Search results for: molecular motion

Authors: Somayeh Akrami, Vali-Allah Mozaffarian, Habib Onsori

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The studied region in this research, watershed Kuhkamar river, is about 112.66 square kilometers, it is located between 45º 48' 9" to 45º 2' 20" N and 38º 34' 15" to 38º 40' 28" E. The gained results of the studies on flora combinations, proved 287 plant species in 190 genera and 51 families. Asteracea with 49 and Lamiaceae with 27 plant species are the major plant families. Among collected species one interesting plant was found and determined as a new record Anemone narcissiflora L. for flora of Iran. This plant is known as a complex species that shows intraspecific speciation and is classified into about 12 subspecies and 10 varieties in world. To identify the infraspecies taxons of this species, in addition to morphological characteristics, the use of appropriate molecular markers for the better isolation of the individuals were needed.

Keywords: Anemone narcissiflora, floristic Study, kuhkamar, molecular marker

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Authors: Soheil Arash Moghadam, Abdol R. Kashani Nia, Ali Akrami Zade

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Considering numerous applications of Autonomous Underwater Vehicles in various industries, there has been plenty of researches and studies on the motion control of such vehicles. One of the useful aspects for studying is the guidance of these vehicles. In this paper, while presenting motion equations with six degrees of freedom for Autonomous Underwater Vehicles, Proportional Navigation Guidance Law and the first order sliding mode control for TAIPAN AUV was used to address its guidance for the purpose of collision with a moving target.

Keywords: Autonomous Underwater Vehicle (AUV), degree of freedom (DOF), hydrodynamic, line of sight(LOS), proportional navigation guidance(PNG), sliding mode control(SMC)

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Authors: Son Nguyen, Thanh Van, Ly Le

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Ca2+ - dependent calmodulin kinase IIa (CaMKIIa) has recently been found to associate with protein tau missorting and polymerization in Alzheimer’s Disease (AD). However, there has yet inhibitors targeting CaMKIIa to investigate the correlation between CaMKIIa activity and protein tau polymer formation. Combining virtual screening and our statistics in binding contribution scoring function (BCSF), we rationally identified potential compounds that bind to specific CaMKIIa active site and specificity-affinity distribution of the ligand within the active site. Using molecular dynamics simulation, we identified structural stability of CaMKIIa and potent inhibitors, and site-directed bonding, separating non-specific and specific molecular interaction features. Despite of variation in confirmation of simulation time, interactions of the potent inhibitors were found to be strongly associated with the unique chemical features extracted from molecular binding poses. In addition, competitive inhibitors within CaMKIIa showed an important molecular recognition pattern toward specific ligand features. Our approach combining virtual screening with BCSF may provide an universally applicable method for precise identification in the discovery of compounds.

Keywords: Alzheimer’s disease, Ca 2+ -dependent calmodulin kinase IIa, protein tau, molecular docking

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Authors: Fathi Soliman

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With the ultimate goal of developing the separation of n-paraffin as phase change material (PCM) by means of molecular dynamic simulations, we attempt to predict the solubility of aromatic n-paraffin in two organic solvents: Butyl Acetate (BA) and Methyl Iso Butyl Ketone (MIBK). A simple model of aromatic paraffin: 2-hexadecylantharacene with amorphous molecular structure and periodic boundary conditions was constructed. The results showed that MIBK is the best solvent to separate ultra-pure phase change materials and this data was compatible with experimental data done to separate ultra-pure n-paraffin from waste petroleum aromatic paraffin wax, the separated n-paraffin was characterized by XRD, TGA, GC and DSC, moreover; data revealed that the n-paraffin separated by using MIBK is better as PCM than that separated using BA.

Keywords: molecular dynamics simulation, n-paraffin, organic solvents, phase change materials, solvent extraction

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Authors: Edgar Teixeira, Eurico Carrapatoso

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As 3D displays become increasingly affordable, while production techniques and computational resources to create stereoscopic content being ever more accessible, a new dimension is literally introduced along with new expressive and immersive potentialities in support of designing for the screen. Prospective design visionaries have already at the reach of their hands an innovative and powerful visualization technology, which enables them to actively envision future trends and vanguardist directions. This paper explores the aesthetic and informational potentialities of stereoscopic motion graphics, providing insight on the application of 3D displays in design practice, proposing strategies to investigate stereoscopic communication, discussing potential repercussions to extant theory and impacts on audience.

