Coarse grained model of entangled polymer melts

A coarse graining procedure aimed at reproducing both the chain structure and dynamics in melts of linear monodisperse polymers is presented. The reference system is a bead-spring-type representation of the melt. The level of coarse graining is selected equal to the number of beads in the entanglement segment, Ne. The coarse model is still discrete and contains blobs each representing Ne consecutive beads in the fine scale model. The mapping is defined by the following conditions: the probability of given state of the coarse system is equal to that of all fine system states compatible with the respective coarse state, the dissipation per coarse grained object is similar in the two systems, constraints to the motion of a representative chain exist in the fine phase space, and the coarse phase space is adjusted such to represent them. Specifically, the chain inner blobs are constrained to move along the backbone of the coarse grained chain, while the end blobs move in the three-dimensional embedding space. The end blobs continuously redefine the diffusion path for the inner blobs. The input parameters governing the dynamics of the coarse grained system are calibrated based on the fine scale model behavior. Although the coarse model cannot reproduce the whole thermodynamics of the fine system, it ensures that the pair and end-to-end distribution functions, the rate of relaxation of segmental and end-to-end vectors, the Rouse modes, and the diffusion dynamics are properly represented.     

Coarse grained model of diffusion in entangled bidisperse polymer melts

Chain diffusion is studied in mixtures of bidisperse linear polymers of same chemical identity by means of simulations. The two subpopulations are moderately to highly entangled, with the shorter chain length N(S), fulfilling N(S)N(e)> or =5. To this end, a coarse grained model calibrated to reproduce both the structure and dynamics of chains in monodisperse entangled melts is used [A. Rakshit and R. C. Picu, J. Chem. Phys. 125, 164907 (2006)]. Its performance in reproducing chain dynamics in a polydisperse melt is tested by extensively comparing the results with those obtained from an equivalent fine scale representation of the same system (a bead-spring model). The coarse grained model is used further to investigate the scaling of the diffusion coefficient with the length of the two types of chains and its dependence on the respective fractions. The model reproduces many features observed experimentally. For example, the diffusion coefficient of one of the chain types decreases with increasing the length of the other type chains. It is shown that, in this model, this effect is not linked to constraint release. When the matrix chains become sufficiently long, their length does not influence the diffusion coefficient of the short chains anymore. The diffusion coefficient of the short chains scales with their weight fraction in a manner consistent with experimental observations. In mixtures, the dynamics of the short chains is slower and that of the long chains is marginally faster than in their respective monodisperse melts.     

Coarse grained models for flexible liquid crystals: parameterization of the bond fluctuation model

We extend the bond fluctuation model, originally devised to investigate polymer systems, to contain anisotropic interactions suitable for the simulation of large flexible molecules such as liquid crystalline polymers and dendrimers. This extended model coarse grains the interaction between the flexible chains at a similar level of detail to the mesogenic units. Suitable interaction parameters are obtained by performing trial simulations on a low molar mass liquid crystalline system. The phase diagram of this system is determined as a function of the molecular stiffness. The nematic to isotropic transition temperature is found to increase with increasing stiffness.     

Artificial neural network modification of simulation-based fitting: application to a protein-lipid system

Simulation-based fitting has been applied to data analysis and parameter determination of complex experimental systems in many areas of chemistry and biophysics. However, this method is limited because of the time costs of the calculations. In this paper it is proposed to approximate and substitute a simulation model by an artificial neural network during the fitting procedure. Such a substitution significantly speeds up the parameter determination. This approach is tested on a model of fluorescence resonance energy transfer (FRET) within a system of site-directed fluorescence labeled M13 major coat protein mutants incorporated into a lipid bilayer. It is demonstrated that in our case the application of a trained artificial neural network for the substitution of the simulation model results in a significant gain in computing time by a factor of 5 x 10(4). Moreover, an artificial neural network produces a smooth approximation of the noisy results of a stochastic simulation.     

