Search results for: molecular docking and dynamics

Authors: Jin Yue

Abstract:

Fresh produces especially fruits, vegetables, meats and aquatic products have limited shelf life and are highly susceptible to deterioration. Essential oils (EOs) extracted from plants have excellent antioxidant and broad-spectrum antibacterial activities, and they can play as natural food preservatives. But EOs are volatile, water insoluble, pungent, and easily decomposing under light and heat. Many approaches have been developed to improve the solubility and stability of EOs such as polymeric film, coating, nanoparticles, nano-emulsions and nanofibers. Construction of active packaging film which can incorporate EOs with high loading efficiency and controlled release of EOs has received great attention. It is still difficult to achieve accurate release of antibacterial compounds at specific target locations in active packaging. In this research, a relative humidity-responsive packaging material was designed, employing the electrospinning technique to fabricate a nanofibrous film loaded with a 4-terpineol/β-cyclodextrin inclusion complexes (4-TA/β-CD ICs). Functioning as an innovative food packaging material, the film demonstrated commendable attributes including pleasing appearance, thermal stability, mechanical properties, and effective barrier properties. The incorporation of inclusion complexes greatly enhanced the antioxidant and antibacterial activity of the film, particularly against Shewanella putrefaciens, with an inhibitory efficiency of up to 65%. Crucially, the film realized controlled release of 4-TA under 98% high relative humidity conditions by inducing the plasticization of polymers caused by water molecules, swelling of polymer chains, and destruction of hydrogen bonds within the cyclodextrin inclusion complex. This film with a long-term antimicrobial effect successfully extended the shelf life of Litopenaeus vannamei shrimp to 7 days at 4 °C. To further improve the loading efficiency and long-acting release of EOs, we synthesized the γ-cyclodextrin-metal organic frameworks (γ-CD-MOFs), and then efficiently anchored γ-CD-MOFs on chitosan-cellulose (CS-CEL) composite film by in situ growth method for controlled releasing of carvacrol (CAR). We found that the growth efficiency of γ-CD-MOFs was the highest when the concentration of CEL dispersion was 5%. The anchoring of γ-CD-MOFs on CS-CEL film significantly improved the surface area of CS-CEL film from 1.0294 m2/g to 43.3458 m2/g. The molecular docking and 1H NMR spectra indicated that γ-CD-MOF has better complexing and stabilizing ability for CAR molecules than γ-CD. In addition, the release of CAR reached 99.71±0.22% on the 10th day, while under 22% RH, the release pattern of CAR was a plateau with 14.71 ± 4.46%. The inhibition rate of this film against E. coli, S. aureus and B. cinerea was more than 99%, and extended the shelf life of strawberries to 7 days. By incorporating the merits of natural biopolymers and MOFs, this active packaging offers great potential as a substitute for traditional packaging materials.

Keywords: active packaging, antibacterial activity, controlled release, essential oils, food quality control

Procedia PDF Downloads 64

Authors: Edwin Cartledge, Jack Clark, Mazaher Molaei-Chalchooghi

Abstract:

The mixing in the crystallization step of active pharmaceutical ingredient manufacturers was studied via advanced modeling tools to enable a successful scale-up. A virtual representation of the vessel was created, and computational fluid dynamics were used to simulate multiphase flow and, thus, the mixing environment within this vessel. The study identified a significant dead zone in the vessel underneath the impeller and found that increasing the impeller speed and power did not improve the mixing. A series of sensitivity analyses found that to improve mixing, the vessel had to be redesigned, and found that optimal mixing could be obtained by adding two extra cylindrical baffles. The same two baffles from the simulated environment were then constructed and added to the process vessel. By identifying these potential issues before starting the manufacture and modifying the vessel to ensure good mixing, this study mitigated a failed crystallization and potential batch disposal, which could have resulted in a significant loss of high-value material.

Keywords: active pharmaceutical ingredient, baffles, computational fluid dynamics, mixing, modelling

Procedia PDF Downloads 97

Authors: Veenu Bala, Yashpal S. Chhonker, Bhavana Kushwaha, Rabi S. Bhatta, Gopal Gupta, Vishnu L. Sharma

Abstract:

According to UNAIDS 2013 estimate nearly 52% of all individuals living with HIV are now women of reproductive age (15–44 years). Seventy-five percent cases of HIV acquisition are through heterosexual contacts and sexually transmitted infections (STIs), attributable to unsafe sexual behaviour. Each year, an estimated 500 million people acquire atleast one of four STIs: chlamydia, gonorrhoea, syphilis and trichomoniasis. Trichomonas vaginalis (TV) is exclusively sexually transmitted in adults, accounting for 30% of STI cases and associated with pelvic inflammatory disease (PID), vaginitis and pregnancy complications in women. TV infection resulted in impaired vaginal milieu, eventually favoring HIV transmission. In the absence of an effective prophylactic HIV vaccine, prevention of new infections has become a priority. It was thought worthwhile to integrate HIV prevention and reproductive health services including unintended pregnancy protection for women as both are related with unprotected sex. Initially, nonoxynol-9 (N-9) had been proposed as a spermicidal agent with microbicidal activity but on the contrary it increased HIV susceptibility due to surfactant action. Thus, to accomplish an urgent need of novel woman controlled non-detergent microbicidal spermicides benzenepropanamine analogues have been synthesized. At first, five benzenepropanamine-dithiocarbamate hybrids have been synthesized and evaluated for their spermicidal, anti-Trichomonas and anti-fungal activities along with safety profiling to cervicovaginal cells. In order to further enhance the scope of above study benzenepropanamine was hybridized with thiourea as to introduce anti-HIV potential. The synthesized hybrid molecules were evaluated for their reverse transcriptase (RT) inhibition, spermicidal, anti-Trichomonas and antimicrobial activities as well as their safety against vaginal flora and cervical cells. simulated vaginal fluid (SVF) stability and pharmacokinetics of most potent compound versus N-9 was examined in female Newzealand (NZ) rabbits to observe its absorption into systemic circulation and subsequent exposure in blood plasma through vaginal wall. The study resulted in the most promising compound N-butyl-4-(3-oxo-3-phenylpropyl) piperazin-1-carbothioamide (29) exhibiting better activity profile than N-9 as it showed RT inhibition (72.30 %), anti-Trichomonas (MIC, 46.72 µM against MTZ susceptible and MIC, 187.68 µM against resistant strain), spermicidal (MEC, 0.01%) and antifungal activity (MIC, 3.12–50 µg/mL) against four fungal strains. The high safety against vaginal epithelium (HeLa cells) and compatibility with vaginal flora (lactobacillus), SVF stability and least vaginal absorption supported its suitability for topical vaginal application. Docking study was performed to gain an insight into the binding mode and interactions of the most promising compound, N-butyl-4-(3-oxo-3-phenylpropyl) piperazin-1-carbothioamide (29) with HIV-1 Reverse Transcriptase. The docking study has revealed that compound (29) interacted with HIV-1 RT similar to standard drug Nevirapine. It may be concluded that hybridization of benzenepropanamine and thiourea moiety resulted into novel lead with multiple activities including RT inhibition. A further lead optimization may result into effective vaginal microbicides having spermicidal, anti-Trichomonas, antifungal and anti-HIV potential altogether with enhanced safety to cervico-vaginal cells in comparison to Nonoxynol-9.