Keywords: design, visual communication, technology, stereoscopy, 3D media

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Authors: Muchun Yu, Xue Gao, Qian Chen

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As a novel passive vibration isolation technology, molecular spring isolator (MSI) is investigated in this paper. An MSI consists of water and hydrophobic zeolites as working medium. Under periodic excitation, water molecules intrude into hydrophobic pores of zeolites when the pressure rises and water molecules extrude from hydrophobic pores when pressure drops. At the same time, energy is stored, released and dissipated. An MSI of piston-cylinder structure was designed in this work. Experiments were conducted to investigate the stiffness properties of MSI. The results show that MSI exhibits high-static-low dynamic (HSLD) stiffness. Furthermore, factors such as the quantity of zeolites, temperature, and ions in water are proved to have an influence on the stiffness properties of MSI.

Keywords: hydrophobic zeolites, molecular spring, stiffness, vibration isolation

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Authors: Milica Karadžić, Lidija Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Anamarija Mandić, Aleksandar Oklješa, Andrea Nikolić, Marija Sakač, Katarina Penov Gaši

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Using chemometric approach, the relationships between the chromatographic lipophilicity and in silico molecular descriptors for twenty-nine selected steroid derivatives were studied. The chromatographic lipophilicity was predicted using artificial neural networks (ANNs) method. The most important in silico molecular descriptors were selected applying stepwise selection (SS) paired with partial least squares (PLS) method. Molecular descriptors with satisfactory variable importance in projection (VIP) values were selected for ANN modeling. The usefulness of generated models was confirmed by detailed statistical validation. High agreement between experimental and predicted values indicated that obtained models have good quality and high predictive ability. Global sensitivity analysis (GSA) confirmed the importance of each molecular descriptor used as an input variable. High-quality networks indicate a strong non-linear relationship between chromatographic lipophilicity and used in silico molecular descriptors. Applying selected molecular descriptors and generated ANNs the good prediction of chromatographic lipophilicity of the studied steroid derivatives can be obtained. This article is based upon work from COST Actions (CM1306 and CA15222), supported by COST (European Cooperation and Science and Technology).

Keywords: artificial neural networks, chemometrics, global sensitivity analysis, liquid chromatography, steroids

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Authors: Qiang Zhang, Chun Yuan

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Since the PU (Prediction Unit) decision process is the most time consuming part of the emerging HEVC (High Efficient Video Coding) standardin intra and inter frame coding, this paper proposes the fast PU decision algorithm and speed up the algorithm using CUDA (Compute Unified Device Architecture). In intra frame coding, the fast PU decision algorithm uses the texture features to skip intra-frame prediction or terminal the intra-frame prediction for smaller PU size. In inter frame coding of HEVC, the fast PU decision algorithm takes use of the similarity of its own two Nx2N size PU's motion vectors and the hierarchical structure of CU (Coding Unit) partition to skip some modes of PU partition, so as to reduce the motion estimation times. The accelerate algorithm using CUDA is based on the fast PU decision algorithm which uses the GPU to make the motion search and the gradient computation could be parallel computed. The proposed algorithm achieves up to 57% time saving compared to the HM 10.0 with little rate-distortion losses (0.043dB drop and 1.82% bitrate increase on average).

Keywords: HEVC, PU decision, inter prediction, intra prediction, CUDA, parallel

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Authors: Mahmoud A. Abdulhamid

