Search results for: molecular simulation

Authors: Asma Poursoroush

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Solid-supported lipid bilayers are often used as a simple model for studies of biological membranes. The presence of a solid substrate that interacts attractively with lipid head-groups is expected to affect the phase behavior of the supported bilayer. Molecular dynamics simulations of a coarse-grained model are thus performed to investigate the phase behavior of supported one-component lipid bilayer membranes. Our results show that the attraction of the lipid head groups to the substrate leads to a phase behavior that is different from that of a free standing lipid bilayer. In particular, we found that the phase behaviors of the two leaflets are decoupled in the presence of a substrate. The proximal leaflet undergoes a clear gel-to-fluid phase transition at a temperature lower than that of a free standing bilayer, and that decreases with increasing strength of the substrate-lipid attraction. The distal leaflet, however, undergoes a change from a homogeneous liquid phase at high temperatures to a heterogeneous state consisting of small liquid and gel domains, with the average size of the gel domains that increases with decreasing temperature. While the chain order parameter of the proximal leaflet clearly shows a gel-fluid phase transition, the chain order parameter of the distal leaflet does not exhibit a clear phase transition. The decoupling in the phase behavior of the two leaflets is due to a non-symmteric lipid distribution in the two leaflets resulting from the presence of the substrate.

Keywords: membrane, substrate, molecular dynamics, simulation

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Authors: Chaudhari S. G., Saxena, S.

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We systematically and quantitatively investigated the effect of glucose as a model of natural molecular crowding agent on the structure and thermodynamics of Watson-Crick base paired three duplexes (named as D1, D2 and D3) of different base compositions and lengths. Structural analyses demonstrated that duplexes (D1 and D2) folded into B-form with different cations in the absence and presence of glucose while duplex (D3) folded into mixed A and B-form. Moreover, we demonstrated that the duplex was more stable in the absence of glucose, and marginally destabilized in its presence because glucose act as a weak structure breaker on the tetrahedral network of water. In the absence of glucose, the values of ΔG°25 for duplex (D1) were -13.56, -13.76, -12.46, and -12.36 kcal/mol, for duplex (D2) were -13.64, -12.93, -12.86, and -12.30 kcal/mol, for duplex (D3) were -10.05, -11.76, -9.91, -9.70 kcal/mol in the presence of Na+, K+, Na+ + Mg++ and K+ + Mg++ respectively. At high concentration of glucose (1:10000), there was increase in ΔG°25 for duplex (D1) -12.47, -12.37, -11.96, -11.55 kcal/mol, for duplex (D2) -12.37, -11.47, -11.98, -11.01 kcal/mol and for duplex (D3) -8.47, -9.17, -9.16, -8.66 kcal/mol. Our results provide the information that structure and stability of DNA duplex depends on the structure of molecular crowding agent present in its close vicinity. In this study, I have taken the hydration of simple sugar as an essential model for understanding interactions between hydrophilic groups and interfacial water molecules and its effect on hydrogen bonded DNA duplexes. On the basis of these relatively simple building blocks I hope to gain some insights for understanding more generally the properties of sugar–water–salt systems with DNA duplexes.

Keywords: natural molecular crowding, DNA Duplex, structure of DNA, bioengineering and life sciences

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Authors: Shuo Tian, Xuepiao Bai, Jianqin Shang, Pengtao Gai, Yuansong Zeng

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Shot peen forming is an essential forming process for aircraft metal wing panel. With the development of computer simulation technology, scholars have proposed a numerical simulation method of shot peen forming based on stress field. Three shot peen forming indexes of crater diameter, shot speed and surface coverage are required as simulation parameters in the stress field method. It is necessary to establish the relationship between simulation and experimental process parameters in order to simulate the deformation under different shot peen forming parameters. The shot peen forming tests of the 2024-T351 aluminum alloy workpieces were carried out using uniform test design method, and three factors of air pressure, feed rate and shot flow were selected. The second-order response surface model between simulation parameters and uniform test factors was established by stepwise regression method using MATLAB software according to the results. The response surface model was combined with the stress field method to simulate the shot peen forming deformation of the workpiece. Compared with the experimental results, the simulated values were smaller than the corresponding test values, the maximum and average errors were 14.8% and 9%, respectively.