Modeling of the triglyceride-rich core in lipoprotein particles

Triglycerides are a major component of many important biological entities such as lipoproteins and lipid droplets. This work focuses on two common triglycerides, tripalmitin and triolein, which have been simulated through atomistic molecular dynamics at temperatures of 310 and 350 K for 300-700 ns. In these systems, both structural and dynamical properties have been characterized, paying particular attention to understanding the packing of triglyceride molecules and their molecular conformations. Additionally, we study the liquid-to-crystalline phase transition of tripalmitin through a temperature quench from the high-temperature isotropic liquid phase to 310 K, corresponding to a polymorphic, crystalline-like phase. The transition is characterized in detail through density, average molecular shape, and, in particular, the relevant order parameter describing the transition.     

Assembly of lipids and proteins into lipoprotein particles

The self-assembly of reconstituted discoidal high-density lipoproteins, known as nanodiscs, was studied using coarse-grained molecular dynamics and small-angle X-ray scattering. In humans, high-density lipoprotein particles transport cholesterol in the blood and facilitate the removal of excess cholesterol from the body. Native high-density lipoprotein exhibits a wide variety of shapes and sizes, forming lipid-free/poor, nascent discoidal, and mature spherical particles. Little is known about how these lipoprotein particles assemble and transform from one state to another. Multiple 10 micros coarse-grained simulations reveal the assembly of discoidal high-density lipoprotein particles from disordered protein-lipid complexes. Small-angle X-ray scattering patterns were calculated from the final assembled structures and compared with experimental measurements carried out for this study to verify the accuracy of the coarse-grained simulations. Results show that hydrophobic interactions assemble, within several microseconds, the amphipathic helical proteins and lipids into roughly discoidal particles, while the proteins assume a final approximate double-belt configuration on a slower time scale.     

Multicut-HDMR with an application to an ionospheric model

A new High Dimensional Model Representation (HDMR) tool, Multicut-HDMR, is introduced and applied to an ionospheric electron density model. HDMR is a general set of quantitative model assessment and analysis tools for improving the efficiency of deducing high-dimensional input-output system behavior. HDMR describes an output [f(x)] in terms of its input variables (x = [x(1), x(2), em leader, x(n)]) via a series of finite, hierarchical, correlated function expansions. Various forms of HDMR are constructed for different purposes such as modeling laboratory or field data, or reproducing a complicated mathematical model. The Cut-HDMR technique, which expresses f(x) with respect to a specified reference point x in the input space, is appropriate when the input space is sampled in an orderly fashion. However, if the desired domain of the input space is too large, the HDMR function expansion may not converge, and Cut-HDMR will be unable to accurately approximate f(x). The new Multicut-HDMR technique addresses this problem through the use of multiple reference points in the input space.     

An anisotropic coarse‐grained model based on Gay–Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model

In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay–Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay–Berne parameters were initially obtained by fitting to atomistic profiles of van der Waals interactions between homodimers of molecular fragments while EMP parameters was directly derived from the expansion of point multipoles at predefined EMP sites. Second, the GB and EMP parameters for DMPC molecule were carefully optimized to be comparable to AMBER atomistic model in the calculations of the dipole moments of DMPC monomers adopting different conformations as well as the nonbonded interactions between two DMPC molecules adopting different conformations and separated at various distances. Finally, the GB parameters for DMPC were slightly adjusted in simulating a 72 DMPC bilayer system so that our GBEMP model would be able to reproduce a few important structural properties, namely, thickness (), area per lipid ( ) and volume per lipid ( ). Meanwhile, the atomistic and experimental results for electron density profiles and order parameters were reproduced reasonably well by the GBEMP model, demonstrating the promising feature of GBEMP model in modeling lipid systems. Finally, we have shown that current GBEMP model is more efficient by a factor of about 25 than AMBER atomistic point charge model. © 2015 Wiley Periodicals, Inc.     

