Search results for: molecular characteristic

Authors: Hideo Sawada

Abstract:

Fluoroalkyl end-capped oligomers [RF-(M)n-RF; RF = fluoroalkyl groups; M = radical polymerizable monomers] can form nanometre size-controlled self-assembled oligomeric aggregates through the aggregations of end-capped fluoroalkyl groups. Fluoroalkyl end-capped oligomeric aggregates can also interact with guest molecules to afford fluorinated aggregate/guest molecule nanocomposites; although the corresponding non-fluorinated oligomers cannot form such molecular aggregates to interact with guest molecules. For example, silica nanoparticles should act as guest molecules in fluorinated oligomeric aggregate cores to give new fluorinated oligomer-coated silica nanoparticles (fluorinated oligomer/silica nanocomposites). In these fluoroalkyl end-capped oligomers/silica nanocomposites, some fluorinated oligomers/silica nanocomposites were found to exhibit no weight loss behavior corresponding to the contents of oligomers in the silica matrices even after calcination at 800 oC. Fluoroalkyl end-capped vinyltrimethoxysilane oligomer-coated silica nanoparticles can be prepared by the sol-gel reaction of the corresponding fluorinated oligomer under alkaline conditions. The modified glass surface treated with this fluorinated oligomeric nanoparticle exhibited a completely super-hydrophobic characteristic. These fluorinated nanoparticles were also applied to the surface modification possessing a super-oleophobic characteristic. Not only fluoroalkyl end-capped oligomers but also low molecular weight fluorinated surfactants such as perfluoro-1,3-propanedisulfonic acid (PFPS) were applied to the preparation of fluorinated surfactants/silica nanocomposites to give no weight loss in proportion to the content of the surfactants in the nanocomposites even after calcination at 800 oC.

Keywords: fluorinated oligomer, silica nanocomposite, nonflammable characteristic, superamphiphobic chracteristic

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Authors: Huang Yong, Chen Qianting, Zhao Shurong

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In order to identify the role and effect of Characteristic Towns as an important means to promote urban-rural integration, this paper uses Flow Theory and complex network analysis methods to jointly construct the identification path of urban-rural integration capabilities of Characteristic Towns. Take the National Characteristic Towns of Yunnan Province as the empirical objects to identify their role laws. The study found that in the implementation of the National Characteristic Town Project in Yunnan Province, (1) the population is more susceptible to the impact of the Characteristic Town Project than the technical elements, but the stability is poor; (2) The flow capacity of urban and rural technical elements is weak, and the quality of the enterprise cooperation network in general; (3) Compared with the batch of Characteristic Towns in 2016, its ability to promote urban-rural integration is higher in 2017; (4) The role of the Characteristic Town Project on urban-rural integration focuses on the improvement of the number of urban and rural flow elements. This paper analyzes the mode of the role of Characteristic Towns on urban-rural integration from the perspective of ‘flow,’ establishes a research paradigm for evaluating the role of Characteristic Towns in urban-rural integration capabilities, and builds a path for the application of Characteristic Towns to support the realization of urban-rural integration goals.

Keywords: characteristic town, urban-rural integration, flow theory, complex network analysis

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Authors: Ewelina Nowak, Anna Wisla-Swider, Krzysztof Danel

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Aqueous suspensions of DNA were illuminated with linearly polarized visible light and ultraviolet for 5, 15, 20 and 40 h. In order to check the nature of modification, DNA interactions were characterized by FTIR spectroscopy. For each illuminated sample, weight average molecular weight and hydrodynamic radius were measured by high pressure size exclusion chromatography. Resulting optical changes for illuminated DNA were investigated using UV-Vis spectra and photoluminescent. Optical properties show potential application in sensors based on modified DNA. Then selected DNA-surfactant complexes were illuminated with electromagnetic radiation for 5h. Molecular structure, optical characteristic were examinated for obtained complexes. Illumination led to changes of complexes physicochemical properties as compared with native DNA. Observed changes were induced by rearrangement of the molecular structure of DNA chains.

