Density functional theory for the selective adsorption of small molecules on a surface modified with polymer brushes

A density functional method based on weighted density approximation is extended to study the selective adsorption of small molecules on a surface modified with end-grafted square-well chains. The excess part of the Helmholtz free energy functional is divided into two components: the hard sphere repulsion and the square-well attraction. The equation of state for hard sphere chain fluids developed by Liu et al. is used to calculate the repulsive part of the excess Helmholtz free energy functional, and the equation of state for square-well chain fluid with variable range developed by Li et al. is employed to calculate the attractive part. With this theoretical model, we examine the physical properties of the grafted polymer and the selective adsorption of small molecules on the modified surface.     

Extending the diffuse layer model of surface acidity constant behaviour: IV. Diffuse layer charge/potential relationships

Abstract

Most current electrostatic surface complexation models describing ionic binding at the particle/water interface rely on the use of Poisson–Boltzmann (PB) theory for relating diffuse layer charge densities to diffuse layer electrostatic potentials. PB theory is known to contain a number of implicit assumptions whose significance in environmental applications is largely unknown. This study seeks to better quantify the impact of these assumptions by: (1) comparing potentials obtained from planar analytical solutions to the PB with those obtained from Hypernetted Chain (HNC) theory (Attard, 2006), (2) assessing the accuracy of the Ohshima et al. (1982) spherical approximate analytical solution to the PB equation by comparison with published numerical values (Loeb et al., 1961), and (3) comparing interfacial potential estimates obtained from the spherical approximate analytical solution to the PB equation at and adjacent to the particle surface with potential estimates obtained from the Entropic Balanced Surface Potential (EB) model (Loux, 1985; Loux and Anderson, 2001) and published potential estimates obtained from the Hypernetted Chain/Mean Spherical Approximation procedure (HNC/MSA; Gonzalez-Tovar and Lozada-Cassou, 1989). EB potential estimates were obtained assuming a surface volume thickness equal to the Bjerrum length (0.357 nm in a room temperature monovalent electrolyte solution). Findings from the study included: (1) the planar, surficial HNC estimates compared favourably with planar surficial PB relationships at charge densities equal to or less than 0.05 C m^?2, (2) the Ohshima et al. (1982) approximate spherical analytical solution to the PB equation replicated the numerical charge density estimates required to obtain 72 datapoints over an e<img>/kT range of one to four with a maximum error of 3.37% and a coefficient of variation of 0.92%, (3) for a 0.1 μm radius particle in a room temperature 0.01 M (1 : 1) ionic strength solution, potential estimates over a surface charge density range of 0 to 0.3C m^?2 occurred in the following order: ψ_HNC/MSA,R >ψ_PB,R >_{ψHNC/MSA,R+0.2125nm} >ψ_PB,R+0.2nm ~ ψ_EB >ψ_{HNC/MSA,R+0.425nm} ~ _ψPB,R+0.4nm and (4) with 45 datapoints including both 1 μm and 10 nm radius particles over an ionic strength range of 1.0 to 0.001 M, the PB potential estimates 0.2 nm from the particle surface (ψ_PBR+02nm) closely tracked the corresponding EB estimates (ψ_EB) with a 5.3% coefficient of variation. If one assumes that interfacial potential values adjacent to the particle surface are most relevant for describing environmental phenomena and that a 10% coefficient of variation in potential estimates is acceptable, then presumably any of the non-surficial charge/potential relationships would be useful below an absolute charge density of 0.125 C m ^?2 (with monovalent electrolyte solutions).     

Statistical mechanics approach to inhomogeneous van der Waals fluids

A general methodology is proposed to formulate density functional approximation (DFA) for inhomogeneous van der Waals fluids. The present methodology needs as input only a hard sphere DFA, second order direct correlation function (DCF) and pressure of coexistence bulk fluid, and therefore can be applicable to both supercitical and subcritical temperature regions. As illustrating example, the present report combines a recently proposed hard sphere “Formally exact truncated non-uniform excess Helmholtz free energy density functional approximation” with the present methodology, and applies the resultant DFA to calculate density profile of the inhomogeneous Lennard-Jones (LJ) fluid in coexistence with a bulk LJ fluid being situated at “dangerous” regions, i.e. the coexistence bulk state is near the critical temperature or the gas-liquid coexistence line. The theoretical predictions are in very good agreement with the recent simulation results, it is concluded that the present DFA is a globally excellent one. A discussion is given why the present methodology can lead to so excellent DFA.     

