Computer simulation of lipid membranes: Methodology and achievements

Rapid development of computer power during the last decade has made molecular simulations of lipid bilayers feasible for many research groups, which, together with the growing general interest in investigations of these very important biological systems has lead to tremendous increase of the number of research on the computational modeling of lipid bilayers. In this review, we give account of the recent progress in computer simulations of lipid bilayers covering mainly the period of the last 7 years, and covering only several selected subjects: methodological (development of the force fields for lipid bilayer simulations, use of coarse-grained models) and scientific (studies of the role of lipid unsaturation, and the effect of cholesterol and other inclusions on properties of the bilayer).     

Computer simulation of diffusion within and through membranes using nonequilibrium molecular dynamics

A novel nonequilibrium molecular dynamics (NEMD) method introduced in 1994 and its recent application to investigations of the transport properties of gases and dense fluids within strongly inhomogeneous pore structures are reviewed. In this technique molecular simulations are conducted under realistic nonequilibrium (experimental) conditions thus enabling direct insight into the underlying microscopic processes taking place during transport within pores. The case studies reviewed in this paper establish the versatility and scope of the NEMD technique and also demonstrate its significant advantages over prior molecular simulation procedures as a tool to assist in the design and tailoring of novel nanopore systems.     

Dinosterol in model membranes: Fluorescence polarization studies

The interaction between the phospholipids ofCrypthecodinium cohnii, a heterotropic marine dinoflagellate, and its major sterol dinosterol was studied using a fluorescence polarization technique. Compared to cholesterol, dinosterol is less soluble in model membranes and as effective in increasing the microviscosity. These results indicate that the unique side chain of dinosterol does not play a special role in terms of complementary interaction with the phospholipids of this organism.     

Computer simulation and preparation of molecularly imprinted polymer membranes with chlorogenic acid as template

A computational approach was developed for screening functional monomers for rational design of molecularly imprinted polymer (MIP) membranes. It was based on a comparison of the binding energy of complexes between a template and various functional monomers. According to the results of theoretical calculations, MIP membranes with chlorogenic acid as a template were prepared with a UV irradiation polymerization method, using 4‐vinylpyridine as a functional monomer and N,N′‐methylenebisacrylamide as a crosslinker, with poly(vinylidene fluoride) microfiltration membranes as the support. Membranes covered with a thin layer of imprinted polymer selective to chlorogenic acid were then obtained and tested using the equilibrium‐adsorption method. The high affinity of these synthetic membranes to chlorogenic acid, together with their straightforward and inexpensive preparation, provides a good basis for the development of applications of imprinted polymers in separation processes such as solid‐phase extraction. Copyright © 2011 Society of Chemical Industry     

Computer simulation studies on overlapping polymer chains confined in narrow channels

Conformation of polymer chains strongly confined in a narrow channel space was studied over a broad range of polymer volume fractions φ using lattice Monte Carlo simulations. The longitudinal component of the chain dimension decreased in a power law of ∼φ⁻¹ as φ exceeded the overlap volume fraction. The conformation changed from the one extended along the channel to a random coil. The change occurred without much overlap between adjacent chains. As the conformational transition was completed, the chains started to penetrate each other. Contraction of the chains became more gradual, and eventually the longitudinal component of the chain dimension approached that of the unconfined chains with the overall chain dimension being smaller than that of the unconfined chains. Predictions of the scaling theory were thus confirmed with additional detailed information on the state of confined chains in each regime of characteristic φ dependence of chain dimensions.     

Computer simulation studies of the selectivity of zeolites for different butene isomers

In the present study simulation methods are applied to investigate butene isomer selectivity in 55 zeolite structures, and to rank the predicted performance of potential zeolite catalysts. The method used is based on a blend of Monte Carlo and molecular dynamics with energy minimization procedures. The TON framework has the highest ‘selectivity’ followed by RHO and MFI. The calculations indicate that the TON (Theta-1) framework is particularly effective in binding differing butene isomers in differing manners. This revised version was published online in July 2006 with corrections to the Cover Date.     

Computer simulation of melt spinning of polypropylene fibers using a steady-state model

A mathematical model that includes crystallization in the spinline and the effect of crystallization on the extensional viscosity and the various physical properties of polypropylene has been developed and used to help in identifying the various factors that can affect the spun yarn characteristics. The model is used to simulate effects of spinning parameters on fiber physical properties, temperature, and stresses. The experimental observation of a minimum in density of the spun yarn at high throughput rates, when density is plotted as a function of take up velocity, has been investigated in some detail. It has been found that all conditions which can substantially affect the rate of cooling and the orientation of the polymer in the spinline, viz, throughput rate, spinning temperature, and spinning speed have an important bearing on the temperature range in which crystallization can take place in the spinline and thus affect the density. It is suggested that in addition to these factors, the formation of different crystal modifications at different spinning speeds could also contribute to the reduction in density of these samples. The model cannot reflect the observation of density changes occurring due to the formation of different crystal modifications. Nevertheless, it can be of use in understanding the effects of various process conditions on the cooling rate and the orientation of the polymer in the spinline. © 1995 John Wiley & Sons, Inc.     

