Search results for: molecular evolution

Authors: I-Ling Chang, Jer-An Chen

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The elastic properties and fracture of two-dimensional graphene were calculated purely from the atomic bonding (stretching and bending) based on molecular mechanics method. Considering the representative unit cell of graphene under various loading conditions, the deformations of carbon bonds and the variations of the interlayer distance could be realized numerically under the geometry constraints and minimum energy assumption. In elastic region, it was found that graphene was in-plane isotropic. Meanwhile, the in-plane deformation of the representative unit cell is not uniform along armchair direction due to the discrete and non-uniform distributions of the atoms. The fracture of graphene could be predicted using fracture criteria based on the critical bond length, over which the bond would break. It was noticed that the fracture behavior were directional dependent, which was consistent with molecular dynamics simulation results.

Keywords: energy minimization, fracture, graphene, molecular mechanics

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Authors: Utkarsh Goley

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Leather has been a valued material for clothing and accessories for centuries, and its use has evolved along with fashion trends and technological advancements. From ancient times when leather was used for practical purposes, to the modern fashion industry, where it is used for both functional and decorative purposes, leather has undergone significant changes in its production and usage. In recent years, there has been a growing awareness of ethical and sustainable fashion, leading to a shift towards alternative materials and production methods. The leather industry has responded to this by exploring new techniques and materials, such as vegetable-tanned leather and leather substitutes made from plant-based materials. The evolution of leather in the fashion industry is also closely tied to cultural and social trends. The use of leather has been associated with rebellion and counterculture in the past, and today it is often used to evoke a sense of luxury and sophistication. Despite the challenges and controversies surrounding its production, leather continues to be a popular material in the fashion industry, with designers and consumers alike valuing its durability, versatility, and aesthetic appeal. As fashion continues to evolve, so will the role and use of leather in the industry. This research paper provides a detailed overview of the evolution of leather in the fashion industry throughout the different decades and centuries.

Keywords: evolution, fashion, leather, sustainable

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Authors: Jing Zhao, Yongqing Bai, Qiaofang Shi, Huaihao Zhang

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Advances in software technology enable computational chemistry to be commonly applied in various research fields, especially in pedagogy. Thus, in order to expand and improve experimental instructions of computational chemistry for undergraduates, we designed an introductory experiment—research on acrylamide molecular structure and physicochemical properties. Initially, students construct molecular models of acrylamide and polyacrylamide in Gaussian and Materials Studio software respectively. Then, the infrared spectral data, atomic charge and molecular orbitals of acrylamide as well as solvation effect of polyacrylamide are calculated to predict their physicochemical performance. At last, rheological experiments are used to validate these predictions. Through the combination of molecular simulation (performed on Gaussian, Materials Studio) with experimental verification (rheology experiment), learners have deeply comprehended the chemical nature of acrylamide and polyacrylamide, achieving good learning outcomes.

Keywords: upper-division undergraduate, computer-based learning, laboratory instruction, molecular modeling

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Authors: Sakina Fatima, Joseph-Patrick W. E. Clarke, Patricia A. Thibault, Subha Kalyaanamoorthy, Michael Levin, Aravindhan Ganesan

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Heteronuclear ribonucleoprotein (hnRNPA1 or A1) is associated with the pathology of different diseases, including neurological disorders and cancers. In particular, the aggregation and dysfunction of A1 have been identified as a critical driver for neurodegeneration (NDG) in Multiple Sclerosis (MS). Structurally, A1 includes a low-complexity domain (LCD) and two RNA-recognition motifs (RRMs), and their interdomain coordination may play a crucial role in A1 aggregation. Previous studies propose that RNA-inhibitors or nucleoside analogs that bind to RRMs can potentially prevent A1 self-association. Therefore, molecular-level understanding of the structures, dynamics, and nucleotide interactions with A1 RRMs can be useful for developing therapeutics for NDG in MS. In this work, a combination of computational modelling and biochemical experiments were employed to analyze a set of RNA-A1 RRM complexes. Initially, the atomistic models of RNA-RRM complexes were constructed by modifying known crystal structures (e.g., PDBs: 4YOE and 5MPG), and through molecular docking calculations. The complexes were optimized using molecular dynamics simulations (200-400 ns), and their binding free energies were computed. The binding affinities of the selected complexes were validated using a thermal shift assay. Further, the most important molecular interactions that contributed to the overall stability of the RNA-A1 RRM complexes were deduced. The results highlight that adenine and guanine are the most suitable nucleotides for high-affinity binding with A1. These insights will be useful in the rational design of nucleotide-analogs for targeting A1 RRMs.