Keywords: shot peen forming, process parameter, response surface model, numerical simulation

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Authors: E. Al Daoud

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In many cases, theoretical treatments are available for models for which there is no perfect physical realization. In this situation, the only possible test for an approximate theoretical solution is to compare with data generated from a computer simulation. In this paper, Monte Carlo tools are used to study and compare the elementary particles models. All the experiments are implemented using 10000 events, and the simulated energy is 13 TeV. The mean and the curves of several variables are calculated for each model using MadAnalysis 5. Anomalies in the results can be seen in the muons masses of the minimal supersymmetric standard model and the two Higgs doublet model.

Keywords: Feynman rules, hadrons, Lagrangian, Monte Carlo, simulation

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Authors: Ilya Kavalchuk, Hayrettin Arisoy, Alex Stojcevski, Aman Maun Than Oo

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Electric vehicles are one of the most complicated electric devices to simulate due to the significant number of different processes involved in electrical structure of it. There are concurrent processes of energy consumption and generation with different onboard systems, which make simulation tasks more complicated to perform. More accurate simulation on energy consumption can provide a better understanding of all energy management for electric transport. As a result of all those processes, electric transport can allow for a more sustainable future and become more convenient in relation to the distance range and recharging time. This paper discusses the problems of energy consumption simulations for electric vehicles using different software packages to provide ideas on how to make this process more precise, which can help engineers create better energy management strategies for electric vehicles.

Keywords: electric vehicles, EV, power consumption, power management, simulation

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Authors: S. Kohestani, R. Amrollahi, P. Daryabor

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Microwave diagnostics such as reflectometry are receiving growing attention in magnetic confinement fusionresearch. In order to obtain the better understanding of plasma confinement physics, more detailed measurements on density profile and its fluctuations might be required. A 2D full-wave simulation of ordinary mode propagation has been written in an effort to model effects seen in reflectometry experiment. The code uses the finite-difference-time-domain method with a perfectly-matched-layer absorption boundary to solve Maxwell’s equations.The code has been used to simulate the reflectometer measurement in Alborz Tokamak.

Keywords: reflectometry, simulation, ordinary mode, tokamak

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Authors: Mehvish Bilal, Navneet Singh, Jasir Mushtaq

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Water pollution puts people's health at risk, and it can also impact the ecology. For practitioners of integrated water resources management (IWRM), water quality modelling may be useful for informing decisions about pollution control (such as discharge permitting) or demand management (such as abstraction permitting). To comprehend the current pollutant load, movement of effective load movement of contaminants generates effective relation between pollutants, mathematical simulation, source, and water quality is regarded as one of the best estimating tools. The current study involves the Qual2k model, which includes manual simulation of the various physiochemical characteristics of water. To this end, various sensors could be installed for the automatic simulation of various physiochemical characteristics of water. An artificial intelligence model has been proposed for the automatic simulation of water quality parameters. Models of water quality have become an effective tool for identifying worldwide water contamination, as well as the ultimate fate and behavior of contaminants in the water environment. Water quality model research is primarily conducted in Europe and other industrialized countries in the first world, where theoretical underpinnings and practical research are prioritized.

Keywords: artificial intelligence, QUAL2K, simulation, physiochemical parameters

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Authors: Robert Ogbanje Okwori

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The research studied expository and simulation method of teaching woodwork at Federal University of Technology, Minna, Niger State, Nigeria. The purpose of the study was to compare expository and simulation method of teaching woodwork and determine the method that is more effective in improving performance of students in woodwork. Two research questions and two hypotheses were formulated to guide the study. Fifteen objective questions and two theory questions were used for data collection. The questions set were on structure of timber. The study used the quasi experimental design. The population of the study consisted of 25 woodwork students of Federal University of Technology, Minna, Niger State, Nigeria and three hundred (300) level students were used for the study. The lesson plans for expository method and questions were validated by three lecturers in the Department of Industrial and Technology Education, Federal University of Technology, Minna, Nigeria. The validators checked the appropriates of test items and all the corrections and inputs were effected before administration of the instrument. Data obtained were analyzed using mean, standard deviation and t-test statistical tool. The null hypotheses were formulated and tested using t-test statistics at 0.05 level of significance. The findings of the study showed that simulation method of teaching has improved students’ performance in woodwork and the performance of the students was not influenced by gender. Based on the findings of the study, it was concluded that there was a significant difference in the mean achievement scores of students taught woodwork using simulation method. This implies that simulation method is more effective than expository method of teaching woodwork. Therefore, woodwork teachers should adopt simulation method of teaching woodwork towards better performance. It was recommended that simulation method should be used by woodwork lecturers to teach woodwork since students perform better using the method and also the teachers needs to be trained and re-trained in using simulation method for teaching woodwork. Teachers should be encouraged to use simulation method for their instructional delivery because it will allow them to identify their areas of strength and weakness when imparting knowledge to woodwork students. Government and different agencies should assist in procuring materials and equipment for wood workshops to enable students effectively practice what they have been taught using simulation method.