Dynamics of the head-neck complex in response to the trunk horizontal vibration: modeling and identification

Although many studies exist concerning the influence of seat vibration on the head in the seated human body, the dynamic response of the head-neck complex (HNC) to the trunk vibration has not been well investigated. Little quantitative knowledge exists about viscoelastic parameters of the neck. In this study, the dynamics of the HNC is identified when it is exposed to the trunk horizontal (fore-and-aft) vibration. The frequency response functions between the HNC angular velocity and the trunk horizontal acceleration, corresponding to four volunteers, are obtained in the frequency range of 0.5 Hz to 10 Hz. A fourth-order mathematical model, derived by considering a double-inverted-pendulum model for the HNC, is designed to simulate the dynamic response of the HNC to the trunk horizontal vibration. The frequency domain identification method is used to determine the coefficients of the mathematical model of the HNC. Good agreement has been obtained between experimental and simulation results. This indicates that the system, similar to the designed fourth-order model, has mainly two resonance frequencies. The viscoelastic parameters of the neck, including the spring and damping coefficients, are then obtained by use of the optimization method.     

Molecular simulation of volume of mixing,Helmholtz free energy of mixing and entropy of mixing in bulk fluid mixtures

We describe a kinetic Monte Carlo molecular simulation procedure to calculate the Helmholtz free energy, the entropy and the chemical potentials of all components in a bulk fluid mixture. This allows us to derive the excess properties (volume, free energy and entropy) resulting from the mixing of homogeneous fluids of pure components at constant temperature and pressure. We have chosen neon–xenon mixtures to illustrate our method because of the large difference in collision diameter and well-depth of the interaction energy. When xenon is predominant in the mixture, the volume of mixing is larger. The excess entropy of mixing correlates with the volume of mixing, since a positive excess volume enables more configurations (more possible molecular distributions). The excess thermodynamic quantities as functions of the total density were found to be insensitive to temperature. To investigate the effects of the molecular parameters, we also studied argon–nitrogen and argon–krypton mixtures. The effect of the difference in molecular parameters is in the order: argon–nitrogen < argon–krypton < neon–xenon. A large difference in the well-depth of the interaction energies results in an increase in the excess thermodynamic variables, which is in agreement with the literature McDonald IR. NpT-ensemble Monte Carlo calculations for binary liquid mixtures. Mol Phys. 1972;23(1):41–58; Singer JVL, Singer K. Monte Carlo calculation of thermodynamic properties of binary mixtures of Lennard-Jones (12-6) liquids. Mol Phys. 1972;24(2):357–390.     

Identification of the head-neck complex in response to trunk horizontal vibration

A method is proposed for identifying the head-neck complex (HNC) in the seated human body when it is exposed to the trunk horizontal (fore-and-aft) vibration. It is assumed that the HNC only has the anteroposterior (flexion/extension) motion in the sagittal plane. An electrohydraulic vibrator is used as a source of vibration. To generate the trunk horizontal vibration, the trunk of the seated subject is fixed to the seatback. The subjects are exposed to the random vibration at a magnitude of 1.60 ms^-2 rms (root-mean-square) for 50 s. The coherence and frequency response function are then obtained in the frequency range 0.5–3 Hz. The results show that the HNC behavior is quasilinear with a resonance frequency between 1 and 1.4 Hz. Accordingly, a two-dimensional single-inverted pendulum is considered as a model for the HNC. The frequency domain identification method is then used to estimate the unknown parameters, including the HNC viscoelastic and inertia parameters. The model is examined in a time domain using the random vibration. Good agreement is obtained between experimental and simulation results, indicating the reliability of the proposed method.     

Allele frequency distribution under recurrent selective sweeps

The allele frequency of a neutral variant in a population is pushed either upward or downward by directional selection on a linked beneficial mutation ("selective sweeps"). DNA sequences sampled after the fixation of the beneficial allele thus contain an excess of rare neutral alleles. This study investigates the allele frequency distribution under selective sweep models using analytic approximation and simulation. First, given a single selective sweep at a fixed time, I derive an expression for the sampling probabilities of neutral mutants. This solution can be used to estimate the time of the fixation of a beneficial allele from sequence data. Next, I obtain an approximation to mean allele frequencies under recurrent selective sweeps. Under recurrent sweeps, the frequency spectrum is skewed toward rare alleles. However, the excess of high-frequency derived alleles, previously shown to be a signature of single selective sweeps, disappears with recurrent sweeps. It is shown that, using this approximation and multilocus polymorphism data, genomewide parameters of directional selection can be estimated.     

