Search results for: molecular characterization

Authors: Keun Woo Lee, Minky Son, Chanin Park, Ayoung Baek

Abstract:

Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.

Keywords: Amino acid discrimination, Binding free energy Leucyl-tRNAsynthetase, Molecular dynamics.

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Authors: Sie-Tiong Ha, Teck-Leong Lee, Yip-Foo Win, Siew-Ling Lee, Guan-Yeow Yeap

Abstract:

A homologous series of aromatic esters, 4-nalkanoyloxybenzylidene- 4--bromoanilines, nABBA, consisting of two 1,4-disubstituted phenyl cores and a Schiff base central linkage was synthesized. All the members can be differed by the number of carbon atoms at terminal alkanoyloxy chain (CnH2n-1COO-, n = 2, 6, 18). The molecular structure of nABBA was confirmed with infrared spectroscopy, nuclear magnetic resonance (NMR) spectroscopy and electron-ionization mass (EI-MS) spectrometry. Mesomorphic properties were studied using differential scanning calorimetry and polarizing optical microscopy.

Keywords: Liquid Crystals, Schiff base, Smectic, Mesomorphic

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Authors: D. Falliano, D. De Domenico, G. Ricciardi, E. Gugliandolo

Abstract:

This paper is focused on the mechanical characterization of foamed concrete specimens with protein-based foaming agent. Unlike classic foamed concrete, a peculiar property of the analyzed foamed concrete is the extrudability, which is achieved via a specific additive in the concrete mix that significantly improves the cohesion and viscosity of the fresh cementitious paste. A broad experimental campaign was conducted to evaluate the compressive strength and the indirect tensile strength of the specimens. The study has comprised three different cement types, two water/cement ratios, three curing conditions and three target dry densities. The variability of the strength values upon the above mentioned factors is discussed.

Keywords: Cement type, curing conditions, density, extrudable concrete, foamed concrete, mechanical characterization.

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Authors: Musammat F. Nahar, Anna Roujeinikova

Abstract:

Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.

Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.

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Authors: Salem El-tohami Ashoor

Abstract:

A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH₂)₃NAr)}^2-((ηⁿ-Cp)Cp)} (Ar = 2,6-Prⁱ₂C₆H₃)(Cp = C₅H₅ and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions.

The optimised of [V(ArN(CH₂)₃NAr)₂Cl(η⁵-Cp)] (Ar = 2,6-Prⁱ₂C₆H₃ and Cp= C₅H₅) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH₂)₃NAr)₂Cl(η¹-Cp)] (Ar = 2,6-Prⁱ₂C₆H₃ and Cp= C₅H₅) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: Vanadium(IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO.

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Authors: V. A. C. Vale, E. T. L. Cöuras Ford

Abstract:

The use of optical technologies in the telecommunications has been increasing due to its ability to transmit large amounts of data over long distances. However, as in all systems of data transmission, optical communication channels suffer from undesirable and non-deterministic effects, being essential to know the same. Thus, this research allows the assessment of these effects, as well as their characterization and beneficial uses of these effects.

Keywords: Optical communication, optical fiber, non-deterministic effects.

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Authors: A. Fakhfakh, N. Ksentini, M. Loulou, N. Masmoudi, J. J. Charlot

Abstract:

Today, design requirements are extending more and more from electronic (analogue and digital) to multidiscipline design. These current needs imply implementation of methodologies to make the CAD product reliable in order to improve time to market, study costs, reusability and reliability of the design process. This paper proposes a high level design approach applied for the characterization and the optimization of Switched-Current Sigma- Delta Modulators. It uses the new hardware description language VHDL-AMS to help the designers to optimize the characteristics of the modulator at a high level with a considerably reduced CPU time before passing to a transistor level characterization.

Keywords: high level design, optimization, switched-Current Sigma-Delta Modulators, VHDL-AMS.