Keywords: biopolymers, deoxyribonucleic acid, ionic liquids, linearly polarized visible light, ultraviolet

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Authors: Vladimir S. Timofeev

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In this article the problem of distributional moments estimation is considered. The new approach of moments estimation based on usage of the characteristic function is proposed. By statistical simulation technique, author shows that new approach has some robust properties. For calculation of the derivatives of characteristic function there is used numerical differentiation. Obtained results confirmed that author’s idea has a certain working efficiency and it can be recommended for any statistical applications.

Keywords: characteristic function, distributional moments, robustness, outlier, statistical estimation problem, statistical simulation

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Authors: Narendra Nath Patra

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Several recent studies reinforce the existence of a thick molecular disc in galaxies along with the dynamically cold thin disc. Assuming a two-component molecular disc, we model the disc of NGC 6946 as a four-component system consists of stars, HI, thin disc molecular gas, and thick disc molecular gas in vertical hydrostatic equilibrium. Following, we set up the joint Poisson-Boltzmann equation of hydrostatic equilibrium and solve it numerically to obtain a three-dimensional density distribution of different baryonic components. Using the density solutions and the observed rotation curve, we further build a three-dimensional dynamical model of the molecular disc and consecutively produce simulated CO spectral cube and spectral width profile. We find that the simulated spectral width profiles distinguishably differs for different assumed thick disc molecular gas fraction. Several CO spectral width profiles are then produced for different assumed thick disc molecular gas fractions and compared with the observed one to obtain the best fit thick disc molecular gas fraction profile. We find that the thick disc molecular gas fraction in NGC 6946 largely remains constant across its molecular disc with a mean value of 0.70 +/- 0.09. We also estimate the amount of extra-planar molecular gas in NGC 6946. We find 60% of the total molecular gas is extra-planar at the central region, whereas this fraction reduces to ~ 35% at the edge of the molecular disc. With our method, for the first time, we estimate the thick disc molecular gas fraction as a function of radius in an external galaxy with sub-kpc resolution.

Keywords: galaxies: kinematics and dynamic, galaxies: spiral, galaxies: structure , ISM: molecules, molecular data

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Authors: Mera-Martínez Daniela

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Dendropsophus minutus, is a species distributed in South America including the slopes of the Andes, the Amazon basin, forests of southeastern Brazil and in Guyana where tropical forests are characteristic. The relationship of amphibians found in this locality is evidenced by molecular markers, with the objective of analyzing if the geographic distance is influencing the structure of the populations of D. minutus in Guyana; we analyzed 65 sequences from the 3 localities of Guyana where haplotype networks, Mantel Test and phylogeny were realized to know the influence. It was evidenced that there is a haplotypic difference in the locality of Guyana compared to Suriname and French Guyana, but this does not have a correlation with the geographic distance, but this one can be influenced by the conditions of the places.

Keywords: phylogeography, Dendropsophus, geographic distance, molecular markers

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Authors: Xiaohan Ye

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Under the new normal situation, some urban spaces with the industrial base and regional features in Zhejiang, China have been selected to build a characteristic town, a kind of environmentally-friendly development platform with city-industry integrated, in an attempt to achieve the most optimized layout of productivity with the least space resource. After analysis on the connotation, mechanism and mode of characteristic town in Zhejiang, it is suggested in this paper that characteristic town should take improving the regional ecological environment as an important object in planning strategy from the perspective of ecological concept. Improved environmental quality, optimized resource allocation, and compact industrial distribution should be realized so as to drive the regional green and sustainable development. Finally, this paper analyzes location selection, industrial distribution, spatial organization and environment construction based on the exploration of the dream town of Zhejiang province, the first batch of provincial-level characteristic towns to demonstrate how to apply the ecological concept to the design of characteristic town.

Keywords: characteristic town, ecological concept, Hangzhou dream town, planning strategy

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Authors: Jeoungsu Na, Jaehawn Lee, Changil Hong, Suhee Kim

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A molecular dynamics simulation in a converging-diverging nozzle was performed to study molecular collisions and their influence to average flow velocity according to a variety of vacuum levels. The static pressures and the dynamic pressure exerted by the molecule collision on the selected walls were compared to figure out the intensity variances of the directional flows. With pressure differences constant between the entrance and the exit of the nozzle, the numerical experiment was performed for molecular velocities and directional flows. The result shows that the velocities increased at the nozzle exit as the vacuum level gets higher in that area because less molecular collisions.