Keywords: comparative, expository, simulation, woodwork

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Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

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Terahertz time-domain spectroscopy (THz-TDS) was used to observe the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different average molecular weights (10,000 g/mol, 40,000 g/mol, 360,000 g/mol). Distinct footprints of phase transition in the THz region (0.4 - 2.2 THz) were analyzed and absorption coefficients and complex refractive indices are obtained and compared in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz, polyvinylpyrrolidone (PVP), THz-TDS, inhibitor

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Authors: Jing Zhao, Yoshiharu Ishikawa, Chuan Xiao, Kento Sugiura

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In order to analyze large-scale scientific data, research on data exploration and visualization has gained popularity. In this paper, we focus on the exploration and visualization of scientific simulation data, and define a spatial V-Optimal histogram for data summarization. We propose histogram construction algorithms based on a general binary hierarchical partitioning as well as a more specific one, the l-grid partitioning. For effective data summarization and efficient data visualization in scientific data analysis, we propose an optimal algorithm as well as a heuristic algorithm for histogram construction. To verify the effectiveness and efficiency of the proposed methods, we conduct experiments on the massive evacuation simulation data.

Keywords: simulation data, data summarization, spatial histograms, exploration, visualization

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Authors: Mahdi Golriz

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The aim of this work is to estimate the change in molecular structure of linear low-density polyethylene (LLDPE) during peroxide modification can be detected by a simple rheological method. For this purpose a commercial grade LLDPE (Exxon MobileTM LL4004EL) was reacted with different doses of dicumyl peroxide (DCP). The samples were analyzed by size-exclusion chromatography coupled with a light scattering detector. The dynamic shear oscillatory measurements showed a deviation of the δ-׀G ׀٭curve from that of the linear LLDPE, which can be attributed to the presence of long-chain branching (LCB). By the use of a simple rheological method that utilizes melt rheology, transformations in molecular architecture induced on an originally linear low density polyethylene during the early stages of reactive modification were indicated. Reasonable and consistent estimates are obtained, concerning the degree of LCB, the volume fraction of the various molecular species produced in peroxide modification of LLDPE.

Keywords: linear low-density polyethylene, peroxide modification, long-chain branching, rheological method

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Authors: A. Hossein Madadi-Najafabadi, Masoud Nasiri

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The discrete element method is a powerful technique for numerical modeling the flow of granular materials such as direct reduced iron. It would enable us to study processes and equipment related to the production and handling of the material. However, the characteristics and properties of the granules have to be adjusted precisely to achieve reliable results in a DEM simulation. The main properties for DEM simulation are size distribution, density, Young's modulus, Poisson's ratio and the contact coefficients of restitution, rolling friction and sliding friction. In the present paper, the mentioned properties are determined for DEM simulation of DRI pellets. A reliable DEM simulation would contribute to optimizing the handling system of DRIs in an iron-making plant. Among the mentioned properties, Young's modulus is the most important parameter, which is usually hard to get for particulate solids. Here, an especial method is utilized to precisely determine this parameter for DRI.

Keywords: discrete element method, direct reduced iron, simulation parameters, granular material

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Authors: Marianna Maiaru, Gregory M. Odegard, Josh Kemppainen, Ivan Gallegos, Michael Olaya

