Computer simulation study of probe-target hybridization in model DNA microarrays: effect of probe surface density and target concentration

We use lattice Monte Carlo simulations to study the thermodynamics of hybridization of single-stranded "target" genes in solution with complementary "probe" DNA molecules immobilized on a microarray surface. The target molecules in our system contain 48 segments and the probes tethered on a hard surface contain 8-24 segments. The segments on the probe and target are distinct, with each segment representing a sequence of nucleotides that interacts exclusively with its unique complementary target segment with a single hybridization energy; all other interactions are zero. We examine how surface density (number of probes per unit surface area) and concentration of target molecules affect the extent of hybridization. For short probe lengths, as the surface density increases, the probability of binding long stretches of target segments increases at low surface density, reaches a maximum at an intermediate surface density, and then decreases at high surface density. Furthermore, as the surface density increases, the target is less likely to bind completely to one probe; instead, it binds simultaneously to multiple probes. At short probe lengths, as the target concentration increases, the fraction of targets binding completely to the probes (specificity) decreases. At long probe lengths, varying the target concentration does not affect the specificity. At all target concentrations as the probe length increases, the fraction of target molecules bound to the probes by at least one segment (sensitivity) increases while the fraction of target molecules completely bound to the probes (specificity) decreases. This work provides general guidelines to maximizing microarray sensitivity and specificity. Our results suggest that the sensitivity and specificity can be maximized by using probes 130-180 nucleotides long at a surface density in the range of 7 x 10(-5)- 3 x 10(-4) probe molecules per nm(2).     

Heat transfer coefficient and pressure drop during refrigerant R-134a condensation in a plate heat exchanger

The condensation heat transfer coefficient and the two-phase pressure drop of refrigerant R-134a in a vertical plate heat exchanger were investigated experimentally. The area of the plate was divided into several segments along the vertical axis. For each of the segments, local values of the heat transfer coefficient and frictional pressure drop were calculated and presented as a function of the mean vapor quality in the segment. Owing to the thermocouples installed along the plate surface, it was possible to determine the temperature distribution and vapor quality profile inside the plate. The influences of the mass flux and the heat flux on the heat transfer coefficient and the pressure drop were also taken into account and a comparison with previously published experimental data and literature correlations was carried out. Presented at the 34th International Conference of the Slovak Society of Chemical Engineering, Tatranské Matliare, 21–25 May 2007.     

Thermodynamic modeling of CO2 solubility in ionic liquid with heterosegmented statistical associating fluid theory

Heterosegmented statistical associating fluid theory is used to represent the CO₂ solubility in ionic liquids. As in our previous work, ionic liquid molecule is divided into several groups representing the alkyls, cation head, and anion. The cation of ionic liquid is modeled as a chain molecule that consists of one spherical segment representing the cation head and groups of segments of different types representing different substituents (alkyls). The anion of ionic liquid is modeled as a spherical segment of different type. To account for the electrostatic/polar interaction between the cation and anion, the spherical segments representing cation head and anion each have one association site, which can only cross associate. Carbon dioxide is modeled as a molecule with three association sites, two sites of type O and one site of type C, where sites of the same type do not associate with each other. The parameters of CO₂ are obtained from the fitting of the density and the saturation vapor pressure of CO₂. For the CO₂-ionic liquid systems, cross association between site of type C in CO₂ and another association site in anion is allowed to occur to account for the Lewis acid–base interaction. The parameters for cross association interactions and the binary interaction parameters used to adjust the dispersive interactions between unlike segments are obtained from the fitting of the available CO₂ solubility in ionic liquids. The model is found to well represent the CO₂ solubility in the imidazolium ionic liquids from 283 to 415 K and up to 200 bar.     

