Search results for: molecular docking

Authors: Tudor Petreuş, Andrei Neamţu, Cristina Dascălu, Paul Dan Sîrbu, Carmen E. Cotrutz

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Matrix metalloproteinases (MMP) are a class of structural and functional related enzymes involved in altering the natural elements of the extracellular matrix. Most of the MMP structures are cristalographycally determined and published in WorldWide ProteinDataBank, isolated, in full structure or bound to natural or synthetic inhibitors. This study proposes an algorithm to replace missing crystallographic structures in PDB database. We have compared the results of a chosen docking algorithm with a known crystallographic structure in order to validate enzyme sites reconstruction there where crystallographic data are missing.

Keywords: matrix metalloproteinases, molecular docking, structure superposition, surface complementarity.

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Authors: Dhananjay C. Joshi, Jung-Hsin Lin

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Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

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Authors: Ching-Wei Tsai, Chih-I Liu, Ruoh-Chyu Ruaana

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A new strategy for oriented immobilization of proteins was proposed. The strategy contains two steps. The first step is to search for a docking site away from the active site on the protein surface. The second step is trying to find a ligand that is able to grasp the targeted site of the protein. To avoid ligand binding to the active site of protein, the targeted docking site is selected to own opposite charges to those near the active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic interactions need to be included. The targeted docking site should therefore contain hydrophobic amino acids. The ligand is then selected through the help of molecular docking simulations. The enzyme α-amylase derived from Aspergillus oryzae (TAKA) was taken as an example for oriented immobilization. The active site of TAKA is surrounded by negatively charged amino acids. All the possible hydrophobic sites on the surface of TAKA were evaluated by the free energy estimation through benzene docking. A hydrophobic site on the opposite side of TAKA-s active site was found to be positive in net charges. A possible ligand, 3,3-,4,4- – Biphenyltetra- carboxylic acid (BPTA), was found to catch TAKA by the designated docking site. Then, the BPTA molecules were grafted onto silica gels and measured the affinity of TAKA adsorption and the specific activity of thereby immobilized enzymes. It was found that TAKA had a dissociation constant as low as 7.0×10-6 M toward the ligand BPTA on silica gel. The increase in ionic strength has little effect on the adsorption of TAKA, which indicated the existence of hydrophobic interaction between ligands and proteins. The specific activity of the immobilized TAKA was compared with the randomly adsorbed TAKA on primary amine containing silica gel. It was found that the orderly immobilized TAKA owns a specific activity twice as high as the one randomly adsorbed by ionic interaction.

Keywords: Protein Oriented immobilization, Molecular docking, ligand design, surface modification.

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Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

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The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: Nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation.

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Authors: Suman Bala, Sunil Kamboj, Vipin Saini

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Quantitative Structure Activity Relationship (QSAR) analysis has been developed to relate antifungal activity of novel substituted 1,3,4-oxadiazole against Candida albicans and Aspergillus niger using computer assisted multiple regression analysis. The study has shown the better relationship between antifungal activities with respect to various descriptors established by multiple regression analysis. The analysis has shown statistically significant correlation with R² values 0.932 and 0.782 against Candida albicans and Aspergillus niger respectively. These derivatives were further subjected to molecular docking studies to investigate the interactions between the target compounds and amino acid residues present in the active site of glucosamine-6-phosphate synthase. All the synthesized compounds have better docking score as compared to standard fluconazole. Our results could be used for the further design as well as development of optimal and potential antifungal agents.

Keywords: 1, 3, 4-Oxadiazole, QSAR, Multiple linear regression, Docking, Glucosamine-6-Phosphate Synthase.

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Authors: Isti Surjandari, Riara Novita

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Maintenance is one of the most important activities in the shipyard industry. However, sometimes it is not supported by adequate services from the shipyard, where inaccuracy in estimating the duration of the ship maintenance is still common. This makes estimation of ship maintenance duration is crucial. This study uses Data Mining approach, i.e., CART (Classification and Regression Tree) to estimate the duration of ship maintenance that is limited to dock works or which is known as dry docking. By using the volume of dock works as an input to estimate the maintenance duration, 4 classes of dry docking duration were obtained with different linear model and job criteria for each class. These linear models can then be used to estimate the duration of dry docking based on job criteria.