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Ceramic matrix composites (CMCs) are typically used in applications that require long-term mechanical integrity at elevated temperatures. CMCs are usually fabricated using a polymer precursor that is initially polymerized in situ with fiber reinforcement, followed by a series of cycles of pyrolysis to transform the polymer matrix into a rigid glass or ceramic. The pyrolysis step typically generates volatile gasses, which creates porosity within the polymer matrix phase of the composite. Subsequent cycles of monomer infusion, polymerization, and pyrolysis are often used to reduce the porosity and thus increase the durability of the composite. Because of the significant expense of such iterative processing cycles, new generations of CMCs with improved durability and manufacturability are difficult and expensive to develop using standard Edisonian approaches. The goal of this research is to develop a computational process-modeling-based approach that can be used to design the next generation of CMC materials with optimized material and processing parameters for maximum strength and efficient manufacturing. The process modeling incorporates computational modeling tools, including molecular dynamics (MD), to simulate the material at multiple length scales. Results from MD simulation are used to inform the continuum-level models to link molecular-level characteristics (material structure, temperature) to bulk-level performance (strength, residual stresses). Processing parameters are optimized such that process-induced residual stresses are minimized and laminate strength is maximized. The multiscale process modeling method developed with this research can play a key role in the development of future CMCs for high-temperature and high-strength applications. By combining multiscale computational tools and process modeling, new manufacturing parameters can be established for optimal fabrication and performance of CMCs for a wide range of applications.

Keywords: digital engineering, finite elements, manufacturing, molecular dynamics

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Authors: N. V. Kuznetsov, O. A. Kuznetsova, G. A. Leonov, M. V. Yuldashev, R. V. Yuldashev

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Nonlinear analysis of the phase locked loop (PLL)-based circuits is a challenging task. Thus, the simulation is widely used for their study. In this work, we consider a mathematical model of the optical Costas loop and demonstrate the limitations of simulation approach related to the existence of so-called hidden oscillations in the phase space of the model.

Keywords: optical Costas loop, mathematical model, simulation, hidden oscillation

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Authors: Soraya Abtouche, Zeyneb Ghoualem, Syrine Daoudi, Lina Ouldmohamed, Xavier Assfeld

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This work reports density functional theory calculations of the optimized geometries, molecular reactivity, energy gap,and thermodynamic properties of the free base (H2P) and their Zn (II) metallated (ZnP), bearing one, two, or three carboxylic acid groups using the hybrid functional B3LYP, Cam-B3lYP, wb97xd with 6-31G(d,p) basis sets. When donating groups are attached to the molecular dye, the bond lengths are slightly decreased, which is important for the easy transfer of an electron from donating to the accepting group. For all dyes, the highest occupied molecular orbital/lowest occupied molecular orbital analysis results in positive outcomes upon electron injection to the semiconductor and subsequent dye regeneration by the electrolyte. The ionization potential increases with increasing conjugation; therefore, the compound dye attached to one carboxylic acid group has the highest ionization potential. The results show higher efficiencies of those sensitized with ZnP. These results have been explained, taking into account the electronic character of the metal ion, which acts as a mediator in the injection step, and, on the other hand, considering the number of anchoring groups to which it binds to the surface of TiO2.

Keywords: DSSC, porphyrin, TD-DFT, electronic properties, donor-acceptor groups

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Authors: Norbert Szulc, Jakub Wilk, Franciszek Górski

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This paper presents an approach for simulating and testing robotic systems based on PX4, using a local Kubernetes cluster. The approach leverages modern cloud-native tools and runs on single-board computers. Additionally, this solution enables the creation of datasets for computer vision and the evaluation of control system algorithms in an end-to-end manner. This paper compares this approach to method commonly used Docker based approach. This approach was used to develop simulation environment for an unmanned surface vehicle (USV) for RoboBoat 2023 by running a containerized configuration of the PX4 Open-source Autopilot connected to ROS and the Gazebo simulation environment.

Keywords: cloud computing, Kubernetes, single board computers, simulation, ROS

Procedia PDF Downloads 51

Authors: Suja Karkada, Jayanthi Radhakrishnan, Jansi Natarajan, Gerald, Amandu Matua, Sujatha Shanmugasundaram