Keywords: cavitation, molecular collision, nozzle, vacuum, velocity increase

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Authors: Elmira Ghanbari, Jan Van Esch, Stephen J. Picken, Sahil Aggarwal

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Low-molecular-weight organogelators form gels by self-assembly into the crystalline network which immobilizes the organic solvent. For single bisamide organogelator systems, the effect of the molecular structure on the molecular interaction and their self-assembly behavior has been explored. The spatial arrangement of bisamide molecules in the gel-state is driven by a combination of hydrogen bonding and Van der Waals interactions. The hydrogen-bonding pattern between the amide groups of bisamide molecules is regulated by the number of methylene spacers; the even number of methylene spacers between two amide groups, in even-spaced bisamides, leads to the antiparallel position of amide groups within a molecule. An even-spaced bisamide molecule with antiparallel amide groups can make two pairs of hydrogen bonding with the molecules on the same plane. The odd-spaced bisamide with a parallel directionality of amide groups can form four independent hydrogen bonds with four other bisamide molecules on different planes. The arrangement of bisamide molecules in the crystalline state and the interaction of these molecules depends on the molecular structure, particularly the parity of the spacer length between the amide groups in the bisamide molecule. In this study, the directionality of amide groups has been exploited as a structural characteristic to affect the arrangement of molecules in the crystalline state and produce different binary bisamide gelators with different degrees of crystallinities. Single odd- and even-spaced single bisamides were synthesized and blended to produce binary bisamide organogelators to be characterized in order to understand the effect of the different directionality of amide groups on the molecular interaction in the crystalline state. The pattern of molecular interactions between these blended molecules, mixing or phase separation, has been monitored via differential scanning calorimetry (DSC) and crystallography techniques; X-ray powder diffraction (XRD) and Small-angle X-ray scattering (SAXS). The formation of lamellar structures for odd- and even-spaced bisamide gelators was confirmed by using SAXS and XRD techniques. DSC results have shown that binary bisamide organogelators with different parity of methylene spacers (odd-even binary blends) have a higher tendency for phase separation compared to the binary bisamides with the same parity (odd-odd or even-even binary blends). Phase separation in binary odd-even bisamides was confirmed by the presence of individual (100) reflections of odd and even lamellar structures. The structural characteristic of bisamide organogelators, the parity of spacer length in binary systems, is a promising tool to control the arrangement of molecules and their crystalline structure.

Keywords: binary bisamide organogelators, crystalline structure, phase separation, self-assembly behavior

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Authors: Zongjie Wang, Zhizhong Guo

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While the regular optimal power flow model focuses on a single time scan, the optimization of power systems is typically intended for a time duration with respect to a desired objective function. In this paper, a temporal optimal power flow model for a time period is proposed. To reduce the computation burden needed for calculating temporal optimal power flow, a characteristic optimal power flow model is proposed, which employs different characteristic load patterns to represent the objective function and security constraints. A numerical method based on the interior point method is also proposed for solving the characteristic optimal power flow model. Both the temporal optimal power flow model and characteristic optimal power flow model can improve the systems’ desired objective function for the entire time period. Numerical studies are conducted on the IEEE 14 and 118-bus test systems to demonstrate the effectiveness of the proposed characteristic optimal power flow model.

Keywords: optimal power flow, time period, security, economy

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Authors: Yu-Han Tao, Hui-Qin Xu

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The present study aimed to explain the protective effect of Cornus officinalis characteristic components, under AGEs damage to HUVEC. After cultured HUVEC adhered, Cornus officinalis characteristic components such as loganin, morroniside, oleanolic acid, ursolic acid and aminoguanidine (positive control dug) hatched, after 1h the AGEs (200 mg/L) were added. After 24h, LDH, SOD, MDA, NO, ET, and AngⅡ, TGF-β, IL-1β, ROS in the supernatant were determined. The results showed the Cornus officinalis characteristic compounds could improve vitality of SOD, NO, reduce the MDA, ET, AngⅡ, TGF-β, IL-1β, ROS significantly when compared with the model groug. Loganin, oleanic acid, ursolic acid, had significant protective effect on AGEs injured HUVEC. As a conclusion, characteristic components in Cornus officinalis had a positive effect after HUVEC injured by AGEs.