Keywords: hnRNPA1, molecular docking, molecular dynamics, RNA-binding proteins

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Authors: Nikolaos Simantiris, Markos Avlonitis

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This work builds a simulation platform, modeling the spatial diffusion of the invasive species Callinectes sapidus (blue crab) as a random walk, incorporating also generation, fatality, and fishing rates modeling the time evolution of its population. Antinioti lagoon in West Greece was used as a testbed for applying the simulation model. Field measurements from June 2020 to June 2021 on the lagoon’s setting, bathymetry, and blue crab juveniles provided the initial population simulation of blue crabs, as well as biological parameters from the current literature were used to calibrate simulation parameters. The scope of this study is to render the authors able to predict the evolution of the blue crab population in confined environments of the Ionian Islands region in West Greece. The first result of the simulation experiments shows the possibility for a robust prediction for blue crab population evolution in the Antinioti lagoon.

Keywords: antinioti lagoon, blue crab, stochastic simulation, random walk

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Authors: Rim Khemiri, Mariam Dammak

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The aim of this study is to trace the historical evolution of Tunisian higher accounting education and to understand and highlight the circumstances of its birth and its development. A documentary study (archival documents, official documents, public speeches, etc.), as well as semi-directive interviews with key actors, were carried out as part of this research work. These interviews aim to fill a lack of information on this subject and to confirm events addressed by other sources, but for which it lacks the elements necessary for a good understanding. After having put forward the specificities of the Tunisian context, we will, first of all, proceed to a review of the literature related to our theme in various contexts of the world. Then, we will present the evolution of the accounting curriculum by highlighting the circumstances of its birth and those of the successive reforms led by the Tunisian government. The study of higher accounting education in Tunisia and its evolution has several interests. The first lies in understanding the circumstances of its birth and its evolution in relation to the historical, socio-economic, and political context of the country. The second is to propose a reading grid that allows an understanding of the reforms that led to the university accountancy accounting course as we know it today. And, the third, aims to complete the literature on the processes of evolution of higher education accounting, by treating a different context, in order to provide additional knowledge necessary to compare experiences in this area around the world.

Keywords: accounting history, higher accounting education, socio-economic and political context, Tunisian context

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Authors: Chinedu Bevis Dibia, Hom Nath Dhakal

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Effective waste management in sub-Saharan Africa has been identified as a means of resolving the wicked problems posed by climate change. Municipal solid waste management in Nigeria could be argued to be ineffective and unsustainable, despite the tag of sustainable ascribed to most municipalities’ waste management. Relatively, few studies have enquired on the evolution of Sustainable Municipal Waste Management (SMWM) in Nigeria. The main objective of this research is to examine the evolution of SMWM in Nigeria using Lagos state as a case study. A qualitative method was used as methodology, soft systems analysis is the main tool of evaluation. Results indicated that effective policy implementation and management is the main challenge to the proper evolution of SMWM. These findings highlight the relevance of effective stakeholder’s engagement and management, policy consistency as major determinants in SMWM.

Keywords: high income localities, low middle income localities, SMWM, upper middle income localities, waste collection, waste disposal

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Authors: Salem El-Tohami Ashoor

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Here we show that the reduction of [Cr(ArN(CH2)3NAr)2Cl2] (1) where (Ar = 2,6-Pri2C6H3) and in presence of NaCp (2) (Cp= C5H5 = cyclopentadien), with a center coordination η5 interaction between Cp as co-ligand and chromium metal center, this was optimization by using density functional theory (DFT) and then was comparing with experimental data, also other possibility of Cp interacted with ion metal were tested like η1 ,η2 ,η3 and η4 under optimization system. 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 [Cr(ArN(CH2)3NAr)2(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of chromium cyclopentadienyl. 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: Chromium(III) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

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Authors: Abdulwahab Kammon, Tan Sheau Wei, Abdul Rahman Omar, Abdunaser Dayhum, Ibrahim Eldghayes, Monier Sharif

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Infectious bronchitis virus (IBV) is a very dynamic and evolving virus which causing major economic losses to the global poultry industry. Recently, the Libyan poultry industry faced severe outbreak of respiratory distress associated with high mortality and dramatic drop in egg production. Tracheal and cloacal swabs were analyzed for several poultry viruses. IBV was detected using SYBR Green I real-time PCR detection based on the nucleocapsid (N) gene. Sequence analysis of the partial N gene indicated high similarity (~ 94%) to IBV strain 3382/06 that was isolated from Taiwan. Even though the IBV strain 3382/06 is more similar to that of the Mass type H120, the isolate has been implicated associated with intertypic recombinant of 3 putative parental IBV strains namely H120, Taiwan strain 1171/92 and China strain CK/CH/LDL/97I. Complete sequencing and antigenicity studies of the Libya IBV strains are currently underway to determine the evolution of the virus and its importance in vaccine induced immunity. In this paper, we documented for the first time the presence of possibly variant IBV strain from Libya which required a dramatic change in the vaccination program.