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Simulation-based learning is an educational strategy designed to simulate actual clinical situations in a safe environment. Globally, simulation is recognized by several landmark studies as an effective teaching-learning method. A systematic review of the literature on simulation revealed simulation as a useful strategy in creating a learning environment which contributes to knowledge, skills, safety, and confidence. However, to the best of the author's knowledge, there are no studies on assessing the anxiety of the students undergoing simulation. Hence the researchers undertook a study with the aim to evaluate the effectiveness of simulation on anxiety and knowledge among novice nursing students. This quasi-experimental study had a total sample of 69 students (35- Intervention group with simulation and 34- Control group with case scenario) consisting of all the students enrolled in the Fundamentals of Nursing Laboratory course during Spring 2016 and Fall 2016 semesters at a college of nursing in Oman. Ethical clearance was obtained from the Institutional Review Board (IRB) of the college of nursing. Informed consent was obtained from every participant. Study received the Dean’s fund for research. The data were collected regarding the demographic information, knowledge and anxiety levels before and after the use of simulation and case scenario for the procedure nasogastric tube feeding in intervention and control group respectively. The intervention was performed by four faculties who were the core team members of the course. Results were analyzed in SPSS using descriptive and inferential statistics. Majority of the students’ in intervention (82.9%) and control (89.9%) groups were equal to or below the age of 20 years, were females (71%), 76.8% of them were from rural areas and 65.2% had a GPA of more than 2.5. The selection of the samples to either the experimental or the control group was from a homogenous population (p > 0.05). There was a significant reduction of anxiety among the students of control group (t (67) = 2.418, p = 0.018) comparing to the experimental group, indicating that simulation creates anxiety among Novice nursing students. However, there was no significant difference in the mean scores of knowledge. In conclusion, the study was useful in that it will help the investigators better understand the implications of using simulation in teaching skills to novice students. Since previous studies with students indicate better knowledge acquisition; this study revealed that simulation can increase anxiety among novice students possibly it is the first time they are introduced to this method of teaching.

Keywords: anxiety, knowledge, novice students, simulation

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Authors: Ahmed Al-Sultan

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The check-in area of airport terminal is one of the busiest sections at airports at certain periods. The passengers are subjected to queues and delays during the check-in process. These delays and queues are due to constraints in the capacity of service facilities. In this project, the airport terminal is decomposed into several check-in areas. The airport check-in scheduling problem requires both a deterministic (integer programming) and stochastic (simulation) approach. Integer programming formulations are provided to minimize the total number of counters in each check-in area under the realistic constraint that counters for one and the same flight should be adjacent and the desired number of counters remaining in each area should be fixed during check-in operations. By using simulation, the airport system can be modeled to study the effects of various parameters such as number of passengers on a flight and check-in counter opening and closing time.

Keywords: airport terminal, integer programming, scheduling, simulation

Procedia PDF Downloads 363

Authors: Abdulatif Abdulsalam Mohamed Shaban

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A.C motors, in general, have superior performance characteristics to their d.c. counterparts. However, despite these advantage a.c. motors lack the controllability and simplicity and so d.c. motors retain a competitive edge where precise control is required. As part of an overall project to develop an improved cycloconverter control strategy for induction motors. Simulation and modelling techniques have been developed. This contribution describes a method used to simulate an induction motor drive using the SIMULINK toolbox within MATLAB software. The cycloconverter fed induction motor is principally modelled using the d-q axis equations. Results of the simulation for a given set of induction motor parameters are also presented.

Keywords: simulation, converter, motor, cycloconverter

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Authors: T. A. Shahul Hameed, P. Predeep, Anju Iqbal, M. R. Baiju

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Research and development in organic photovoltaic cells and Organic Light Emitting Diodes have gained wider acceptance due to the advent of many advanced techniques to enhance the efficiency and operational hours. Here we report our work on design, simulation and characterizationracterize the bulk heterojunction organic photo cell and polymer light emitting diodes in different layer configurations using ATLAS, a licensed device simulation tool. Bulk heterojuction and multilayer devices were simulated for comparing their performance parameters.

Keywords: HOMO, LUMO, PLED, OPV

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Authors: Tzu-Hsuan Lei, Shu-Chien Wu, Kuang-Che Lo, Shu-Chi Liu, Yu-Cheng Liu

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The focus of this study was on the effects of air propagation associated with vented holes on acoustic resistance properties. A cylindrical hole with diameter and depth of 0.7 mm and 1.0 mm, respectively, was the research target. By constructing a finite element analytical model of its sound field properties, the acoustic-specific airflow resistance relationships were obtained for the differences in sound pressure and flow velocity at the two ends of this vented hole. In addition, the acoustic properties of this vented hole were included in the in-ear earphone simulation model to complete the sound pressure curve simulation analysis of the in-ear earphone system with a vented hole of corresponding size. Then, the simulation results were compared with actual measurements obtained from the standard system. Based on the results, when the in-ear earphone vented hole simulation model considered the simulated specific airflow resistance values of this cylindrical hole, the overall simulated sound pressure performance was highly consistent with that of measured values. The difference in the first peak values of sound pressure at mid-to-low frequencies was reduced from 5.64% when the simulation model did not consider the specific airflow resistance of the cylindrical hole to 1.18%, and the accuracy of the overall simulation was around 70%. This indicates the importance of the acoustic resistance properties of vented holes. Moreover, as specific airflow resistance values were able to be further quantified, the accuracy of the entire in-ear earphone simulation was ultimately and effectively elevated.