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Poly(ether-ether-ketone) (PEEK) has received increased attention due to its outstanding performance in different membrane applications including gas and liquid separation. However, it suffers from a semi-crystalline morphology, bad solubility and low porosity. To fabricate membranes from PEEK, the usage of harsh acid such as sulfuric acid is essential, regardless its hazardous properties. In this work, we report the molecular design of poly(ether-ether-ketones) (iPEEKs) with intrinsic porosity character, by incorporating kinked units into PEEK backbone such as spirobisindane, Tröger's base, and triptycene. The porous polymers were used to fabricate stable membranes for organic solvent nanofiltration application. To better understand the mechanism, we conducted molecular dynamics simulations to evaluate the possible interactions between the polymers and the solvents. Notable enhancement in separation performance was observed confirming the importance of molecular engineering of high-performance polymers. The iPEEKs demonstrated good solubility in polar aprotic solvents, a high surface area of 205–250 m² g⁻¹, and excellent thermal stability. Mechanically flexible nanofiltration membranes were prepared from N-methyl-2-pyrrolidone dope solution at iPEEK concentrations of 19–35 wt%. The molecular weight cutoff of the membranes was fine-tuned in the range of 450–845 g mol⁻¹ displaying 2–6 fold higher permeance (3.57–11.09 L m⁻² h⁻¹ bar⁻¹) than previous reports. The long-term stabilities were demonstrated by a 7 day continuous cross-flow filtration.

Keywords: molecular engineering, polymer synthesis, membrane fabrication, liquid separation

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Authors: Ross Calvert, Colin Whittaker, Alison Raby, Alistair G. L. Borthwick, Ton S. van den Bremer

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Large concentrations of plastic have polluted the seas in the last half century, with harmful effects on marine wildlife and potentially to human health. Plastic pollution will have lasting effects because it is expected to take hundreds or thousands of years for plastic to decay in the ocean. The question arises how waves transport plastic in the ocean. The predominant motion induced by waves creates ellipsoid orbits. However, these orbits do not close, resulting in a drift. This is defined as Stokes drift. If a particle is infinitesimally small and the same density as water, it will behave exactly as the water does, i.e., as a purely Lagrangian tracer. However, as the particle grows in size or changes density, it will behave differently. The particle will then have its own inertia, the fluid will exert drag on the particle, because there is relative velocity, and it will rise or sink depending on the density and whether it is on the free surface. Previously, plastic pollution has all been considered to be purely Lagrangian. However, the steepness of waves in the ocean is small, normally about α = k₀a = 0.1 (where k₀ is the wavenumber and a is the wave amplitude), this means that the mean drift flows are of the order of ten times smaller than the oscillatory velocities (Stokes drift is proportional to steepness squared, whilst the oscillatory velocities are proportional to the steepness). Thus, the particle motion must have the forces of the full motion, oscillatory and mean flow, as well as a dynamic buoyancy term to account for the free surface, to determine whether inertia is important. To track the motion of a floating inertial particle under wave action requires the fluid velocities, which form the forcing, and the full equations of motion of a particle to be solved. Starting with the equation of motion of a sphere in unsteady flow with viscous drag. Terms can added then be added to the equation of motion to better model floating plastic: a dynamic buoyancy to model a particle floating on the free surface, quadratic drag for larger particles and a slope sliding term. Using perturbation methods to order the equation of motion into sequentially solvable parts allows a parametric equation for the transport of inertial finite-sized floating particles to be derived. This parametric equation can then be validated using numerical simulations of the equation of motion and flume experiments. This paper presents a parametric equation for the transport of inertial floating finite-size particles by ocean waves. The equation shows an increase in Stokes drift for larger, less dense particles. The equation has been validated using numerical solutions of the equation of motion and laboratory flume experiments. The difference in the particle transport equation and a purely Lagrangian tracer is illustrated using worlds maps of the induced transport. This parametric transport equation would allow ocean-scale numerical models to include inertial effects of floating plastic when predicting or tracing the transport of pollutants.

Keywords: perturbation methods, plastic pollution transport, Stokes drift, wave flume experiments, wave-induced mean flow

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Authors: Qazi Umer Jamil, Abubakr Siddique, Mubeen Ur Rehman, Nida Aziz, Mohsin I. Tiwana

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This paper discusses a brain controlled robotic gait trainer for neurorehabilitation of Spinal Cord Injury (SCI) patients. Patients suffering from Spinal Cord Injuries (SCI) become unable to execute motion control of their lower proximities due to degeneration of spinal cord neurons. The presented approach can help SCI patients in neuro-rehabilitation training by directly translating patient motor imagery into walkers motion commands and thus bypassing spinal cord neurons completely. A non-invasive EEG based brain-computer interface is used for capturing patient neural activity. For signal processing and classification, an open source software (OpenVibe) is used. Classifiers categorize the patient motor imagery (MI) into a specific set of commands that are further translated into walker motion commands. The robotic walker also employs fall detection for ensuring safety of patient during gait training and can act as a support for SCI patients. The gait trainer is tested with subjects, and satisfactory results were achieved.

