On estimation of bias field in MRI images: polynomial vs Gaussian surface fitting method

Surface fitting is one of the well‐known retrospective methods for bias field estimation from magnetic resonance imaging (MRI) images. Bias field in MRI images is primarily caused because of radio frequency–coil nonuniformity, improper image acquisition process, patient movement, and so on. The bias field can be characterized by any slow variant and smooth function because of its slow variant nature. In this paper, we present a comparative study between polynomial and Gaussian surface fitting methods. In particular, we have used both the second‐ and third‐order polynomial functions to estimate the bias field. In this study, we approximate the bias field in two different ways. In the first method, the surfaces are fitted on the anatomical tissue regions individually and then fused to estimate the bias field. Conversely, in the second method, we have done the same over the entire image region. We have tested on three volumes of simulated and one volume of real‐patient MRI brain images and validated the results by both the qualitative and quantitative analyses. The quantitative analyses are presented in standard deviation and coefficient of joint variation. The analysis of the simulation results show that the Gaussian surface fitting method yields better results in both the cases, where the surface fitting is done on entire image and individual tissue regions.     

Sulfur hexafluoride's liquid-vapor coexistence curve, interfacial properties, and diffusion coefficients as predicted by a simple rigid model

We present here molecular-dynamics simulation results of the vapor-liquid coexistence curve, surface tension, and self-diffusion coefficients of sulfur hexafluoride. Sulfur hexafluoride is modeled as a rigid molecule, following the model proposed by Pawley [Mol. Phys. 43, 1321 (1981)]. Vapor-liquid coexistence curve and surface tension are obtained through direct molecular-dynamic simulations in the NVT ensemble. Simulation results are able to reproduce the qualitative shape of the vapor-liquid envelope. However, lower densities, a higher critical temperature, and an overestimated surface tension are obtained here. Those deviations are explained on the basis of the rigidity of the molecular model used. Self-diffusion coefficients are calculated from simulations in the NVE ensemble for different gas states at atmospheric pressure. The rigid model performs better for dynamical properties since simulation results provide very good agreement with available experimental data in this case.     

On the mode-coupling theory of vibrational line broadening in near-critical fluids

Molecular-dynamics simulations of a neat atomic fluid, coupled with a simple model for vibrational frequency perturbations, are used to investigate vibrational line broadening near the liquid-gas critical point. All features of our simulations are in qualitative agreement with recent Raman experiments on nitrogen. We also use our simulation results to assess the validity of the mode-coupling theories that have been used to analyze experiment. We find that the theoretical results are not in good agreement with simulation, both for the temperature dependence of the linewidth, and for the frequency time-correlation functions. However, the mode-coupling prediction that critical line broadening is due to the diverging correlation time of the frequency fluctuations is shown to be correct.     

Molecular Dynamics Simulations of a β-Hairpin Fragment of Protein G by Means of Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics (ABEEMσπ/MM)

There are some controversial opinions about the origin of folding β‐hairpin stability in aqueous solution. In this study, the structural and dynamic behavior of a 16‐residue β‐hairpin from B1 domain of protein G has been investigated at 280, 300, 350 and 450 K using molecular dynamics (MD) simulations by means of Atom‐Bond Electronegativity Equalization Method Fused into Molecular Mechanics i.e., ABEEMδπ/MM and the explicit ABEEM‐7P water solvent model. In addition, a 300 K simulation of one mutant having the aromatic residues substituted with alanines has been performed. The hydrophobic surface area, hydrophilic surface area and some structural properties have been used to measure the role of the hydrophobic interactions. It is found that the aromatic residues substituted with alanines have shown an evident destabilization of the structure and unfolding started after 1.5 ns. It is also found that the number of the main chain hydrogen bonds have different distributions through three different simulations. All above demonstrate that the hydrophobic interactions and the main chain hydrogen bonds play an important role in the stability of the folding structure of β‐hairpin in solution. Furthermore, through the structural analyses of the β‐hairpin structures from four temperature simulations and the comparison with other MD simulations of β‐hairpin peptides, the new ABEEMδπ force field can reproduce the structural data in good agreement with the experimental data.     

