Search results for: molecular individualism

Authors: Ela Ari, Aysi̇ma Findikoglu

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Consumers’ switching GSM operators’ has been an important research issue since the rise of their competitive offers. Recent research has looked at consumer switching behavior through the theory of planned behavior, but not yet extended the theory with identity, psycho-social and cultural influences within the service context. This research explores an extended version of the theory of planned behavior including social and financial risks and brand loyalty. Moreover, the role of individualism and collectivism at the individual level is investigated in a collectivistic culture that moves toward to individualism due to changing family relationships, use of technology and education. Our preliminary analysis showed that financial risk and vertical individualism prove to be a significant determinant of intention to switch. The study also investigates social risk and intention, subjective norm, perceived behavioral control relationship. The effect of individualism and collectivism and attitudes relationship has been also examined within a service industry. Implications for marketing managers and scholars are also discussed.

Keywords: attitude, individualism, intention, subjective norm

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Authors: Tsai-Hsiu Lin

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Three dimensions of teacher culture hinder educational improvement: individualism, conservatism and presentism. To promote the professional development of teachers, these three aspects in teacher culture should be eliminated. Classroom observation may be a useful method of eliminating individualism. The Ministry of Education in Taiwan has attempted to reduce the isolation of teachers to promote their professional growth. Because classroom observation discourse varies, teachers are generally unwilling to allow their teaching to be observed. However, classroom observations take place in the country in the form of school evaluations. The main purpose of this study was to explore the differences in teachers’ conservatism, individualism and presentism after classroom observations had been conducted at an elementary school in Taiwan. The research method was a qualitative case study involving interviews with the school principal, the director of academic affairs, and two classroom teachers. The following conclusions were drawn: (1) Educators in different positions viewed classroom observations differently; (2) The classroom teachers did not highly value classroom observation; (3) There was little change in the teachers’ conservatism, individualism and presentism after classroom observation.

Keywords: classroom observation, Lortie’s Trinity, teacher culture, teacher professional development

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Authors: Sarthak S. Salunke

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Development, as a notion, is seen in perspective of western philosophical conceptions, and the western developed nations have become a yardstick for setting up development goals for developing and underdeveloped nations around the world. This blanket term of development becomes superficial and materialistic in context of the vast geopolitical, territorial, cultural and behavioral diversities existing in countries of the Africa and the Asia, and tends to undermine the atomistic aspect of development. Indian political theories, which are often seen as religious philosophies, have inherent structure of development of human being as an individual and as a part of the society, and, in result, development of the State. These theories, primarily individualistic in nature, have a combination of altruism and rationalism which guides human beings towards constructing a collectively developed and morally sustainable society. This research focuses on the application of this Indian thought in combination of classical liberal thought to tackle the issues of development in diverse societies. The proposed restructured model of development is based on molecular individualism, instead of atomic individual approach of liberalists, which lets development modelers to target meaningful clusters for designating goals for development based on the particular needs based on geopolitical, cultural and ethical requirements, and making it meaningful in conjunction with global development to establish a harmony between western and eastern worlds.

Keywords: Indian political thought, development, liberalism, molecular individualism

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Authors: Irene Bruna Seu

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This paper draws on a three-year research project investigating everyday moral reasoning in relation to donations and prosocial behaviour in the humanitarian context. The analysis focuses on the principle of deservingness by which members of the public decide who and under which conditions to help and illustrates how the speakers engage in ideological dilemmas. The paper focuses on the theme ‘Something for nothing’ to examine how the position of ‘deserving’ and the speaker’s rights and duties in relation to victims of humanitarian crises are negotiated. Discursive analyses of this dilemmatic storyline of deservingness illuminate the cultural and ideological resources buttressing this construction. They also illustrate how humanitarianism intersects and clashes with other ideologies and value systems. The presentation will focus on the role of Individualism underpinned by Neo-liberalism ideology. The data propose that neo-liberal ideology, which endorses self-gratification, materialistic and individualistic ethics play an important role in decisions regarding humanitarian helping. The paper argues for the need for psychological research to engage more actively with the dilemmatic nature of moral reasoning in the humanitarian context, and to contextualize decisions about giving and helping within the socio-cultural and ideological landscape in which the helpers operate.