Keywords: Cornus officinalis, morroniside, oganin, oleanolic acid, ursolic acid

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Authors: Muhammad Luqman, Yusuf Kurniawan

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S-Boxes is one of the linear parts of the cryptographic algorithm. The existence of S-Box in the cryptographic algorithm is needed to maintain non-linearity of the algorithm. Nowadays, modern cryptographic algorithms use an S-Box as a part of algorithm process. Despite the fact that several cryptographic algorithms today reuse theoretically secure and carefully constructed S-Boxes, there is an evaluation characteristic that can measure security properties of S-Boxes and hence the corresponding primitives. Analysis of an S-Box usually is done using manual mathematics calculation. Several S-Boxes are presented as a Truth Table without any mathematical background algorithm. Then, it’s rather difficult to determine the strength of Truth Table S-Box without a mathematical algorithm. A comprehensive analysis should be applied to the Truth Table S-Box to determine the characteristic. Several important characteristics should be owned by the S-Boxes, they are Nonlinearity, Balancedness, Algebraic degree, LAT, DAT, differential delta uniformity, correlation immunity and global avalanche criterion. Then, a comprehensive tool will be present to automatically calculate the characteristics of S-Boxes and determine the strength of S-Box. Comprehensive analysis is done on a deterministic process to produce a sequence of S-Boxes characteristic and give advice for a better S-Box construction.

Keywords: cryptographic properties, Truth Table S-Boxes, S-Boxes characteristic, deterministic process

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Authors: Mohammad Hossein Modarressi, Mozhgan Mondeali, Khabat Barkhordari, Ali Etemadi

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The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant concerns worldwide due to its catastrophic effects on public health. The SARS-CoV-2 infection is initiated with the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Due to the error-prone entity of the viral RNA-dependent polymerase complex, the virus genome, including the coding region for the RBD, acquires new mutations, leading to the appearance of multiple variants. These variants can potentially impact transmission, virulence, antigenicity and evasive immune properties. S477N mutation located in the RBD has been observed in the SARS-CoV-2 omicron (B.1.1. 529) variant. In this study, we investigated the consequences of S477N mutation at the molecular level using computational approaches such as molecular dynamics simulation, protein-protein interaction analysis, immunoinformatics and free energy computation. We showed that displacement of Ser with Asn increases the stability of the spike protein and its affinity to ACE2 and thus increases the transmission potential of the virus. This mutation changes the folding and secondary structure of the spike protein. Also, it reduces antibody neutralization, raising concern about re-infection, vaccine breakthrough and therapeutic values.

Keywords: S477N, COVID-19, molecular dynamic, SARS-COV2 mutations

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Authors: Adel Belayadi, Ahmed Mougari, Boualem Bourahla

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Molecular junctions are currently considered a promising style in the miniaturization of electronic devices. In this contribution, we provide a tight-binding model to investigate the quantum transport properties across-molecular junctions sandwiched between 2D-graphene nanoribbons in the zigzag direction. We investigate, in particular, the effect of embedded atoms such as Gold and Silicon across the molecular junction. The results exhibit a resonance behavior in terms of incident Fermi levels, depending on the molecular junction type. Additionally, the transport properties under a perpendicular magnetic field exhibit an oscillation for the transmittance versus the magnetic field strength.

Keywords: molecular junction, 2D-graphene nanoribbons, quantum transport properties, magnetic field

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Authors: Lokesh Soni, Sushanta Kumar Sethi, Gaurav Manik