Keywords: microbicidal, nonoxynol-9, reverse transcriptase, spermicide

Procedia PDF Downloads 344

Authors: Fakhrosadat Sajjadian, Ramin Ghasemi Shayan

Abstract:

The tumor microenvironment plays an fundamental part in tumor start, movement, metastasis, and treatment resistance. It varies from ordinary tissue in terms of its extracellular network, vascular and lymphatic arrange, as well as physiological conditions. The clinical application of atomic cancer imaging is regularly prevented by the tall commercialization costs of focused on imaging operators as well as the constrained clinical applications and little showcase measure of a few operators. . Since numerous cancer types share comparable characteristics of the tumor microenvironment, the capacity to target these biomarkers has the potential to supply clinically translatable atomic imaging advances for numerous types encompassing cancer and broad clinical applications. Noteworthy advance has been made in focusing on the tumor microenvironment for atomic cancer imaging. In this survey, we summarize the standards and methodologies of later progresses in atomic imaging of the tumor microenvironment, utilizing distinctive imaging modalities for early discovery and conclusion of cancer. To conclude, The tumor microenvironment (TME) encompassing tumor cells could be a profoundly energetic and heterogeneous composition of safe cells, fibroblasts, forerunner cells, endothelial cells, flagging atoms and extracellular network (ECM) components.

Keywords: molecular, imaging, TME, medicine

Procedia PDF Downloads 46

Authors: Owolabi Kolade Matthew

Abstract:

In this work, we investigate both the analytical and numerical studies of the dynamical model comprising of three species system. We analyze the linear stability of stationary solutions in the one-dimensional multi-system modeling the interactions of two predators and one prey species. The stability analysis has a lot of implications for understanding the various spatiotemporal and chaotic behaviors of the species in the spatial domain. The analysis results presented have established the possibility of the three interacting species to coexist harmoniously, this feat is achieved by combining the local and global analyzes to determine the global dynamics of the system. In the presence of diffusion, a viable exponential time differencing method is applied to multi-species nonlinear time-dependent partial differential equation to address the points and queries that may naturally arise. The scheme is described in detail, and justified by a number of computational experiments.

Keywords: asymptotically stable, coexistence, exponential time differencing method, global and local stability, predator-prey model, nonlinear, reaction-diffusion system

Procedia PDF Downloads 412

Authors: Ahmed E. Hodaib, Mohamed A. Hashem

Abstract:

In engineering applications, a design has to be as fully perfect as possible in some defined case. The designer has to overcome many challenges in order to reach the optimal solution to a specific problem. This process is called optimization. Generally, there is always a function called “objective function” that is required to be maximized or minimized by choosing input parameters called “degrees of freedom” within an allowed domain called “search space” and computing the values of the objective function for these input values. It becomes more complex when we have more than one objective for our design. As an example for Multi-Objective Optimization Problem (MOP): A structural design that aims to minimize weight and maximize strength. In such case, the Pareto Optimal Frontier (POF) is used, which is a curve plotting two objective functions for the best cases. At this point, a designer should make a decision to choose the point on the curve. Engineers use algorithms or iterative methods for optimization. In this paper, we will discuss the Evolutionary Algorithms (EA) which are widely used with Multi-objective Optimization Problems due to their robustness, simplicity, suitability to be coupled and to be parallelized. Evolutionary algorithms are developed to guarantee the convergence to an optimal solution. An EA uses mechanisms inspired by Darwinian evolution principles. Technically, they belong to the family of trial and error problem solvers and can be considered global optimization methods with a stochastic optimization character. The optimization is initialized by picking random solutions from the search space and then the solution progresses towards the optimal point by using operators such as Selection, Combination, Cross-over and/or Mutation. These operators are applied to the old solutions “parents” so that new sets of design variables called “children” appear. The process is repeated until the optimal solution to the problem is reached. Reliable and robust computational fluid dynamics solvers are nowadays commonly utilized in the design and analyses of various engineering systems, such as aircraft, turbo-machinery, and auto-motives. Coupling of Computational Fluid Dynamics “CFD” and Multi-Objective Evolutionary Algorithms “MOEA” has become substantial in aerospace engineering applications, such as in aerodynamic shape optimization and advanced turbo-machinery design.