Keywords: humanitarianism, individualism, ideological dilemmas, discourse, neo-liberalism, prosocial behaviour

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Authors: Lina Khashogji

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This study highlights on analysing the educational experience of female Saudi Arabian students in private schools in Islamic studies subjects. Exploring how school environment, teachers’ authority and textbooks could influence the level of individuality. Considering the complex interaction between religious is social and political power in Saudi Arabia. The study draws on phenomenology as a guiding theoretical framework using multi methods. It includes a vertical/horizontal individualism measurement tool “survey” used on 120 students of two age groups (9-12) and (13-15). Semi-structured interviews with eight school teachers, observational notes in the classroom, and textbook analysis. The study links the interactions between the student mind, the teacher, the classroom and the curriculum.

Keywords: education, individualism, identity development, Islamic studies, Saudi Arabia

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Authors: Hong Im Shin

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Previous research demonstrated that self-objectification (women view themselves as objects for use) is related to system-justification. Three studies investigated whether cultural disposition as its system-justifying function could have an impact on self-objectification and dehumanization of sexualized women and men. Study 1 (N = 91) employed a survey methodology to examine the relationship between cultural disposition (collectivism vs. individualism), trait of system-justification, and self-objectification. The results showed that the higher tendency of collectivism was related to stronger system-justification and self-objectification. Study 2 (N = 60 females) introduced a single category implicit association task (SC-IAT) to assess the extent to which sexually objectified women were associated with uniquely human attributes (i.e., culture) compared to animal-related attributes (i.e., nature). According to results, female participants associated sexually objectified female targets less with human attributes compared to animal-related attributes. Study 3 (N = 46) investigated whether priming to individualism or collectivism was associated to system justification and sexual objectification of men and women with the use of a recognition task involving upright and inverted pictures of sexualized women and men. The results indicated that the female participants primed to individualism showed an inversion effect for sexualized women and men (person-like recognition), whereas there was no inversion effect for sexualized women in the priming condition of collectivism (object-like recognition). This implies that cultural disposition plays a mediating role for rationalizing the gender status, implicit dehumanization of sexualized females and self-objectification. Future research directions are discussed.

Keywords: cultural disposition, dehumanization, implicit test, self-objectification

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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: 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: Waisu Iliyasu

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It is a well-known fact that the Hausa people have, since time immemorial, had a distinct culture of living together and assisting one another. In fact, the communal bond has been an important aspect that bound society together. Over the years, this communal bond has been eroded, giving way to an individualistic society whereby everyone lives a different way of life free from social cohesion and family bonds. It is against this backdrop the paper examines the forces of change in Hausa society and their effect on communal living. The paper also highlights the factors and actors involved in such change and how, in the later years of Nigeria’s independence, such factors transformed the social, political and economic structures of Hausa society in Northern Nigeria. In writing this paper, qualitative research is used in which questionnaires and oral interviews were used as a method of data collection. Along this way, other sources like primary and secondary are also used extensively in writing the paper. The concluding part of the paper reveals that unless the problems of elitism, corruption and poverty are addressed, the gap between have and have-nots, wealthy and poor, literate and illiterate, will continue to widen, thereby leading to an individualistic society that negates all forms of communal living.

Keywords: communalism, individualism, historical insights, Hausa land

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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: Niranjani Ruba Pandian

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In today’s multicultural global business community, most of the businesses and industries are linked with various countries in which different nationalities have different roles and responsibilities throughout the project. The purpose of this research is to examine the cross-cultural challenges between Indian and French and the ways to minimize these challenges to manage effectively the cross-cultural aspect of human resources for the success of global business in an automotive industry. The conducted study utilized quantitative methodology to analyze the data on Indian and French employees' perceptions of 6 cultural dimensions such as power versus distance, individualism versus collectivism, masculinity versus femininity, uncertainty versus avoidance, pragmatic versus normative and indulgence versus restraint. Employees of 4 multinational companies filled in the questionnaire based on the 5-point Likert scale to present quantitative results. The data was analysed with the correlation and multiple regression statistical analyses. It was found that Indian and French have major gap in uncertainty versus avoidance followed by individualism versus collectivism. However, this article highlights the way to minimize these gaps by adopting certain sequenced methodologies.

