Computational Modeling of Realistic Cell Membranes

Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead

Isotherms of Fluids in Native and Defective Zeolite and Alumino-Phosphate Crystals: Monte-Carlo Simulations with “On-the-Fly”

We use periodic Density Functional Theory (DFT) method to generate the electrostatic potentials of adsorption materials and use them in Grand Canonical Monte Carlo simulations of fluid adsorption isotherms. This permits us to consider complex solids showing defects and without a priori knowledge of their electrostatic parameters for the Monte Carlo simulations. We apply the method to aluminophosphate and silicate solids of ZON type and evaluate their affinity to adsorb and separate CO2-N2(H2O) mixtures

Rheological behavior of aqueous polyacrylamide solutions determined by dissipative particle dynamics and comparison to experiments

Based on molecular-dynamics simulations and experimental data, a new coarse-grained forcefield is proposed for the polyacrylamide (PAM)-water system that allows to study dynamical properties of chains at several concentrations with molecular weight up to 17000 g/mol. Non-equilibrium simulations were used to compute relative viscosities, enabling a direct comparison with experimental values. High-shear-rate measurements for low-molecular-weight PAM (10000 g/mol) were done using a microfluidic rheometer Rheosense to decrease the gap between experimental and simulated shear rates. DPD simulations reproduced qualitatively and quantitatively structural properties as well as rheological properties in the dilute regime and qualitatively in the semi-dilute regime

Isotherms of Fluids in Native and Defective Zeolite and Alumino-Phosphate Crystals: Monte-Carlo Simulations with “On-the-Fly” ab initio

We use periodic Density Functional Theory (DFT) method to generate the electrostatic potentials of adsorption materials and use them in Grand Canonical Monte Carlo simulations of fluid adsorption isotherms. This permits us to consider complex solids showing defects and without a priori knowledge of their electrostatic parameters for the Monte Carlo simulations. We apply the method to aluminophosphate and silicate solids of ZON type and evaluate their affinity to adsorb and separate CO2-N2(H2O) mixtures

United atom forcefield for vapor-liquid equilibrium (VLE) properties of cyclic and polycyclic compounds from Monte Carlo simulations

International audienceGibbs ensemble Monte Carlo and NPT simulations are applied to the prediction of VLE properties for cyclic and polycyclic molecules with internal flexibility. An extension of the TraPPE-UA forcefield is defined, considering the molecules fully flexible with appropriate intramolecular potential terms (bond stretching, bending, torsion, Van der Waals) in cycles as well as in side chains. New United Atom types are proposed to handle the ternary and quaternary carbons involved in naphthenes and aromatics bearing alkyl groups or naphthenoaromatics, and published TraPPE-UA parameters are kept unchanged for other groups. The extended forcefield is tested for accuracy and internal consistency on a set of 34 compounds comprising between 5 and 28 carbon atoms including naphthenic hydrocarbons, aromatic hydrocarbons, naphthenoaromatics, and thiophenic compounds. This set of compounds contains several multi-functional polycyclic molecules which can now be described with the forcefield extensions provided by this work (e.g. 5α cholestane, 1-hexyl tetralin) and that are representative of a much wider range of compounds for which predictions through theoretical methods are difficult to be achieved. Comparison with available experimental data on normal boiling temperature, vapor pressure, and liquid density, reveals average absolute deviations of 6.4 K on normal boiling temperature and 0.91% on standard liquid density, without noticeable increase of deviations with molecular weight. Computational efficiency allows simulations for compounds containing up to 30 carbon atoms

Molecular Simulation of Adsorption in Microporous Materials

The development of industrial software, the decreasing cost of computing time, and the availability of well-tested forcefields make molecular simulation increasingly attractive for chemical engineers. We present here several applications of Monte-Carlo simulation techniques, applied to the adsorption of fluids in microporous solids such as zeolites and model carbons (pores < 2 nm). Adsorption was computed in the Grand Canonical ensemble with the MedeA®-GIBBS software, using energy grids to decrease computing time. MedeA®-GIBBS has been used for simulations in the NVT or NPT ensembles to obtain the density and fugacities of fluid phases. Simulation results are compared with experimental pure component isotherms in zeolites (hydrocarbon gases, water, alkanes, aromatics, ethanethiol, etc.), and mixtures (methane-ethane, n-hexane-benzene), over a large range of temperatures. Hexane/benzene selectivity inversions between silicalite and Na-faujasites are well predicted with published forcefields, providing an insight on the underlying mechanisms. Also, the adsorption isotherms in Na-faujasites for light gases or ethane-thiol are well described. Regarding organic adsorbents, models of mature kerogen or coal were built in agreement with known chemistry of these systems. Obtaining realistic kerogen densities with the simple relaxation approach considered here is encouraging for the investigation of other organic systems. Computing excess sorption curves in qualitative agreement with those recently measured on dry samples of gas shale is also favorable. Although still preliminary, such applications illustrate the strength of molecular modeling in understanding complex systems in conditions where experiments are difficult