Keywords: brain computer interface (BCI), gait trainer, spinal cord injury (SCI), neurorehabilitation

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

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

Keywords: enhanced ideal gas molecular movement (EIGMM), ideal gas molecular movement (IGMM), model updating method, probability-based damage detection (PBDD), uncertainty quantification

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Authors: Christy Rosaline, Rathankar Roa, Waheeta Hopper

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Persistence of tuberculosis, emergence of multidrug-resistance and extensively drug-resistant forms of the disease, has increased the interest in developing new antitubercular drugs. Developing inhibitors for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtbDAH7Ps), an enzyme involved in shikimate pathway, gives a selective target for antitubercular agents. MtbDAH7Ps was screened against ZINC database, and shortlisted compounds were subjected to induce fit docking. Prime/Molecular Mechanics Generalized Born Surface Area calculation was used to validate the binding energy of ligand-protein complex. Molecular Dynamics analysis for of the lead compounds–MtbDAH7Ps complexes showed that the backbone of MtbDAH7Ps in their complexes were stable. These results suggest that the shortlisted lead compounds ZINC04097114, ZINC15163225, ZINC16857013, ZINC06275603, and ZINC05331260 could be developed into novel drug leads to inhibit DAH7Ps in Mycobacterium tuberculosis.

Keywords: MtbDAH7Ps, Mycobacterium tuberculosis, HTVS, molecular dynamics

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Authors: Radoslaw Pytlak, Damian Suski

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The aim of the paper is to provide a computational tool for planning a haemodialysis process. It is shown that optimization methods can be used to obtain the most effective treatment focused on removing both urea and phosphorus during the process. In order to achieve that, the IV–compartment model of phosphorus kinetics is applied. This kinetics model takes into account a rebound phenomenon that can occur during haemodialysis and results in a hybrid model of the process. Furthermore, vector fields associated with the model equations are such that it is very likely that using the most intuitive objective functions in the planning problem could lead to solutions which include sliding motions. Therefore, building computational tools for solving the problem of planning a haemodialysis process has required constructing numerical algorithms for solving optimal control problems with hybrid systems. The paper concentrates on minimum time control of hybrid systems since this control objective is the most suitable for the haemodialysis process considered in the paper. The presented approach to optimal control problems with hybrid systems is different from the others in several aspects. First of all, it is assumed that a hybrid system can exhibit sliding modes. Secondly, the system’s motion on the switching surface is described by index 2 differential–algebraic equations, and that guarantees accurate tracking of the sliding motion surface. Thirdly, the gradients of the problem’s functionals are evaluated with the help of adjoint equations. The adjoint equations presented in the paper take into account sliding motion and exhibit jump conditions at transition times. The optimality conditions in the form of the weak maximum principle for optimal control problems with hybrid systems exhibiting sliding modes and with piecewise constant controls are stated. The presented sensitivity analysis can be used to construct globally convergent algorithms for solving considered problems. The paper presents numerical results of solving the haemodialysis planning problem.

Keywords: haemodialysis planning process, hybrid systems, optimal control, sliding motion

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Authors: Micheale Yifter Weldemichael, Stefaan Werbrouck, Hailay Mehari Gebremedhn

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Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: molecular breeding, oil, sesame, shattering

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Authors: Nikhil Agrawal, Adam A. Skelton

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Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

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Authors: Sangbaek Park, Seungju Lee, Soo-Won Chae