Keywords: automotive industry, cross cultural challenges, globalization, global business

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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: Allison Streutker, Josephine Tan

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Universities across Canada have experienced unprecedented growth in international student enrollment from across the world. As cultural diversity in Canada and other countries increases, understanding the social support needs of all students is important for providing them with the assistance they need to thrive psychologically and academically. Those from individualistic cultural orientations tend to seek explicit social support, which involves expressly asking for assistance in times of stress. However, those from collectivistic cultural orientations are more likely to seek implicit social support, where encouragement is obtained from spending time among valued social groups without explicitly talking about problems. This study explored whether the relationship between the type of social support needs (implicit or explicit) and psychological and academic functioning might be moderated by cultural orientations (individualistic, collectivistic) among university students. Participants were 110 university students (70 women, 40 men; mean age = 24.8 years, SD = 6.6). They completed the Individualism and Collectivism Scale (ICS), Perceived Stress Scale (PSS), Interpersonal Support Evaluation List (ISEL) which assesses implicit and explicit social support, Satisfaction with Life Scale (SWLS), Scale of Positive and Negative Experience (SPANE) which yields positive and negative experience scores, Flourishing Scale (FS), and reported their grade point average (GPA) as a measure of academic performance. Moderated regression analysis demonstrated that, for those scoring lower on individualism, reporting lower level of implicit support predicted higher levels of perceived stress. For those scoring higher on individualism, lower levels of explicit social support predicted higher levels of perceived stress and a greater number of negative experiences. Generally, higher levels of implicit support were associated with greater satisfaction with life for all students, with the association becoming stronger among students with higher collectivism scores. No other significant findings were found. The results point to the value of considering the cultural orientations of students when designing programs to maintain and improve their sense of well-being.

Keywords: cultural orientation, social support, university students, well-being

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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: Said Abdullah Al Saifi

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The goal of this research is to examine the impact of trust, motivation, and national culture on knowledge sharing within the context of electronic mail. This study is quantitative and survey based. In order to conduct the research, 200 students from a leading university in New Zealand were chosen randomly to participate in a questionnaire survey. Motivation and trust were found to be significantly and positively related to knowledge sharing. The research findings illustrated that face saving, face gaining, and individualism positively moderates the relationship between motivation and knowledge sharing. In addition, collectivism culture negatively moderates the relationship between motivation and knowledge sharing. Moreover, the research findings reveal that face saving, individualism, and collectivism culture positively moderate the relationship between trust and knowledge sharing. In addition, face gaining culture negatively moderates the relationship between trust and knowledge sharing. This study sets out several implications for researchers and practitioners. The study produces an integrative model that shows how attributes of national culture impact knowledge sharing through the use of emails. A better understanding of the relationship between knowledge sharing and trust, motivation, and national culture differences will increase individuals’ ability to make wise choices when sharing knowledge with those from different cultures.

Keywords: knowledge sharing, motivation, national culture, trust

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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: 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

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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

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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

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Authors: Sunatda Arayachukiat, Shogo Nobukawa, Masayuki Yamaguchi

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A new self-healing material was developed utilizing molecular entanglements for poly(vinyl butyral) (PVB) containing plasticizers. It was found that PVB shows autonomic self-healing behavior even below the glass transition temperature Tg because of marked molecular motion at surface. Moreover, the plasticizer addition enhances the chain mobility, leading to good healing behavior.

Keywords: Poly(vinyl butyral) (PVB), rheological properties, self-healing behaviour, molecular diffusion

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Authors: Rajandeep Kaur, Rajeev Gupta

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Background: Chronic myeloid leukemia (CML) is the most common leukaemia in India. The annual incidence of chronic myeloid leukemia in India was originally reported to be 0.8 to 2.2 per 1,00,000 population. CML is a clonal disorder that is usually easily diagnosed because the leukemic cells of more than 95% of patients have a distinctive cytogenetic abnormality, the Philadelphia chromosome (Ph1). The approval of tyrosine kinase inhibitors (TKIs), which target BCR-ABL1 kinase activity, has significantly reduced the mortality rate associated with chronic myeloid leukemia (CML) and revolutionized treatment. Material and Methods: 80 diagnosed cases of CML were taken. Investigations were done. Bone marrow and molecular studies were also done and with EUTOS, patients were stratified into low and high-risk groups and then treatment with Imatinib was given to all patients and the molecular response was evaluated at 6 months and 12 months follow up with BCR-ABL by RT-PCR quantitative assay. Results: In the study population, out of 80 patients in the study population, 40 were females and 40 were males, with M: F is 1:1. Out of total 80 patients’ maximum patients (54) were in 31-60 years age group. Our study showed a most common symptom of presentation is abdominal discomfort followed by fever. Out of the total 80 patients, 25 (31.3%) patients had high EUTOS scores and 55 (68.8%) patients had low EUTOS scores. On 6 months follow up 36.3% of patients had Complete Molecular Response, 16.3% of patients had Major Molecular Response and 47.5% of patients had No Molecular Response but on 12 months follow up 71.3% of patients had Complete Molecular Response, 16.25% of patients had Major Molecular Response and 12.5% patients had No Molecular Response. Conclusion: In this study, we found a significant correlation between EUTOS score and Molecular response at 6 months and 12 months follow up after Imatinib therapy.