Computer simulation method for calculating concentration profiles in polyurethane/polystyrene interpenetrating polymer network membranes

Interpenetrating polymer networks (IPNs) of polyurethane (PU) and polystyrene (PS; 90/10 and 75/25) were synthesized by the condensation reaction of castor oil with methylene diisocyanate and styrene, with benzoyl peroxide as an initiator. The IPN membranes were characterized for physicomechanical, optical, and X‐ray diffraction properties. Computer‐simulated concentration profiles of aqueous salt solutions through PU/PS IPN membranes were generated with Fick's second‐order differential equation, and the results were examined in terms of diffusion anomalies. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 122–128, 2003     

Computational simulation of gas separation using nonporous polymeric membranes: Experimental and theoretical studies

In this study, preparation and simulation of polydimethylsiloxane (PDMS) membranes for gas separation is carried out. The membranes are synthesized by solution‐casting method via silicon oil as precursor. Gas permeation experiments for single gases of CH₄ and N₂ were conducted at different feed pressures (2–10 bars). PDMS membrane as a rubbery polymer showed that are more permeable toward more condensable gases, i.e., CH₄ compared to N₂. It was indicated that increasing feed pressure enhances permeability of CH₄ through the membrane slightly, but the permeability of nitrogen was almost constant over enhancement of feed pressure. Moreover, a mathematical model was developed to predict the permeation of gases across PDMS membrane. The model is based on solving conservation equations for gases in the membrane phase. Finite element analysis was utilized for numerical simulation of the governing equations. The simulation results were used to predict the concentration of gases inside the membrane. POLYM. ENG. SCI., 55:54–59, 2015. © 2014 Society of Plastics Engineers     

Computer simulation of stiff-chain polymers

A review of studies on the computer simulation of the phase behavior of various stiff-chain polymer systems is presented. Methods for calculating phase diagrams of a polymer solution in a computer experiment are discussed, including the methods of extended ensembles, entropic simulation, and the Wang-Landau algorithm to obtain the density-of-states function. The authors’ original results on studying the intramolecular orientational and spatial ordering of monomer units in a single stiff-chain macromolecule in the bulk and near a planar adsorbing surface by means of the Wang-Landau algorithm and using the bond-fluctuation lattice model are presented. Corresponding state diagrams are presented for these two cases. For systems of multiple chains, the phenomenon of nematic liquid-crystalline ordering in semi-dilute solutions in the bulk and in a planar layer is considered, and the phase diagrams for these cases are presented. A survey of the published data on some other promising directions of investigation of stiff-chain polymer systems is presented.     

Computer simulation of urethane formation

Computer model calculations have been used to simulate the reaction of polyoxypropylene triol with hexamethylene diisocyanate. Various molecular weight distributions and degrees of polymerisation are used in the calculation. The effect of side reactions is investigated and compared with experiment. Good agreement for both cyclisation and gel points is found for bulk and concentrated solutions. The model can be used to simulate random polycondensation reactions with a reliability approaching that of experiments, and it gives crucial results that cannot be obtained in any other way.     

Computer simulation of injection molding

The injection-molding process consists of three consecutive stages: filling, packing, and cooling. In order to obtain some insight into the phenomena involved in the process, and particularly in order to evaluate the moldability of certain resins and to predict the microstructure and properties of products molded therefrom, a number of workers have employed a variety of techniques based on mathematical simulation of the process. Mathematical simulation involves writing the relevant continuity, momentum, and energy equations governing the system, with appropriate boundary and initial conditions representing the prevailing conditions in the cavity and delivery channels. In order to obtain meaningful solutions to the above equations, detailed information is required regarding the thermodynamic, thermal, and rheological properties of the resin. Moreover, the prediction of the microstructure and ultimate properties of the molded article requires a knowledge of the morphological, crystallization, and orientation phenomena that take place under the influence of the thermo-mechanical history experienced by the resin. The complexity of the equations involved results in the utilization of a number of simplifying assumptions and the resort to computer simulation and numerical solutions of these equations. A variety of numerical schemes based on finite difference and finite element methods has been employed by various researchers.     