Keywords: mathematical optimization, multi-objective evolutionary algorithms "MOEA", computational fluid dynamics "CFD", aerodynamic shape optimization

Procedia PDF Downloads 256

Authors: Getachew Tilahun, Oluwole Makinde, David Malonza

Abstract:

We propose and analyze a non-linear mathematical model for the transmission dynamics of pneumonia disease in a population of varying size. The deterministic compartmental model is studied using stability theory of differential equations. The effective reproduction number is obtained and also the local and global asymptotically stability conditions for the disease free and as well as for the endemic equilibria are established. The model exhibit a backward bifurcation and the sensitivity indices of the basic reproduction number to the key parameters are determined. Using Pontryagin’s maximum principle, the optimal control problem is formulated with three control strategies; namely disease prevention through education, treatment and screening. The cost effectiveness analysis of the adopted control strategies revealed that the combination of prevention and treatment is the most cost effective intervention strategies to combat the pneumonia pandemic. Numerical simulation is performed and pertinent results are displayed graphically.

Keywords: cost effectiveness analysis, optimal control, pneumonia dynamics, stability analysis, numerical simulation

Procedia PDF Downloads 327

Authors: Lubem Matthew Kwaghkor

Abstract:

Terrorism, which remains one of the largest threats faced by various nations and communities around the world, including Nigeria, is the calculated use of violence to create a general climate of fear in a population to attain particular goals that might be political, religious, or economical. Several terrorist groups are currently active in Nigeria, leading to attacks on both civil and military targets. Among these groups, Boko Haram is the deadliest terrorist group operating majorly in Borno State. The southern part of Borno State in North-Eastern Nigeria has been plagued by terrorism, insurgency, and conflict for several years. Understanding the dynamics of terrorism is crucial for developing effective strategies to mitigate its impact on communities and to facilitate peace-building efforts. This research aims to develop a mathematical model that captures the dynamics of terrorism within the southern part of Borno State, Nigeria, capturing both government and local community intervention strategies as control measures in combating terrorism. A compartmental model of five nonlinear differential equations is formulated. The model analyses show that a feasible solution set of the model exists and is bounded. Stability analyses show that both the terrorism free equilibrium and the terrorism endermic equilibrium are asymptotically stable, making the model to have biological meaning. Optimal control theory will be employed to identify the most effective strategy to prevent or minimize acts of terrorism. The research outcomes are expected to contribute towards enhancing security and stability in Southern Borno State while providing valuable insights for policymakers, security agencies, and researchers. This is an ongoing research.

Keywords: modelling, terrorism, optimal control, susceptible, non-susceptible, community intervention

Procedia PDF Downloads 24

Authors: Masoud Safdari, Jacob Fish

Abstract:

Despite vast amount of existing theoretical knowledge, the implementation of a universal multiscale modeling, analysis, and simulation software framework remains challenging. Existing multiscale software and solutions are often domain-specific, closed-source and mandate a high-level of experience and skills in both multiscale analysis and programming. Furthermore, tools currently existing for Atomistic-to-Continuum (AtC) multiscaling are developed with the assumptions such as accessibility of high-performance computing facilities to the users. These issues mentioned plus many other challenges have reduced the adoption of multiscale in academia and especially industry. In the current work, we introduce Multiscale Hub (MsHub), an effort towards making AtC more accessible through cloud services. As a joint effort between academia and industry, MsHub provides a universal web-enabled framework for practical multiscaling. Developed on top of universally acclaimed scientific programming language Python, the package currently provides an open-source, comprehensive, easy-to-use framework for AtC coupling. MsHub offers an easy to use interface to prominent molecular dynamics and multiphysics continuum mechanics packages such as LAMMPS and MFEM (a free, lightweight, scalable C++ library for finite element methods). In this work, we first report on the design philosophy of MsHub, challenges identified and issues faced regarding its implementation. MsHub takes the advantage of a comprehensive set of tools and algorithms developed for AtC that can be used for a variety of governing physics. We then briefly report key AtC algorithms implemented in MsHub. Finally, we conclude with a few examples illustrating the capabilities of the package and its future directions.

Keywords: atomistic, continuum, coupling, multiscale

Procedia PDF Downloads 177

Authors: Mohamad Alkhalidi, S. Neelamani, Noor Alanjari

Abstract:

The main purpose of harbors and marinas is to create a calm and safe docking space for marine vessels. Standard rubble mound breakwaters, although widely used, occupy port space and require large amounts of stones or rocks. Kuwait does not have good quality stone, so they are imported at a very high cost. Therefore, there is a need for a new wave energy dissipating structure where stones and rocks are scarce. While permeable slotted vertical walls have been proved to be a suitable alternative to rubble mound breakwaters, the introduction of sloped slotted walls may be more efficient in dissipating wave energy. For example, two slotted barriers with 60degree inclination may be equivalent to three vertical slotted barriers from wave energy dissipation point of view. A detailed physical model study is carried out to determine the effects of slope angle, porosity, and a number of walls on wave energy dissipation for a wide range of random and regular waves. The results of this study can be used to improve and optimize energy dissipation and reduce construction cost.

Keywords: porosity, slope, wave reflection, wave transmission

Procedia PDF Downloads 290

Authors: Liu Ying-jie, Lu Wen-bo, Peng Cheng-jian

Abstract:

With the development of the automotive technology and electric vehicle, the contribution of the wind noise on the interior noise becomes the main source of noise. The main transfer path which the exterior excitation is transmitted through is the greenhouse panels and side windows. Simulating the wind noise transmitted into the vehicle accurately in the early development stage can be very challenging. The basic methodologies of this study were based on the Lighthill analogy; the exterior flow field around a passenger car was computed using unsteady Computational Fluid Dynamics (CFD) firstly and then a Finite Element Method (FEM) was used to compute the interior acoustic response. The major findings of this study include: 1) The Sound Pressure Level (SPL) response at driver’s ear locations is mainly induced by the turbulence pressure fluctuation; 2) Peaks were found over the full frequency range. It is found that the methodology used in this study could predict the interior wind noise induced by the exterior aerodynamic excitation in industry.