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Authors: S. Yaglikci, B. Salgara, F. Soysal, B. Cicek

Abstract:

Chemical vapor deposition method was used to produce carbon nanotubes on an iron based catalyst from acetylene. Gas-phase samples collected from the different positions of the tubular reactor were analyzed by GC/MS. A variety of species ranging from hydrogen to naphthalene were observed and changes in their concentrations were plotted against the reactor position. Briefly benzene, toluene, styrene, indene and naphthalene were the main higher molecular weight species and vinylacetylene and diacetylene were the important intermediates. Nanotube characterization was performed by scanning electron microscopy and transmission electron microscopy.

Keywords: Carbon nanotubes, chemical vapor deposition, GC/MS, species profile

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Authors: Lina Paola Orozco-Marín, Yuliet Montoya, John Bustamante

Abstract:

Ischemic events can culminate in acute myocardial infarction with irreversible cardiac lesions that cannot be restored due to the limited regenerative capacity of the heart. Tissue engineering proposes therapeutic alternatives by using biomaterials to resemble the native extracellular medium combined with healthy and functional cells. This research focused on developing a natural thermosensitive hydrogel, its physical-chemical characterization and in vitro biocompatibility determination. Hydrogels’ morphological characterization was carried out through scanning electron microscopy and its chemical characterization by employing Infrared Spectroscopy technic. In addition, the biocompatibility was determined using fetal human ventricular cardiomyocytes cell line RL-14 and the MTT cytotoxicity test according to the ISO 10993-5 standard. Four biocompatible and thermosensitive hydrogels were obtained with a three-dimensional internal structure and two gelation times. The results show the potential of the hydrogel to increase the cell survival rate to the cardiac cell therapies under investigation and lay the foundations to continue with its characterization and biological evaluation both in vitro and in vivo models.

Keywords: cardiac cell therapy, cardiac ischemia, natural polymers, thermosensitive hydrogel

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Authors: S. Kulsri, M. Jaroensutasinee, K. Jaroensutasinee

Abstract:

We developed a method based on quasi-molecular modelling to simulate the fall of water drops on horizontally smooth and rough surfaces. Each quasi-molecule was a group of particles that interacted in a fashion entirely analogous to classical Newtonian molecular interactions. When a falling water droplet was simulated at low impact velocity on both smooth and rough surfaces, the droplets moved periodically (i.e. the droplets moved up and down for a certain period, finally they stopped moving and reached a steady state), spreading and recoiling without splash or break-up. Spreading rates of falling water droplets increased rapidly as time increased until the spreading rate reached its steady state at time t ~ 0.25 s for rough surface and t ~ 0.40 s for smooth surface. The droplet height above both surfaces decreased as time increased, remained constant after the droplet diameter attained a maximum value and reached its steady state at time t ~ 0.4 s. However, rough surface had higher spreading rates of falling water droplets and lower height on the surface than smooth one.

Keywords: Quasi-molecular modelling, particle modelling, molecular aggregate approach.

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Authors: M. Gómez-Gómez, M. E. Sánchez-Vergara

Abstract:

Many sustainable approaches to generate electric energy have emerged in the last few decades; one of them is through solar cells. Yet, this also has the disadvantage of highly polluting inorganic semiconductor manufacturing processes. Therefore, the use of molecular semiconductors must be considered. In this work, allene compounds C24H26O4 and C24H26O5 were used as dopants to manufacture semiconductor films based on PbPc by high-vacuum evaporation technique. IR spectroscopy was carried out to determine the phase and any significant chemical changes which may occur during the thermal evaporation. According to UV-visible spectroscopy and Tauc’s model, the deposition process generated thin films with an activation energy range of 1.47 eV to 1.55 eV for direct transitions and 1.29 eV to 1.33 eV for indirect transitions. These values place the manufactured films within the range of low bandgap semiconductors. The flexible devices were manufactured: polyethylene terephthalate (PET), Indium tin oxide (ITO)/organic semiconductor/Cubic Close Packed (CCP). The characterization of the devices was carried out by evaluating electrical conductivity using the four-probe collinear method. I-V curves were obtained under different lighting conditions at room temperature. OS1 (PbPc/C24H26O4) showed an Ohmic behavior, while OS2 (PbPc/C24H26O5) reached higher current values at lower voltages. The results obtained show that the semiconductor devices doped with allene compounds can be used in the manufacture of optoelectronic devices.