Keywords: chronic myeloid leukemia, European treatment and outcome study score, hematological response, molecular response, tyrosine kinase inhibitor

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Authors: Sanja O. Podunavac-Kuzmanović, Lidija R. Jevrić, Strahinja Z. Kovačević

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Benzimidazoles are a group of compounds with significant antibacterial, antifungal and anticancer activity. The studied compounds consist of the main benzimidazole structure with different combinations of substituens. This study is based on the two-dimensional and three-dimensional molecular modeling and calculation of molecular descriptors (physicochemical and lipophilicity descriptors) of structurally diverse benzimidazoles. Molecular modeling was carried out by using ChemBio3D Ultra version 14.0 software. The obtained 3D models 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. The obtained set of molecular descriptors was used in principal component analysis (PCA) of possible similarities and dissimilarities among the studied derivatives. After the molecular modeling, the quantitative structure-property relationship (QSPR) analysis was applied in order to get the mathematical models which can be used in prediction of pKb values of structurally similar benzimidazoles. The obtained models are based on statistically valid multiple linear regression (MLR) equations. The calculated cross-validation parameters indicate the high prediction ability of the established QSPR models. This study is financially supported by COST action CM1306 and the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina.

Keywords: benzimidazoles, chemometrics, molecular modeling, molecular descriptors, QSPR

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Authors: Jannes Quer, Amir Niknejad, Marcus Weber

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Computational Drug Design is often based on Molecular Dynamics simulations of molecular systems. Molecular Dynamics can be used to simulate, e.g., the binding and unbinding event of a small drug-like molecule with regard to the active site of an enzyme or a receptor. However, the time-scale of the overall binding event is many orders of magnitude longer than the time-scale of simulation. Thus, there is a need to speed-up molecular simulations. In order to speed up simulations, the molecular dynamics trajectories have to be ”steared” out of local minimizers of the potential energy surface – the so-called metastabilities – of the molecular system. Increasing the kinetic energy (temperature) is one possibility to accelerate simulated processes. However, with temperature the entropy of the molecular system increases, too. But this kind ”stearing” is not directed enough to stear the molecule out of the minimum toward the saddle point. In this article, we give a new mathematical idea, how a potential energy surface can be changed in such a way, that entropy is kept under control while the trajectories are still steared out of the metastabilities. In order to compute the unsteared transition behaviour based on a steared simulation, we propose to use extrapolation methods. In the end we mathematically show, that our method accelerates the simulations along the direction, in which the curvature of the potential energy surface changes the most, i.e., from local minimizers towards saddle points.

Keywords: extrapolation, Eyring-Kramers, metastability, multilevel sampling

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Authors: A. Azari, S. S. K. Seyyedi

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One of the unaddressed and open challenges in the nano-networking is the characteristics of noise. The previous analysis, however, has concentrated on end-to-end communication model with no separate modelings for propagation channel and noise. By considering a separate signal propagation and noise model, the design and implementation of an optimum receiver will be much easier. In this paper, we justify consideration of a separate additive Gaussian noise model of a nano-communication system based on the molecular communication channel for which are applicable for MSK and MOSK modulation schemes. The presented noise analysis is based on the Brownian motion process, and advection molecular statistics, where the received random signal has a probability density function whose mean is equal to the mean number of the received molecules. Finally, the justification of received signal magnitude being uncorrelated with additive non-stationary white noise is provided.