Extension of CAVS coarse‐grained model to phospholipid membranes: The importance of electrostatics

It is evident from experiment that electrostatic potential (or dipole potential) is positive inside PC or PE lipid bilayers in the absence of ions. MARTINI coarse‐grained (CG) model, which has been widely used in simulating physical properties of lipid bilayers, fails to reproduce the positive value for the dipole potential in the membrane interior. Although the total dipole potential can be correctly described by the BMW/MARTINI model, the contribution from the ester dipoles, playing a nontrivial role in the electrostatic potential across lipid membranes, is neglected by this hybrid approach. In the ELBA CG model, the role of the ester dipoles is considered, but it is overweighed because various atomistic models have consistently shown that water is actually the leading contributor of dipole potential. Here, we present a CG approach by combining the BMW‐like water model (namely CAVS model) with the ELBA‐like lipid model proposed in this work. Our CG model was designed not only to correctly reproduce the positive values for the dipole potential inside PC and PE lipid bilayers but also to properly balance the individual contributions from the ester dipoles and water, surmounting the limitations of current CG models in the calculations of dipole potential. © 2017 Wiley Periodicals, Inc.     

The MARTINI force field: coarse grained model for biomolecular simulations

We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.     

Coating of open tubular capillaries with discoidal and spherical high-density lipoprotein particles in electrochromatography

A new method was developed for the coating of fused-silica capillaries with human high-density lipoproteins (HDLs) for use in electrochromatography. The HDL particles used for the coating differed in particle shape and composition. Both discoidal and spherical particles formed a monolayer on the inner silica wall as confirmed by atomic force microscopy. The effect of coating conditions, such as HDL concentration and coating time, was investigated with spherical HDL particles. Examination of the influence of pH on the coating stability also allowed the determination of pI values for the HDL particles attached to the capillary wall. The pI values for spherical and discoidal HDL particles were close to 5.0. The repeatabilities of the EOF mobility and the retention factors of the uncharged steroid hormones used as model compounds were exploited in the evaluation of the coating stability. The optimal coating was achieved with 0.1 mg/mL HDL protein and 50 min flushing with coating solution followed by 15 min standing time. Electrochromatography with HDL-coated open tubular capillaries offers a new tool for the study of HDL particle structure and transformations.     

Phase diagram of model anisotropic particles with octahedral symmetry

The phase diagram for a system of model anisotropic particles with six attractive patches in an octahedral arrangement has been computed. This model for a relatively narrow value of the patch width where the lowest-energy configuration of the system is a simple cubic crystal. At this value of the patch width, there is no stable vapor-liquid phase separation, and there are three other crystalline phases in addition to the simple cubic crystal that is most stable at low pressure. First, at moderate pressures, it is more favorable to form a body-centered-cubic crystal, which can be viewed as two interpenetrating, and almost noninteracting, simple cubic lattices. Second, at high pressures and low temperatures, an orientationally ordered face-centered-cubic structure becomes favorable. Finally, at high temperatures a face-centered-cubic plastic crystal is the most stable solid phase.     

Interaction of bacterial endotoxine (lipopolysaccharide) with latex particles: application to latex agglutination immunoassays

The latex agglutination immunoassay technique uses polymer colloids as carriers for antibodies or antigens to enhance the immunological reaction. In this work, the interaction of a lipopolysaccharide (LPS) of Brucella Melitensis with two conventional latexes has been studied. Some experiments on the physical adsorption of the LPS onto these polystyrene beads have been performed and several complexes with different coverage degrees were obtained by modifying the incubation conditions. Regarding the application in the development of diagnostic test systems, it is advisable to study the latex-LPS complexes from an electrokinetic and colloidal stability point of view. The complexes were electrokinetically characterized by measuring the electrophoretic mobility under different redispersion conditions. The colloidal stability was determined by simple turbidity measurements. Experimental and theoretical data have been employed to study the molecular disposition of the LPS in the latex particle surface to compare with the outer membrane of bacterial cells. Latex complexes covered by different LPS amounts showed high colloidal stability and adequate immunoreactivity that remains for a long time period.     

Monte Carlo simulations of a coarse grained model for an athermal all-polystyrene nanocomposite system

The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as random walks and the system is described through a coarse grained Hamiltonian. This approach is related to self-consistent-field theory but does not invoke a saddle point approximation and is suitable for treating large three-dimensional systems. The local structure of the polymer matrix in the vicinity of the nanoparticles is found to be different in many ways from that of the corresponding bulk, both at the segment and the chain level. The local polymer density profile near to the particle displays a maximum and the bonds develop considerable orientation parallel to the nanoparticle surface. The depletion layer thickness is also analyzed. The chains orient with their longest dimension parallel to the surface of the particles. Their intrinsic shape, as characterized by spans and principal moments of inertia, is found to be a strong function of position relative to the interface. The dispersion of many nanoparticles in the polymeric matrix leads to extension of the chains when their size is similar to the radius of the dispersed particles.     