Effect of simple olive biophenols and analogues on the thermotropic behavior of biological model membranes

Some foods, in particular fruits and vegetables, are known to have protective effects against cardiovascular disease and cancer. This is believed to be due to the presence of antioxidant substances such as hydroxyaromatic compounds present in these foods. We investigated the effect exerted by protochatechuic and benzoic acid, simple biophenols (BPs) present in olive oils, and their substitute analogues, veratric and xylylic acids, on the thermotropic behavior of model membranes (dimyristoylphosphatidylcholine multilamellar vesicles) by differential scanning calorimetry (DSC) DSC analysis was carried out at two different pHs (4.0 and 7.4). The acids, when dispersed in liposomes during their preparation, were found to modify the gel to liquidcrystal phase transition of the lipid vesicles at pH 4, causing a temperature shift towards lower values and a variation in enthalpy changes. The magnitude of the temperature shift and enthalpy change was a function of the concentration of BP in the lipid dispersions and their lipophilic character. The examined compounds were unable to appreciably modify the thermotropic behavior of the liposomes at pH 7.4 suggesting that the interactions and their absorption are highly influenced by the lipophilic character induced by structural factors and by the polarity of the acidic group.     

Molecular simulation study of polyurethane membranes

Structural, physical and separation properties of polyurethane membrane were investigated by configuration bias grand canonical Monte Carlo and molecular dynamic methods and the effects of degree of polymerization on these properties were studied. To understand the effect of degree of polymerization of polyurethane membrane on its separation property, the adsorption of furfural as pure and binary mixture with water was studied for polyurethane membrane with varied degrees of polymerization from 5 to 100. The temperature range for simulation calculation was 298 K–360 K and the pressure range was 0–10 bar. Also the effects of feed composition, density and free volume of polyurethane membrane on its separation property were studied. It was found that the adsorption of furfural and water in polyurethane membrane depends on free volume of polyurethane and this dependency is more significant for the adsorption of water molecule. The results indicate that the maximum adsorption of furfural and water occurs on polyurethane membrane with polymerization degree of 10.     

Computer simulation of high-discharge-rate battery systems

Simulations were carried out for a proposed two-dimensional high-discharge-rate cell under load with an interelectrode gap of the order of 100 m. A finite difference program was written to solve the set of coupled, partial differential equations governing the behaviour of this system. Cell dimensions, cell loads, and kinetic parameters were varied to study the effects on voltage, current and specific energy. Trends in cell performance are noted, and suggestions are made for development of cells to meet specific design criteria. Modelling difficulties are discussed and suggestions are made for improvement.Nomenclature A surface area of unit cell (cm²) - A _k conductivity parameter (cm^{2 –1} mol^–1) - b Tafel slope (V) - c concentration (mol cm^–3) - c ₀ concentration of bulk electrolyte (mol cm^–3) - D diffusivity (cm² s^–1) - D _h lumped diffusion parameter (J s cm^–2 mol^–1) - D _s lumped diffusion coefficient (A cm² mol^–1) - E rest potential of electrode (V) - F Faraday constant (96 500 C mol^–1) - i current density (A cm^–2) - I total current for unit cell (A) - i ₀ exchange current density (A cm^–2) - N flux of charged species (mol cm² s^–1) - R gas constant (8.314 J mol^–1 K^–1) - R _ext resistance external to cell () - t time (s) - T temperature (K) - t ₀ transference number - u mobility (cm² mol J^–1 s^–1) - V volume of an element in the cell (cm³) - V _ext voltage external to cell (V) - z charge on an ion - _c concentration overpotential (V) - _s surface overpotential (V) - conductivity (^–1 cm^–1) - stoichiometric coefficient - electric potential in solution (V)     

Computer simulation of wastewater treatment plant

The computer simulation of wastewater treatment systems is finding increasingly wide application. Simulation studies of complete municipal waste treatment plants have been successfully accomplished. This paper describes an attempt to simulate the operation of the Kitchener, Ontario, Waste Treatment plant taking data from the last six months of 1975. It is shown that, provided some parameter values are taken from the actual plant, it is possible to closely match the mean monthly performance of the system. Steady-state mathematical models of the major waste treatment units are presented together with a discussion of the structure and operation of the SEPSIM computer program. Detailed cost relationships for a complete municipal waste treatment plant are also shown.     

Computer simulation of granule microstructure formation

The diagenesis (porous microstructure evolution) of granules formed by a layering growth mechanism in a wet granulation process has been modelled. The model includes the packing of primary particles with a given size and shape distribution, and the deposition, spreading, and solidification of binder droplets within the growing granule. The dependence of granule porosity on the binder/solids ratio, primary particle size and morphology, and the rates of binder spreading and solidification has been investigated. The results are presented in the form of structure maps relating volume-averaged microstructure parameters with dimensionless groups including the ratio of droplet spreading and solidification times and the mean time between particle collisions. These graphs can guide the selection of process operating conditions or formulation ingredient properties required to obtain a particular granule microstructure.