Keywords: Classification and regression tree (CART), data mining, dry docking, maintenance duration.

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Authors: L. K. Davis

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The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time based DNA codes, writing DNA code from scratch.

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Authors: Leonardo Herrera, Shield B. Lin, Stephen J. Montgomery-Smith, Ziraguen O. Williams

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A one-directional dynamic model of a Stewart Platform was developed to assist NASA in analyzing the dynamic response in spacecraft docking operations. A simplified mechanical drawing was created, capturing the physical structure's main features. A simplified schematic diagram was developed into a lumped mass model from the mechanical drawing. Three differential equations were derived according to the schematic diagram. A Simulink diagram was created using MATLAB to represent the three equations. System parameters, including spring constants and masses, are derived in detail from the physical system. The model can be used for further analysis via computer simulation in predicting dynamic response in its main docking direction, i.e., up-and-down motion.

Keywords: Stewart platform, docking operation, spacecraft, spring constant.

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

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3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) catalyzes the conversion of HMG-CoA to mevalonate using NADPH and the enzyme is involved in rate-controlling step of mevalonate. Inhibition of HMGR is considered as effective way to lower cholesterol levels so it is drug target to treat hypercholesterolemia, major risk factor of cardiovascular disease. To discover novel HMGR inhibitor, we performed structure-based pharmacophore modeling combined with molecular dynamics (MD) simulation. Four HMGR inhibitors were used for MD simulation and representative structure of each simulation were selected by clustering analysis. Four structure-based pharmacophore models were generated using the representative structure. The generated models were validated used in virtual screening to find novel scaffolds for inhibiting HMGR. The screened compounds were filtered by applying drug-like properties and used in molecular docking. Finally, four hit compounds were obtained and these complexes were refined using energy minimization. These compounds might be potential leads to design novel HMGR inhibitor.

Keywords: Anti-hypercholesterolemia drug, HMGR inhibitor, Molecular dynamics simulation, Structure-based pharmacophore modeling.

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Authors: Y. Fathi, B. Karimi, S. M. J. Mirzapour Al-e-Hashem

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Cross-docking includes receiving products supplied by a set of suppliers, unloading them from inbound trucks (ITs) at strip doors, consolidating and handling these products to stack doors based on their destinations, loading them into outbound trucks (OTs); then, delivering these products to customers. An effective assignment of the trucks to the doors would enhance the advantages of the cross-docking (e.g. reduction of the handling costs). This paper addresses the truck-to-door assignment problem in a cross-dock in which assignment of the ITs to the strip doors as well as assignment of the OTs to the stacks doors is determined so that total material handling cost in the cross-dock is minimized. Capacity constraints are applied for the ITs, OTs, strip doors, and stack doors. We develop a Quadratic Programming (QP) to formulate the problem. To solve it, the model is coded in LINGO software to specify the best assignment of the trucks to the doors.

Keywords: Cross-docking, truck-to-door assignment, supply chain, quadratic programming.

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Authors: Jayashree Ramana

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An alarming emergence of multidrug-resistant strains of the tuberculosis pathogen Mycobacterium tuberculosis and continuing high worldwide incidence of tuberculosis has invigorated the search for novel drug targets. The enzyme glutamate racemase (MurI) in bacteria catalyzes the stereoconversion of L-glutamate to D-glutamate which is a component of the peptidoglycan cell wall of the bacterium. The inhibitors targeted against MurI from several bacterial species have been patented and are advocated as promising antibacterial agents. However there are none available against MurI from Mycobacterium tuberculosis, due to the lack of its threedimensional structure. This work accomplished two major objectives. First, the tertiary structure of MtMurI was deduced computationally through homology modeling using the templates from bacterial homologues. It is speculated that like in other Gram-positive bacteria, MtMurI exists as a dimer and many of the protein interactions at the dimer interface are also conserved. Second, potent candidate inhibitors against MtMurI were identified through docking against already known inhibitors in other organisms.