Keywords: Libya, infectious bronchitis, molecular characterization, viruses, vaccine

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Authors: Milica Karadzic, Lidija Jevric, Sanja Podunavac-Kuzmanovic, Strahinja Kovacevic, Sinisa Markov, Aleksandar Okljesa, Andrea Nikolic, Marija Sakac, Katarina Penov Gasi

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This study considered the microbiological activity determination and molecular docking study for selected steroid derivatives of biomedical importance. Minimal inhibitory concentration (MIC) was determined for steroid derivatives against Staphylococcus aureus using macrodilution method. Some of the investigated steroid derivatives express bacteriostatic effect against Staphylococcus aureus. Molecular docking approaches are the most widely used techniques for predicting the binding mode of a ligand. Molecular docking study was done for steroid derivatives for androgen receptor negative prostate cancer cell line (PC-3) toward Human Cytochrome P450 CYP17A1. The molecules that had the smallest experimental IC50 values confirmed their ability to dock into active place using suitable molecular docking procedure. The binding disposition of those molecules was thoroughly investigated. Microbiological analysis and molecular docking study were conducted with aim to additionally characterize selected steroid derivatives for future investigation regarding their biological activity and to estimate the binding-affinities of investigated derivatives. This article is based upon work from COST Action (TD1305), supported by COST (European Cooperation and Science and Technology).

Keywords: binding affinity, minimal inhibitory concentration, molecular docking, pc-3 cell line, staphylococcus aureus, steroids

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

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The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene

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Authors: Ayaz Ahmad

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TOPIC: A study of the formation ,existness and stability of localised pulses in pde Ayaz Ahmad ,NITP, Abstract:In this paper we try to govern the evolution deterministic variable over space and time .We analysis the behaviour of the model which allows us to predict and understand the possible behaviour of the physical system .Bifurcation theory provides a basis to systematically investigate the models for invariant sets .Exploring the behaviour of PDE using bifurcation theory which provides many challenges both numerically and analytically. We use the derivation of a non linear partial differential equation which may be written in this form ∂u/∂t+c ∂u/∂x+∈(∂^3 u)/(∂x^3 )+¥u ∂u/∂x=0 We show that the temperature increased convection cells forms. Through our work we look for localised solution which are characterised by sudden burst of aeroidic spatio-temporal evolution. Key word: Gaussian pulses, Aeriodic ,spatio-temporal evolution ,convection cells, nonlinearoptics, Dr Ayaz ahmad Assistant Professor Department of Mathematics National institute of technology Patna ,Bihar,,India 800005 [email protected] +91994907553

Keywords: Gaussian pulses, aeriodic, spatio-temporal evolution, convection cells, nonlinear optics

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Authors: Ali Rahnamoun, Adri van Duin

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The concept of high velocity particle impact on the spacecraft surface materials has been one of the important issues in the design of such materials. Among these particles, water clusters might be the most abundant and the most important particles to be studied. The importance of water clusters is that upon impact on the surface of the materials, they can cause damage to the material and also if they are sub-cooled water clusters, they can attach to the surface of the materials and cause ice accumulation on the surface which is very problematic in spacecraft and also aircraft operations. The dynamics of the collisions between amorphous silica structures and water clusters with impact velocities of 1 km/s to 10 km/s are studied using the ReaxFF reactive molecular dynamics simulation method. The initial water clusters include 150 water molecules and the water clusters are collided on the surface of amorphous fully oxidized and suboxide silica structures. These simulations show that the most abundant molecules observed on the silica surfaces, other than reflecting water molecules, are H3O+ and OH- for the water cluster impacts on suboxide and fully oxidized silica structures, respectively. The effect of impact velocity on the change of silica mass is studied. At high impact velocities the water molecules attach to the silica surface through a chemisorption process meaning that water molecule dissociates through the interaction with silica surface. However, at low impact velocities, physisorbed water molecules are also observed, which means water molecule attaches and accumulates on the silica surface. The amount of physisorbed waters molecules at low velocities is higher on the suboxide silica surfaces. The evolution of the temperatures of the water clusters during the collisions indicates that the possibility of electron excitement at impact velocities less than 10 km/s is minimal and ReaxFF reactive molecular dynamics simulation can predict the chemistry of these hypervelocity impacts. However, at impact velocities close to 10 km/s the average temperature of the impacting water clusters increase to about 2000K, with individual molecules oocasionally reaching temperatures of over 8000K and thus will be prudent to consider the concept of electron excitation at these higher impact velocities which goes beyond the current ReaxFF ability.