Keywords: Electrical properties, optical gap, phthalocyanine, thin film.

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Authors: N. Reehana, A. Parveez Ahamed, D. Mubarak Ali, A. Suresh, R. Arvind Kumar, N. Thajuddin

Abstract:

Cyanobacteria play a vital role in the production of phycobiliproteins that includes phycocyanin and phycoerythrin pigments. Phycocyanin and related phycobiliproteins have wide variety of application that is used in the food, biotechnology and cosmetic industry because of their color, fluorescent and antioxidant properties. The present study is focused to understand the pigment at molecular level in the Cyanobacteria Oscillatoria terebriformis NTRI05 and Oscillatoria foreaui NTRI06. After extraction of genomic DNA, the amplification of C-Phycocyanin gene was done with the suitable primer PCβF and PCαR and the sequencing was performed. Structural and Phylogenetic analysis was attained using the sequence to develop a molecular model.

Keywords: Cyanobacteria, C-Phycocyanin gene, Phylogenetic analysis, Structural analysis.

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Authors: J. Subbalakshmi, G. Dhruvasamhith, S. M. Hussain

Abstract:

Polyaniline (PANI) is one of the most extensively studied material among the conducting polymers due to its simple synthesis by chemical and electrochemical routes. PANIs have advantages of chemical stability and high conductivity making their commercial applications quite attractive. However, to our knowledge, very little work has been reported on the tensile strength properties of templated PANIs processed with polyvinyl alcohol and also, detailed study has not been carried out. We have investigated the effect of small molecule and polymers as templates on PANI. Stable aqueous colloidal suspensions of trisodium citrate (TSC), poly(ethylenedioxythiophene)-polystyrene sulfonate (PEDOT-PSS), and polyethylene glycol (PEG) templated PANIs were prepared through chemical synthesis, processed with polyvinyl alcohol (PVA) and were fabricated into films by solution casting. Absorption and infra-red spectra were studied to gain insight into the possible molecular interactions. Surface morphology was studied through scanning electron microscope and optical microscope. Interestingly, tensile testing studies revealed least strain for pure PVA when compared to the blends of templated PANI. Furthermore, among the blends, TSC templated PANI possessed maximum elasticity. The ultimate tensile strength for PVA processed, PEG-templated PANI was found to be five times more than other blends considered in this study. We establish structure–property correlation with morphology, spectral characterization and tensile testing studies.

Keywords: Processed films, polyvinyl alcohol, spectroscopy, surface morphology, templated polyanilines, tensile test.

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Authors: I. Restrepo, S. Solorzano

Abstract:

This work was focused in to study the compatibility, dispersion and exfoliation of modified nanoclays in biodegradable polymers and evaluate its effect on the physical, mechanical and thermal properties on the biodegradable matrix used. The formulations have been developed with polylactic acid (PLA) and organically modified montmorillonite-type commercial nanoclays (Cloisite 15, Cloisite 20, and Cloisite 30B) in the presence of a plasticizer agent, specifically Polyethylene Glycol of low molecular weight. Different compositions were evaluated, in order to identify the influence of each nanoclayin the polymeric matrix. The mixtures were characterized by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction (DRX), transmission electron microscopy (TEM) and Tensile Test. These tests have allowed understanding the behavior of each of the mixtures developed.

Keywords: Biopolymers, Nanoclays, polylacticacid (PLA), polymer blends.