Keywords: Glutamate racemase, homology modeling, docking, drug resistance.

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Authors: Wen-Shyong Tzou, Chih-Ching Huang, Chin-Hwa Hu, Ying-Tsang Lo, Tun-Wen Pai, Chia-Yin Chiang, Chung-Hao Li, Hong-Jyuan Jian

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Plasmin plays an important role in the human circulatory system owing to its catalytic ability of fibrinolysis. The immediate injection of plasmin in patients of strokes has intrigued many scientists to design vectors that can transport plasmin to the desired location in human body. Here we predict the structure of human plasmin and investigate the interaction of plasmin with the gold-nanoparticle. Because the crystal structure of plasminogen has been solved, we deleted N-terminal domain (Pan-apple domain) of plasminogen and generate a mimic of the active form of this enzyme (plasmin). We conducted a simulated annealing process on plasmin and discovered a very large conformation occurs. Kringle domains 1, 4 and 5 had been observed to leave its original location relative to the main body of the enzyme and the original doughnut shape of this enzyme has been transformed to a V-shaped by opening its two arms. This observation of conformational change is consistent with the experimental results of neutron scattering and centrifugation. We subsequently docked the plasmin on the simulated gold surface to predict their interaction. The V-shaped plasmin could utilize its Kringle domain and catalytic domain to contact the gold surface. Our findings not only reveal the flexibility of plasmin structure but also provide a guide for the design of a plasmin-gold nanoparticle.

Keywords: Docking, gold nanoparticle, molecular simulation, plasmin.

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Authors: Carlo Cernicchiaro, Pedro D. Gaspar, Martim L. Aguiar

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The agricultural sector is becoming more critical than ever in view of the expected overpopulation of the Earth. The introduction of robotic solutions in this field is an increasingly researched topic to make the most of the Earth's resources, thus going to avoid the problems of wear and tear of the human body due to the harsh agricultural work, and open the possibility of a constant careful processing 24 hours a day. This project is realized for a terrestrial autonomous robot aimed to navigate in an orchard collecting fallen peaches below the trees. When it receives the signal indicating the low battery, it has to return to the docking station where it will replace its battery and then return to the last work point and resume its routine. Considering a preset path in orchards with tree rows with variable length by which the robot goes iteratively using the algorithm D*. In case of low battery, the D* algorithm is still used to determine the fastest return path to the docking station as well as to come back from the docking station to the last work point. MATLAB simulations were performed to analyze the flexibility and adaptability of the developed algorithm. The simulation results show an enormous potential for adaptability, particularly in view of the irregularity of orchard field, since it is not flat and undergoes modifications over time from fallen branch as well as from other obstacles and constraints. The D* algorithm determines the best route in spite of the irregularity of the terrain. Moreover, in this work, it will be shown a possible solution to improve the initial points tracking and reduce time between movements.

Keywords: Path planning, fastest return path, agricultural terrestrial robot, autonomous, docking station.

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Authors: R. Chanajaree, D. Luanwiset, K. Pongpratea

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Dye removal is an environmental concern because the textile industries have been increasing by world population and industrialization. Adsorption is the technique to find adsorbents to remove dyes from wastewater. This method is low-cost and effective for dye removal. This work tries to develop effective adsorbents using the computational approach because it will be able to predict the possibility of the adsorbents for specific dyes in terms of binding free energies. The computational approach is faster and cheaper than the experimental approach in case of finding the best adsorbents. All starting structures of dyes and adsorbents are optimized by quantum calculation. The complexes between dyes and adsorbents are generated by the docking method. The obtained binding free energies from docking are compared to binding free energies from the experimental data. The calculated energies can be ranked as same as the experimental results. In addition, this work also shows the possible orientation of the complexes. This work used two experimental groups of the complexes of the dyes and adsorbents. In the first group, there are chitosan (adsorbent) and two dyes (reactive red (RR) and direct sun yellow (DY)). In the second group, there are poly(1,2-epoxy-3-phenoxy) propane (PEPP), which is the adsorbent, and 2 dyes of bromocresol green (BCG) and alizarin yellow (AY).