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Unstable shoes are known to strengthen lower extremity muscles and improve gait ability and to change the user’s gait pattern. The change in gait pattern affects human body enormously because the walking is repetitive and steady locomotion in daily life. It is possible to estimate the joint motion including joint moment, force and inertia effect using kinematic and kinetic analysis. However, the change of internal stress at the articular cartilage has not been possible to estimate. The purpose of this research is to evaluate the internal stress of human body during gait with unstable shoes. In this study, FE analysis was combined with motion capture experiment to obtain the boundary condition and loading condition during walking. Motion capture experiments were performed with a participant during walking with normal shoes and with unstable shoes. Inverse kinematics and inverse kinetic analysis was performed with OpenSim. The joint angle and muscle forces were estimated as results of inverse kinematics and kinetics analysis. A detailed finite element (FE) lower extremity model was constructed. The joint coordinate system was added to the FE model and the joint coordinate system was coincided with OpenSim model’s coordinate system. Finally, the joint angles at each phase of gait were used to transform the FE model’s posture according to actual posture from motion capture. The FE model was transformed into the postures of three major phases (1st peak of ground reaction force, mid stance and 2nd peak of ground reaction force). The direction and magnitude of muscle force were estimated by OpenSim and were applied to the FE model’s attachment point of each muscle. Then FE analysis was performed to compare the stress at knee cartilage during gait with normal shoes and unstable shoes.

Keywords: finite element analysis, gait analysis, human model, motion capture

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Authors: Milica Ž. Karadžić, Lidija R. Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Z. Kovačević, Anamarija I. Mandić, Katarina Penov-Gaši, Andrea R. Nikolić, Aleksandar M. Oklješa

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This study considered selection of the in silico molecular descriptors and the models for newly synthesized steroid derivatives description and their characterization using chemometric techniques. Multiple linear regression (MLR) models were established and gave the best molecular descriptors for quantitative structure-retention relationship (QSRR) modeling of the retention of the investigated molecules. MLR models were without multicollinearity among the selected molecular descriptors according to the variance inflation factor (VIF) values. Used molecular descriptors were ranked using generalized pair correlation method (GPCM). In this method, the significant difference between independent variables can be noticed regardless almost equal correlation between dependent variable. Generated MLR models were statistically and cross-validated and the best models were kept. Models were ranked using sum of ranking differences (SRD) method. According to this method, the most consistent QSRR model can be found and similarity or dissimilarity between the models could be noticed. In this study, SRD was performed using average values of experimentally observed data as a golden standard. Chemometric analysis was conducted in order to characterize newly synthesized steroid derivatives for further investigation regarding their potential biological activity and further synthesis. This article is based upon work from COST Action (CM1105), supported by COST (European Cooperation in Science and Technology).

Keywords: generalized pair correlation method, molecular descriptors, regression analysis, steroids, sum of ranking differences

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Authors: O. Punjarat, S. Chucheepsakul, T. Phanyasahachart

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This paper focuses on a variational formulation of large amplitude free vibration behavior of a very sag marine cable. In the static equilibrium state, the marine cable has a very large sag configuration. In the motion state, the marine cable is assumed to vibrate in in-plane motion with large amplitude from the static equilibrium position. The total virtual work-energy of the marine cable at the dynamic state is formulated which involves the virtual strain energy due to axial deformation, the virtual work done by effective weight, and the inertia forces. The equations of motion for the large amplitude free vibration of marine cable are obtained by taking into account the difference between the Euler’s equation in the static state and the displaced state. Based on the Galerkin finite element procedure, the linear and nonlinear stiffness matrices, and mass matrices of the marine cable are obtained and the eigenvalue problem is solved. The natural frequency spectrum and the large amplitude free vibration behavior of marine cable are presented.

Keywords: axial deformation, free vibration, Galerkin finite element method, large amplitude, variational method

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Authors: Y. Johnson

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Study of multi-satellite formation flight systems has drawn wide attention recently due to so many potential advantages. The present work aims to model the relative motion dynamics in terms of change in classical orbital parameters between the two satellites-chief and deputy- under Earth’s oblateness effect. The required impulsive thrust control is calculated to minimize these orbital parameter changes. The formation configuration is initialized by selecting a set of orbital parameters for the chief and deputy satellites such that bounded motion is maintained for a long time in a J_2-invariant relative non-circular orbit between the satellites. The solution of J_2-modified Hill’s equations is also derived in this paper.