Nonthermal plasma induces head and neck cancer cell death: the potential involvement of mitogen-activated protein kinase-dependent mitochondrial reactive oxygen species

Nonthermal plasma (NTP) is generated by ionization of neutral gas molecules, which results in a mixture of energy particles including electrons and ions. Recent progress in the understanding of NTP has led to its application in the treatment of various diseases, including cancer. However, the molecular mechanisms of NTP-induced cell death are unclear. The purpose of this study was to evaluate the molecular mechanism of NTP in the induction of apoptosis of head and neck cancer (HNC) cells. The effects of NTP on apoptosis were investigated using MTT, terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end labeling, Annexin V assays, and western blot analysis. The cells were examined for production of reactive oxygen species (ROS) using DCFCA or MitoSOX staining, intracellular signaling, and an animal model. NTP reduced HNC cell viability in a dose-dependent manner and induced apoptosis. NTP resulted in alteration of mitochondrial membrane potential and accumulation of intracellular ROS generated from the mitochondria in HNC cells. Blockade of ROS production by N-acetyl-L-cysteine inhibited NTP-induced apoptosis. NTP led to the phosphorylation of c-JUN N-terminal kinase (JNK) and p38, but not extracellular-regulated kinase. Treatment with JNK and p38 inhibitors alleviated NTP-induced apoptosis via ROS generation. Taken together, these results show that NTP induced apoptosis of HNC cells by a mechanism involving MAPK-dependent mitochondrial ROS. NTP inhibited the growth of pre-established FaDu tumors in a nude mouse xenograft model and resulted in accumulation of intracellular ROS. In conclusion, NTP induced apoptosis in HNC cells through a novel mechanism involving MAPK-mediated mitochondrial ROS. These findings show the therapeutic potential of NTP in HNC.     

Architecture, electronic structure and stability of TM@Ge(n) (TM = Ti, Zr and Hf; n = 1-20) clusters: a density functional modeling

The present study reports the geometry, electronic structure and properties of neutral and anionic transition metal (TM = Ti, Zr and Hf)) doped germanium clusters containing 1 to 20 germanium atoms within the framework of linear combination of atomic orbitals density functional theory under spin polarized generalized gradient approximation. Different parameters, like, binding energy (BE), embedding energy (EE), energy gap between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO), ionization energy (IP), electron affinity (EA), chemical potential etc. of the energetically stable clusters (ground state cluster) in each size are calculated. From the variation of these parameters with the size of the clusters the most stable cluster within the range of calculation is identified. It is found that the clusters having 20 valence electrons turn out to be relatively more stable in both the neutral and the anionic series. The sharp drop in IP as the valence electron count increases from 20 to 21 in neutral cluster is in agreement with predictions of shell models. To study the vibrational nature of the clusters, IR and Raman spectrum of some selected TM@Ge_n (n = 15,16,17) clusters are also calculated and compared. In the end, relevance of calculated results to the design of Ge-based super-atoms is discussed.     

Inhibition of intracellular proteolysis in muscle cultures by multiplication-stimulating activity. Comparison of effects of multiplication-stimulating activity and insulin on proteolysis, protein synthesis, amino acid uptake, and sugar transport

The effects of the insulin-like growth factor, multiplication-stimulating activity (MSA), on chick myotube cultures were investigated. In serum-free media, MSA at levels reported to be present in fetal serum (5 ng/ml) significantly inhibited overall rates of protein degradation and stimulated protein synthesis and amino acid uptake. Half-maximal effects on protein degradation (-30%), synthesis (+25%), and amino acid uptake (+50%) occurred at approximately 0.05 micrograms/ml. In contrast, 10(2)-10(3)-fold higher concentrations (5 micrograms/ml) were required to stimulate transport of the glucose analog 2-deoxyglucose. The results indicate that MSA is an effective anabolic agent regulating protein metabolism and amino acid uptake, but not sugar transport in these cells. Parallel studies conducted with insulin demonstrated similar size effects on protein metabolism and amino acid uptake in serum-free media. However, unlike MSA, insulin levels (10(-2) units/ml) well in excess of its normal physiological range were required to produce significant effects. In addition, the relative sensitivity of sugar transport with respect to protein metabolic effects differed for insulin and MSA. Thus, 2-deoxyglucose transport was approximately 10 times more sensitive to insulin than protein synthesis, proteolysis, or amino acid uptake in contrast to MSA where the reverse was true. However, despite the relatively higher sensitivity of sugar transport to insulin, supraphysiological levels (10(-3) units/ml) of this hormone were still required for significant stimulation. These results suggest a generally low insulin sensitivity in cultured chick myotubes relative to adult tissues. In contrast, the effects of MSA are consistent with a possible role of this or similar factors in regulating growth and development of embryonic muscle.     