Keywords: Dye removal, binding free energies, quantum calculation, docking.

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Authors: S. Al-Asheh, K. Al-Emadi

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In recent years, there have been attempts to store natural gas in adsorptive form. This is called adsorptive natural gas, or ANG. The problem with this technology is the low sorption capacity. The purpose is to achieve compressed natural gas (CNG) capacity of 230 V/V. Further research is required to achieve such target. Several research studies have been performed with this target; through either the modification or development of new sorbents or the optimization of the operation sorption process itself. In this work, storage of methane on molecular sieves 5A and 13X was studied on dry basis, and on wet basis to certain extent. The temperature and the pressure dynamics were investigated. The results indicated that regardless of the charge pressure, the time for the peak temperature during the methane charge process is always the same. This can be used as a characteristic of the adsorbent. The total achieved deliveries using molecular sieves were much lower than that of activated carbons; 53.0 V/V for the case of 13X molecular sieves and 43 V/V for the case of 5A molecular sieves, both at 2oC and 4 MPa (580 psi). Investigation of charge pressure dynamic using wet molecular sieves at 2oC and a mass ratio of 0.5, revealed slowness of the process and unexpected behavior.

Keywords: Methane, Molecular sieves, Adsorption, Delivery, Storage.

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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: Homa Torabizadeh

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This study proposes a basic molecular formula for all proteins. A total of 10,739 proteins belonging to 9 different protein groups classified on the basis of their functions were selected randomly. They included enzymes, storage proteins, hormones, signalling proteins, structural proteins, transport proteins, immunoglobulins or antibodies, motor proteins and receptor proteins. After obtaining the protein molecular formula using the ProtParam tool, the H/C, N/C, O/C, and S/C ratios were determined for each randomly selected sample. In this case, H, N, O, and S coefficients were specified per carbon atom. Surprisingly, the results demonstrated that H, N, O, and S coefficients for all 10,739 proteins are similar and highly correlated. This study demonstrates that despite differences in the structure and function, all known proteins have a similar basic molecular formula CnH1.58 ± 0.015nN0.28 ± 0.005nO0.30 ± 0.007nS0.01 ± 0.002n. The total correlation between all coefficients was found to be 0.9999.

Keywords: Protein molecular formula, Basic unit formula, Protparam tool.

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Authors: Vicente F. P. Aleixo, Augusto C. F. Saraiva, Jordan Del Nero

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The production of devices in nanoscale with specific molecular rectifying function is one of the most significant goals in state-of-art technology. In this work we show by ab initio quantum mechanics calculations coupled with non-equilibrium Green function, the design of an organic two-terminal device. These molecular structures have molecular source and drain with several bridge length (from five up to 11 double bonds). Our results are consistent with significant features as a molecular rectifier and can be raised up as: (a) it can be used as bi-directional symmetrical rectifier; (b) two devices integrated in one (FET with one operational region, and Thyristor thiristor); (c) Inherent stability due small intrinsic capacitance under forward/reverse bias. We utilize a scheme for the transport mechanism based on previous properties of ¤Ç bonds type that can be successfully utilized to construct organic nanodevices.

Keywords: ab initio, Carotenoid, Charge Transfer, Nanodevice

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Authors: Salem El-tohami Ashoor

Abstract:

Here, we have shown the reaction of [Cr(ArN(CH2)3NAr)2Cl2] (1) where (Ar = 2,6-Pri 2C6H3) and in presence of NaCp (2) (Cp= C5H5 = cyclopentadien), with a center coordination η5 interaction between Cp as co-ligand and chromium metal center, for optimization we used density functional theory (DFT), under methods, explicitly including electrons correlations, for the final calculations as MB3LYP (Becke) (Lee–Yang–Parr) level of theory we used to obtain more exact results. This complex was calculated as electronic energy for molecular system, because the calculation accounting all electrons correlations interactions. The optimised of [Cr(ArN(CH2)3NAr)2(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp = C5H5) was found to be thermally stable. 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: Virupakshaiah DBM, Madiha Ahmed, Smita T. Patil, Chandrakanth Kelmani