Keywords: wind noise, computational fluid dynamics, finite element method, passenger car

Procedia PDF Downloads 172

Authors: Pragathi Gurumurthy, Christina Hagen, Patricia Ulloa, Martin A. Koch, Thorsten M. Buzug

Abstract:

Obstructive sleep apnea (OSA) is a sleep disorder where the patient suffers a disturbed airflow during sleep due to partial or complete occlusion of the pharyngeal airway. Recently, numerical simulations have been used to better understand the mechanism of pharyngeal collapse. However, to gain confidence in the solutions so obtained, an experimental validation is required. Therefore, in this study an experimental validation of computational fluid dynamics (CFD) used for the study of human pharyngeal flow patterns during OSA is performed. A stationary incompressible Navier-Stokes equation solved using the finite element method was used to numerically study the flow patterns in a computed tomography-based human pharynx model. The inlet flow rate was set to 250 ml/s and such that a flat profile was maintained at the inlet. The outlet pressure was set to 0 Pa. The experimental technique used for the validation of CFD of fluid flow patterns is phase contrast-MRI (PC-MRI). Using the same computed tomography data of the human pharynx as in the simulations, a phantom for the experiment was 3 D printed. Glycerol (55.27% weight) in water was used as a test fluid at 25°C. Inflow conditions similar to the CFD study were simulated using an MRI compatible flow pump (CardioFlow-5000MR, Shelley Medical Imaging Technologies). The entire experiment was done on a 3 T MR system (Ingenia, Philips) with 108 channel body coil using an RF-spoiled, gradient echo sequence. A comparison of the axial velocity obtained in the pharynx from the numerical simulations and PC-MRI shows good agreement. The region of jet impingement and recirculation also coincide, therefore validating the numerical simulations. Hence, the experimental validation proves the reliability and correctness of the numerical simulations.

Keywords: computational fluid dynamics, experimental validation, phase contrast-MRI, obstructive sleep apnea

Procedia PDF Downloads 311

Authors: Konrad Pietrykowski, Michal Bialy, Pawel Karpinski, Radoslaw Maczka

Abstract:

The nozzle is an element of the rocket engine in which the conversion of the potential energy of gases generated during combustion into the kinetic energy of the gas stream takes place. The design parameters of the nozzle have a decisive influence on the ballistic characteristics of the engine. Designing a nozzle assembly is, therefore, one of the most responsible stages in developing a rocket engine design. The paper presents the results of the simulation of three types of rocket propulsion nozzles. Calculations were made using CFD (Computational Fluid Dynamics) in ANSYS Fluent software. The next types of nozzles differ in shape. The analysis was made of a conical nozzle, a bell type nozzle with a conical supersonic part and a bell type nozzle. Calculation results are presented in the form of pressure, velocity and kinetic energy distributions of turbulence in the longitudinal section. The courses of these values along the nozzles are also presented. The results show that the cone nozzle generates strong turbulence in the critical section. Which negatively affect the flow of the working medium. In the case of a bell nozzle, the transformation of the wall caused the elimination of flow disturbances in the critical section. This reduces the probability of waves forming before or after the trailing edge. The most sophisticated construction is the bell type nozzle. It allows you to maximize performance without adding extra weight. The bell type nozzle can be used as a starter and auxiliary engine nozzle due to its advantages. The project/research was financed in the framework of the project Lublin University of Technology-Regional Excellence Initiative, funded by the Polish Ministry of Science and Higher Education (contract no. 030/RID/2018/19).

Keywords: computational fluid dynamics, nozzle, rocket engine, supersonic flow

Procedia PDF Downloads 158

Authors: Sorin Muraru

Abstract:

Computational generation of carbon nanostructures is still a very demanding process. This work provides an alternative to manual molecular modeling through an algorithm meant to automate the design of such structures. Specifically, carbon nanochimneys are obtained through the bonding of a carbon nanotube with the smaller edge of an open carbon nanocone. The methods of connection rely on mathematical, geometrical and chemical properties. Non-hexagonal rings are used in order to perform the correct bonding of dangling bonds. Once obtained, they are useful for thermal transport, gas storage or other applications such as gas separation. The carbon nanochimneys are meant to produce a less steep connection between structures such as the carbon nanotube and graphene sheet, as in the pillared graphene, but can also provide functionality on its own. The method relies on connecting dangling bonds at the edges of the two carbon nanostructures, employing the use of two different types of auxiliary structures on a case-by-case basis. The code is implemented in Python 3.7 and generates an output file in the .pdb format containing all the system’s coordinates. Acknowledgment: This work was supported by a grant of the Executive Agency for Higher Education, Research, Development and innovation funding (UEFISCDI), project number PN-III-P1-1.1-TE-2016-24-2, contract TE 122/2018.

Keywords: carbon nanochimneys, computational, carbon nanotube, carbon nanocone, molecular modeling, carbon nanostructures

Procedia PDF Downloads 170

Authors: Justin Zhengjie Tan, Yang Zhao

Abstract:

Adiabatic Rapid Passage, a popular method of achieving population inversion, is studied in a Rabi dimer model in the presence of noise which acts as a dissipative environment. The integration of the multi-Davydov D2 Ansatz into the time-dependent variational framework enables us to model the intricate quantum system accurately. By influencing the system with a driving field strength resonant with the energy spacing, the probability of adiabatic rapid passage, which is modelled after the Landau Zener model, can be derived along with several other observables, such as the photon population. The effects of a dissipative environment can be reproduced by coupling the system to a common phonon mode. By manipulating the strength and frequency of the driving field, along with the coupling strength of the phonon mode to the qubits, we are able to control the qubits and photon dynamics and subsequently increase the probability of Adiabatic Rapid Passage happening.