Keywords: spacecraft materials, hypervelocity impact, reactive molecular dynamics simulation, amorphous silica

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Authors: Jayanthi Sivaraman

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Claudins are the important components of the tight junctions that play a key role in paracellular permeability. Among various members of Claudin family, Claudin 4 (CLDN4) is found to be overexpressed in ovarian, pancreatic carcinomas and other epithelial malignancies. Therefore, in this study, an attempt has been made to identify potent inhibitors for CLDN4 from the ZINC database using virtual screening, molecular docking and molecular dynamics simulations. A well refined molecular model of CLDN4 was built using Prime of Schrodinger v10.2(Template- PDB ID: 4P79). Approximately, 6 million compounds from ZINC database are subjected to high-throughput virtual screening (HTVS) against the active site of CLDN4. Molecular docking using GLIDE predicted ARG31, ASN142, ASP146 and ARG158 as critically important residues. Furthermore, three compounds from ZINC database (ZINC96331839, ZINC36533519 and ZINC75819394) showed highly promising ADME properties and binding affinity with stable conformation. The therapeutic efficiency of these lead compounds is evaluated and confirmed by in-vitro and in-vivo studies which leads to the development of novel anti-cancer drugs.

Keywords: ADME property, inhibitors, molecular docking, virtual screening

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Authors: Guohua Cao, Xu Dong

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X-ray Fluorescence Molecular Imaging (XFMI) holds great promise as a low-cost molecular imaging modality for biomedical applications with high chemical sensitivity. However, for in vivo biomedical applications, a key technical bottleneck is the relatively low chemical sensitivity of XFMI, especially at a reasonably low radiation dose. In laboratory x-ray source based XFMI, one of the main factors that limits the chemical sensitivity of XFMI is the scattered x-rays. We will present our latest findings on improving the chemical sensitivity of XFMI using excitation beam spectrum optimization. XFMI imaging experiments on two mouse-sized phantoms were conducted at three different excitation beam spectra. Our results show that the minimum detectable concentration (MDC) of iodine can be readily increased by five times via excitation spectrum optimization. Findings from this investigation could find use for in vivo pre-clinical small-animal XFMI in the future.

Keywords: molecular imaging, X-ray fluorescence, chemical sensitivity, X-ray scattering

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Authors: Shu-Yu Hsu, Chen-Chien Hsu, Wei-Yen Wang

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Color segmentation is a basic and simple way for recognizing the visual markers in a robotic tracking system. In this paper, we propose a new method for color segmentation by incorporating differential evolution algorithm and connected component labeling to autonomously preset the HSV threshold of visual markers. To evaluate the effectiveness of the proposed algorithm, a ROBOTIS OP2 humanoid robot is used to conduct the experiment, where five most commonly used color including red, purple, blue, yellow, and green in visual markers are given for comparisons.

Keywords: color segmentation, differential evolution, connected component labeling, humanoid robot

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Authors: Begüm Terzi, Özlem Ateş Sönmezoğlu, Ahmet Yildirim

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Drought is the most important factor that limiting the production and productivity of wheat in the world. The yield of wheat, which is one of the most important crop in the world, reduced depend on drought. Researches to minimize effects of drought are one of the most important about breeding of drought resistant varieties. In recent years, benefiting from the drought resistance wild species and rapid advances in molecular biology studies, researches about drought have been accelerated and number of studies were made on molecular plant breeding which included the molecular mechanisms related to drought resistance. The aim of the present study was characterization of some bread wheat lines for drought tolerance which commonly cultivated in different location of Turkey. In this study, registered 9 bread wheat varieties which on the physiological tests about drought tolerance and 10 bread wheat line has been developed by Transitional Zone Agricultural Research Institute were used. SSR, STS, RAPD and SNP markers that associated with drought tolerance were used. The polymorphisms of the markers were determined by screening of two control varieties. For these purpose 40 molecular markers were used and 12 markers of them were polymorphic among the drought tolerance and the drought sensitive varieties. Control varieties were screened using polymorphic markers. All the DNAs on the genotypes will be searched for the presence of QTLs mapped to different chromosomes. Result of the research, the studied genotypes will be grouped according to drought tolerance and will be detected drought tolerance varieties by molecular markers. In addition, the results will be compared also with physiological tests. The drought tolerant wheat genotypes may be used in breeding studies related to drought stress.