Keywords: specific airflow resistance, vented holes, in-ear earphone, finite element method

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Authors: Mohammad H. Almomani

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In this paper, we argue the effect of the initial sample size, and the increment in simulation samples on the performance of a sequential approach that used in selecting the top m designs when the number of alternative designs is very large. The sequential approach consists of two stages. In the first stage the ordinal optimization is used to select a subset that overlaps with the set of actual best k% designs with high probability. Then in the second stage the optimal computing budget is used to select the top m designs from the selected subset. We apply the selection approach on a generic example under some parameter settings, with a different choice of initial sample size and the increment in simulation samples, to explore the impacts on the performance of this approach. The results show that the choice of initial sample size and the increment in simulation samples does affect the performance of a selection approach.

Keywords: Large Scale Problems, Optimal Computing Budget Allocation, ordinal optimization, simulation optimization

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Authors: Wenjing Ding, Weiwei Shan, Zijuan, Wang, Chao He

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Liquid spray heat exchanger is the critical equipment of temperature regulating system by gaseous nitrogen which realizes the environment temperature in the range of -180 ℃~+180 ℃. Liquid nitrogen is atomized into smaller liquid drops through liquid nitrogen sprayer and then contacts with gaseous nitrogen to be cooled. By adjusting the pressure of liquid nitrogen and gaseous nitrogen, the flowrate of liquid nitrogen is changed to realize the required outlet temperature of heat exchanger. The temperature accuracy of shrouds is ±1 ℃. Liquid nitrogen spray heat exchanger is simulated by CATIA, and the numerical simulation is performed by FLUENT. The comparison between the tests and numerical simulation is conducted. Moreover, the results help to improve the design of liquid nitrogen spray heat exchanger.

Keywords: liquid nitrogen spray, temperature regulating system, heat exchanger, numerical simulation

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Authors: Arunima Verma, Padmabati Mondal

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Serotonin-receptor binding plays a key role in several neurological and biological processes, including mood, sleep, hunger, cognition, learning, and memory. In this article, we performed molecular dynamics simulation to examine the key residues that play an essential role in the binding of serotonin to the G-protein-coupled 5-HT₁ᴮ receptor (5-HT₁ᴮ R) via electrostatic interactions. An end-point free energy calculation method (MM-PBSA) determines the stability of the 5-HT1B R due to serotonin binding. The single-point mutation of the polar or charged amino acid residues (Asp129, Thr134) on the binding sites and the calculation of binding free energy validate the importance of these residues in the stability of the serotonin-receptor complex. Principal component analysis indicates the serotonin-bound 5-HT1BR is more stabilized than the apo-receptor in terms of dynamical changes. The difference dynamic cross-correlations map shows the correlation between the transmembrane and mini-Go, which indicates signal transduction happening between mini-Go and the receptor. Allosteric communication reveals the key nodes for signal transduction in 5-HT1BR. These results provide useful insights into the signal transduction pathways and mutagenesis study to regulate the functionality of the complex. The developed protocols can be applied to study local non-covalent interactions and long-range allosteric communications in any protein-ligand system for computer-aided drug design.

Keywords: allostery, CADD, MD simulations, MM-PBSA

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Authors: Amir Doustgani

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Melt electrospinning is a safe and simple technique for the production of micro and nanofibers which can be an alternative to conventional solvent electrospinning. The effects of various melt-electrospinning parameters, including molecular weight, electric field strength, flow rate and temperature on the morphology and fiber diameter of polylactic acid were studied. It was shown that molecular weight was the predominant factor in determining the obtainable fiber diameter of the collected fibers. An orthogonal design was used to examine process parameters. Results showed that molecular weight is the most effective parameter on the average fiber diameter of melt electrospun PLA nanofibers and the flow rate has the less important impact. Mean fiber diameter increased by increasing MW and flow rate, but decreased by increasing electric field strength and temperature. MFD of optimized fibers was below 100 nm and the result of software was in good agreement with the experimental condition.