Water vapor nucleation on an infinite substrate with complementary structure: 1. The mechanism of nucleation

The nucleation of water vapor on the infinite surface of a silver iodide crystal at 260 K is simulated. Long-range electrostatic and polarization interactions are taken into account by the Ewald method. The free energy and work of equilibrium formation of nuclei are calculated at the molecular level by the method of bicanonical statistical ensemble. It is shown that, at the initial stage, the substrate is completely covered with a water monolayer. The substrate tends to decrease by two orders of magnitude the vapor pressure required to form the critical nucleus of a monomolecular film with a size of 10² molecules, the nucleation rate being increased by tens of orders of magnitude as compared to homogeneous nucleation. The saturation pressure above the adsorbed monomolecular film is 12 times lower than that above the flat ice surface. The free energy at the edges of “spots” per unit length is 1.4 × 10^?11 J/m. The critical size of the spot increases with a decrease in vapor pressure as the inverse second power of the logarithm of pressure.     

Rapid Estimation of Thermodynamic Parameters and Vapor Pressures of Volatile Materials at Nanoscale

Non‐isothermal measurements of thermodynamic parameters and vapor pressures of low‐volatile materials are favored when time is a crucial factor to be considered, such as in the case of detection of hazardous materials. In this article, we demonstrate that optical absorbance spectroscopy can be used non‐isothermally to estimate the thermodynamic properties and vapor pressures of volatile materials with good accuracy. This is the first method to determine such parameters in nanoscale in just minutes. Trinitrotoluene (TNT) is chosen because of its low melting temperature, which makes it impossible to determine its thermodynamic parameter by other rising‐temperature techniques, such as thermogravimetric analysis (TGA). The well‐characterized vapor pressure of benzoic acid is used to calibrate the spectrometer in order to determine the vapor pressure of low‐volatile TNT. The estimated thermodynamic properties of both benzoic acid and TNT are in excellent agreement with the literature. The estimated vapor pressure of TNT is one order of magnitude larger than that determined isothermally using the same method. However, the values are still within the range reported in the literature. The data indicate the high potential for use of rising‐temperature absorbance spectroscopy in determining vapor pressures of materials at nanometer scale in minutes instead of hours or days.     

In Situ Direct Measurement of Vapor Pressures and Thermodynamic Parameters of Volatile Organic Materials in the Vapor Phase: Benzoic Acid,Ferrocene, and Naphthalene

We report the direct determination of vapor pressures and optical and thermodynamic parameters of powders of low‐volatile materials in their vapor phase using a commercial UV/Vis spectrometer. This methodology is based on the linear proportionality between the density of the saturated gas of the material and the absorbance of the gas at different temperatures. The vapor pressure values determined for benzoic acid and ferrocene are in good agreement with those reported in the literature with ～2–7 % uncertainty. Thermodynamic parameters of benzoic acid, ferrocene, and naphthalene are determined in situ at temperatures below their melting points. The sublimation enthalpies of the investigated organic molecules are in excellent agreement with the ICTAC recommended values (less than 1 % difference). This method has been used to measure vapor pressures and thermodynamic parameters of organic volatile materials with vapor pressures of ～0.5–355 Pa in the 50–100 °C temperature range.     

Synthesis and self-organization of rod–dendron and dendron–rod–dendron molecules

We synthesized molecules containing one or two dendritic segments and a rigid-rod-like segment with their structures in the solid state. The molecules with rod–dendron or dendron–rod–dendron architecture had biphenyl ester rigid segments and 3,4,5 tris(n-dodecyloxy)benzoate of first or second generation as their dendritic segments. The variables investigated included the rod segment length as well as dendron generation, and all materials obtained were characterized by optical microscopy, differential scanning calorimetry, and X-ray scattering. Depending on the size of the rod segment and generation number of the dendritic segment, molecules organized into smectic, columnar, or cubic phases, and the symmetries observed were dominated by the anisotropic rod–rod interactions. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 3501–3518, 2003     

Modeling phase equilibria of alkanols with the simplified PC-SAFT equation of state and generalized pure compound parameters

