Interactions between spherical colloids mediated by a liquid crystal: a molecular simulation and mesoscale study

Monte Carlo simulations and dynamic field theory (DyFT) are used to study the interactions between dilute spherical particles, dispersed in nematic and isotropic phases of a liquid crystal. A recently developed simulation method (expanded ensemble density of states) was used to determine the potential of mean force (PMF) between the two spheres as a function of their separation and size. The PMF was also calculated by a dynamic field theory that describes the evolution of the local tensor order parameter. Both methods reveal an overall attraction between the colloids in the nematic phase; in the isotropic phase, the overall attraction between the colloids is much weaker, whereas the repulsion at short range is stronger. In addition, both methods predict a new topology of the disclination lines, which arises when the particles approach each other. The theory is found to describe the results of simulations remarkably well, down to length scales comparable to the size of the molecules. At separations corresponding to the width of individual molecular layers on the particles' surface, the two methods yield different defect structures. We attribute this difference to the neglect of density inhomogeneities in the DyFT. We also investigate the effects of the size of spherical colloids on their interactions.     

The Protective Effects of Sour Orange (Citrus aurantium L.) Polymethoxyflavones on Mice Irradiation-Induced Intestinal Injury

Sour orange (Citrus aurantium L.) is one of the biological sources of polymethoxyflavones (PMFs), which are often used to deal with gastrointestinal diseases. The intestine is highly sensitive to irradiation damage. However, limited certain cures have been released for irradiation-induced gastrointestinal injury, and the potentials of sour orange PMFs as radio-resistance agents have not been fully discussed yet. The present study aims to (1) investigate the PMF components in 12 sour orange cultivars, (2) determine the protective effects of PMFs on irradiation-induced intestinal injury by treating mice that received 12 Gy abdominal irradiation with different doses of PMFs and observing the changes in organ indexes and pathological sections and (3) test cytotoxicity of PMFs by CCK-8 method. The results showed that sour orange PMFs appeared to have high intraspecies similarity. Besides, PMFs protected mice from irradiation-induced injury by alleviating body weight loss, reliving organ index changing and maintaining the intestinal structure. Finally, IC₅₀ concentrations to cell line CCD 841 CoN of PMFs and nobiletin were calculated as 42.23 μg/mL and 51.58 μg/mL, respectively. Our study uncovered PMF contents in 12 sour orange materials and determined the protective effects on irradiation-induced intestinal injuries, providing guidance for the utilization of sour orange resources.     

Prediction and phase segregation in thin‐film of conjugated polymer blends

Blending conjugated polymers is an efficient method to improve the properties of the films. The phase diagram of poly(9,9‐dihexylfluorene) (PF) and poly(2‐methoxy‐5‐(2′‐ethyl‐hexyloxyl)‐p‐phenylene vinylene) (MEHPPV) was predicted by a modified Flory–Huggins theory based on the topological method (graph theory) for the structure‐property correlations. It shows that the two polymers have a strong trend to separate. Atomic/friction force microscopy (AFM/FFM) measurements show there exist microphase separations in film prepared at room temperature. After annealing at 160 °C, serious phase segregations took place in both the lateral and vertical direction. The photoluminescence of the thin films was also measured by a fluorophotometer. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1382–1391, 2005     

Influence of the electric field on a particle in a space with a disclination

We consider a quantum particle in a space with a linear topological defect, i.e., disclination. The effect of the uniform electric field in this space, on the particle, is shown to cause a translation of the wave function. In addition, the electric field is not found to be affected by the defect. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Validated reversed phase LC method for quantitative analysis of polymethoxyflavones in citrus peel extracts

Polymethoxyflavones (PMFs), which exist exclusively in the citrus genus, have biological activities including anti-inflammatory, anticarcinogenic, and antiatherogenic properties. A validated RPLC method was developed for quantitative analysis of six major PMFs, namely nobiletin, tangeretin, sinensetin, 5,6,7,4'-tetramethoxyflavone, 3,5,6,7,3',4'-hexamethoxyflavone, and 3,5,6,7,8,3',4'-heptamethoxyflavone. The polar embedded LC stationary phase was able to fully resolve the six analogues. The developed method was fully validated in terms of linearity, accuracy, precision, sensitivity, and system suitability. The LOD of the method was calculated as 0.15 microg/mL and the recovery rate was between 97.0 and 105.1%. This analytical method was successfully applied to quantify the individual PMFs in four commercially available citrus peel extracts (CPEs). Each extract shows significant difference in the PMF composition and concentration. This method may provide a simple, rapid, and reliable tool to help reveal the correlation between the bioactivity of the PMF extracts and the individual PMF content.     