Keywords: bread wheat, drought, molecular marker, Triticum aestivum

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Authors: Asli Faiza, Khamouli Saida

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With the development of computer tools over the past 20 years. Molecular modeling and, more precisely, molecular docking has very quickly entered field of pharmaceutical research. EGFR enzyme involved in cancer disease.Our work consists of studying the inhibition of EGFR (1M17) with deferent inhibitors derived from quinazoline and quinoline by molecular docking. The values of ligands L148 and L177 are the best ligands for inhibit the activity of 1M17 since it forms a stable complex with this enzyme by better binding to the active site. The results obtained show that the ligands L148 and L177 give weak interactions with the active site residues EGFR (1M17), which stabilize the complexes formed of this ligands, which gives a better binding at the level of the active site, and an RMSD of L148 [1,9563 Å] and of L177 [ 1,2483 Å]. [1, 9563, 1.2483] Å

Keywords: docking, EGFR, quinazoline, quinoliène, MOE

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Authors: Mohamad Mohsen Yavarizadeh

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Polystyrene (PS) and related homopolymers are brittle materials that typically fail in tensile tests at very low strains. These polymers can be toughened by the addition of rubbery particles which initiate a large number of crazes that produce substantial plastic strain at relatively low stresses. Considerable energy is dissipated in the formation of these crazes, producing a relatively tough material that shows an impact toughness of more than 5 times of pure PS. While cross linking of rubbery phase is necessary in aforementioned mechanism of toughening, another mechanism of toughening was also introduced in which low molecular weight liquid rubbers can also toughen PS when dispersed in the form of small pools in the glassy matrix without any cross linking. However, this new mechanism which is based on local plasticization, fails to act properly at high strain rate deformations, i.e. impact tests. In this work, the idea of combination of these two mechanisms was tried. To do so, Polybutadiene rubbers (PB) with bimodal distribution of molecular weight were prepared in which, comparable fractions of very high and very low molecular weight rubbers were mixed. Incorporation of these materials in PS matrix in a reactive process resulted in more significant increases in toughness of PS. In other words, although low molecular weight PB is ineffective in high strain rate impact test by itself, it showed a significant synergistic effect when combined with high molecular weight PB. Surprisingly, incorporation of just 10% of low molecular weight PB doubled the impact toughness of regular high impact PS (HIPS). It was observed that most of rubbery particles could initiate crazes. The effectiveness of low molecular weight PB in impact test was attributed to low strain rate deformation of each individual craze as a result of producing a large number of crazes in this material. In other words, high molecular weight PB chains make it possible to have an appropriate dispersion of rubbery phase in order to create a large number of crazes in the PS matrix and consequently decrease the velocity of each craze. Low molecular weight PB, in turn, would have enough time to locally plasticize craze fibrils and enhance the energy dissipation.

Keywords: molecular weight distribution, polystyrene, toughness, homopolymer

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Authors: Moulay Driss Mellaoui, Khadija Zaki, Khalid Abbiche, Abdallah Imjjad, Rachid Boutiddar, Abdelouahid Sbai, Aaziz Jmiai, Souad El Issami, Al Mokhtar Lamsabhi, Hanane Zejli

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This study presents a comprehensive analysis of six isoxazolidine and isoxazoline derivatives, leveraging a multifaceted approach that combines Density Functional Theory (DFT), AdmetSAR analysis, and molecular docking simulations to explore their electronic, pharmacokinetic, and anticancer properties. Through DFT analysis, using the B3LYP-D3BJ functional and the 6-311++G(d,p) basis set, we optimized molecular geometries, analyzed vibrational frequencies, and mapped Molecular Electrostatic Potentials (MEP), identifying key sites for electrophilic attacks and hydrogen bonding. Frontier Molecular Orbital (FMO) analysis and Density of States (DOS) plots revealed varying stability levels among the compounds, with 1b, 2b, and 3b showing slightly higher stability. Chemical potential assessments indicated differences in binding affinities, suggesting stronger potential interactions for compounds 1b and 2b. AdmetSAR analysis predicted favorable human intestinal absorption (HIA) rates for all compounds, highlighting compound 3b superior oral effectiveness. Molecular docking and molecular dynamics simulations were conducted on isoxazolidine and 4-isoxazoline derivatives targeting the EGFR receptor (PDB: 1JU6). Molecular docking simulations confirmed the high affinity of these compounds towards the target protein 1JU6, particularly compound 3b, among the isoxazolidine derivatives, compound 3b exhibited the most favorable binding energy, with a g score of -8.50 kcal/mol. Molecular dynamics simulations over 100 nanoseconds demonstrated the stability and potential of compound 3b as a superior candidate for anticancer applications, further supported by structural analyses including RMSD, RMSF, Rg, and SASA values. This study underscores the promising role of compound 3b in anticancer treatments, providing a solid foundation for future drug development and optimization efforts.

Keywords: isoxazolines, DFT, molecular docking, molecular dynamic, ADMET, drugs.

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Authors: Yuan Zhang

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Along with large population and great demands for urban development, Hong Kong serves as a typical high-density city with multiple altitudes, advanced three-dimensional traffic system, rich city open space, etc. This paper contributes to analyzing its complex urban form and evolution mechanism from three aspects of view, separately as time, space and buildings. Taking both horizontal and vertical dimension into consideration, this paper provides a perspective to explore the fascinating process of growing and space folding in the urban form of high-density city, also as a research reference for related high-density urban design.