The simplified PC-SAFT equation of state has been applied to liquid–liquid, vapor–liquid and solid–liquid equilibria for mixtures containing 1- or 2-alkanols with alkanes, aromatic hydrocarbons, CO₂ and water. For the alkanols we use generalized pure compound parameters. This means that two of the physical pure compound parameters, m (segment number) and σ (segment diameter), are obtained from linear extrapolations, since m and mσ³, increase linearly with respect to the molar mass, and moreover, the two association parameters (association energy and association volume) were assumed to be constant for all alkanols. Only the dispersion energy is fitted to experimental data. Thus it is possible to estimate parameters for several 1- and 2-alkanols. The final aim is to develop a group contribution approach for PC-SAFT which is suitable for complex compounds, considering that the motivation of this project is to obtain a thermodynamic model which can be used in the development of sophisticated products such as pharmaceuticals, polymers, detergents or food ingredients. One of the severe limitations in applying SAFT-type equations of state to these compounds is that the procedure for obtaining the pure compound parameters is usually based on fitting to saturated vapor pressure and liquid density data over an extended temperature range. However, such data are rarely available for complex compounds. To verify the new pure compound parameters, comparisons to ordinary optimized alkanol parameters, where all five pure compound parameters were fitted to experimental liquid density and vapor pressure data, were made. The results show that the new generalized alkanol parameters from this work perform at least as well as other alkanol parameter sets.     

A generalized technique to obtain pure component parameters for two-parameter equations of state

A generalized technique is presented for the calculation of the pure component parameters for use in a general two-parameter equation of state. The method requires as input data the vapor pressure and saturated liquid volume of a component at a given temperature, and is both accurate and simple to use.Correlations for the calculation of the parameters are presented for the van der Waals, Redlich—Kwong and Peng—Robinson forms of cubic equations of state. A comparison is made between the new method and the corresponding-states approach.     

The role of fluid wall association on adsorption of chain molecules at functionalized surfaces: a density functional approach

We present a density functional theory to describe adsorption in systems where selected segments of chain molecules of fluids can bond (or associate) with functional groups attached to the surfaces. Association of active segments with the surface is modeled within the framework of the first-order thermodynamic perturbation theory. We discuss the influence of several parameters such as the density of surface active sites, the energy of association, the chain length, and the number of the active segment in the chain molecule on the structure of the fluid adjacent to the wall. The proposed model can be considered as a first step towards developing a density functional theory of molecular brushes chemically bonded to solid surfaces.     

Formation of carbon nanoparticles by the condensation of supersaturated atomic vapor obtained by the laser photolysis of C3O2

A new technique is suggested for obtaining nanoparticles from highly supersaturated vapor resulting from the laser photolysis of volatile compounds. The growth of carbon nanoparticles resulting from C₃O₂ photolysis has been studied in detail. Absorbing UV quanta (from an Ar-F excimer laser), C₃O₂ molecules decompose to yield atomic carbon vapor with precisely known and readily controllable parameters. This is followed by the condensation of supersaturated carbon vapor and the formation of carbon nanoparticles. These processes have been investigated by the laser extinction and laser-induced incandescence (LII) methods in wide ranges of experimental conditions (carbon vapor concentration, nature of the diluent gas, and gas pressure). The current and ultimate particle sizes and the kinetic parameters of particle growth have been determined. The characteristic time of particle growth ranges between 20 and 1000 μs, depending on photolysis conditions. The ultimate particle size determined by electron microscopy is 5–12 nm for all experimental conditions. It increases with increasing total gas pressure and carbon vapor partial pressure and depends on the diluent gas. The translational energy accommodation coefficients for the Ar, He, CO, and C₃O₂ molecules interacting with the carbon particle surface have been determined by comparing the LII and electron microscopic particle sizes. A simple model has been constructed to describe the condensation of carbon nanoparticles from supersaturated atomic vapor. According to this model, the main process in nanoparticle formation is surface growth through the addition of separate atoms to the nucleation cluster. The nucleus concentrations for various condensation parameters have been determined by comparing experimental and calculated data.     

两亲性嵌段聚醚酯在空气-水界面上的Langmuir单分子膜

聚醚酯是一种新型弹性材料,目前已成为工业化产品[1].对这种嵌段聚醚酯的合成和弹性行为[2]、熔体的流变性能[3]、以及纤维在拉伸状态下的聚集态结构和分子运动[4]已有一些报道.     