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This work attempts to use molecular simulations to create equilibrated structures of a range of commercially used polymers. Generated equilibrated structures for polyvinyl acetate (isotactic), polyvinyl alcohol (atactic), polystyrene, polyethylene, polyamide 66, poly dimethyl siloxane, poly carbonate, poly ethylene oxide, poly amide 12, natural rubber, poly urethane, and polycarbonate (bisphenol-A) and poly ethylene terephthalate are employed to estimate the correct chain length that will correctly predict the chain parameters and properties. Further, the equilibrated structures are used to predict some properties like density, solubility parameter, cohesive energy density, surface energy, and Flory-Huggins interaction parameter. The simulated densities for polyvinyl acetate, polyvinyl alcohol, polystyrene, polypropylene, and polycarbonate are 1.15 g/cm3, 1.125 g/cm3, 1.02 g/cm3, 0.84 g/cm3 and 1.223 g/cm3 respectively are found to be in good agreement with the available literature estimates. However, the critical repeating units or the degree of polymerization after which the solubility parameter showed saturation were 15, 20, 25, 10 and 20 respectively. This also indicates that such properties that dictate the miscibility of two or more polymers in their blends are strongly dependent on the chosen polymer or its characteristic properties. An attempt has been made to correlate such properties with polymer properties like Kuhn length, free volume and the energy term which plays a vital role in predicting the mentioned properties. These results help us to screen and propose a useful library which may be used by the research groups in estimating the polymer properties using the molecular simulations of chains with the predicted critical lengths. The library shall help to obviate the need for researchers to spend efforts in finding the critical chain length needed for simulating the mentioned polymer properties.

Keywords: Kuhn length, Flory Huggins interaction parameter, cohesive energy density, free volume

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Authors: K. Ivandic, F. Dodigovic, D. Stuhec, S. Strelec

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A characteristic value of certain geotechnical parameter results from an engineering assessment. Its selection has to be based on technical principles and standards of engineering practice. It has been shown that the results of engineering assessment of different authors for the same problem and input data are significantly dispersed. A survey was conducted in which participants had to estimate the force that causes a 10 cm displacement at the top of a axially in-situ compressed pile. Fifty experts from all over the world took part in it. The lowest estimated force value was 42% and the highest was 133% of measured force resulting from a mentioned static pile load test. These extreme values result in significantly different technical solutions to the same engineering task. In case of selecting a characteristic value of a geotechnical parameter the importance of the influence of an engineering assessment can be reduced by using statistical methods. An informative annex of Eurocode 1 prescribes the method of selecting the characteristic values of material properties. This is followed by Eurocode 7 with certain specificities linked to selecting characteristic values of geotechnical parameters. The paper shows the procedure of selecting characteristic values of a geotechnical parameter by using a statistical method with different initial conditions. The aim of the paper is to quantify an engineering assessment in the example of determining a characteristic value of a specific geotechnical parameter. It is assumed that this assessment is a random variable and that its statistical features will be determined. For this purpose, a survey research was conducted among relevant experts from the field of geotechnical engineering. Conclusively, the results of the survey and the application of statistical method were compared.

Keywords: characteristic values, engineering judgement, Eurocode 7, statistical methods

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Authors: Diana Larisa Vladoiu, Vasile Ostafe, Adriana Isvoran

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Molecular docking calculations reveal that pesticides provide favorable interactions with the bacterial chitinases. Pesticides interact with both hydrophilic and aromatic residues involved in the active site of the enzymes, their positions partially overlapping the substrate and the inhibitors locations. Molecular docking outcomes, in correlation with experimental literature data, suggest that the pesticides may be degraded or having an inhibitor effect on the activity of these enzymes, depending of the application dose and rate.

Keywords: chitinases, inhibition, molecular docking, pesticides

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Authors: Samy Madbouly

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The relaxation behavior of biorenewable castor oil-based polyurethane-lignin thin films synthesized in homogenous waterborne dispersions was investigated as a function of concentration at different temperatures and frequencies using broadband dielectric relaxation spectroscopy (BDRS). The molecular dynamics of the glass relaxation process and the local relaxation process of the PU-LS thin films were studied over a wide range of temperatures (-70 to 30 ℃) and frequencies (5 × 10−2 to 0.5 × 107 Hz) for different lignin concentration. Four relaxation processes have been observed namely; ?-, β-, γ-relaxations and ionic conductivity for pure castor oil-based PU and castor oil-lignin-based PU thin films at different temperatures and frequencies ranges. The Vogel-Fulcher-Tammann equation was found to be well described the temperature dependence of the characteristic relaxation times of the ?-relaxation process. However, on the other hand, the molecular dynamics of both β- and γ-relaxation processes were given by the Arrhenius equation. The incorporation of lignin into the castor oil-based PU significantly increased the glass transition temperature and primitivity of the thin films. In addition, the broadness, intensity, and molecular dynamics of the only observed ?-relaxation process were found to be strongly dependent on lignin concentration.