Keywords: evolution mechanism, high-density city, Hong Kong, urban form

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Authors: Saroj Poudel, Joshua Mancini, Douglas Pike, Jennifer Timm, Alexei Tyryshkin, Vikas Nanda, Paul Falkowski

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On the early Earth, protein-metal complexes likely harvested energy from a reduced environment. These complexes would have been precursors to the metabolic enzymes of ancient organisms. Hydrogenase is an essential enzyme in most anaerobic organisms for the reduction and oxidation of hydrogen in the environment and is likely one of the earliest evolved enzymes. To attempt to reinvent a precursor to modern hydrogenase, we computationally designed a short thirteen amino acid peptide that binds the often-required catalytic transition metal Nickel in hydrogenase. This simple complex can achieve hundreds of hydrogen evolution cycles using light energy in a broad range of temperature and pH. Biophysical and structural investigations strongly indicate the peptide forms a di-nickel active site analogous to Acetyl-CoA synthase, an ancient protein central to carbon reduction in the Wood-Ljungdahl pathway and capable of hydrogen evolution. This work demonstrates that prior to the complex evolution of multidomain enzymes, early peptide-metal complexes could have catalyzed energy transfer from the environment on the early Earth and enabled the evolution of modern metabolism

Keywords: hydrogenase, prebiotic enzyme, metalloenzyme, computational design

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Authors: C. M. Priesnitz, G. Zanandrea, J. P. Fabris, S. L. Russo, M. E. Camargo

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This study aimed to the prospection the physiotherapy area technological production registered with the National Intellectual Property Institute (INPI) in Brazil, for understand the evolution of the technological production in the country over time and visualize the distribution this production request in Brazil. There was an evolution in the technology landscape, where the average annual deposits had an increase of 102%, from 3.14 before the year 2004 to 6,33 after this date. It was found differences in the distribution of the number the deposits requested to each Brazilian region, being that of the 132 request, 68,9% were from the southeast region. The international patent classification evaluated the request deposits, and the more found numbers were A61H and A63B. So even with an improved panorama of technology production, this should still have incentives since it is an important tool for the development of the country.

Keywords: distribution, evolution, patent, physiotherapy, technological prospecting

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Authors: Proficiency Munsaka, Peter Baricholo, Erich Rohwer

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Pulse evolutions along the 5 cm long, 6.0 ×4.2 μm² cross-section silicon germanium (SiGe) photonic waveguides were simulated and compared with experiments. Simulations were carried out by solving a generalized nonlinear Schrodinger equation (GNLSE) for an optical pulse evolution along the length of the SiGe photonic waveguides by the split-step Fourier method (SSFM). The solution obtained from the SSFM gave the pulse envelope in both time and spectral domain calculated at each distance step along the propagation direction. The SiGe photonic waveguides were pumped in an anomalous group velocity dispersion (GVD) regime using a 4.7 μm, 210 fs femtosecond laser to produce a significant supercontinuum (SC). The simulated propagation of ultrafast pulse along the SiGe photonic waveguides produced an SC covering the atmospheric window (2.5-8.5 μm) containing the molecular fingerprints for important gases. Thus, the mid-infrared supercontinuum generation in SiGe photonic waveguides system can be commercialized for gas spectroscopy for detecting gases that include CO₂, CH₄, H₂O, SO₂, SO₃, NO₂, H₂S, CO, and NO at trace level using absorption spectroscopy technique. The simulated profile evolutions are spectrally and temporally similar to those obtained by other researchers. Obtained evolution profiles are characterized by pulse compression, Soliton fission, dispersive wave generation, stimulated Raman Scattering, and Four Wave mixing.

Keywords: silicon germanium photonic waveguide, supercontinuum generation, spectroscopy, mid infrared

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Authors: Alena Semeradtova, Marcel Stofik, Lucie Mareckova, Petr Maly, Ondrej Stanek, Jan Maly

Abstract:

Recently, novel strategies based on so-called molecular evolution were shown to be effective for the production of various peptide ligand libraries with high affinities to molecular targets of interest comparable or even better than monoclonal antibodies. The major advantage of these peptide scaffolds is mainly their prevailing low molecular weight and simple structure. This study describes a new high-affinity binding molecules based immunesensor using a simple optical system for human serum albumin (HSA) detection as a model molecule. We present a comparison of two variants of recombinant binders based on albumin binding domain of the protein G (ABD) performed on micropatterned glass chip. Binding domains may be tailored to any specific target of interest by molecular evolution. Micropatterened glass chips were prepared using UV-photolithography on chromium sputtered glasses. Glass surface was modified by (3-aminopropyl)trietoxysilane and biotin-PEG-acid using EDC/NHS chemistry. Two variants of high-affinity binding molecules were used to detect target molecule. Firstly, a variant is based on ABD domain fused with TolA chain. This molecule is in vivo biotinylated and each molecule contains one molecule of biotin and one ABD domain. Secondly, the variant is ABD domain based on streptavidin molecule and contains four gaps for biotin and four ABD domains. These high-affinity molecules were immobilized to the chip surface via biotin-streptavidin chemistry. To eliminate nonspecific binding 1% bovine serum albumin (BSA) or 6% fetal bovine serum (FBS) were used in every step. For both variants range of measured concentrations of fluorescently labelled HSA was 0 – 30 µg/ml. As a control, we performed a simultaneous assay without high-affinity binding molecules. Fluorescent signal was measured using inverse fluorescent microscope Olympus IX 70 with COOL LED pE 4000 as a light source, related filters, and camera Retiga 2000R as a detector. The fluorescent signal from non-modified areas was substracted from the signal of the fluorescent areas. Results were presented in graphs showing the dependence of measured grayscale value on the log-scale of HSA concentration. For the TolA variant the limit of detection (LOD) of the optical immunosensor proposed in this study is calculated to be 0,20 µg/ml for HSA detection in 1% BSA and 0,24 µg/ml in 6% FBS. In the case of streptavidin-based molecule, it was 0,04 µg/ml and 0,07 µg/ml respectively. The dynamical range of the immunosensor was possible to estimate just in the case of TolA variant and it was calculated to be 0,49 – 3,75 µg/ml and 0,73-1,88 µg/ml respectively. In the case of the streptavidin-based the variant we didn´t reach the surface saturation even with the 480 ug/ml concentration and the upper value of dynamical range was not estimated. Lower value was calculated to be 0,14 µg/ml and 0,17 µg/ml respectively. Based on the obtained results, it´s clear that both variants are useful for creating the bio-recognizing layer on immunosensors. For this particular system, it is obvious that the variant based on streptavidin molecule is more useful for biosensing on glass planar surfaces. Immunosensors based on this variant would exhibit better limit of detection and wide dynamical range.

Keywords: high affinity binding molecules, human serum albumin, optical immunosensor, protein G, UV-photolitography

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Authors: Ashkan Forootan, Reza Rashedi

Abstract:

Polyethylene has wide usage areas such as blow molding, pipe, film, cable insulation. However, regardless to its growing applications, it has some constraints such as the limited 70C operating temperature. Polyethylene thermo setting procedure whose molecules are knotted and 3D-molecular-network formed , is developed to conquer the above problem and to raise the applicable temperature of the polymer. This paper reports the cross-linking for two different molecular weight grades of LLDPE by adding 0.5, 1, and 2% of DCP (Dicumyl Peroxide). DCP was chosen for its prevalence among various cross-linking agents. Structural parameters such as molecular weight, melt flow index, comonomer, number of branches,etc. were obtained through the use of relative tests as Gel Permeation Chromatography and Fourier Transform Infra Red spectrometer. After calculating the percentage of gel content, properties of the pure and cross-linked samples were compared by thermal and mechanical analysis with DMTA and FTIR and the effects of cross-linking like viscous and elastic modulus were discussed by using various structural paprameters such as MFI, molecular weight, short chain branches, etc. Studies showed that cross-linked polymer, unlike the pure one, had a solid state with thermal mechanical properties in the range of 110 to 120C and this helped overcome the problem of using polyethylene in temperatures near the melting point.

Keywords: LLDPE, cross-link, structural parameters, DCP, DMTA, GPC

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

Abstract:

The relationship between antibacterial activity of eighteen different substituted benzimidazole derivatives and their molecular characteristics was studied using chemometric QSAR (Quantitative Structure–Activity Relationships) approach. QSAR analysis has been carried out on inhibitory activity towards Staphylococcus aureus, by using molecular descriptors, as well as minimal inhibitory activity (MIC). Molecular descriptors were calculated from the optimized structures. Principal component analysis (PCA) followed by hierarchical cluster analysis (HCA) and multiple linear regression (MLR) was performed in order to select molecular descriptors that best describe the antibacterial behavior of the compounds investigated, and to determine the similarities between molecules. The HCA grouped the molecules in separated clusters which have the similar inhibitory activity. PCA showed very similar classification of molecules as the HCA, and displayed which descriptors contribute to that classification. MLR equations, that represent MIC as a function of the in silico molecular descriptors were established. The statistical significance of the estimated models was confirmed by standard statistical measures and cross-validation parameters (SD = 0.0816, F = 46.27, R = 0.9791, R2CV = 0.8266, R2adj = 0.9379, PRESS = 0.1116). These parameters indicate the possibility of application of the established chemometric models in prediction of the antibacterial behaviour of studied derivatives and structurally very similar compounds.