Keywords: molecular, noise, diffusion, channel

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Authors: Paweł Stączek, Tomasz Plech, Aleksandra Strzelczyk, Katarzyna Dzitko, Monika Wujec, Edyta Kuśmierz, Piotr Paneth, Agata Paneth

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In this contribution, we will describe the inhibitory potency of nine thiosemicarbazide derivatives against bacterial type IIA topoisomerases, their antibacterial profile, and molecular modeling evaluation. We have found that one of the tested compounds, 4-benzoyl-1-(2-methyl-furan-3-ylcarbonyl) thiosemicarbazide, remarkably inhibits the activity of S. aureus DNA gyrase with the IC50 below 5 μM. Besides, this compound displays antibacterial activity on Staphylococcus spp. and E. faecalis at non-cytotoxic concentrations in mammalian cells, with minimal inhibitory concentrations (MICs) values at 25 μg/mL. Based on the enzymatic and molecular modeling studies we propose two factors, i.e. geometry of molecule and hydrophobic/hydrophilic balance as important molecular properties for developing thiosemicarbazide derivatives as potent Staphylococcus aureus DNA gyrase inhibitors.

Keywords: bioactivity, drug design, topoisomerase, molecular modeling

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Authors: Hai Hoang, Thanh Xuan Nguyen Thi, Guillaume Galliero

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Coarse-Grained (CG) molecular simulations have shown to be an efficient way to estimate thermophysical (static and dynamic) properties of fluids. Several strategies have been developed and reported in the literature for defining CG molecular models. Among them, those based on a top-down strategy (i.e. CG molecular models related to macroscopic observables), despite being heuristic, have increasingly gained attention. This is probably due to its simplicity in implementation and its ability to provide reasonable results for not only simple but also complex systems. Regarding simple Force-Fields associated with these CG molecular models, it has been found that the four parameters Mie chain model is one of the best compromises to describe thermophysical static properties (e.g. phase diagram, saturation pressure). However, parameterization procedures of these Mie-chain GC molecular models given in literature are generally insufficient to simultaneously provide static and dynamic (e.g. viscosity) properties. To deal with such situations, we have extended the corresponding states by using a quantity associated with the liquid viscosity. Results obtained from molecular simulations have shown that our approach is able to yield good estimates for both static and dynamic thermophysical properties for various real non-associating fluids. In addition, we will show that on simple (e.g. phase diagram, saturation pressure) and complex (e.g. thermodynamic response functions, thermodynamic energy potentials) static properties, results of our scheme generally provides improved results compared to existing approaches.

Keywords: coarse-grained model, mie potential, molecular simulations, thermophysical properties, phase equilibria

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Authors: Manel Boulakoud, Abdelkader Chouaih, Fodil Hamzaoui

Abstract:

In the present work we are interested in the determination of the Molecular electrostatic potential (MEP) in Z-3N(2-Ethoxyphenyl), 2-N’(2-Ethoxyphenyl) imino thiazolidin-4-one molecule by ab initio and Density Functional Theory (DFT) in the ground state. The MEP is related to the electronic density and is a very useful descriptor in understanding sites for electrophilic attack and nucleophilic reactions as well as hydrogen bonding interactions. First, geometry optimization was carried out using Hartree–Fock (HF) and DFT methods with 6-311G(d,p) basis set. In order to get more information on the molecule, its stability has been analyzed by natural bond orbital (NBO) analysis. Mulliken population analyses have been calculated. Finally, the molecular electrostatic potential (MEP) and HOMO-LUMO energy levels have been performed. The calculated HOMO and LUMO energies show also the charge transfer within the molecule. The energy gap obtained is about 4 eV which explain the stability of the studied compound. The obtained molecular electrostatic potential from the two methods confirms the nature of the electron charge transfer at the molecular shell and locate the electropositive part and the electronegative part in molecular scale of the title compound.

Keywords: DFT, ab initio, HOMO-LUMO, organic compounds

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Authors: Efendi Zaenudin, Chien-Hung Huang, Ka-Lok Ng

Abstract:

Essential genes play an important role in the survival of an organism. It has been shown that cancer-associated essential genes are genes necessary for cancer cell proliferation, where these genes are potential therapeutic targets. Also, it was demonstrated that mutations of the cancer-associated essential genes give rise to the resistance of immunotherapy for patients with tumors. In the present study, we focus on studying the biological effects of the essential genes from a network perspective. We hypothesize that one can analyze a biological molecular network by decomposing it into both three-node and four-node digraphs (subgraphs). These network subgraphs encode the regulatory interaction information among the network’s genetic elements. In this study, the frequency of occurrence of the subgraph-associated essential genes in a molecular network was quantified by using the statistical parameter, odds ratio. Biological effects of subgraph-associated essential genes are discussed. In summary, the subgraph approach provides a systematic method for analyzing molecular networks and it can capture useful biological information for biomedical research.

Keywords: biological molecular networks, essential genes, graph theory, network subgraphs

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