• Title/Summary/Keyword: Molecular Simulation

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Adsorption Kinetics for Polymeric Additives in Papermaking Aqueous Fibrous Media by UV Spectroscopic Analysis

  • Yoon, Sung-Hoon;Chai, Xin-Sheng
    • Bulletin of the Korean Chemical Society
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    • v.27 no.11
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    • pp.1819-1824
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    • 2006
  • The general objective of the present study was to investigate the potential application of the UV spectroscopic method for determination of the polymeric additives present in papermaking fibrous stock solutions. The study also intended to establish the surface-chemical retention model associated with the adsorption kinetics of additives on fiber surfaces. Polyamide epichlorohydrin (PAE) wet strength resin and imidazolinium quaternary (IZQ) softening agents were selected to evaluate the analytical method. Concentrations of PAE and IZQ in solution were proportional to the UV absorption at 314 and 400 nm, respectively. The time-dependent behavior of polymeric additives obeyed a mono-molecular layer adsorption as characterized in Langmuir-type expression. The kinetic modeling for polymeric adsorption on fiber surfaces was based on a concept that polymeric adsorption on fiber surfaces has two distinguishable stages including initial dynamic adsorption phase and the final near-equilibrium state. The simulation model predicted not only the real-time additive adsorption behavior for polymeric additives at high accuracy once the kinetic parameters were determined, but showed a good agreement with the experimental data. The spectroscopic method examined on the PAE and IZQ adsorption study could potentially be considered as an effective tool for the wet-end retention control as applied to the paper industry.

Interaction at the nanoscale of fundamental biological molecules with minerals

  • Valdre, Giovanni;Moro, Daniele;Ulian, Gianfranco
    • Advances in nano research
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    • v.1 no.3
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    • pp.133-151
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    • 2013
  • The availability of advanced nanotechnological methodologies (experimental and theoretical) has widened the investigation of biological/organic matter in interaction with substrates. Minerals are good candidates as substrates because they may present a wide variety of physico-chemical properties and surface nanostructures that can be used to actively condense and manipulate the biomolecules. Scanning Probe Microscopy (SPM) is one of the best suited techniques used to investigate at a single molecule level the surface interactions. In addition, the recent availability of high performance computing has increased the possibility to study quantum mechanically the interaction phenomena extending the number of atoms involved in the simulation. In the present paper, firstly we will briefly introduce new SPM technological developments and applications to investigate mineral surfaces and mineral-biomolecule interaction, then we will present results on the specific RNA-mineral interaction and recent basics and applicative achievements in the field of the interactions between other fundamental biological molecules and mineral surfaces from both an experimental and theoretical point of view.

Calculation on Electronic State of Y-doped ZnO (Y이 도핑된 ZnO의 전자상태 계산)

  • Lee, Dong-Yoon;Lee, Won-Jae;Song, Jae-Sung;Koo, Bo-Kun;Kim, Hyun-Ju
    • Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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    • 2005.07a
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    • pp.172-173
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    • 2005
  • The electronic state of ZnO doped with Y was calculated using the density functional theory. In this study, the program used for the calculation on theoretical structures of ZnO and doped ZnO was Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The detail of electronic structure was obtained by the descrite variational $X\alpha$ (DV-$X\alpha$) method, which is a sort of molecular orbital full potential method. The optimized crystal structures obtained by calculations were compared to the measured structure. The density of state and energy levels of dopant elements was shown and discussed in association with optical properties.

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The study of electron drift velocity in $CF_4+Ar$ molecular gas mixture by 2-term and multi-term approximation of the Boltzmann equation (다항근사 및 2항근사 볼츠만 방정식을 이용한 $CF_4+Ar$ 혼합기체의 전자이동속도 연구)

  • Song, Byoung-Doo;Ha, Sung-Chul;Jeon, Byoung-Hoon
    • Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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    • 2004.07b
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    • pp.1179-1182
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    • 2004
  • This paper describes the information for quantitative simulation of weakly ionized plasma. In previous paper, we calculated the electron transport coefficients in $CF_4+Ar$ gas mixture by using two-term approximation of Boltzmann equation. but there is difference between the result of the two-term and the multi-term approximation of the Boltzmann equation in $CF_4$ gas. Therefore, in this paper, we calculated the electron drift velocity (W) in $CF_4+Ar$ gas mixture for range of E/N values from $0.01\sim500[Td}$ at the temperature was 300[K] and pressure was 1[Torr] by multi-term approximation of the Boltzmann equation by Robson and Ness. The results of two-term and multi-term approximation of the Boltzmann equation has been compared with each other for a range of E/N.