Keywords: satellite, formation flight, j2 effect, control

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Authors: Wei Liu, Shuquan Wang, Yang Gao

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Microgravity Science Experiment Rack (MSER) will be onboard TianHe (TH) spacecraft planned to be launched in 2018. TH is one module of Chinese Space Station. Microgravity Vibration Isolation System (MVIS), which is MSER’s core part, is used to isolate disturbance from TH and provide high-level microgravity for science experiment payload. MVIS is two stage vibration isolation system, consisting of Follow Unit (FU) and Experiment Support Unit (ESU). FU is linked to MSER by umbilical cables, and ESU suspends within FU and without physical connection. The FU’s position and attitude relative to TH is measured by binocular vision measuring system, and the acceleration and angular velocity is measured by accelerometers and gyroscopes. Air-jet thrusters are used to generate force and moment to control FU’s motion. Measurement module on ESU contains a set of Position-Sense-Detectors (PSD) sensing the ESU’s position and attitude relative to FU, accelerometers and gyroscopes sensing ESU’s acceleration and angular velocity. Electro-magnetic actuators are used to control ESU’s motion. Firstly, the linearized equations of FU’s motion relative to TH and ESU’s motion relative to FU are derived, laying the foundation for control system design and simulation analysis. Subsequently, two control schemes are proposed. One control scheme is that ESU tracks FU and FU tracks TH, shorten as E-F-T. The other one is that FU tracks ESU and ESU tracks TH, shorten as F-E-T. In addition, motion spaces are constrained within ±15 mm、±2° between FU and ESU, and within ±300 mm between FU and TH or between ESU and TH. A Proportional-Integrate-Differentiate (PID) controller is designed to control FU’s position and attitude. ESU’s controller includes an acceleration feedback loop and a relative position feedback loop. A Proportional-Integrate (PI) controller is designed in the acceleration feedback loop to reduce the ESU’s acceleration level, and a PID controller in the relative position feedback loop is used to avoid collision. Finally, simulations of E-F-T and F-E-T are performed considering variety uncertainties, disturbances and motion space constrains. The simulation results of E-T-H showed that control performance was from 0 to -20 dB for vibration frequency from 0.01 to 0.1 Hz, and vibration was attenuated 40 dB per ten octave above 0.1Hz. The simulation results of T-E-H showed that vibration was attenuated 20 dB per ten octave at the beginning of 0.01Hz.

Keywords: microgravity science experiment rack, microgravity vibration isolation system, PID control, vibration isolation performance

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Authors: Ambrish Singh

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The corrosion inhibition performance of pyran derivatives (AP) on mild steel in 15% HCl was investigated by electrochemical impedance spectroscopy (EIS), potentiodynamic polarization, weight loss, contact angle, and scanning electron microscopy (SEM) measurements, DFT and molecular dynamic simulation. The adsorption of APs on the surface of mild steel obeyed Langmuir isotherm. The potentiodynamic polarization study confirmed that inhibitors are mixed type with cathodic predominance. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface. The theoretical data obtained are, in most cases, in agreement with experimental results.

Keywords: acidizing inhibitor, pyran derivatives, DFT, molecular simulation, mild steel, EIS

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Authors: Danish Idrees, Vijay Kumar, Samudrala Gourinath

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Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1). The use of small molecules has been shown to stabilize the SOD1 dimer and preventing its dissociation and aggregation. In this study, we employed molecular docking, molecular dynamics simulation and surface plasmon resonance (SPR) to study the interactions between SOD1 and natural polyphenolic compounds. In order to explore the noncovalent interaction between SOD1 and natural polyphenolic compounds, molecular docking and molecular dynamic (MD) simulations were employed to gain insights into the binding modes and free energies of SOD1-polyphenolic compounds. MM/PBSA methods were used to calculate free energies from obtained MD trajectories. The compounds, Hesperidin, Ergosterol, and Rutin showed the excellent binding affinity in micromolar range with SOD1. Ergosterol and Hesperidin have the strongest binding affinity to SOD1 and was subjected to further characterization. Biophysical experiments using Circular Dichroism and Thioflavin T fluorescence spectroscopy results show that the binding of these two compounds can stabilize SOD1 dimer and inhibit the aggregation of SOD1. Molecular simulation results also suggest that these compounds reduce the dissociation of SOD1 dimers through direct interaction with the dimer interface. This study will be helpful to develop other drug-like molecules which may have the effect to reduce the aggregation of SOD1.