Molecular dynamics simulations of pressure effects on hydrophobic interactions.

We report results on the pressure effects on hydrophobic interactions obtained from molecular dynamics simulations of aqueous solutions of methanes in water. A wide range of pressures that is relevant to pressure denaturation of proteins is investigated. The characteristic features of water-mediated interactions between hydrophobic solutes are found to be pressure-dependent. In particular, with increasing pressure we find that (1) the solvent-separated configurations in the solute-solute potential of mean force (PMF) are stabilized with respect to the contact configurations; (2) the desolvation barrier increases monotonically with respect to both contact and solvent-separated configurations; (3) the locations of the minima and the barrier move toward shorter separations; and (4) pressure effects are considerably amplified for larger hydrophobic solutes. Together, these observations lend strong support to the picture of the pressure denaturation process proposed previously by Hummer et al. (Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1552): with increasing pressure, the transfer of water into protein interior becomes key to the pressure denaturation process, leading to the dissociation of close hydrophobic contacts and subsequent swelling of the hydrophobic protein interior through insertions of water molecules. The pressure dependence of the PMF between larger hydrophobic solutes shows that pressure effects on the interaction between hydrophobic amino acids may be considerably amplified compared to those on the methane-methane PMF.     

Two-dimensional director configurations in a nematic-filled cylindrical capillary with the hybrid director alignment on its surface

ABSTRACT

We analytically calculate two-dimensional equilibrium configurations of the nematic liquid crystal (NLC) director in a right cylindrical capillary with the hybrid director alignment on its inner surface. A part of this surface is treated to impose the strong homeotropic alignment, while on the remaining part the strong circular alignment, perpendicular to the capillary axis, is imposed. Owing to the system homogeneity along the capillary axis, a disclination line emerges in the bulk of the NLC, which runs parallel to the axis. It is shown that there exist either one or two equilibrium locations of the disclination line depending on the ratio of capillary surface parts with homeotropic and circular alignment. The technique that allows to obtain an analytical expression for the system free energy as a function of a disclination line location is presented. It considerably simplifies calculations and can be used while solving a variety of problems in which a defect location is sought.     

Numerical analysis of the radial-axial structure transition with an applied field in a nematic droplet

In this paper the director configurations and the free energies of a nematic droplet with a surface normal anchoring condition are calculated numerically. For this surface anchoring, a transition occurs between the radial and axial structures with respect to an applied field. In the calculation of the director configurations, the position of a disclination has been fixed. Comparing the free energies for different disclinations, the stable position which gives the minimum free energy is found. In calculating the free energy of a droplet, it is assumed that the free energy density of the nematic phase does not exceed the isotropic free energy density, so that the large distortion in the vicinity of the disclination causes a nematic-isotropic transition and the free energy density of the disclination core becomes equal to the isotropic free energy density. The director configuration in a droplet is calculated as a function of an applied field for different isotropic free energy densities, elastic constant ratios and droplet shapes. The relation between the radial-axial structure transition and these factors are clarified.     

Potential of mean force of hydrophobic association: dependence on solute size

The potentials of mean force (PMFs) were determined for systems involving formation of nonpolar dimers composed of methane, ethane, propane, isobutane, and neopentane, respectively, in water, using the TIP3P water model, and in vacuo. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field was carried out for each pair in either water or in vacuo. The PMFs were calculated by using the weighted histogram analysis method (WHAM). The shape of the PMFs for dimers of all five nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule, that is, for larger molecules they shift toward larger distances. The PMF of the neopentane dimer is similar to those of other small nonpolar molecules studied in this work, and hence the neopentane dimer is too small to be treated as a nanoscale hydrophobic object. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from the PMF in explicit solvent. The molecular surface area model correctly describes the solvent contribution to the PMF together with the changes of the height and positions of the desolvation barrier for all dimers investigated. The water molecules in the first solvation sphere of the dimer are more ordered compared to bulk water, with their dipole moments pointing away from the surface of the dimer. The average number of hydrogen bonds per water molecule in this first hydration shell is smaller compared to that in bulk water, which can be explained by coordination of water molecules to the hydrocarbon surface. In the second hydration shell, the average number of hydrogen bonds is greater compared to bulk water, which can be explained by increased ordering of water from the first hydration shell; the net effect is more efficient hydrogen bonding between the water molecules in the first and second hydration shells.     

