Gianluca Marcelli

Molecular simulation of the phase behavior of noble gases using accurate two-body and three-body intermolecular potentials

Gibbs ensemble Monte Carlo simulations are reported for the vapor–liquid phase coexistence of argon, krypton, and xenon. The calculations employ accurate two-body potentials in addition to contributions from three-body dispersion interactions resulting from third-order triple-dipole, dipole–dipole–quadrupole, dipole–quadrupole–quadrupole, quadrupole–quadrupole–quadrupole, and fourth-order triple-dipole terms. It is shown that vapor–liquid equilibria are affected substantially by three-body interactions. The addition of three-body interactions results in good overall agreement of theory with experimental data. In particular, the subcritical liquid-phase densities are predicted accurately.

Inferring biological mechanisms from spatial analysis: Prediction of a local inhibitor in the ovary

Female mammals are born with a lifetimes supply of oocytes individually enveloped in flattened epithelial cells to form primordial follicles. It is not clear how sufficient primordial follicles are maintained to sustain the reproductive lifespan, while providing an adequate supply of mature oocytes for ovulation. Locally produced growth factors are thought to be critical regulators of early follicle growth, but knowledge of their identity and source remains incomplete. Here, we have used a simple approach of spatial analysis of structures in histological tissue sections to identify likely sources of such regulatory molecules, narrowing the field for future screening for candidate growth factors or antagonists. We have quantified the relative spatial positions of primordial (resting) follicles and growing follicles in mice on days 4, 8, and 12 after birth, and calculated interfollicular distances. Follicles were significantly less likely to have started growing if they had 1 or more primordial follicles close by (within 10 μm), predicting that primordial follicles inhibit each other. This approach allows us to hypothesize that primordial follicles produce a diffusible inhibitor that prevents neighboring primordial follicles from growing. Such an approach has wide applicability within many branches of developmental and cell biology for studying spatial signaling within tissues and cells.

Models of electron trapping and transport in polyethylene: Current–voltage characteristics

We present a unified method to estimate current–voltage characteristics of insulators starting from ab initio electronic calculations of the properties of the dielectric material. The method consists of three stages: (1) computation of trap energy distributions for excess electrons by means of density functional theory, (2) computation of local electron mobilities from a multiple trapping electron transport model which includes trap filling effects and (3) macroscopic integration of the Poisson and current–field equations, using local electron mobility data from stage (2) to predict the current–voltage characteristics for a material of a given width. The only input to this procedure is the chemical composition of the insulating material. We compare our model results with experimental studies of the current–voltage curve of cross-linked polyethylene.

On the estimation of the curvatures and bending rigidity of membrane networks via a local maximum-entropy approach

We present a meshfree method for the curvature estimation of membrane networks based on the local maximum entropy approach recently presented in [1]. A continuum regularization of the network is carried out by balancing the maximization of the information entropy corresponding to the nodal data, with the minimization of the total width of the shape functions. The accuracy and convergence properties of the given curvature prediction procedure are assessed through numerical applications to benchmark problems, which include coarse grained molecular dynamics simulations of the fluctuations of red blood cell membranes [2,3]. We also provide an energetic discrete-to-continuum approach to the prediction of the zero-temperature bending rigidity of membrane networks, which is based on the integration of the local curvature estimates. The local maximum entropy approach is easily applicable to the continuum regularization of fluctuating membranes, and the prediction of membrane and bending elasticities of molecular dynamics models.

A link between the two-body and three-body interaction energies of fluids from molecular simulation

Molecular simulation data are reported that indicate that there is a simple empirical relationship between two-body and three-body interaction energies. The significance of this relationship is that three-body interactions can be estimated accurately from two-body interactions without incurring the computational penalty of three-body calculations. The relationship is tested by performing Gibbs ensemble simulations for the vapor–liquid equilibria of argon. The results are in good agreement with calculations that explicitly evaluate all three-body interactions.

On the relationship between two-body and three-body interactions from nonequilibrium molecular dynamics simulation

Nonequilibrium molecular dynamics (NEMD) simulations are performed for argon at different strain rates using accurate two-body and three-body intermolecular potentials. The contributions of two- and three-body interactions to the configurational energy of argon at different strain rates are reported. The NEMD data indicate that there is the same simple relationship between two- and three-body interactions as reported previously [Marcelli and Sadus, J. Chem. Phys. 112, 6382 (2000)] from equilibrium Monte Carlo simulations. The relationship is largely independent of strain rate. NEMD calculations using this relationship for shear viscosity at different strain rates indicate good agreement with full two-body+three-body calculations. This means that the effect of three-body interactions on transport properties might be achieved in a conventional two-body NEMD simulation without incurring the computational penalty of three-body calculations.