Influence of image‐analysis software on quantitation of two‐dimensional gel electrophoresis data

Image analysis of two‐dimensional gels is a crucial step in a proteomic workflow and has a direct impact on obtained qualitative and quantitative data. Since the analysis is a complex process and creates large data amounts, the use of a respective software is inevitable. There are only a few papers published addressing the issue of analysis‐based variance; therefore, our aim was to highlight the discrepancy of received results when different commercially available image‐tools are used for gel analysis especially in terms of comparability of the obtained outcome when the same digital image set is used. A set of six gels (three replicates per group) of real‐life samples was created and examined with two different versions of PD‐Quest (Bio‐Rad) (version 6.1 and its update version 8.0) and with an external image‐tool Delta 2D (Decodon) (version 3.6). Replicate groups were analyzed and compared with each other with regard to volume ratios of a group of significantly changed spots. The study points out significant variations among results depending on the software package used, underlining the importance of a careful investigation of post‐experimental processes to receive comparable and reliable results.     

Atomic force microscopy application for degradation diagnostics in library heritage

Atomic Force Microscopy was used on pure cotton cellulose paper to characterize the relationship between surface topographies and cellulose degradation patterns. Whatman N.1 chromatography paper and Fabriano Umbria paper artificially aged with different procedures and then naturally aged‐were evaluated together with a sample from an original book. Evidence is found of a clear distinction between surface heights distribution of chiefly oxidised samples with respect to those where hydrolysis is the dominant process. In both cases, deteriorated paper shows surface features well different from the paper in good preservation state, in agreement to results from previous experiments. This is a first step that could open the way to AFM application as a qualitative diagnostic tool for library materials. The only way to achieve such a goal is to extend the experimentation to a wider population of paper samples, so to improve the statistical evaluation. Copyright © 2008 John Wiley & Sons, Ltd.     

Effect of Endfunctionality of Reactive Polymers on the Reaction Kinetics at Immiscible Polymer Interfaces: A Monte Carlo Study

Reactions at the interface of two immiscible polymers containing different reactive groups at either one end or both ends are studied with Monte Carlo (MC) simulations. The MC simulation shows that the copolymer concentration at the interface is shown to dramatically increase during the early stage of reaction and then levels off at a constant value. The effect of endfunctionality, i. e., the effect of the number of endfunctional groups, is also investigated. While the saturation value of interfacial coverage is proportional to the initial reactive polymer density for the case of mono‐endfunctional polymer, the simulation results with di‐endfunctional polymers show that the saturation copolymer coverage is not exactly proportional to the initial reactive polymer density in the case of high concentrations of the initial reactive polymer. This is believed to be caused by the change of conformation of block copolymers formed at the interface due to reaction: the fraction of loop conformation decreases while the tail fraction increases with a large amount of initial reactive di‐endfunctional polymer. Also, the experimentally determined time‐dependent interfacial fracture toughness, which is, in turn, related to the copolymer coverage at the interface, is in good qualitative agreement with the simulation results.     

Adhesion between graphite and modified polyester surfaces: a theoretical study

This study examines the adhesion of graphite to functionalized polyester surfaces using a range of qualitative and quantitative measures of theoretical adhesion. Modifications to the polyester surfaces include the addition of hydroxyl, carboxyl, or fluorine substituents with coverages of 0.4 and 0.9 groups per nm(2). In each case, the introduction of substituents to the surface of the polyester was calculated to lead to reduced adhesion to graphite. Effects of surface relaxation on adhesion are studied by employing different simulation protocols. The theoretical results suggest one mechanism to reduce adhesion to carbonaceous solids is to increase atomic roughness using strongly hydrophilic or alternatively strongly hydrophobic substituents.     