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Tuberculosis (TB) is a bacterial infectious disease caused by the obligate human pathogen, Mycobacterium tuberculosis. Multidrug-resistant tuberculosis (MDR-TB) is a global reality that threatens tuberculosis control. Resistance to antibiotic Rifampicin, occurs in 95% of cases through nucleotide substitutions in an 81-bp core region of the rpoB i.e; beta subunit of DNA dependant RNA polymerase. In this paper, we studied the Rifampicin-rpoB receptor interactions In silico. First, homology modeling was performed to obtain the three dimensional structure of Mycobacterium rpoB. Sixty analogs of Rifampicin were prepared using Marvin sketch software. Both original Rifampicin and the analogs were docked with rpoB and energy values were obtained. Out of sixty analogs, 43 analogs had lesser energy values than conventional Rifampicin and hence are predicted to have greater binding affinity to rpoB. Thus, this study offers a route for the development of Rifampicin analogs against multi drug resistant Mycobacterium rpoB.

Keywords: Marvin Sketch, Mycobacterium tuberculosis, Rifampicin, rpoB.

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Authors: M. R. Naghavi, M. Maleki, S. F. Tabatabaei

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In order to study floristic and molecular classification of common wild wheat (Triticum boeoticum Boiss.), an analysis was conducted on populations of the Triticum boeoticum collected from different regions of Iran. Considering all floristic compositions of habitats, six floristic groups (syntaxa) within the populations were identified. A high level of variation of T. boeoticum also detected using SSR markers. Our results showed that molecular method confirmed the grouping of floristic method. In other word, the results from our study indicate that floristic classification are still useful, efficient, and economic tools for characterizing the amount and distribution of genetic variation in natural populations of T. boeoticum. Nevertheless, molecular markers appear as useful and complementary techniques for identification and for evaluation of genetic diversity in studied populations.

Keywords: T. boeoticum, diversity, floristic, SSRs.

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

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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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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: Zhao Jing, Bai Yongqing, Shi Qiaofang, Zang Yang, Zhang Huaihao

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Advances in software technology enable the 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, amides, molecular modeling, spectroscopy.

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Authors: A. Ito, S. Okamoto

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We constructed an atomic structure model for a PAN-based carbon fiber containing amorphous structures using molecular dynamics methods. It was found that basic physical properties such as crystallinity, Young’s modulus, and thermal conductivity of our model were nearly identical to those of real carbon fibers. We then obtained the tensile strength of a carbon fiber, which has no macro defects. We finally determined that the limitation of the tensile strength was 19 GPa.

Keywords: Amorphous, carbon fiber, molecular dynamics, tensile strength.

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

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

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

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Authors: Leonor Varandas, Pedro D. Gaspar, Martim L. Aguiar

Abstract:

One of the biggest concerns in the field of agriculture is around the energy efficiency of robots that will perform agriculture’s activity and their charging methods. In this paper, two different charging methods for agricultural standalone docking stations are shown that will take into account various variants as field size and its irregularities, work’s nature to which the robot will perform, deadlines that have to be respected, among others. Its features also are dependent on the orchard, season, battery type and its technical specifications and cost. First charging base method focuses on wireless charging, presenting more benefits for small field. The second charging base method relies on battery replacement being more suitable for large fields, thus avoiding the robot stop for recharge. Existing many methods to charge a battery, the CC CV was considered the most appropriate for either simplicity or effectiveness. The choice of the battery for agricultural purposes is if most importance. While the most common battery used is Li-ion battery, this study also discusses the use of graphene-based new type of batteries with 45% over capacity to the Li-ion one. A Battery Management Systems (BMS) is applied for battery balancing. All these approaches combined showed to be a promising method to improve a lot of technical agricultural work, not just in terms of plantation and harvesting but also about every technique to prevent harmful events like plagues and weeds or even to reduce crop time and cost.

Keywords: Agricultural mobile robot, charging base methods, battery replacement method, wireless charging method.

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Authors: Musammat F. Nahar, Anna Roujeinikova

Abstract:

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

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

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Authors: Salem El-tohami Ashoor

Abstract:

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

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

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

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