Temperature- and pressure-dependent phase behavior of monoacylglycerides monoolein and monoelaidin.

We used x-ray and neutron diffraction to study the temperature- and pressure-dependent structure and phase behavior of the monoacylglycerides 1-monoelaidin (ME) and 1-monoolein (MO) in excess water. The monoacylglycerides were chosen for investigation of their phase behavior because they exhibit mesomorphic phases with one-, two-, and three-dimensional periodicity, such as lamellar, an inverted hexagonal and bicontinuous cubic phases, in a rather easily accessible temperature and pressure range. We studied the structure, stability, and transformations of the different phases over a wide temperature and pressure range, explored the epitaxial relations that exist between different phases, and established a relationship between the chemical structure of the lipid molecules and their phase behavior. For both systems, a temperature-pressure phase diagram has been determined in the temperature range from 0 to 100 degrees C at pressures from ambient up to 1400 bar, and drastic differences in phase behavior are found for the two systems. In MO-water dispersions, the cubic phase Pn3m extends over a large phase field in the T,p-plane. At temperatures above 95 degrees C, the inverted hexagonal phase is found. In the lower temperature region, a crystalline lamellar phase is induced at higher pressures. The phases found in ME-water include the lamellar crystalline Lc phase, the L beta gel phase, the L alpha liquid-crystalline phase, and two cubic phases belonging to the crystallographic space groups Im3m and Pn3m. In addition, the existence of metastable phases has been exploited. Between coexisting metastable cubic structures, a metric relationship has been found that is predicted theoretically on the basis of the curvature elastic energy approximation only.     

DNA-lipid complexes: stability of honeycomb-like and spaghetti-like structures.

A molecular level theory is presented for the thermodynamic stability of two (similar) types of structural complexes formed by (either single strand or supercoiled) DNA and cationic liposomes, both involving a monolayer-coated DNA as the central structural unit. In the "spaghetti" complex the central unit is surrounded by another, oppositely curved, monolayer, thus forming a bilayer mantle. The "honeycomb" complex is a bundle of hexagonally packed DNA-monolayer units. The formation free energy of these complexes, starting from a planar cationic/neutral lipid bilayer and bare DNA, is expressed as a sum of electrostatic, bending, mixing, and (for the honeycomb) chain frustration contributions. The electrostatic free energy is calculated using the Poisson-Boltzmann equation. The bending energy of the mixed lipid layers is treated in the quadratic curvature approximation with composition-dependent bending rigidity and spontaneous curvature. Ideal lipid mixing is assumed within each lipid monolayer. We found that the most stable monolayer-coated DNA units are formed when the charged/neutral lipid composition corresponds (nearly) to charge neutralization; the optimal monolayer radius corresponds to close DNA-monolayer contact. These conclusions are also valid for the honeycomb complex, as the chain frustration energy is found to be negligible. Typically, the stabilization energies for these structures are on the order of 1 k(B)T/A of DNA length, reflecting mainly the balance between the electrostatic and bending energies. The spaghetti complexes are less stable due to the additional bending energy of the external monolayer. A thermodynamic analysis is presented for calculating the equilibrium lipid compositions when the complexes coexist with excess bilayer.     

A visco-hyperelastic model for skeletal muscle tissue under high strain rates

In this paper, a visco-hyperelastic skeletal muscle model is developed. The constitutive relation is based on the definition of a Helmholtz free energy function. It is assumed that the Helmholtz energy can be decomposed into volumetric and isochoric parts; furthermore, the isochoric energy can be decoupled into hyperelastic and viscous parts. The model developed involves 14 material parameters and its performance is evaluated by comparing the finite element simulation results with the published experimental studies on the New Zealand white rabbit tibialis anterior muscle. Results show that this model is able to describe the visco-hyperelastic behaviour of both passive and active skeletal muscle tissues under high strain rates (10/s and 25/s).     