Keywords: castor oil, lignin, polyurethane, dielectric, dispersions

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Authors: Eric Chabrol, Sidonia B.G. Eckle, Renate de Boer, James McCluskey, Jamie Rossjohn, Mirjam H.M. Heemskerk, Stephanie Gras

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αβ and γδ T-cells are disparate T-cell lineages that, via their use of either αβ or γδ T-cell antigen receptors (TCRs) respectively, can respond to distinct antigens. Here we characterise a new population of human T-cells, term δβ T-cells, that express TCRs comprising a TCR-δ variable gene fused to a Joining-α/Constant-α domain, paired with an array of TCR-β chains. We characterised the cellular, functional, biophysical and structural characteristic feature of this new T-cells population that reveal some new insight into TCR diversity. We provide molecular bases of how δβ T-cells can recognise viral peptide presented by Human Leukocyte Antigen (HLA) molecule. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer antigen specificity thus expanding our understanding of T-cell biology and TCR diversity.

Keywords: new delta-beta TCR, HLA, viral peptide, structural immunology

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Authors: Bhupeshwaran Mani, S. Radha, A. Jawahar, A. Sivasubramanian

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Here, we study the characteristic feature of conventional (ON-OFF keying) and soliton based transmission system. We consider 20 Gbps transmission system implemented with Conventional Single Mode Fiber (C-SMF) to examine the role of Gaussian pulse which is the characteristic of conventional propagation and hyperbolic-secant pulse which is the characteristic of soliton propagation in it. We note the influence of these pulses with respect to different dispersion lengths and soliton period in conventional and soliton system, respectively, and evaluate the system performance in terms of quality factor. From the analysis, we could prove that the soliton pulse has more consistent performance even for long distance without dispersion compensation than the conventional system as it is robust to dispersion. For the length of transmission of 200 Km, soliton system yielded Q of 33.958 while the conventional system totally exhausted with Q=0.

Keywords: dispersion length, retrun-to-zero (rz), soliton, soliton period, q-factor

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Authors: Xiaoli Zhang, Xiongfei Li, Yuncong Feng

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ROC curves, as a widely used evaluating tool in machine learning field, are the tradeoff of true positive rate and negative rate. However, they are blamed for ignoring some vital information in the evaluation process, such as the amount of information about the target that each instance carries, predicted score given by each classification model to each instance. Hence, in this paper, a new classification performance method is proposed by extending the Receiver Operator Characteristic (ROC) curves to 3D space, which is denoted as 3D ROC Histogram. In the histogram, the

Keywords: classification, performance evaluation, receiver operating characteristic histogram, hardness prediction

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Authors: Kamel Agroui, George Collins, Rydha Yaiche

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The objective of this study is to better understand the thermal characteristics and molecular behaviour of cured EVA before and after outdoor exposure. Thermal analysis methods as DSC, TSC and DMTA studies were conducted on EVA material. DSC experiments on EVA show a glass transition at about -33.1° C which is characteristic of crystalline phase and an endothermic peak at temperature of 55 °C characteristic of amorphous phase. The magnitude of the integrated temperature DSC peak for EVA is 14.4 J/g. The basic results by TSC technique is that there are two relaxations that are reproducibly observed in cured EVA encapsulant material. At temperature polarization 85°C, a low temperature relaxation occurs at –24.4°C and a high temperature relaxation occurs at +30.4ºC. DMTA results exhibit two tan peaks located at -14.9°C and +66.6°C. After outdoor exposure cured EVA by DSC analysis revealed two endothermic peaks due to post crystallization phenomenon and TSC suggests that prolonged exposure selectively effects the poly(vinyl acetate)-rich phase, with much less impact on the polyethylene-rich phase.

Keywords: EVA, encapsulation process, PV module, thermal analysis, quality control

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Authors: R. Mohan, V. Jadhav, A. Ahmed, J. Rivas, A. Kelkar

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Cementitious materials are an excellent example of a composite material with complex hierarchical features and random features that range from nanometer (nm) to millimeter (mm) scale. Multi-scale modeling of complex material systems requires starting from fundamental building blocks to capture the scale relevant features through associated computational models. In this paper, molecular dynamics (MD) modeling is employed to predict the effect of plasticizer additive on the mechanical properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown molecular configuration of CSH, a representative configuration widely accepted in the field of mineral Jennite is employed. The effectiveness of the Molecular Dynamics modeling to understand the predictive influence of material chemistry changes based on molecular/nanoscale models is demonstrated.

