molecule reactions at low temperatures and application to the H2+_2^+ + H2_2 →\rightarrow H3+_3^+ + H reaction

Studies of ion-molecule reactions at low temperatures are difficult because stray electric fields in the reaction volume affect the kinetic energy of charged reaction partners. We describe a new experimental approach to study ion-molecule reactions at low temperatures and present, as example, a measurement of the ${\rm H}_2^+ + {\rm H}_2\rightarrow {\rm H}_3^+ + {\rm H}$ reaction with the ${\rm H}_2^+$ ion prepared in a single rovibrational state at collision energies in the range $E_{\rm col}/k_{\rm B} = 5$-60 K. To reach such low collision energies, we use a merged-beam approach and observe the reaction within the orbit of a Rydberg electron, which shields the ions from stray fields. The first beam is a supersonic beam of pure ground-state H$_2$ molecules and the second is a supersonic beam of H$_2$ molecules excited to Rydberg-Stark states of principal quantum number $n$ selected in the range 20-40. Initially, the two beams propagate along axes separated by an angle of 10$^\circ$. To merge the two beams, the Rydberg molecules in the latter beam are deflected using a surface-electrode Rydberg-Stark deflector. The collision energies of the merged beams are determined by measuring the velocity distributions of the two beams and they are adjusted by changing the temperature of the pulsed valve used to generate the ground-state ${\rm H}_2$ beam and by adapting the electric-potential functions to the electrodes of the deflector. The collision energy is varied down to below $E_{\rm col}/k_{\rm B}= 10$ K, i.e., below $E_{\rm col}\approx 1$ meV, with an energy resolution of 100 $\mu$eV. We demonstrate that the Rydberg electron acts as a spectator and does not affect the cross sections, which are found to closely follow a classical-Langevin-capture model in the collision-energy range investigated. Because all neutral atoms and molecules can be excited to Rydberg states, this method of studyingComment: 39 pages, 10 figure

Beyond direct simulation Monte Carlo (DSMC) modelling of collision environments

The raw data behind the results presented in the paper are provided here

A topology framework for macromolecular complexes and condensates

Macromolecular assemblies such as protein complexes and protein/RNA condensates are involved in most fundamental cellular processes. The arrangement of subunits within these nano-assemblies is critical for their biological function and is determined by the topology of physical contacts within and between the subunits forming the complex. Describing the spatial arrangement of these interactions is of central importance to understand their functional and stability consequences. In this concept article, we propose a circuit topology-based formalism to define the topology of a complex consisting of linear polymeric chains with inter- and intrachain interactions. We apply our method to a system of model polymer chains as well as protein assemblies. We show that circuit topology can categorize different forms of chain assemblies. Our multi-chain circuit topology should aid analysis and predictions of mechanistic and evolutionary principles in the design of macromolecular assemblies