Keywords: fiber formation, processing, spinning, melt blowing

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Authors: M. Ali Mandegari, S. Farzad, J. F. Görgens

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Sugar is one of the main agricultural industries in South Africa and approximately livelihoods of one million South Africans are indirectly dependent on sugar industry which is economically struggling with some problems and should re-invent in order to ensure a long-term sustainability. Second generation bio-refinery is defined as a process to use waste fibrous for the production of bio-fuel, chemicals animal food, and electricity. Bio-ethanol is by far the most widely used bio-fuel for transportation worldwide and many challenges in front of bio-ethanol production were solved. Bio-refinery annexed to the existing sugar mill for production of bio-ethanol and electricity is proposed to sugar industry and is addressed in this study. Since flow-sheet development is the key element of the bio-ethanol process, in this work, a bio-refinery (bio-ethanol and electricity production) annexed to a typical South African sugar mill considering 65ton/h dry sugarcane bagasse and tops/trash as feedstock was simulated. Aspen PlusTM V8.6 was applied as simulator and realistic simulation development approach was followed to reflect the practical behavior of the plant. Latest results of other researches considering pretreatment, hydrolysis, fermentation, enzyme production, bio-ethanol production and other supplementary units such as evaporation, water treatment, boiler, and steam/electricity generation units were adopted to establish a comprehensive bio-refinery simulation. Steam explosion with SO2 was selected for pretreatment due to minimum inhibitor production and simultaneous saccharification and fermentation (SSF) configuration was adopted for enzymatic hydrolysis and fermentation of cellulose and hydrolyze. Bio-ethanol purification was simulated by two distillation columns with side stream and fuel grade bio-ethanol (99.5%) was achieved using molecular sieve in order to minimize the capital and operating costs. Also boiler and steam/power generation were completed using industrial design data. Results indicates 256.6 kg bio ethanol per ton of feedstock and 31 MW surplus power were attained from bio-refinery while the process consumes 3.5, 3.38, and 0.164 (GJ/ton per ton of feedstock) hot utility, cold utility and electricity respectively. Developed simulation is a threshold of variety analyses and developments for further studies.

Keywords: bio-refinery, bagasse, tops, trash, bio-ethanol, electricity

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Authors: Abiodun Ladanu Ajala, Wuyi Oke

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Mathematical simulation and optimization models packaged within interactive computer programs provide a common way for planners and managers to predict the behaviour of any proposed water resources system design or management policy before it is implemented. Modeling presents a principal technique of predicting the behaviour of the proposed infrastructural designs or management policies. Models can be developed and used to help identify specific alternative plans that best meet those objectives. This study discusses various types of models, their development, architecture, data requirements, and applications in the field of engineering. It also outlines the advantages and limitations of each the optimization and simulation models presented. The techniques explored in this review include; dynamic programming, linear programming, fuzzy optimization, evolutionary algorithms and finally artificial intelligence techniques. Previous studies carried out using some of the techniques mentioned above were reviewed, and most of the results from different researches showed that indeed optimization and simulation provides viable alternatives and predictions which form a basis for decision making in building engineering structures and also in engineering planning and management.

Keywords: linear programming, mutation, optimization, simulation

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Authors: Murali Aarthy, Sanjeev Kumar Singh

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High risk human papillomaviruses are highly associated with the carcinoma of the cervix and the other genital tumors. Cervical cancer develops through the multistep process in which increasingly severe premalignant dysplastic lesions called cervical intraepithelial neoplastic progress to invasive cancer. The oncoprotein E7 of human papillomavirus expressed in the lower epithelial layers drives the cells into S-phase creating an environment conducive for viral genome replication and cell proliferation. The replication of the virus occurs in the terminally differentiating epithelium and requires the activation of cellular DNA replication proteins. To date, no suitable drug molecule is available to treat HPV infection whereas identification of potential drug targets and development of novel anti-HPV chemotherapies with unique mode of actions are expected. Hence, our present study aimed to identify the potential inhibitors analogous to EGCG, a green tea molecule which is considered to be safe to use for mammalian systems. A 3D similarity search on the natural small molecule library from natural product database using EGCG identified 11 potential hits based on their similarity score. The structure based docking strategies were implemented in the potential hits and the key interacting residues of protein with compounds were identified through simulation studies and binding free energy calculations. The conformational changes between the apoprotein and the complex were analyzed with the simulation and the results demonstrated that the dynamical and structural effects observed in the protein were induced by the compounds and indicated the dominance to the oncoprotein. Overall, our study provides the basis for the structural insights of the identified potential hits and EGCG and hence, the analogous compounds identified can be potent inhibitors against the HPV 16 E7 oncoprotein.