Keywords: cement composite, mechanical properties, molecular dynamics, plasticizer additives

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Authors: Monisha Isaac

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Use of molecular markers for selecting plants with desired traits has been started long back. Due to their heritable characteristics, they are useful for identification and characterization of specific genotypes. The study involves various types of molecular markers used to select multiple desired characters in plants, their properties, and advantages to improve crop productivity in adverse climatological conditions for the purpose of providing food security to fast-growing global population. The study shows that genetic similarities obtained from molecular markers provide more accurate information and the genetic diversity can be better estimated from the genetic relationship obtained from the dendrogram. The information obtained from markers assisted characterization is more suitable for the crops of economic importance like sugarcane.

Keywords: molecular markers, crop productivity, genetic diversity, genotype

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Authors: Yuanhao Chang, Senbo Xiao, Zhiliang Zhang, Jianying He

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The role of nanoparticles (NPs) in enhanced oil recovery (EOR) is being increasingly emphasized. In this study, the motion of NPs and local stress distribution of tapped oil droplet/nanofluid in nanochannels are studied with coarse-grained modeling and molecular dynamic simulations. The results illustrate three motion patterns for NPs: hydrophilic NPs are more likely to adsorb on the channel and stay near the three-phase contact areas, hydrophobic NPs move inside the oil droplet as clusters and more mixed NPs are trapped at the oil-water interface. NPs in each pattern affect the flow of fluid and the interfacial thickness to various degrees. Based on the calculation of atomistic stress, the characteristic that the higher value of stress occurs at the place where NPs aggregate can be obtained. Different occurrence patterns correspond to specific local stress distribution. Significantly, in the three-phase contact area for hydrophilic NPs, the local stress distribution close to the pattern of structural disjoining pressure is observed, which proves the existence of structural disjoining pressure in molecular dynamics simulation for the first time. Our results guide the design and screen of NPs for EOR and provide a basic understanding of nanofluid applications.

Keywords: local stress distribution, nanoparticles, enhanced oil recovery, molecular dynamics simulation, trapped oil droplet, structural disjoining pressure

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Authors: Ferid Hammami

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The molecular geometries of the possible conformations of pyruvic acid-water complexes (PA-(H₂O)ₙ = 1- 4) have been fully optimized at DFT/B3LYP/6-311G ++ (d, p) levels of calculation. Among several optimized molecular clusters, the most stable molecular arrangements obtained when one, two, three, and four water molecules are hydrogen-bonded to a central pyruvic acid molecule are presented in this paper. Apposite topological and geometrical parameters are considered as primary indicators of H-bond strength. Atoms in molecules (AIM) analysis shows that pyruvic acid can form a ring structure with water, and the molecular structures are stabilized by both strong O-H...O and C-H...O hydrogen bonds. In large clusters, classical O-H...O hydrogen bonds still exist between water molecules, and a cage-like structure is built around some parts of the central molecule of pyruvic acid. The electrostatic potential energy map (MEP) and the HOMO-LUMO molecular orbital (highest occupied molecular orbital-lowest unoccupied molecular orbital) analysis has been performed for all considered complexes.

Keywords: pyruvic acid, PA-water complex, hydrogen bonding, DFT, AIM, MEP, HOMO-LUMO

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Authors: Mei Hong, Wei Liu, Xuemin Dai, Yanxiong Pan, Xiangling Ji