Keywords: antibacterial, benzimidazole, molecular descriptors, QSAR

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Authors: Sohail Ahmed, Ke Xing

Abstract:

This research theoretically explored the evolution mechanism of enterprise technological innovation capability system (ETICS) from the perspective of complex adaptive systems (CAS). This research proposed an analytical framework for ETICS, its concepts, and theory by integrating CAS methodology into the management of the technological innovation capability of enterprises and discusses how to use the principles of complexity to analyze the composition, evolution, and realization of the technological innovation capabilities in complex dynamic environments. This paper introduces the concept and interaction of multi-agent, the theoretical background of CAS, and summarizes the sources of technological innovation, the elements of each subject, and the main clusters of adaptive interactions and innovation activities. The concept of multi-agents is applied through the linkages of enterprises, research institutions, and government agencies with the leading enterprises in industrial settings. The study was exploratory and based on CAS theory. Theoretical model is built by considering technological and innovation literature from foundational to state of the art projects of technological enterprises. On this basis, the theoretical model is developed to measure the evolution mechanism of the enterprise's technological innovation capability system. This paper concludes that the main characteristics for evolution in technological systems are based on the enterprise’s research and development personnel, investments in technological processes, and innovation resources are responsible for the evolution of enterprise technological innovation performance. The research specifically enriched the application process of technological innovation in institutional networks related to enterprises.

Keywords: complex adaptive system, echo model, enterprise technological innovation capability system, research institutions, multi-agents

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Authors: Sohail Ahmed, Ke Xing

Abstract:

This research theoretically explored the evolution mechanism of enterprise technological innovation capability system (ETICS) from the perspective of complex adaptive systems (CAS). Starting from CAS theory, this study proposed an analytical framework for ETICS, its concepts and theory by integrating CAS methodology into the management of technological innovation capability of enterprises and discusses how to use the principles of complexity to analyze the composition, evolution and realization of the technological innovation capabilities in complex dynamic environment. This paper introduces the concept and interaction of multi-agent, the theoretical background of CAS and summarizes the sources of technological innovation, the elements of each subject and the main clusters of adaptive interactions and innovation activities. The concept of multi-agents is applied through the linkages of enterprises, research institutions and government agencies with the leading enterprises in industrial settings. The study was exploratory based on CAS theory. Theoretical model is built by considering technological and innovation literature from foundational to state of the art projects of technological enterprises. On this basis, the theoretical model is developed to measure the evolution mechanism of enterprise technological innovation capability system. This paper concludes that the main characteristics for evolution in technological systems are based on enterprise’s research and development personal, investments in technological processes and innovation resources are responsible for the evolution of enterprise technological innovation performance. The research specifically enriched the application process of technological innovation in institutional networks related to enterprises.

Keywords: complex adaptive system, echo model, enterprise knowledge system, research institutions, multi-agents.

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Authors: Kamran Dastafkan, Chuan Zhao

Abstract:

Improving surface chemistry is a promising approach in addition to the rational alteration in the catalyst composition to advance water electrolysis. Here, we demonstrate an evident enhancement of oxygen evolution on an iron-nickel vanadate catalyst synthesized by a facile successive ionic adsorption and reaction method. The vanadate-modified catalyst demonstrates a highly efficient oxygen evolution in 1 M KOH by requiring low overpotentials of 274 and 310 mV for delivering large current densities of 100 and 400 mA cm⁻², respectively where vigorous gas bubble evolution occurs. Vanadate modification augments the OER activity from three aspects. (i) Both the electrochemical surface area (47.1 cm²) and intrinsic activity (318 mV to deliver 10 mA cm⁻² per unit ECSA) of the catalytic sites are improved. (ii) The amorphous and roughened nanoparticle-comprised catalyst film exhibits a high surface wettability and a low-gas bubble-adhesion, which is beneficial for the accelerated mass transport and gas bubble dissipation at large current densities. The gas bubble dissipation behavior is studied by operando dynamic specific resistance measurements where a significant change in the variation of the interfacial resistance during the OER is detected for the vanadate-modified catalyst. (iii) The introduced vanadate poly-oxo-anions with high charge density have electronic interplay with Fe and Ni catalytic centers. Raman study reveals the structural evolution of β-NiOOH and γ-FeOOH phases during the OER through the vanadate-active site synergistic interactions. Achievement of a high catalytic turnover of 0.12 s⁻¹ put the developed FeNi vanadate among the best recent catalysts for water oxidation.

Keywords: gas bubble dissipation, iron-nickel vanadate, low-gas bubble-adhesion catalyst, oxygen evolution reaction

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