Keywords: quantum electrodynamics, adiabatic rapid passage, Landau-Zener transitions, dissipative environment

Procedia PDF Downloads 87

Authors: Seul-Ki Park, Jong-Chun Park, Gyu-Mok Jeon, Dae-Kyung Ock, Seung-Gyu Jeong

Abstract:

Rogue waves cause frequent accidents of ships and offshore structures, which can result in severe damage to the structures. The Rogue waves, which are also known as big waves, freak waves, extreme waves, monster waves, focused waves, giant waves and abnormal waves, are unexpected and suddenly appearing, and can have a breaking force to destroy the structure even though modern structures are designed to tolerate a breaking wave. In the present study, a series of focused waves are numerically reproduced by concentrating nonlinear multi-directional waves into a target point using a commercial CFD software, Star-CCM+. A flow analysis for investigating the physical characteristics of the focused waves is performed using the Star-CCM+, while it has several difficulties to examine the inner properties of the waves in existing potential theory and experiments. Additionally, the 6-DOF (Degree of Freedom) motion of a floating body interacting with the focused waves are simulated, and the dynamic response of the body are discussed.

Keywords: multidirectional waves, focused waves, rogue waves, wave-structure interaction, numerical wave tank, computational fluid dynamics

Procedia PDF Downloads 251

Authors: Ehsan Alishahi, Chuang Deng

Abstract:

Commercial applications of bulk metallic glasses (BMGs) were restricted due to the sudden brittle failure mode which was the main drawback in these new class of materials. Therefore, crystalline-amorphous (C-A) composites were introduced as a toughening strategy in BMGs. In spite of numerous researches in the area of metallic C-A composites, the fundamental structure-property relation in these composites that are not exactly known yet. In this study, it is aimed to investigate the fundamental properties of crystalline-amorphous interface in a model system of Cu/CuZr by using molecular dynamics simulations. Several parameters including interface energy and mechanical properties were investigated by means of atomic models and employing Embedded Atom Method (EAM) potential function. It is found that the crystalline-amorphous interfacial energy weakly depends on the orientation of the crystalline layer, which is in stark contrast to that in a regular crystalline grain boundary. Additionally, the results showed that the interface controls the yielding of the crystalline-amorphous composites during uniaxial tension either by serving as sources for dislocation nucleation in the crystalline layer or triggering local shear transformation zones in amorphous layer. The critical resolved shear stress required to nucleate the first dislocation is also found to strongly depend on the crystalline orientation. Furthermore, it is found that the interaction between dislocations and shear localization at the crystalline-amorphous interface oriented in different directions can lead to a change in the deformation mode. For instance, while the dislocation and shear banding are aligned to each other in {0 0 1} interface plane, the misorientation angle between these failure mechanisms causing more homogeneous deformation in {1 1 0} and {1 1 1} crystalline-amorphous interfaces. These results should help clarify the failure mechanism of crystalline-amorphous composites under various loading conditions.

Keywords: crystalline-amorphous, composites, orientation, plasticity

Procedia PDF Downloads 293

Authors: S. A. Hashemi, A. Khoshraftar

Abstract:

This paper presents the influence of the vertical seismic component on the non-linear dynamics analysis of three different structures. The subject structures were analyzed and designed according to recent codes. This paper considers three types of buildings: 5-, 10-, and 15-story buildings. The non-linear dynamics analysis of the structures with assuming elastic-perfectly-plastic behavior was performed using Ram Perform-3D software; the horizontal component was taken into consideration with and without the incorporation of the corresponding vertical component. Dynamic responses obtained for the horizontal component acting alone were compared with those obtained from the simultaneous application of both seismic components. The results show that the effect of the vertical component of the ground motion may increase the axial load significantly in the interior columns and consequently, the stories. The plastic mechanisms would be changed. The P-Delta effect is expected to increase. The punching base plate shear of the columns should be considered. Moreover, the vertical component increases the input energy when the structures exhibit inelastic behavior and are taller.

Keywords: inelastic behavior, non-linear dynamic analysis, steel structure, vertical component

Procedia PDF Downloads 317

Authors: Lokesh Soni, Sushanta Kumar Sethi, Gaurav Manik

Abstract:

This work attempts to use molecular simulations to create equilibrated structures of a range of commercially used polymers. Generated equilibrated structures for polyvinyl acetate (isotactic), polyvinyl alcohol (atactic), polystyrene, polyethylene, polyamide 66, poly dimethyl siloxane, poly carbonate, poly ethylene oxide, poly amide 12, natural rubber, poly urethane, and polycarbonate (bisphenol-A) and poly ethylene terephthalate are employed to estimate the correct chain length that will correctly predict the chain parameters and properties. Further, the equilibrated structures are used to predict some properties like density, solubility parameter, cohesive energy density, surface energy, and Flory-Huggins interaction parameter. The simulated densities for polyvinyl acetate, polyvinyl alcohol, polystyrene, polypropylene, and polycarbonate are 1.15 g/cm3, 1.125 g/cm3, 1.02 g/cm3, 0.84 g/cm3 and 1.223 g/cm3 respectively are found to be in good agreement with the available literature estimates. However, the critical repeating units or the degree of polymerization after which the solubility parameter showed saturation were 15, 20, 25, 10 and 20 respectively. This also indicates that such properties that dictate the miscibility of two or more polymers in their blends are strongly dependent on the chosen polymer or its characteristic properties. An attempt has been made to correlate such properties with polymer properties like Kuhn length, free volume and the energy term which plays a vital role in predicting the mentioned properties. These results help us to screen and propose a useful library which may be used by the research groups in estimating the polymer properties using the molecular simulations of chains with the predicted critical lengths. The library shall help to obviate the need for researchers to spend efforts in finding the critical chain length needed for simulating the mentioned polymer properties.