High translational energy release in H2 (D2) associative desorption from H (D) chemisorbed on C(0001)

Highly energetic translational energy distributions are reported for hydrogen and deuterium molecules desorbing associatively from the atomic chemisorption states on highly oriented pyrolytic graphite (HOPG). Laser assisted associative desorption is used to measure the time of flight of molecules desorbing from a hydrogen (deuterium) saturated HOPG surface produced by atomic exposure from a thermal atom source at around 2100 K. The translational energy distributions normal to the surface are very broad, from approximately 0.5 to approximately 3 eV, with a peak at approximately 1.3 eV. The highest translational energy measured is close to the theoretically predicted barrier height. The angular distribution of the desorbing molecules is sharply peaked along the surface normal and is consistent with thermal broadening contributing to energy release parallel to the surface. All results are in qualitative agreement with recent density functional theory calculations suggesting a lowest energy para-type dimer recombination path.     

Computer‐aided design and synthesis of magnetic molecularly imprinted polymers with high selectivity for the removal of phenol from water

A molecular simulation method was introduced to compute the phenol–monomer pre‐assembled system of a molecularly imprinted polymer. The interaction type and intensity between phenol and monomer were evaluated by combining binding energy and charge transfer with complex conformation. The simulation results indicate that interaction energies are simultaneously affected by the type of monomer and the ratio between phenol and monomers. At the same time, we considered that by increasing the amount of functional monomer is not always better for preparing molecularly imprinter polymers. In this study, three kinds of novel magnetic phenol‐imprinted polymers with favorable specific adsorption effects were prepared by the surface imprinting technique combined with atom transfer radical polymerization. Various measures were selected to characterize the structure and morphology to obtain the optimal polymer. The characterization results show that the optimal polymer has suitable features for further adsorption process. A series of static adsorption experiments were conducted to analyze its adsorption performance, which follows the Elovich model from the kinetic analysis and the Sips equation from the isothermal analysis. To further verify the reliability and accuracy of the simulation results, the effects of different monomers on the adsorption selectivity were also determined. They display higher selectivity towards phenol than 4‐nitrophenol.The results from the simulation of the pre‐assembled complexes are in reasonable agreement with those from the experiment.     

Inversion of the Side‐Chain Stereochemistry of Indvidual Thr or Ile Residues in a Protein Molecule: Impact on the Folding,Stability, and Structure of the ShK Toxin

ShK toxin is a cysteine‐rich 35‐residue protein ion‐channel ligand isolated from the sea anemone Stichodactyla helianthus. In this work, we studied the effect of inverting the side chain stereochemistry of individual Thr or Ile residues on the properties of the ShK protein. Molecular dynamics simulations were used to calculate the free energy cost of inverting the side‐chain stereochemistry of individual Thr or Ile residues. Guided by the computational results, we used chemical protein synthesis to prepare three ShK polypeptide chain analogues, each containing either an allo‐Thr or an allo‐Ile residue. The three allo‐Thr or allo‐Ile‐containing ShK polypeptides were able to fold into defined protein products, but with different folding propensities. Their relative thermal stabilities were measured and were consistent with the MD simulation data. Structures of the three ShK analogue proteins were determined by quasi‐racemic X‐ray crystallography and were similar to wild‐type ShK. All three ShK analogues retained ion‐channel blocking activity.     

Inversion of the Side‐Chain Stereochemistry of Indvidual Thr or Ile Residues in a Protein Molecule: Impact on the Folding,Stability, and Structure of the ShK Toxin

ShK toxin is a cysteine‐rich 35‐residue protein ion‐channel ligand isolated from the sea anemone Stichodactyla helianthus. In this work, we studied the effect of inverting the side chain stereochemistry of individual Thr or Ile residues on the properties of the ShK protein. Molecular dynamics simulations were used to calculate the free energy cost of inverting the side‐chain stereochemistry of individual Thr or Ile residues. Guided by the computational results, we used chemical protein synthesis to prepare three ShK polypeptide chain analogues, each containing either an allo‐Thr or an allo‐Ile residue. The three allo‐Thr or allo‐Ile‐containing ShK polypeptides were able to fold into defined protein products, but with different folding propensities. Their relative thermal stabilities were measured and were consistent with the MD simulation data. Structures of the three ShK analogue proteins were determined by quasi‐racemic X‐ray crystallography and were similar to wild‐type ShK. All three ShK analogues retained ion‐channel blocking activity.     