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SPH SIMULATIONS OF BARRED GALAXIES: DYNAMICAL EVOLUTION OF GASEOUS DISK

  • ANN HONG BAE;LEE HVUNG MOK
    • Journal of The Korean Astronomical Society
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    • v.33 no.1
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    • pp.1-17
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    • 2000
  • We have performed extensive simulations of response of gaseous disk in barred galaxies using SPH method. The gravitational potential is assumed to be generated by disk, bulge, halo, and bar. The mass of gaseous disk in SPH simulation is assumed to be negligible compared to the stellar and dark mass component, and the gravitational potential generated by other components is fixed in time. The self-gravity of the gas is not considered in most simulations, but we have made a small set of simulations including the self-gravity of the gas. Non-circular component of velocity generated by the rotating, non-axisymmetric potential causes many interesting features. In most cases, there is a strong tendency of concentration of gas toward the central parts of the galaxy. The morphology of the gas becomes quite complex, but the general behavior can be understood in terms of simple linear approximations: the locations and number of Lindblad resonances play critical role in determining the general distribution of the gas. We present our results in the form of 'atlas' of artificial galaxies. We also make a brief comment on the observational implications of our calculations. Since the gaseous component show interesting features while the stellar component behaves more smoothly, high resolution mapping using molecular emission line for barred galaxies would be desirable.

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Speckle Removal of SAR Imagery Using a Point-Jacobian Iteration MAP Estimation

  • Lee, Sang-Hoon
    • Korean Journal of Remote Sensing
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    • v.23 no.1
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    • pp.33-42
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    • 2007
  • In this paper, an iterative MAP approach using a Bayesian model based on the lognormal distribution for image intensity and a GRF for image texture is proposed for despeckling the SAR images that are corrupted by multiplicative speckle noise. When the image intensity is logarithmically transformed, the speckle noise is approximately Gaussian additive noise, and it tends to a normal probability much faster than the intensity distribution. MRFs have been used to model spatially correlated and signal-dependent phenomena for SAR speckled images. The MRF is incorporated into digital image analysis by viewing pixel types as slates of molecules in a lattice-like physical system defined on a GRF Because of the MRF-SRF equivalence, the assignment of an energy function to the physical system determines its Gibbs measure, which is used to model molecular interactions. The proposed Point-Jacobian Iterative MAP estimation method was first evaluated using simulation data generated by the Monte Carlo method. The methodology was then applied to data acquired by the ESA's ERS satellite on Nonsan area of Korean Peninsula. In the extensive experiments of this study, The proposed method demonstrated the capability to relax speckle noise and estimate noise-free intensity.

Electron Redistribution of Clavalanate on Binding to a $\beta$-Lactamase

  • Sang-Hyun Park;Hojing Kim
    • Bulletin of the Korean Chemical Society
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    • v.14 no.4
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    • pp.491-496
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    • 1993
  • A class A ${\beta}$-lactamase from Staphylococcus aureus PC1 complexed with 3R,5R-clavulanate is studied. The starting geometry for the computation is the crystal structure of the ${\beta}$-lactamase. Docking of the clavulanate to the enzyme is done exploiting the requirements of electrostatic and shape complementarity between the enzyme and clavulanate. This structure is then hydrated by water molecules and refined by energy minimization and short molecular dynamics simulation. In the energy refined structure of this complex, the carboxyl group of the clavulanate is hydrogen bonded to Lys-234, and the the carbonyl carbon atom of the clavulanate is adjacent to the $O_{\gamma}$ of Ser-70. It is found that a crystallographic water molecule initially located at the oxyanion hole, which is formed by the two -NH group of Ser-70 and Gln-237, is replaced by the carbonyl oxygen atom of the 3R,5R-clavulanate after docking and energy reginement. The crystallographic water molecules are proved to be important in ligand binding. Glu-166 residue is found to be repulsive to the binding of clavulanate, which is in agreement with experimental observation. Arg-244 residue is found to be important to the binding of clavulanate as well as to interaction with C2 side chain of the clavulanate. The electron density redistribution of the clavulanate on binding to the ${\beta}$-lactamase in studied by an ab initio quantum-mechanical calculation. A significant redistribution of electron density of the clavulanate is induced by the enzyme, toward the enzyme, toward the transition state of the enzymatic reaction.