Effects of molecular structure on positive and negative azeotropies in mixed monolayers of lipids

In order to clarify the effect of molecular structure on the nature of azeotropic transformations in mixed monolayers, many systems of the positive and negative azeotropic types are examined in this study. Two-dimensional phase diagrams and apparent molar energy changes which are associated with the phase transition from the liquid-expanded to the liquid-condensed state are evaluated using a previously developed thermodynamic treatment. There is a maximum in the phase diagram of the positive azeotropic type and the excess apparent molar energy change is positive over the entire compositional range. Steric hindrance of the hydrophilic groups seems to be the important factor in the behavior of the positive azeotropic type. For the negative azeotropic type there is a minimum in the phase diagram and the excess apparent molar energy change is negative over the entire compositional range. The two long acyl chains of dipalmitoyl lecithin leads to a strong interaction between the two components.     

Molecular dynamics simulations and 2H NMR study of the GalCer/DPPG lipid bilayer

Molecular dynamics simulations were performed on a two-component lipid bilayer system in the liquid crystalline phase at constant pressure and constant temperature. The lipid bilayers were composed of a mixture of neutral galactosylceramide (GalCer) and charged dipalmitoylphosphatidylglycerol (DPPG) lipid molecules. Two lipid bilayer systems were prepared with GalCer:DPPG ratio 9:1 (10%-DPPG system) and 3:1 (25%-DPPG system). The 10%-DPPG system represents a collapsed state lipid bilayer, with a narrow water space between the bilayers, and the 25%-DPPG system represents an expanded state with a fluid space of approximately 10 nm. The number of lipid molecules used in each simulation was 1024, and the length of the production run simulation was 10 ns. The simulations were validated by comparing the results with experimental data for several important aspects of the bilayer structure and dynamics. Deuterium order parameters obtained from (2)H NMR experiments for DPPG chains are in a very good agreement with those obtained from molecular dynamics simulations. The surface area per GalCer lipid molecule was estimated to be 0.608 +/- 0.011 nm(2). From the simulated electron density profiles, the bilayer thickness defined as the distance between the phosphorus peaks across the bilayer was calculated to be 4.21 nm. Both simulation systems revealed a tendency for cooperative bilayer undulations, as expected in the liquid crystalline phase. The interaction of water with the GalCer and DPPG oxygen atoms results in a strong water ordering in a spherical hydration shell and the formation of hydrogen bonds (H-bonds). Each GalCer lipid molecule makes 8.6 +/- 0.1 H-bonds with the surrounding water, whereas each DPPG lipid molecule makes 8.3 +/- 0.1 H-bonds. The number of water molecules per GalCer or DPPG in the hydration shell was estimated to be 10-11 from an analysis of the radial distribution functions. The formation of the intermolecular hydrogen bonds was observed between hydroxyl groups from the opposing GalCer sugar headgroups, giving an energy of adhesion in the range between -1.0 and -3.4 erg/cm(2). We suggest that this value is the contribution of the hydrogen-bond component to the net adhesion energy between GalCer bilayers in the liquid crystalline phase.     

Thermodynamic properties of strongly coupled plasma in the presence of an external magnetic field

Thermodynamic properties of a Yukawa system consisting of dust particles in plasma are studied in the presence of an external magnetic field. It is assumed that dust particles interact with each other by a modified potential in the presence of a magnetic field. A molecular dynamics code is developed to calculate this internal energy for the entire system. Based on the values of the internal energy given by the code, the Helmholtz free energy and pressure are calculated for the system.     

Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation

This study explores the use of multiple sequence alignment (MSA) information and global measures of hydrophobic core formation for improving the Rosetta ab initio protein structure prediction method. The most effective use of the MSA information is achieved by carrying out independent folding simulations for a subset of the homologous sequences in the MSA and then identifying the free energy minima common to all folded sequences via simultaneous clustering of the independent folding runs. Global measures of hydrophobic core formation, using ellipsoidal rather than spherical representations of the hydrophobic core, are found to be useful in removing non-native conformations before cluster analysis. Through this combination of MSA information and global measures of protein core formation, we significantly increase the performance of Rosetta on a challenging test set. Proteins 2001;43:1-11.     

Thermodynamic properties of two-dimensional nonideal structures with isotropic pair potential

An approximation is proposed for energy density in two-dimensional nonideal systems for a wide class of isotropic repulsive pair interparticle potentials. The approximation allows one to determine the main thermodynamic functions and characteristics of the system by using well-known thermodynamic formulas. The results obtained with the help of this approximation are compared with the data of numerical simulations of thermodynamic properties of the structures under study. The simulations were performed in a wide range of parameters typical of laboratory dusty plasmas. Main attention was paid to the screened Coulomb potential.