Understanding changes in uptake and release of serotonin from gastrointestinal tissue using a novel electroanalytical approach

Serotonin (5-HT) is well known to be a key neurotransmitter within the gastrointestinal (GI) tract, where it is responsible for influencing motility. Obtaining dynamic information about the neurotransmission process (specifically the release and reuptake of 5-HT) requires the development of new approaches to measure the extracellular 5-HT concentration profile. In this work constant-potential amperometry has been utilised at +650 mV vs. Ag|AgCl to measure in vitro the overflow of 5-HT. Steady-state levels of 5-HT have been observed, due to continuous mechanical stimulation of the tissue from the experimental protocol. Measurements are conducted at varying tissue-electrode distances in the range of 5 to 1100 microm. The difference in the current from the bulk media and that from each tissue-electrode distance is obtained, and the natural log of this current is plotted versus the tissue-electrode distance. The linear fit to the log of the current is derived, and its intercept, I(0), with the vertical axis and its slope are calculated. The reciprocal of the slope, indicated as slope(-1), is used as a marker of reuptake. The ratio between intercept, I(0), and the reciprocal of the slope, I(0)/slope(-1), is a measure of the flux at the tissue surface and it can be used as a marker for the 5-HT release rate. Current measurements for ileum and colon tissue indicated a significantly higher reuptake rate in the colon, showed by a lower slope(-1). In addition, the ratio, I(0)/slope(-1), indicated that the colon has a higher 5-HT flux compared to the ileum. Following the application of the serotonin selective reuptake inhibitor (SSRI), fluoxetine, both tissues showed a higher value of slope(-1), as the reuptake process is blocked preventing clearance of 5-HT. No differences were observed in the ratio, I(0)/slope(-1), in the ileum, but a decrease was observed in the colon. These results indicate that ileum and colon are characterised by different reuptake and release processes. The new approach we propose provides pivotal information on the variations in the signalling mechanism, where steady state levels are observed and can be a vital tool to study differences between normal and diseased tissue and also the efficacy of pharmacological agents.

Molecular simulation of the vapour–liquid phase coexistence of neon and argon using ab initio potentials

Gibbs ensemble simulations using ab initio intermolecular potentials are reported for the vapour–liquid phase coexistence of neon and argon. For neon two different quantum chemical ab initio potentials of well-known quality are used to investigate the effect of the quality of pair interactions. In addition calculations are also reported for neon using a potential that includes three-body interactions. For argon, simulations are compared with results obtained from NPH-ensemble molecular dynamics simulations. It is found that the results of a perfect pair potential must occur outside the experimental temperature–density phase envelope. Therefore, if a perfect pair potential is used, many-body interactions and quantum effects must be considered to obtain good agreement with experiment.

The strain rate dependence of shear viscosity, pressure and energy from two-body and three-body interactions

Non-equilibrium molecular dynamics simulations (NEMD) are reported for the shear viscosity of xenon using accurate two- and three-body potentials. The hydrostatic pressure and energy are observed to vary proportionally with the square of the strain rate. This is in contrast to the non-analytic three-halves power dependence on strain rate predicted by mode-coupling theory. This result is attributed solely to the two-body potential. The main effect of the three-body potential is to alter the magnitude of the pressure, energy and viscosity profiles.

Erratum: On the relationship between two-body and three-body interactions from nonequilibrium molecular dynamics simulation [J. Chem. Phys. 115, 9410 (2001)]

where the angle brackets represent ensemble averages, E2 is the two-body energy per particle and the remaining terms defined in the original paper. The contribution from the th term on the right-hand side of this equation was miss from the values of pressure reported in Fig. 3. The corr pressure-strain rate behavior is given here in Fig. 3 ~c!. It is now apparent that there is very good agreement of the p sure calculated using the effective intermolecular poten compared with full two-body 1three-body calculations. In our original paper, we conjectured that the failure of Eq. ~2! for pressure was due to differences in the three-body dis bution function and spatial derivatives of the Axilrod–Tell potential compared with Eq. ~2!. The very good agreemen for pressure reported here make these conjectures unn sary. Equation~2! can be used as an accurate alternative such calculations for both energy and pressure. We note that the expression for pressure is strictly va only at equilibrium. Nonetheless, agreement between th pressures and those evaluated for the full two-body p three-body potential is very good for the range of strain r considered. The revised calculation procedure may also fect the calculation of viscosities. However, the effect three-body interactions on viscosities 2 i relatively small and the additional uncertainty from this source is only likely have a very small influence on the viscosity results.