Keywords: amyotrophic lateral sclerosis, molecular dynamics simulation, surface plasmon resonance, superoxide dismutase

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Authors: Salma M. Wakil

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Advances in the field of genetics overwhelmed detecting large number of inherited disorders at the molecular level and directed to the development of innovative technologies. These innovations have led to gene sequencing, prenatal mutation detection, pre-implantation genetic diagnosis; population based carrier screening and genome wide analyses using microarrays. Microarrays are widely used in establishing clinical and diagnostic setup for genetic anomalies at a massive level, with the advent of cytoscan molecular karyotyping as a clinical utility card for detecting chromosomal aberrations with high coverage across the entire human genome. Unlike a regular karyotype that relies on the microscopic inspection of chromosomes, molecular karyotyping with cytoscan constructs virtual chromosomes based on the copy number analysis of DNA which improves its resolution by 100-fold. We have been investigating a large number of patients with Developmental Delay and Intellectual disability with this platform for establishing micro syndrome deletions and have detected number of novel CNV’s in the Arabian population with the clinical relevance.

Keywords: microarrays, molecular karyotyping, developmental delay, genetics

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Authors: Sajjad Seifoori

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

Keywords: impact, molecular dynamic, graphene, spring mass

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Authors: Teng lin, Li Yuxing, Han Hui, Zhao Pengfei, Zhang Datong

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With the development of carbon capture and storage (CCS), the flow assurance of CO2 transportation becomes more important, particularly for supercritical CO2 pipelines. The relieving system using the choke valve is applied to control the pressure in CO2 pipeline. However, the temperature of fluid would drop rapidly because of Joule-Thomson cooling (JTC), which may cause solid CO2 form and block the pipe. In this paper, a Computational Fluid Dynamic (CFD) model, using the modified Lagrangian method, Reynold's Stress Transport model (RSM) for turbulence and stochastic tracking model (STM) for particle trajectory, was developed to predict the deposition characteristic of solid carbon dioxide. The model predictions were in good agreement with the experiment data published in the literature. It can be observed that the particle distribution affected the deposition behavior. In the region of the sudden expansion, the smaller particles accumulated tightly on the wall were dominant for pipe blockage. On the contrary, the size of solid CO2 particles deposited near the outlet usually was bigger and the stacked structure was looser. According to the calculation results, the movement of the particles can be regarded as the main four types: turbulent motion close to the sudden expansion structure, balanced motion at sudden expansion-middle region, inertial motion near the outlet and the escape. Furthermore the particle deposits accumulated primarily in the sudden expansion region, reattachment region and outlet region because of the four type of motion. Also the Stokes number had an effect on the deposition ratio and it is recommended for Stokes number to avoid 3-8St.

Keywords: carbon capture and storage, carbon dioxide pipeline, gas-particle flow, deposition

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Authors: Tokuei Sako, Paul-Antoine Hervieux

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The energy-level structure of a pair of electron and positron confined in a quasi-one-dimensional nano-scale potential well has been investigated focusing on its trend in the small limit of confinement strength ω, namely, the Wigner molecular regime. An anisotropic Gaussian-type basis functions supplemented by high angular momentum functions as large as l = 19 has been used to obtain reliable full configuration interaction (FCI) wave functions. The resultant energy spectrum shows a band structure characterized by ω for the large ω regime whereas for the small ω regime it shows an energy-level pattern dominated by excitation into the in-phase motion of the two particles. The observed trend has been rationalized on the basis of the nodal patterns of the FCI wave functions.