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Authors: Atif Zafar, Fan Haijun

Abstract:

A sequence of different Reservoir Engineering methods and tools in reservoir characterization and field development are presented in this paper. The real data of Jin Gas Field of L-Basin of Pakistan is used. The basic concept behind this work is to enlighten the importance of well test analysis in a broader way (i.e. reservoir characterization and field development) unlike to just determine the permeability and skin parameters. Normally in the case of reservoir characterization we rely on well test analysis to some extent but for field development plan, the well test analysis has become a forgotten tool specifically for locations of new development wells. This paper describes the successful implementation of well test analysis in Jin Gas Field where the main uncertainties are identified during initial stage of field development when location of new development well was marked only on the basis of G&G (Geologic and Geophysical) data. The seismic interpretation could not encounter one of the boundary (fault, sub-seismic fault, heterogeneity) near the main and only producing well of Jin Gas Field whereas the results of the model from the well test analysis played a very crucial rule in order to propose the location of second well of the newly discovered field. The results from different methods of well test analysis of Jin Gas Field are also integrated with and supported by other tools of Reservoir Engineering i.e. Material Balance Method and Volumetric Method. In this way, a comprehensive way out and algorithm is obtained in order to integrate the well test analyses with Geological and Geophysical analyses for reservoir characterization and field development. On the strong basis of this working and algorithm, it was successfully evaluated that the proposed location of new development well was not justified and it must be somewhere else except South direction.

Keywords: Field development, reservoir characterization, reservoir engineering, well test analysis.

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Authors: Yoshihiro Ochiai

Abstract:

Globin superfamily proteins including myoglobin and hemoglobin, have welcome new members recently, namely, cytoglobin, neuroglobin and globin X, though their physiological functions are still to be addressed. Fish are the excellent models for the study of these globins, but their characteristics have not yet been discussed to date. In the present study, attempts have been made to characterize their structural uniqueness by making use of proteomics approach. This is the first comparative study on the characterization of globin superfamily proteins from fish.

Keywords: Globin, Superfamily, Protein, Fish, Structure

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

Abstract:

Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: Enhanced ideal gas molecular movement, ideal gas molecular movement, model updating method, probability-based damage detection, uncertainty quantification.

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Authors: David L. Azevedo, Jordan Del Nero

Abstract:

In this paper we study a system composed by carbon nanotube (CNT) and bundle of carbon nanotube (BuCNT) interacting with a specific fatty acid as molecular probe. Full system is represented by open nanotube (or nanotubes) and the linoleic acid (LA) relaxing due the interaction with CNT and BuCNT. The LA has in his form an asymmetric shape with COOH termination provoking a close BuCNT interaction mainly by van der Waals force field. The simulations were performed by classical molecular dynamics with standard parameterizations. Our results show that these BuCNT and CNT are dynamically stable and it shows a preferential interaction position with LA resulting in three features: (i) when the LA is interacting with CNT and BuCNT (including both termination, CH2 or COOH), the LA is repelled; (ii) when the LA terminated with CH2 is closer to open extremity of BuCNT, the LA is also repelled by the interaction between them; and (iii) when the LA terminated with COOH is closer to open extremity of BuCNT, the LA is encapsulated by the BuCNT. These simulations are part of a more extensive work on searching efficient selective molecular devices and could be useful to reach this goal.

Keywords: Carbon Nanotube, Linoleic Acid, MolecularDynamics.

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Authors: Sajjad Seifoori

Abstract:

Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).

Keywords: Impact, molecular dynamic, graphene, nanotube.

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Authors: Sihana Ahmeti Lika, Merita Dauti, Ledjan Malaj

Abstract:

The objective of this study is to analyze the prophylactic usage of low molecular weight heparin (LMWH) along pregnancy and the correlation between their usage and month/week of pregnancy, in the Department of Gynecology and Obstetrics, at Clinical Hospital in Tetovo. A retrospective study was undertaken during 01 January – 31 December 2012. Over of one year, the total number of patients was 4636. Among the 1447 (32.21%) pregnant women, 298 (20.59%) of them were prescribed LMWH. The majority of patients given LMWH, 119 (39.93%) were diagnosed hypercoagulable. The age group with the highest attendance was 25- 35, 141 patients (47.32%). For 195 (65.44%) patients, this was their first pregnancy. Earliest stage of using LMWH was the second month of pregnancy 4 (1.34%) cases. The most common patients were 70 women along the seventh month (23.49%), followed by 68 in the ninth month of pregnancy (22.81%). Women in the 28th gestational week, were found to be the most affected, a total of 55 (78.57%) were in that week. Clexane 2000 and Fraxiparine 0.3 were the most common for which low molecular weight heparin was prescribed. The number of patients which received Clexane 2000 was 84 (28.19%), followed by those with Fraxiparine 0.3 81 (27.18%). The administration of LMWH is associated with long hospitalization (median 14,6 days).