Keywords: EGCG, oncoprotein, molecular dynamics simulation, analogues

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Authors: Yan Lyu, Yiqun Pan, Zhizhong Huang

Abstract:

In the design stage of a new building, the energy model of this building is often required for the analysis of the performance on energy efficiency. In practice, a certain degree of geometric simplification should be done in the establishment of building energy models, since the detailed geometric features of a real building are hard to be described perfectly in most energy simulation engine, such as ESP-r, eQuest or EnergyPlus. Actually, the detailed description is not necessary when the result with extremely high accuracy is not demanded. Therefore, this paper analyzed the relationship between the error of the simulation result from building energy models and the geometric simplification of the models. Finally, the following two parameters are selected as the indices to characterize the geometric feature of in building energy simulation: the southward projected area and total side surface area of the building, Based on the parameterization method, the simplification from an arbitrary column building to a typical shape (a cuboid) building can be made for energy modeling. The result in this study indicates that this simplification would only lead to the error that is less than 7% for those buildings with the ratio of southward projection length to total perimeter of the bottom of 0.25~0.35, which can cover most situations.

Keywords: building energy model, simulation, geometric simplification, design, regression

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Authors: Sundaram Arulmozhiraja, Kanade Shimizu, Yuta Yamamoto, Satoshi Ichikawa, Maenaka Katsumi, Hiroaki Tokiwa

Abstract:

Drug discovery is shifting from small molecule based drugs targeting local active site to middle molecules (MM) targeting large, flat, and groove-shaped binding sites, for example, protein-protein interface because at least half of all targets assumed to be involved in human disease have been classified as “difficult to drug” with traditional small molecules. Hence, MMs such as peptides, natural products, glycans, nucleic acids with various high potent bioactivities become important targets for drug discovery programs in the recent years as they could be used for ‘undruggable” intracellular targets. Cell membrane permeability is one of the key properties of pharmacodynamically active MM drug compounds and so evaluating this property for the potential MMs is crucial. Computational prediction for cell membrane permeability of molecules is very challenging; however, recent advancement in the molecular dynamics simulations help to solve this issue partially. It is expected that MMs with high membrane permeability will enable drug discovery research to expand its borders towards intracellular targets. Further to understand the chemistry behind the permeability of MMs, it is necessary to investigate their conformational changes during the permeation through membrane and for that their interactions with the membrane field should be studied reliably because these interactions involve various non-bonding interactions such as hydrogen bonding, -stacking, charge-transfer, polarization dispersion, and non-classical weak hydrogen bonding. Therefore, parameters-based classical mechanics calculations are hardly sufficient to investigate these interactions rather, quantum mechanical (QM) calculations are essential. Fragment molecular orbital (FMO) method could be used for such purpose as it performs ab initio QM calculations by dividing the system into fragments. The present work is aimed to study the cell permeability of middle molecules using molecular dynamics simulations and FMO-QM calculations. For this purpose, a natural compound syringolin and its analogues were considered in this study. Molecular simulations were performed using NAMD and Gromacs programs with CHARMM force field. FMO calculations were performed using the PAICS program at the correlated Resolution-of-Identity second-order Moller Plesset (RI-MP2) level with the cc-pVDZ basis set. The simulations clearly show that while syringolin could not permeate the membrane, its selected analogues go through the medium in nano second scale. These correlates well with the existing experimental evidences that these syringolin analogues are membrane-permeable compounds. Further analyses indicate that intramolecular -stacking interactions in the syringolin analogues influenced their permeability positively. These intramolecular interactions reduce the polarity of these analogues so that they could permeate the lipophilic cell membrane. Conclusively, the cell membrane permeability of various middle molecules with potent bioactivities is efficiently studied using molecular dynamics simulations. Insight of this behavior is thoroughly investigated using FMO-QM calculations. Results obtained in the present study indicate that non-bonding intramolecular interactions such as hydrogen-bonding and -stacking along with the conformational flexibility of MMs are essential for amicable membrane permeation. These results are interesting and are nice example for this theoretical calculation approach that could be used to study the permeability of other middle molecules. This work was supported by Japan Agency for Medical Research and Development (AMED) under Grant Number 18ae0101047.

Keywords: fragment molecular orbital theory, membrane permeability, middle molecules, molecular dynamics simulation

Procedia PDF Downloads 153