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Polyamic acid (PAA) is the precursor of polyimide (PI) prepared by a two-step method, its molecular weight and molecular weight distribution not only play an important role during the preparation and processing, but also influence the final performance of PI. However, precise characterization on molecular weight of PAA is still a challenge because of the existence of very complicated interactions in the solution system, including the electrostatic interaction, hydrogen bond interaction, dipole-dipole interaction, etc. Thus, it is necessary to establisha suitable strategy which can completely suppress these complex effects and get reasonable data on molecular weight. Herein, the gel permeation chromatography (GPC) coupled with differential refractive index (RI) and multi-angle laser light scattering (MALLS) detectors were applied to measure the molecular weight of (6FDA-DMB) PAA using different mobile phases, LiBr/DMF, LiBr/H3PO4/THF/DMF, LiBr/HAc/THF/DMF, and LiBr/HAc/DMF, respectively. It was found that combination of LiBr with HAc can shield the above-mentioned complex interactions and is more conducive to the separation of PAA than only addition of LiBr in DMF. LiBr/HAc/DMF was employed for the first time as a mild mobile phase to effectively separate PAA and determine its molecular weight. After a series of conditional experiments, 0.02M LiBr/0.2M HAc/DMF was fixed as an optimized mobile phase to measure the relative and absolute molecular weights of (6FDA-DMB) PAA prepared, and the obtained Mw from GPC-MALLS and GPC-RI were 35,300 g/mol and 125,000 g/mol, respectively. Particularly, such a mobile phase is also applicable to other PAA samples with different structures, and the final results on molecular weight are also reproducible.

Keywords: Polyamic acids, Polyelectrolyte effects, Gel permeation chromatography, Mobile phase, Molecular weight

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Authors: Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Lidija Jevrić, Evgenija Djurendić, Jovana Ajduković

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In the present study, the molecular modeling of a series of 24 17-picolyl and 17-picolinylidene androstane derivatives whit significant anticancer activity was carried out. Modelling of studied compounds was performed by CS ChemBioDraw Ultra v12.0 program for drawing 2D molecular structures and CS ChemBio3D Ultra v12.0 for 3D molecular modelling. The obtained 3D structures were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. Full geometry optimization was done by the Austin Model 1 (AM1) until the root mean square (RMS) gradient reached a value smaller than 0.0001 kcal/Åmol using Molecular Orbital Package (MOPAC) program. The obtained physicochemical, lipophilicity and topological descriptors were used for analysis of molecular similarities and dissimilarities applying suitable chemometric methods (principal component analysis and cluster analysis). These results are the part of the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina and CMST COST Action CM1306.

Keywords: androstane derivatives, anticancer activity, chemometrics, molecular descriptors

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Authors: K. Veluraja

Abstract:

Glycan of glycolipids and glycoproteins is playing a significant role in living systems particularly in molecular recognition processes. Molecular recognition processes are attributed to their occurrence on the surface of the cell, sequential arrangement and type of sugar molecules present in the oligosaccharide structure and glyosidic linkage diversity (glycoinformatics) and conformational diversity (glycoconformatics). Molecular Dynamics Simulation study is a theoretical-cum-computational tool successfully utilized to establish glycoconformatics of glycan. The study on various oligosaccharides of glycan clearly indicates that oligosaccharides do exist in multiple conformational states and these conformational states arise due to the flexibility associated with a glycosidic torsional angle (φ,ψ) . As an example: a single disaccharide structure NeuNacα(2-3) Gal exists in three different conformational states due to the differences in the preferential value of glycosidic torsional angles (φ,ψ). Hence establishing three dimensional structural and conformational models for glycan (cartesian coordinates of every individual atoms of an oligosaccharide structure in a preferred conformation) is quite crucial to understand various molecular recognition processes such as glycan-toxin interaction and glycan-virus interaction. The gycoconformatics models obtained for various glycan through Molecular Dynamics Simulation stored in our 3DSDSCAR (3DSDSCAR.ORG) a public domain database and its utility value in understanding the molecular recognition processes and in drug design venture will be discussed.

Keywords: glycan, glycoconformatics, molecular dynamics simulation, oligosaccharide

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Authors: Amir Bahrami

Abstract:

In the fields of chemical graph theory, molecular topology, and mathematical chemistry, a topological index or a descriptor index also known as a connectivity index is a type of a molecular descriptor that is calculated based on the molecular graph of a chemical compound. Topological indices are numerical parameters of a graph which characterize its topology and are usually graph invariant. Topological indices are used for example in the development of quantitative structure-activity relationships (QSARs) in which the biological activity or other properties of molecules are correlated with their chemical structure. In this paper some descriptor index (descriptor index) of single-walled carbon nanotubes, is determined.

Keywords: chemical graph theory, molecular topology, molecular descriptor, single-walled carbon nanotubes

Procedia PDF Downloads 299