Synthesis of submicrometer-sized titania spherical particles with a sol-gel method and their application to colloidal photonic crystals

A synthetic method for preparing submicrometer-sized titania particles is proposed, which is based on hydrolysis of titanium alkoxide with the use of a cosolvent and an amine catalyst for alkoxide hydrolysis. The preparation was performed with different amines of ammonia, methylamine (MA), and dimethylamine (DMA) in different solvents of ethanol/acetonitrile, ethanol/methanol, ethanol/acetone, ethanol/acetonitrile, and ethanol/formamide for 0.1-0.3 M water and 0.03 M titanium tetraisopropoxide (TTIP) at temperatures of 10-50 degrees C. The use of the ethanol/acetonitrile solvent with MA was required for preparing monodispersed, spherical particles. The number average of the titania particle sizes and their coefficient of variation were varied from 143 to 551 nm and from 5.7 to 20.6%, respectively, with reaction temperature and concentrations of water and MA. Colloidal crystals of titania particles fabricated with a sedimentation method revealed reflection peaks attributed to Bragg's diffraction. Annealing at 100-1000 degrees C led to shrinkage and crystallization of titania particles followed by an increase in the refractive index of titania particles.     

Self-assembly of model amphiphilic Janus particles

We apply molecular dynamics simulations to investigate the structure formation of amphiphilic Janus particles in the bulk phase. The Janus particles are modeled as (soft) spheres composed of a hydrophilic and hydrophobic part. Their orientation is described by a vector representing an internal degree of freedom. Investigating energy fluctuations and cluster size distributions, we determine the aggregation line in a temperature-density-diagram, where the reduced temperature is an inverse measure for the anisotropic coupling. Below this aggregation line clusters of various sizes depending on density and reduced temperature are found. For low densities in the range ρ? ≤ 0.3, the cluster size distribution has a broad maximum, indicating simultaneous existence of various cluster sizes between 5 and 10. We find no hint of a condensation transition of these clustered systems. In the case of higher densities (ρ? = 0.5 and 0.6), the cluster size distribution shows an extremely narrow peak at clusters of size 13. In these icosahedrons, the particles are arranged in a closed-packed manner, thereby maximizing the number of bonds. Analyzing the translational mean-square displacement we also observe indications of hindered diffusion due to aggregation.     

Thermal conductivity of polymers filled with dispersed particles: A model

A method for calculating the thermal conductivity coefficient in polymers filled with dispersed particles is proposed. This model is based on estimation of the mean width of a polymer layer between the particles that are randomly distributed in space. This model makes it possible to allow for the effect of particle dimensions, interaction between components, and their characteristics in the course of processing via extrusion.     

Charge density profiling of circulating human low-density lipoprotein particles by capillary zone electrophoresis

Capillary zone electrophoresis (CZE) has been utilized to profile the low-density (LDL) particles in human blood serum in this study. A 5 mM sodium phosphate buffer, pH 7.40, was chosen as the most suitable CE buffer and an extensive ultrafiltration (UF) procedure was applied to purify the LDL sample. Two LDL particle species, LDL with lower mobility and LDL- with higher mobility were observed. The electropherograms were highly reproducible with good precision of effective mobilities, corrected peak areas (CPAs) and CPA ratio of LDL-/LDL. LDL particles shown on the electropherogram were also characterized by several procedures. The applications of Sigma HDL cholesterol reagent and CE on-line 2-propanol precipitation indicated that the two particle species shown in the electropherogram belong to LDL. The LDL particles were found to associate with the buoyant LDL fraction and the LDL- particles associate with the dense LDL fraction. This study utilizes CZE for the profiling of LDL isoforms and provides a new analytical method for the resolution of LDL subspecies. It demonstrates a high-mobility LDL particle which circulates in healthy subjects and diminishes in atherosclerotic patients. Diminution of the high-mobility LDL subspecies may be linked to minimal formation of arterial plaque in atherosclerotic patients.