Keywords: Hypercoagulable state, low molecular weight heparin, month of pregnancy, pregnant women.

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Authors: Srikanta Bose, Sudip K. Mazumder

Abstract:

We report here, the results of molecular dynamics simulation of p-doped (Ga-face)GaN over n-doped (Siface)( 0001)4H-SiC hetero-epitaxial material system with one-layer each of Ga-flux and (Al-face)AlN, as the interface materials, in the form of, the total Density of States (DOS). It is found that the total DOS at the Fermi-level for the heavily p-doped (Ga-face)GaN and ndoped (Si-face)4H-SiC hetero-epitaxial system, with one layer of (Al-face)AlN as the interface material, is comparatively higher than that of the various cases studied, indicating that there could be good vertical conduction across the (Ga-face)GaN over (Si-face)(0001)4HSiC hetero-epitaxial material system.

Keywords: Molecular dynamics, GaN, 4H-SiC, hetero-epitaxy.

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Authors: C. Temaneh-Nyah, J. Makiche, J. Nujoma

Abstract:

This paper considers the characterization of a complex electromagnetic environment due to multiple sources of electromagnetic radiation as a five-dimensional surface which can be described by a set of several surface sections including: instant EM field intensity distribution maps at a given frequency and altitude, instantaneous spectrum at a given location in space and the time evolution of the electromagnetic field spectrum at a given point in space. This characterization if done over time can enable the exposure levels of Radio Frequency Radiation at every point in the analysis area to be determined and results interpreted based on comparison of the determined RFR exposure level with the safe guidelines for general public exposure given by recognized body such as the International commission on non-ionizing radiation protection (ICNIRP), Institute of Electrical and Electronic Engineers (IEEE), the National Radiation Protection Authority (NRPA).

Keywords: Electromagnetic Environment, Electric Field Strength, Mathematical Models.

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Authors: Sanwu Wang, Hongli Dang, Wenhua Xue, Darwin Shields, Xin Liu, Friederike C. Jentoft, Daniel E. Resasco

Abstract:

The bonding configuration and the heat of adsorption of a furfural molecule on the Pd(111) surface were determined by ab initio density-functional-theory calculations. The dynamics of pure liquid water, the liquid-solid interface formed by liquid water and the Pd(111) surface, as well as furfural at the water-Pd interface, were investigated by ab initio molecular dynamics simulations at finite temperatures. Calculations and simulations suggest that the bonding configurations at the water-Pd interface promote decarbonylation of furfural.

Keywords: Ab initio molecular dynamics simulations, bio-fuels, density functional theory, liquid-solid interfaces.

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Authors: J. Davoodi, F. Katouzi

Abstract:

The aim of this research was to calculate the thermal properties of Au3Ni Nanowire. The molecular dynamics (MD) simulation technique was used to obtain the effect of radius size on the energy, the melting temperature and the latent heat of fusion at the isobaric-isothermal (NPT) ensemble. The Quantum Sutton-Chen (Q-SC) many body interatomic potentials energy have been used for Gold (Au) and Nickel (Ni) elements and a mixing rule has been devised to obtain the parameters of these potentials for nanowire stats. Our MD simulation results show the melting temperature and latent heat of fusion increase upon increasing diameter of nanowire. Moreover, the cohesive energy decreased with increasing diameter of nanowire.