Effect of Surface Roughness on Structure and Dynamics in Thin Films

We performed Monte Carlo simulations of free‐standing, amorphous polyethylene (PE) thin films at 509 K. The three films are constructed from 9, 36, or 144 independent parent PE chains, with 100 carbon atoms per chain. The two‐dimensional periodic cross‐sectional area of the simulation box is proportional to the number of independent parent chains, with the 144‐chain film having an area four times larger than the 36‐chain film. All three films have a similar bulk density and a comparable thickness between the two free surfaces. The 144‐chain film with the largest periodic surface area has a broader density profile due to the increased roughness of its surfaces. Snapshots of its surfaces along the trajectory indicate dynamic changes in the high and low regions of the rough surfaces. Diffusion of the chains parallel to the free surfaces is suppressed in the 144‐chain film, due to increased surface roughness. The tendency of bonds to orient parallel to the free surface is less pronounced in films with higher surface roughness.     

Research and application of a new rapid heat cycle molding with electric heating and coolant cooling to improve the surface quality of large LCD TV panels

The usage of rapid heat cycle molding (RHCM) has gained increasing attention in overcoming the limits of conventional injection molding (CIM) and improving the surface quality and mechanical properties of molded plastic products. In RHCM, the vario‐thermal mold temperature control system is the key technique because it directly affects the molding cycle time and the final part quality. In this study, a new RHCM technology with electric heating and coolant cooling was studied in detail. Two different RHCM mold structures for a large LCD TV panel were proposed and designed. The numerical simulation method was used to analyze the thermal response of the mold cavity surface at the heating stage and the thermal response of the resin melt at the cooling stage. The heating/cooling efficiency of the proposed electric heating RHCM system was evaluated. The thermal expansion analysis of mold cavity was implemented and the fixation of the cavity in molds was also optimized. The results showed that the electric‐heating mold with a separate cooling plate can efficiently enhance the heating efficiency. The thermal expansion of the cavity surface can be reduced by increasing the alleviating‐gap between the cavity and the cavity‐retainer plate. Then, the service lifetime of the electric‐heating mold can be improved. A RHCM production line with electric heating for the large LCD TV panel was constructed. Both the simulation and test production results indicate that the proposed electric heating RHCM technique can realize high‐temperature injection molding without increasing the molding cycle time. The surface appearance of the LCD TV panels was dramatically improved and the surface marks that usually occur in CIM process were eliminated completely. Copyright © 2009 John Wiley & Sons, Ltd.     

Monte‐Carlo simulation of x‐ray photoelectron emission from silver

Silver 3d x‐ray photoelectron spectroscopy (XPS) spectra were simulated with the Monte‐Carlo method using an effective energy‐loss function that was derived from a reflected electron energy‐loss spectroscopy (REELS) analysis based on an extended Landau approach. After confirming that Monte‐Carlo simulation based on the use of the effective energy‐loss function can successfully describe the experimental REELS spectrum and Ag 3d XPS spectrum, we applied Monte‐Carlo simulation to predict the angular distribution of Ag 3d x‐ray photoelectrons for different x‐ray incidence angles and different photoelectron take‐off angles. The experimental photoelectron emission microscope that we are constructing was confirmed as being close to the optimum configuration, in which the x‐ray incident angle as measured from the surface normal direction is 74° and the photoelectron take‐off angle is set normal to the surface. The depth distribution functions of the Ag 3d X‐ray photoelectrons for different energy windows suggest that the photoelectron emission microscope will exhibit greater surface sensitivity for narrower photoelectron energy windows. Copyright © 2003 John Wiley & Sons, Ltd.     