Protegrin‐1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations

Protegrin‐1 (PG‐1) belongs to the family of antimicrobial peptides. It interacts specifically with the membrane of a pathogen and kills the pathogen by releasing its cellular contents. To fully understand the energetics governing the orientation of PG‐1 in different membrane environments and its effects on the physicochemical properties of the peptide and membrane bilayers, we have performed the potential of mean force (PMF) calculations as a function of its tilt angle at four distinct rotation angles in explicit membranes composed of either DLPC (1,2‐dilauroylphosphatidylcholine) or POPC (1‐palmitoyl‐2‐oleoylphosphatidylcholine) lipid molecules. The resulting PMFs in explicit lipid bilayers were then used to search for the optimal hydrophobic thickness of the EEF1/IMM1 implicit membrane model in which a two‐dimensional PMF in the tilt and rotation space was calculated. The PMFs in explicit membrane systems clearly reveal that the energetically favorable tilt angle is affected by both the membrane hydrophobic thickness and the PG‐1 rotation angle. Local thinning of the membrane around PG‐1 is observed upon PG‐1 tilting. The thinning is caused by both hydrophobic mismatch and arginine‐lipid head group interactions. The two‐dimensional PMF in the implicit membrane is in good accordance with those from the explicit membrane simulations. The ensemble‐averaged Val16 ¹⁵N and ¹³CO chemical shifts weighted by the two‐dimensional PMF agree fairly well with the experimental values, suggesting the importance of peptide dynamics in calculating such ensemble properties for direct comparison with experimental observables. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Normal‐stress differences and the detection of disclinations in nematic elastomers

We used a continuum model to investigate the isochoric radial expansion of a right circular cylindrical specimen composed of a nematic elastomer that is crosslinked in a uniaxial state and then annealed. Numerical solutions show that, above a certain radial expansion, the material has a definitive energetic preference for a state involving a disclination of strength +1 along the cylinder axis. Surrounding such a disclination is a core with radial dimension on the order of 10^?2 μm, which coincides with observations in conventional liquid‐crystal melts. Examination of the normal‐stress differences indicates that the first of these differences depends nonmonotically on the extent of radial expansion and possesses a local minimum at the point where a disclination becomes energetically preferred. This suggests a practical experimental method for testing the predictions of our model. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2098–2106, 2002     

Linking atomistic and mesoscale simulations of water-soluble polymers

A link between molecular and mesoscopic simulations for water-soluble polymers is made using the potential of mean force (PMF) method. Mesoscale parameters are adjusted to match selected thermodynamic quantities such as the monomer second virial coefficient or the limiting slope of the monomer adsorption isotherm, which are computed directly from atomistic PMFs. The method is illustrated by computing the bulk and surface interaction parameters (chi parameters in self-consistent field theory) for the adsorption of ethylene oxide (EO) and propylene oxide (PO) polymers from aqueous solution onto silica.     

Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling

Potential of mean force (PMF) calculations provide a reliable method for determination of the absolute binding free energies for protein-ligand systems. The common method used for this purpose -- umbrella sampling with weighted histogram analysis -- is computationally very laborious, which limits its applications. Recently, a much simpler alternative for PMF calculations has become available, namely, using Jarzynski's equality in steered molecular dynamics simulations. So far, there have been a few comparisons of the two methods and mostly in simple systems that do not reflect the complexities of protein-ligand systems. Here, we use both methods to calculate the PMF for ion permeation and ligand binding to ion channels. Comparison of results indicate that Jarzynski's method suffers from relaxation problems in complex systems and would require much longer simulation times to yield reliable PMFs for protein-ligand systems.     

Spectroscopic properties and potential energy curves of low-lying electronic states of RuC

The RuC molecule has been a challenging species due to the open-shell nature of Ru resulting in a large number of low-lying electronic states. We have carried out state-of-the-art calculations using the complete active space multiconfiguration self-consistent field followed by multireference configuration interaction methods that included up to 18 million configurations, in conjunction with relativistic effects. We have computed 29 low-lying electronic states of RuC with different spin multiplicities and spatial symmetries with energy separations less than 38,000 cm(-1). We find two very closely low-lying electronic states for RuC, viz., 1Sigma+ and 3Delta with the 1Sigma+ being stabilized at higher levels of theory. Our computed spectroscopic constants and dipole moments are in good agreement with experiment although we have reported more electronic states than those that have been observed experimentally. Our computations reveal a strongly bound 1Sigma+ state with a large dipole moment which is most likely the experimentally observed ground state and an energetically close 3Delta state with a smaller dipole moment. Overall our computed spectroscopic constants of the excited states with energy separations less than 18,000 cm(-1) agree quite well with those of the corresponding observed states.     

Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis

Peptide mass fingerprinting (PMF) is a powerful tool for identification of proteins separated by two-dimensional electrophoresis (2-DE). With the increase in sensitivity of peptide mass determination it becomes obvious that even spots looking well separated on a 2-DE gel may consist of several proteins. As a result the number of mass peaks in PMFs increased dramatically leaving many unassigned after a first database search. A number of these are caused by experiment-specific contaminants or by neighbor spots, as well as by additional proteins or post-translational modifications. To understand the complete protein composition of a spot we suggest an iterative procedure based on large numbers of PMFs, exemplified by PMFs of 480 Helicobacter pylori protein spots. Three key iterations were applied: (1) Elimination of contaminant mass peaks determined by MS-Screener (a software developed for this purpose) followed by reanalysis; (2) neighbor spot mass peak determination by cluster analysis, elimination from the peak list and repeated search; (3) re-evaluation of contaminant peaks. The quality of the identification was improved and spots previously unidentified were assigned to proteins. Eight additional spots were identified with this procedure, increasing the total number of identified spots to 455.     

Equation of state for high density solid and melt polyethylene

Pressure‐volume‐temperature (PVT) measurements for high‐density linear polyethylene (LPE) are studied experimentally over a temperature range of 290 to 470 K and pressures up to 3.1 kbar. For melt, the results can be represented by the Tait equation within the precision of the data. It is noticed that for each isotherm, an abrupt departure from the Tait representation occurs at a particular pressure. This is ascribed to onset of solidification due to pressure. Further, variation of the degree of crystallinity with pressure at various temperatures has been investigated. Finally, the PVT data has been analyzed in terms of the LJD cell theory in its original form without any modifications or simplifications of the cell potential. Satisfactory agreement is obtained between experiment and theory over the entire range of PVT data both in solids and melt states. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1618–1623, 2005     

Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions

We investigated the convergence behavior of potential of mean force (PMF) calculations using free energy perturbation (FEP), thermodynamic integration (TI), and “slow growth” (SG) techniques. The critical comparison of these alternative approaches is illustrated by the study of three different systems: two tagged argon atoms in a periodic box of argon, two methane molecules, and two benzene molecules maintained in a “T-shaped” conformation, both dimers embedded in a periodic box of water. The complete PMF simulations were carried out considering several protocols, in which the number of intermediate “λ” states, together with the amount of sampling per individual state, were varied. In most cases, as much as 1 ns of molecular dynamics (MD) sampling was used to derive each free energy profile. For the different systems examined, we find that FEP and TI unquestionably constitute robust computational methods leading to results of comparable accuracy. We also show that proper convergence of the free energy calculations, and further quantitative interpretation of the PMFs, requires total simulation times much higher than has been hitherto estimated. In some circumstances, the free energy profiles derived from FEP calculations tend to be slightly poorer than those obtained with TI, as a probable consequence of the greater sensitivity of FEP to the window spacing δλ. In the context of TI, and to a lesser extent FEP, simulations, it appears preferable to employ a limited number of “λ” points of the integrand involving extensive sampling, rather than numerous points with fewer samplings. Finally, we note that, at least in the case of nonpolar interactions, PMFs of reasonable quality can be generated using SG, and at a substantially lower cost than with either FEP or TI. © 1996 by John Wiley & Sons, Inc.     

New way of presenting the universal calibration of gel permeation chromatography to include macromolecules with very high segment density

The universal calibration of gel permeation chromatography presents deviations when star‐shaped polymers are used, especially when they present high segment density. Polymers presenting high segment density also have higher values of Flory's parameter Φ than the corresponding flexible, linear polymers. This deviation disappears if we express the hydrodynamic volume of the polymers with the quantity [η]M/Φ (where [η] is the intrinsic viscosity and M is the molecular mass) instead of the commonly used quantity [η]M. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2388–2391, 2005