A consistent estimation of sublimation pressures using a cubic equation of state and fusion properties

In many cases of industrial fluid–solid separation process design, a thermodynamic key parameter may be the sublimation pressure of pure components. A new trend in chemical applications is the use of supercritical solvents either in purifying operations on mixtures of complex pharmaceutical molecules or in stripping on polluted stuff. Measurements of very low sublimation pressures of heavy components are very difficult to perform although their values are of most importance in the process evaluation. Unfortunately, the prediction tools available in the literature for the estimation of sublimation pressures are poor. This paper deals with a consistent approach of sublimation pressure estimation, applicable to any pure material using on one hand easy measurements of normal fusion temperature and fusion enthalpy, and on the other hand vapor pressure data. The influence of all the uncertainties is discussed and the method is proposed as a new reference with emphasis on extrapolating reliably to very heavy compounds. By computing vapor liquid equilibrium using a cubic equation of state (EOS), the estimation of sublimation pressures is discussed in a new perspective.     

Generation of larger numbers of separated microbial populations by cultivation in segmented-flow microdevices

The high speed production of fluid segments for the highly parallelized cultivation of monoclonal cell populations was carried out by the use of microchip segmentor modules. Aqueous fluid segments, embedded in a non-miscible carrier liquid, were produced with frequencies up to 30 s(-1) and showed a high homogeneity in size. This corresponds with the production of about 2.5 million samples per day. The segment volumes can be adapted between about 4 nl and 100 nl. The typical segment size for cultivation experiments is in the range between 40 nl and 80 nl. Nutrient medium can be applied instead of pure water. It is possible to aliquot a cell suspension in such a way that most of the aqueous fluid segments contain only one cell. In model experiments with four microbial species chip-produced aliquots of 60 nl, each containing one or a few cells, were incubated in Teflon capillary tubes. Rapid growth of the microcultures was observed. Cell densities were found to be as high as in conventional shake flask cultures.     

Density-functional theory for fluid mixtures of charged chain particles and spherical counterions in contact with charged hard wall: Adsorption, double layer capacitance, and the point of zero charge

We consider a density-functional theory to describe nonuniform fluids composed of chain molecules, containing a charged segment each, and spherical counterions. The chain molecules are modeled as freely jointed chains of hard spheres, the counterions are oppositely charged spheres of the same diameter as all segments of chain molecules. The theory is applied to study the structure of adsorbed layers, the excess adsorption isotherms, the capacitance of the double layer, and the potential of the zero charge. We show that all electric properties are strongly dependent on the length of the chain molecules. Moreover, these properties are also dependent on the position of the charged segment in the chain.     

A viscosity equation for polyatomic fluids under normal and high pressures

In this work, we relate the self-diffusion coefficient to the residual entropy of the system according to the free volume theory and scaling principle. The viscosity equation for a freely jointed Lennard-Jones chain fluid is then obtained from the expression of self-diffusion coefficient by applying the Stokes–Einstein equation. The real polyatomic compounds are modeled as chains of tangent Lennard-Jones segments. The segment size and energy parameter as well as chain length (expressed by the number of segments) are obtained from the experimental viscosity data. The proposed viscosity equation reproduces the experimental viscosity data with an average absolute deviation of 5.12% for 18 polyatomic compounds (1600 data points) over wide ranges of temperature and pressure. For engineering applications, the generalized model parameters for normal alkanes with the number of carbon atoms n > 3 are proposed. The segment energy parameter is suggested to be evaluated from the critical temperature, and the segment size parameter and chain length are correlated with the number of carbon atoms in an alkane molecule.     

Critical points of hydrocarbon mixtures with the Peng–Robinson,SAFT, and PC-SAFT equations of state

The phase behavior of fluids at high pressures can be rather complex, even for mixtures of relatively simple molecules, such as hydrocarbons. In this work, we use the Hicks and Young algorithm to calculate mixture critical points, comparing five modeling options: Peng–Robinson EOS: (1) original and (2) with parameters fitted from molar volume and vapor pressure data; (3) SAFT EOS; and PC-SAFT EOS: (4) original and (5) with refitted parameters to match pure component critical data. Calculations were carried out for binary hydrocarbon mixtures and 29 multicomponent mixtures. The SAFT EOS provided the worst representation of the systems tested and, interestingly, the conventional cubic EOS provided, in general, the best representation.