Aggregation Behavior of Cationic Copolymer Methacryloxyethyl Trimethyl Ammonium Chloride‐Butyl Acrylate‐Acrylamide in Aqueous Solution

The aggregation behavior of cationic copolymer methacryloxyethyl trimethyl ammonium chloride‐butyl acrylate‐acrylamide (MTAC‐BA‐AM) was investigated via surface property and fluorescence spectroscopy measurements, as well as Mesodyn simulation, etc. The experimental results indicate that MTAC‐BA‐AM has the ability for decreasing surface tension of water and there are two break points in the surface tension isotherm; and its surface dilational viscoelasticity and apparent viscosity in aqueous solution depend upon aggregate structure. The Mesodyn simulation results show that spherical, cylindrical aggregates, and network structures form in aqueous solution with the concentration increasing. The aggregation process is driven by enthalpy and can be divided into two stages. The first stage is controlled by diffusion, while the second one is controlled by hydrophobic interaction.     

A Constant Potential Molecular Dynamics Simulation Study of the Atomic‐Scale Structure of Water Surfaces Near Electrodes

Novel and technologically important processes and phenomena arise at water surfaces in the presence of electric fields. However, experimental measurements on water surfaces are challenging, and the results are scarce and inconclusive. In this work, the constant potential molecular dynamics method, in which the electrode charges are allowed to fluctuate to keep the electric potential fixed, was implemented in the study of a near‐electrode water surface systems. This simulation system was set up with a vapor/liquid‐water/vapor slab and two electrodes under different sets of applied electrostatic potential, yielding i) a detailed characterization of the external E‐field dependent electrostatic potential/density/dipole moment density profiles, and ii) the relationship between the water surface width and the applied electrode voltage differences which has been rarely reported. The adjustments in the number density profiles in the vicinity of water surfaces due to external E‐fields were observed, while the capillary interfacial widths for the surfaces near both cathode and anode were found with different increment rates under increasing E‐fields. By examining dipole density profiles across the water surfaces, we found that external E‐field induced polarization occurs in both bulk and surface regimes, yet the surface polarization densities vary asymmetrically with respect to the increasing E‐fields. Detailed discussions were carried out to explain the correlation between water surface tension and surface widths, as well as the interplay between the surface polarization densities and the hydrogen bond network structure. We conclude that the mechanical and structural properties of the water surfaces could be tuned by both magnitude and direction of the strong external E‐fields. We also recognize that more surface properties with application value, such as dielectric permittivity tensor or surface potential, could also be regulated by the external E‐fields.     

Effect of the Linking Structure of Nonlinear Optical Side Groups on the Phase Behavior of an Aromatic Polyester Backbone

Summary: The phase behavior of poly(p‐phenylene terephthalate)s (PPT) with pendant side groups, N‐(4‐nitrophenyl)ethylaminoethanol (NPE) and N‐(4‐nitrophenyl)‐L ‐prolinol (NPP) has been studied by using differential scanning calorimetry (DSC), wide‐angle X‐ray scattering (WAXS), and second harmonic generation (SHG). PPT‐NPE showed a layered liquid crystalline morphology while PPT‐NPP showed a completely amorphous structure. Compressive or shear stress applied on the polymer melt surface at 210 °C induced a more prominent layered structure of PPT‐NPE whereas the amorphous structure of PPT‐NPP remained unchanged under the stress. In order to understand this phase difference in terms of the repeat structure, we attempted theoretical ab initio Hartree‐Fock, and DFT calculations for the monomers and molecular dynamics for the bulk state. The results indicated that molecular configurations are a good way of microscopically understanding the phases of rigid backbone polymers with functional side groups: The NPT (constant particle number, pressure, and temperature) simulation data at 210 °C agree qualitatively with the experimental data and the difference between PPT‐NPE and PPT‐NPP could be understood using rotational energy barrier, steric hindrance and inter‐chain interactions. X‐ray diffractometer (XRD) simulation patterns for the oligomers are also in qualitative agreement with the experimental WAXS data and the structural parameters of stacks of PPT‐NPE chains are estimated to be layer distance (4.6 Å), backbone distance (21.5 Å), and side distance (12 Å).