Keywords: Au3Ni Nanowire, Thermal properties, Molecular dynamics simulation

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Authors: I. F. Fiţigău, F. Peter, C. G. Boeriu

Abstract:

Five lignin samples were fractionated with Acetone/Water mixtures and the obtained fractions were subjected to extensive structural characterization, including Fourier Transform Infrared (FT-IR), Gel permeation Chromatography (GPC) and Phosphorus-31 NMR spectroscopy (31P-NMR). The results showed that for all studied lignins the solubility increases with the increment of the acetone concentration. Wheat straw lignin has the highest solubility in 90/10 (v/v) Acetone/Water mixture, 400 mg lignin being dissolved in 1 mL mixture. The weight average molecular weight of the obtained fractions increased with the increment of acetone concentration and thus with solubility. 31P-NMR analysis based on lignin modification by reactive phospholane into phosphitylated compounds was used to differentiate and quantify the different types of OH groups (aromatic, aliphatic, and carboxylic) found in the fractions obtained with 70/30 (v/v) Acetone/Water mixture.

Keywords: Lignin, fractionation, FT-IR, GPC, 31P-NMR.

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Authors: R. O. Ocaya, J. J. Terblans

Abstract:

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Keywords: C-language, molecular dynamics, simulation, embedded atom method.

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Authors: Emma K. Sales, Nilda G. Butardo

Abstract:

The project was undertaken to determine the effects of modified tissue culture protocols e.g. age of culture and hormone levels (2,4-D) in generating somaclonal variation. Moreover, the utility of molecular markers (SSR and MSAP) in sorting off types/somaclones were investigated.

Results show that somaclonal variation is in effect due to prolonged subculture and high 2,4-D concentration. The resultant variation was observed to be due to high level of methylation events specifically cytosine methylation either at the internal or external cytosine and was identified by methylation sensitive amplification polymorphism (MSAP).Simple sequence repeats (SSR) on the other hand, was able to associate a marker to a trait of interest.

These therefore, show that molecular markers can be an important tool in sorting out variation/mutants at an early stage.

Keywords: Methylation, MSAP, somaclones, SSR, subculture, 2, 4-D.

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Authors: M. Rahimnejad, B. Vahidi, B. Ebrahimi Hoseinzadeh, F. Yazdian, P. Motamed Fath, R. Jamjah

Abstract:

In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.

Keywords: Anti-cancer drug, center of Mass, interaction energy, molecular dynamics simulation, nanocarrier.

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Authors: Jhalique Jane R. Fojas, Rizalinda L. De Leon, Lucille V. Abad

Abstract:

The characterization of κ-carrageenan could provide a better understanding of its functions in biological, medical and industrial applications. Chemical and physical analyses of carrageenan from seaweeds, Euchema cottonii L., were done to offer information on its properties and the effects of Co-60 γ-irradiation on its thermochemical characteristics. The structural and morphological characteristics of κ-carrageenan were determined using scanning electron microscopy (SEM) while the composition, molecular weight and thermal properties were determined using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), gel permeation chromatography (GPC), thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC). Further chemical analysis was done using hydrogen-1 nuclear magnetic resonance (1H NMR) and functional characteristics in terms of biocompatibility were evaluated using cytotoxicity test.

Keywords: Biocompatibility, carrageenan, DSC, FTIR, GPC, irradiation, NMR, physicochemical, SEM, TGA.

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Authors: Swapnoneel Roy, Ashok Kumar Thakur, Minhazur Rahman

Abstract:

The Block Sorting problem is to sort a given permutation moving blocks. A block is defined as a substring of the given permutation, which is also a substring of the identity permutation. Block Sorting has been proved to be NP-Hard. Until now two different 2-Approximation algorithms have been presented for block sorting. These are the best known algorithms for Block Sorting till date. In this work we present a different characterization of Block Sorting in terms of a transposition cycle graph. Then we suggest a heuristic, which we show to exhibit a 2-approximation performance guarantee for most permutations.

Keywords: Block Sorting, Optical Character Recognition, Genome Rearrangements, Sorting Primitives, ApproximationAlgorithms

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