Temperature Effect on the Configurational Properties of an n-Decane Chain in Solution

  • Oh, In-Joon;Ree, Tai-Kyue
    • Bulletin of the Korean Chemical Society
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    • v.5 no.4
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    • pp.162-167
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    • 1984
  • Equilibrium and dynamical behaviors of an n-alkane poymer (decane) in solution have been investigated by a molecuar dynamics simulation method. The polymer is assumed to be a chain of elements $(CH_2)$ interconnected by bonds having a fixed bond length and bond angle, but esch bond of the polymer is allowed to execute hindered internal rotation. The calculation explicitly considers the molecular naturer of solvent by including the intermolecular interactions between slovent-solvent molecules and chain element-solvent molecule. We present the results of calculations on (1) equilibrium properties (the solvent molecule-chain element pair correlation function, chain element-chain element pair correlation function, the mean square end-to-end distance and the mean square radius of gyration of the polymer) and (2) dynamic properties (four different autocorrelation functions, namely, the autocorrelation functions for the end-to-end distance and the radius of gyration, and the velocity autocorrelation functions for the center of mass and the end point of the chain). We found that the physical properties of the polymer chain depends sensitively on temperature. Comparison of the present work with other authors' results is also presented.

A Study on the Design of High-Stength Titanium Alloys Using DV-Xα Molecular Orbital Method (DV-Xα 분자 궤도법을 이용한 고강도 타이타늄 합금 설계)

  • Baek, Min-Sook;Yoon, Dong-Joo;Won, Dae-Hee;Kim, Byung-Il
    • Korean Journal of Metals and Materials
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    • v.49 no.9
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    • pp.739-745
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    • 2011
  • Beta-type alloys are the most versatile class of titanium alloys. They offer the highest strength to weight ratios and very attractive combinations of strength, toughness, and fatigue resistance inlarge cross sections [1]. The present study was made to obtain useful information for the design of ${\beta}$-type titanium alloys with high-strength properties by using the $DV-X{\alpha}$ method. Employing two calculated parameters, the bond order (Bo) and the d-orbital energy level (Md) of alloying elements in ${\beta}$-type titanium alloy was introduced and used for prediction of mechanical properties. Thus, high-strength titanium alloys were designed by calculating the Md and Bo values of the previous and present titanium alloys.

Investigation of gamma radiation shielding properties of polyethylene glycol in the energy range from 8.67 to 23.19 keV

  • Akhdar, H.;Marashdeh, M.W.;AlAqeel, M.
    • Nuclear Engineering and Technology
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    • v.54 no.2
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    • pp.701-708
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    • 2022
  • The mass attenuation coefficients (μm) of polyethylene glycol (PEG) of different molecular weights (1000-200,000) were measured using single-beam photon transmission. The X-ray fluorescent (XRF) photons from Zinc (Zn), Zirconium (Zr), Molybdenum (Mo), Silver (Ag) and Cadmium (Cd) targets were used to determine the attenuation of gamma radiation of energy range between 8.67 and 23.19 keV in PEG samples. The results were compared to theoretical values using XCOM and Monte Carlo simulation using Geant4 toolkit which was developed to validate the experiment at those certain energies. The mass attenuation coefficients were then used to compute the effective atomic numbers, electron density and half value layers for the studied samples. The outcomes showed good agreement between experimental and simulated results with those calculated theoretically by XCOM within 5% deviation. The PEG 1000 sample showed slightly higher μm value compared with the other samples. The dependence of the photon energy and PEG composition on the values of μm and HVL were investigated and discussed. In addition, the values of Zeff and Neff for all PEG samples behaved similarly in the given photon energy range, and they decreased as the photon energy increased.