Keywords: confined systems, positron, wave function, Wigner molecule, quantum dots

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Authors: Afsheen Aman, Shah Ali Ul Qader

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Dextransucrase [EC 2.4.1.5] is a glucosyltransferase that catalysis the biosynthesis of a natural biopolymer called dextran. It can catalyze the transfer of D-glucopyranosyl residues from sucrose to the main chain of dextran. This unique biopolymer has multiple applications in several industries and the key utilization of dextran lies on its molecular weight and the type of branching. Extracellular dextransucrase from Leuconostoc mesenteroides is most extensively studied and characterized. Limited data is available regarding cell-bound or intracellular dextransucrase and on the characterization of dextran produced by in-vitro reaction of intracellular dextransucrase. L. mesenteroides AA1 is reported to produce extracellular dextransucrase that catalyzes biosynthesis of a high molecular weight dextran with only α-(1→6) linkage. Current study deals with the characterization of an intracellular dextransucrase and in vitro biosynthesis of low molecular weight dextran from L. mesenteroides AA1. Intracellular dextransucrase was extracted from cytoplasm and purified to homogeneity for characterization. Kinetic constants, molecular weight and N-terminal sequence analysis of intracellular dextransucrase reveal unique variation with previously reported extracellular dextransucrase from the same strain. In vitro synthesized biopolymer was characterized using NMR spectroscopic techniques. Intracellular dextransucrase exhibited Vmax and Km values of 130.8 DSU ml-1 hr-1 and 221.3 mM, respectively. Optimum catalytic activity was detected at 35°C in 0.15 M citrate phosphate buffer (pH-5.5) in 05 minutes. Molecular mass of purified intracellular dextransucrase is approximately 220.0 kDa on SDS-PAGE. N-terminal sequence of the intracellular enzyme is: GLPGYFGVN that showed no homology with previously reported sequence for the extracellular dextransucrase. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions and this biopolymer can be hydrolyzed into different molecular weight fractions for various applications.

Keywords: characterization, dextran, dextransucrase, leuconostoc mesenteroides

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Authors: Alfonsina Buoniconto

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The aim of this study is to investigate the degree of cross-linguistic and intra-linguistic variation in the encoding of motion events (MEs) in English and Italian, these being typologically different languages both showing signs of disobedience to their respective types. As a matter of fact, the traditional typological classification of MEs encoding distributes languages into two macro-types, based on the preferred locus for the expression of Path, the main ME component (other components being Figure, Ground and Manner) characterized by conceptual and structural prominence. According to this model, Satellite-framed (SF) languages typically express Path information in verb-dependent items called satellites (e.g. preverbs and verb particles) with main verbs encoding Manner of motion; whereas Verb-framed languages (VF) tend to include Path information within the verbal locus, leaving Manner to adjuncts. Although this dichotomy is valid altogether, languages do not always behave according to their typical classification patterns. English, for example, is usually ascribed to the SF type due to the rich inventory of postverbal particles and phrasal verbs used to express spatial relations (i.e. the cat climbed down the tree); nevertheless, it is not uncommon to find constructions such as the fog descended slowly, which is typical of the VF type. Conversely, Italian is usually described as being VF (cf. Paolo uscì di corsa ‘Paolo went out running’), yet SF constructions like corse via in lacrime ‘She ran away in tears’ are also frequent. This paper will try to demonstrate that such a typological overlapping is due to the fact that the semantic units making up MEs are distributed within several loci of the sentence –not only verbs and satellites– thus determining a number of different constructions stemming from convergent factors. Indeed, the linguistic expression of motion events depends not only on the typological nature of languages in a traditional sense, but also on a series morphological, lexical, and syntactic resources, as well as on inferential, discursive, usage-related, and cultural factors that make semantic information more or less accessible, frequent, and easy to process. Hence, rather than describe English and Italian in dichotomic terms, this study focuses on the investigation of cross-linguistic and intra-linguistic variation in the use of all the strategies made available by each linguistic system to express motion. Evidence for these assumptions is provided by parallel corpora analysis. The sample texts are taken from two contemporary Italian novels and their respective English translations. The 400 motion occurrences selected (200 in English and 200 in Italian) were scanned according to the MODEG (an acronym for Motion Decoding Grid) methodology, which grants data comparability through the indexation and retrieval of combined morphosyntactic and semantic information at different levels of detail.

Keywords: construction typology, motion event encoding, parallel corpora, satellite-framed vs. verb-framed type

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

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

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

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