Keywords: Kuhn length, Flory Huggins interaction parameter, cohesive energy density, free volume

Procedia PDF Downloads 193

Authors: P. M. Fonseca Alfonso, E. A. Murillo Ruiz, M. Diaz Lagos

Abstract:

Understanding the physicochemical properties and mineralogy of fly ash from a particular source is essential for to protect the environment and considering its possible applications, specifically, in the production of geopolymeric materials that solidify/stabilize heavy metals ions. The results of the characterization of three fly ash samples are shown in this paper. The samples were produced in the TERMOPAIPA IV thermal power plant in the State of Boyaca, Colombia. The particle size distribution, chemical composition, mineralogy, and molecular structure of three samples were analyzed using laser diffraction, X-ray fluorescence, inductively coupled plasma mass spectrometry, X-ray diffraction, and infrared spectroscopy respectively. The particle size distribution of the three samples probably ranges from 0.128 to 211 μm. Approximately 59 elements have been identified in the three samples. It is noticeable that the ashes are made up of aluminum and silicon compounds. Besides, the iron phase in low content was also found. According to the results found in this study, the fly ash samples type F has a great potential to be used as raw material for the manufacture of geopolymers with potential use in the stabilization/solidification of heavy metals; mainly due to the presence of amorphous aluminosilicates typical of this type of ash, which react effectively with alkali-activator.

Keywords: fly ash, geopolymers, molecular structure, physicochemical properties.

Procedia PDF Downloads 118

Authors: Jos Olijve

Abstract:

Introduction and Purpose: Endotoxins are found in the outer membrane of gram-negative bacteria and have profound in vitro and in vivo responses. They can trigger strong immune responses and negatively affect various cellar activities particular cells expressing toll-like receptors. They are therefore unwanted contaminants of biomaterials sourced from natural raw materials, and their activity must be as low as possible. Collagen and gelatin are natural extracellular matrix components and have, due to their low allergenic potential, suitable biological properties, and tunable physical characteristics, high potential in biomedical applications. The purpose of this study was to determine the influence of autoclave sterilization of gelatin on physical properties and endotoxin level compared to surfactant purified gelatin. Methods: Type A gelatin from Sigma-Aldrich (G1890) with endotoxin level of 35000 endotoxin units (EU) per gram gelatin and type A gelatins from Rousselot Gent with endotoxin activity of 30000 EU per gram were used. A 10 w/w% G1890 gelatin solution was autoclave sterilized during 30 minutes at 121°C and 1 bar over pressure. The physical properties and the endotoxin level of the sterilized G1890 gelatin were compared to a type A gelatin from Rousselot purified with Triton X100 surfactant. The Triton X100 was added to a concentration of 0.5 w/w% which is above the critical micellar concentration. The gelatin surfactant mixtures were kept for 30-45 minutes under constant stirring at 55-60°C. The Triton X100 was removed by active carbon filtration. The endotoxin levels of the gelatins were measured using the Endozyme recombinant factor C method from Hyglos GmbH (Germany). Results and Discussion: Autoclave sterilization significantly affect the physical properties of gelatin. Molecular weight of G1890 decreased from 140 to 50kDa, and gel strength decreased from 300 to 40g. The endotoxin level of the gelatin reduced after sterilization from 35000 EU/g to levels of 400-500 EU/g. These endotoxin levels are however still far above the upper endotoxin level of 0.05 EU/ml, which resembles 5 EU/g gelatin based on a 1% gelatin solution, to avoid cell proliferation alteration. Molecular weight and gel strength of Rousselot gelatin was not altered after Triton X100 purification and remained 150kDa and 300g respectively. The endotoxin levels of Triton X100 purified Rousselot gelatin was < 5EU/g gelatin. Conclusion: Autoclave sterilization of gelatin is, in comparison to Triton X100 purification, not efficient to inactivate endotoxin levels in gelatin to levels below the upper limit to avoid cell proliferation alteration. Autoclave sterilization gave a significant decrease in molecular weight and gel strength which makes autoclave sterilized gelatin, in comparison to Triton X100 purified gelatin, not suitable for 3D printing.

Keywords: endotoxin, gelatin, molecular weight, sterilization, Triton X100

Procedia PDF Downloads 234

Authors: Thiyam Tamphasana Devi, Bimlesh Kumar

Abstract:

A Computational Fluid Dynamics (CFD) technique has been applied to simulate the gas-liquid phase in double stirred tank of Rushton impeller. Eulerian-Eulerian model was adopted to simulate the multiphase with standard correlation of Schiller and Naumann for drag co-efficient. The turbulence was modeled by using standard k-ε turbulence model. The present CFD model predicts flow pattern, local gas hold-up, and local specific area. It also predicts local kLa (mass transfer rate) for single impeller. The predicted results were compared with experimental and CFD results of published literature. The predicted results are slightly over predicted with the experimental results; however, it is in reasonable agreement with other simulated results of published literature.

Keywords: Eulerian-Eulerian, gas-hold up, gas-liquid phase, local mass transfer rate, local specific area, Rushton Impeller

Procedia PDF Downloads 234

Authors: Chukwuebuka Vincent Azuka, Chidimma Peace Odoh

Abstract:

Changes in agricultural practices and land use influence the storage and release of soil organic carbon and soil structural dynamics. To investigate this in Nsukka, southeastern Nigeria, soil samples were collected at 0-10 cm, 10-20 cm and 20-30 cm from three locations; Ovoko (OV), Obukpa (OB) and University of Nigeria, Nsukka (UNN) and three land use types; cultivated land (CL), forest land (FL) and grassland (GL)). Data were subjected to analysis of variance (ANOVA) using SPSS. Also, correlations between organic carbon stock, structural stability indices and other soil properties were established. The result showed that Ksat was significantly (p < 0.05) influenced by location with mean values of 68 cmhr⁻¹,121.63 cmhr⁻¹, 8.42 cmhr⁻¹ in OV, OB and UNN respectively. The MWD and aggregate stability (AS) were significantly (p < 0.05) influenced by land use and depth. The mean values of MWD are 0.85 (CL), 1.35 (FL) and 1.45 (GL), and 1.66 at 0-10 cm, 1.08 at 10-20 cm and 0.88 mm at 20-30 cm. The mean values of AS are; 27.66% (CL), 46.39% (FL) and 49.81% (GL), and 53.96% at 0-10cm, 40.22% at 10-20cm and 29.57% at 20-30cm. Clay flocculation (CFI) and dispersion indices (CDI) differed significantly (p < 0.05) among the land use. Soil pH differed significantly (p < 0.05) across the land use and locations with mean values ranging from 3.90-6.14. Soil organic carbon (SOC) significantly (p < 0.05) differed across locations and depths. SOC decreases as depth increases depth with mean values of 15.6 gkg⁻¹, 10.1 gkg⁻¹, and 8.6 gkg⁻¹ at 0-10 cm, 10-20 cm, and 20-30 cm respectively. SOC in the three land use was 8.8 g kg-1, 15.2 gkg⁻¹ and 10.4 gkg⁻¹ at CL, FL, and GL respectively. The highest aggregate-associated carbon was recorded in 0.5 mm across the land use and depth except in cultivated land and at 20-30 cm which recorded their highest SOC at 1mm. SOC stock, total nitrogen (TN) and CEC were significantly (p < 0.05) different across the locations with highest values of 23.43 t/ha, 0.07g/kg and 14.27 Cmol/kg respectively recorded in UNN. SOC stock was significantly (p < 0.05) influenced by depth as follows; 0-10>10-20>20-30 cm. TN was low with mean values ranging from 0.03-0.07 across the locations, land use and depths. The mean values of CEC ranged from 9.96-14.27 Cmol kg⁻¹ across the locations and land use. SOC stock showed correlation with silt, coarse sand, N and CEC (r = 0.40*, -0.39*, -0.65** and 0.64** respectively. AS showed correlation with BD, Ksat, pH in water and KCl, and SOC (r = -0.42*, 0.54**, -0.44*, -0.45* and 0.49** respectively. Thus, land use and location play a significant role in sustainable management of soil resources.

Keywords: agricultural practices, structural dynamics, sequestration, soil resources, management

Procedia PDF Downloads 146

Authors: Leo Nnamdi Ozurumba-Dwight

Abstract:

Messenger ribooxynucleic acid (mRNA) molecules are compositional, protein-based. These proteins, encoding mRNA molecules (which collectively connote the transcriptome), when analyzed by RNA sequencing (RNAseq), unveils the nature of gene expression in the RNA. The obtained gene expression provides clues of cellular traits and their dynamics in presentations. These can be studied in relation to function and responses. RNAseq is a practical concept in Genomics as it enables detection and quantitative analysis of mRNA molecules. Single cell and spatial transcriptomics both present varying avenues for expositions in genomic characteristics of single cells and pooled cells in disease conditions such as cancer, auto-immune diseases, hematopoietic based diseases, among others, from investigated biological tissue samples. Single cell transcriptomics helps conduct a direct assessment of each building unit of tissues (the cell) during diagnosis and molecular gene expressional studies. A typical technique to achieve this is through the use of a single-cell RNA sequencer (scRNAseq), which helps in conducting high throughput genomic expressional studies. However, this technique generates expressional gene data for several cells which lack presentations on the cells’ positional coordinates within the tissue. As science is developmental, the use of complimentary pre-established tissue reference maps using molecular and bioinformatics techniques has innovatively sprung-forth and is now used to resolve this set back to produce both levels of data in one shot of scRNAseq analysis. This is an emerging conceptual approach in methodology for integrative and progressively dependable transcriptomics analysis. This can support in-situ fashioned analysis for better understanding of tissue functional organization, unveil new biomarkers for early-stage detection of diseases, biomarkers for therapeutic targets in drug development, and exposit nature of cell-to-cell interactions. Also, these are vital genomic signatures and characterizations of clinical applications. Over the past decades, RNAseq has generated a wide array of information that is igniting bespoke breakthroughs and innovations in Biomedicine. On the other side, spatial transcriptomics is tissue level based and utilized to study biological specimens having heterogeneous features. It exposits the gross identity of investigated mammalian tissues, which can then be used to study cell differentiation, track cell line trajectory patterns and behavior, and regulatory homeostasis in disease states. Also, it requires referenced positional analysis to make up of genomic signatures that will be sassed from the single cells in the tissue sample. Given these two presented approaches to RNA transcriptomics study in varying quantities of cell lines, with avenues for appropriate resolutions, both approaches have made the study of gene expression from mRNA molecules interesting, progressive, developmental, and helping to tackle health challenges head-on.

Keywords: transcriptomics, RNA sequencing, single cell, spatial, gene expression.

Procedia PDF Downloads 122

Authors: Valentina A. Mikhailova, Serguei V. Feskov, Anatoly I. Ivanov

Abstract:

In the last decade the nonequilibrium charge transfer have attracted considerable interest from the scientific community. Examples of such processes are the charge recombination in excited donor-acceptor complexes and the intramolecular electron transfer from the second excited electronic state. In these reactions the charge transfer proceeds predominantly in the nonequilibrium mode. In the excited donor-acceptor complexes the nuclear nonequilibrium is created by the pump pulse. The intramolecular electron transfer from the second excited electronic state is an example where the nuclear nonequilibrium is created by the forward electron transfer. The kinetics of these nonequilibrium reactions demonstrate a number of peculiar properties. Most important from them are: (i) the absence of the Marcus normal region in the free energy gap law for the charge recombination in excited donor-acceptor complexes, (ii) extremely low quantum yield of thermalized charge separated state in the ultrafast charge transfer from the second excited state, (iii) the nonexponential charge recombination dynamics in excited donor-acceptor complexes, (iv) the dependence of the charge transfer rate constant on the excitation pulse frequency. This report shows that most of these kinetic features can be well reproduced in the framework of stochastic point-transition multichannel model. The model involves an explicit description of the nonequilibrium excited state formation by the pump pulse and accounts for the reorganization of intramolecular high-frequency vibrational modes, for their relaxation as well as for the solvent relaxation. The model is able to quantitatively reproduce complex nonequilibrium charge transfer kinetics observed in modern experiments. The interpretation of the nonequilibrium effects from a unified point of view in the terms of the multichannel point transition stochastic model allows to see similarities and differences of electron transfer mechanism in various molecular donor-acceptor systems and formulates general regularities inherent in these phenomena. The nonequilibrium effects in photoinduced ultrafast charge transfer which have been studied for the last 10 years are analyzed. The methods of suppression of the ultrafast charge recombination, similarities and dissimilarities of electron transfer mechanism in different molecular donor-acceptor systems are discussed. The extremely low quantum yield of the thermalized charge separated state observed in the ultrafast charge transfer from the second excited state in the complex consisting of 1,2,4-trimethoxybenzene and tetracyanoethylene in acetonitrile solution directly demonstrates that its effectiveness can be close to unity. This experimental finding supports the idea that the nonequilibrium charge recombination in the excited donor-acceptor complexes can be also very effective so that the part of thermalized complexes is negligible. It is discussed the regularities inherent to the equilibrium and nonequilibrium reactions. Their fundamental differences are analyzed. Namely the opposite dependencies of the charge transfer rates on the dynamical properties of the solvent. The increase of the solvent viscosity results in decreasing the thermal rate and vice versa increasing the nonequilibrium rate. The dependencies of the rates on the solvent reorganization energy and the free energy gap also can considerably differ. This work was supported by the Russian Science Foundation (Grant No. 16-13-10122).

Keywords: Charge recombination, higher excited states, free energy gap law, nonequilibrium

Procedia PDF Downloads 326

Authors: Mohammad Ebrahim Arbabian

Abstract:

This paper investigates the impact of 3D printing, also known as additive manufacturing, on a multi-item supply chain comprising a manufacturer and retailer. Operating under a wholesale-price contract and catering to stochastic customer demand, this study delves into the largely unexplored realm of how 3D printing technology reshapes supply chain dynamics. A distinguishing aspect of 3D printing is its versatility in producing various product types, yet its slower production pace compared to traditional methods poses a challenge. We analyze the trade-off between 3D printing's limited capacity and its enhancement of production flexibility. By delineating the economic circumstances favoring 3D printing adoption by the manufacturer, we establish the Stackelberg equilibrium in the retailer-manufacturer game. Additionally, we determine optimal order quantities for the retailer considering 3D printing as an option for the manufacturer, ascertain optimal wholesale prices in the presence of 3D printing, and compute optimal profits for both parties involved in the supply chain.

Keywords: additive manufacturing, supply chain management, contract theory, Stackelberg game, optimization

Procedia PDF Downloads 61

Authors: Sedat Yayla, Azhin Abdullah

Abstract:

In the process of constructing hydroelectric power plants, the Pelton turbine, which is characterized by its simple manufacturing and construction, is performed in high head and low water flow. Parameters of the turbine have to be comprised in the designing process for obtaining hydraulic turbine with the highest efficiency during different operating conditions. The present investigation applied three-dimensional computational fluid dynamics (CFD). In addition, the bucket of Pelton turbine models with different splitter angle and inlet velocity values were examined for determining the force and visualizing the flow pattern on the bucket. The study utilized two diverse bucket models at various inlet velocities (20, 25, 30,35and 40m/s) and four different splitter angles (55, 75,90and 115 degree) for finding out the impacts of every single parameter on the effective force on the bucket. The acquired outcomes revealed that there is a linear relationship between force and inlet velocity on the bucket. Furthermore, the results also uncovered that the relationship between splitter angle and force on the bucket is linear until 90 degree.

Keywords: bucket design, computational fluid dynamics (CFD), free surface flow, two-phase flow, volume of fluid (VOF)

Procedia PDF Downloads 271

Authors: Atul K. Desai, Jigar K. Sevalia, Sandip A. Vasanwala

Abstract:

When a building is located in an urban area, it is exposed to a wind of different characteristics then wind over an open terrain. This is development of turbulent wake region behind an upstream building. The interaction with upstream building can produce significant changes in the response of the tall building. Here, in this paper, an attempt has been made to study wind induced interference effects on tall building. In order to study wind induced interference effect (IF) on Tall Building, initially a tall building (which is termed as Principal Building now on wards) with square plan shape has been considered with different Height to Width Ratio and total drag force is obtained considering different terrain conditions as well as different incident wind direction. Then total drag force on Principal Building is obtained by considering adjacent building which is termed as Interfering Building now on wards with different terrain conditions and incident wind angle. To execute study, Computational Fluid Dynamics (CFD) Code namely Fluent and Gambit have been used.

Keywords: computational fluid dynamics, tall building, turbulent, wake region, wind

Procedia PDF Downloads 553

Authors: Marina Passero, Tianhua Zhai, Zuyi (Jacky) Huang

Abstract:

Alzheimer’s disease has become a major public health issue, as indicated by the increasing populations of Americans living with Alzheimer’s disease. After decades of extensive research in Alzheimer’s disease, only seven drugs have been approved by Food and Drug Administration (FDA) to treat Alzheimer’s disease. Five of these drugs were designed to treat the dementia symptoms, and only two drugs (i.e., Aducanumab and Lecanemab) target the progression of Alzheimer’s disease, especially the accumulation of amyloid-b plaques. However, controversial comments were raised for the accelerated approvals of either Aducanumab or Lecanemab, especially with concerns on safety and side effects of these two drugs. There is still an urgent need for further drug discovery to target the biological processes involved in the progression of Alzheimer’s disease. Excessive cholesterol has been found to accumulate in the brain of those with Alzheimer’s disease. Cholesterol can be synthesized in both the blood and the brain, but the majority of biosynthesis in the adult brain takes place in astrocytes and is then transported to the neurons via ApoE. The blood brain barrier separates cholesterol metabolism in the brain from the rest of the body. Various proteins contribute to the metabolism of cholesterol in the brain, which offer potential targets for Alzheimer’s treatment. In the astrocytes, SREBP cleavage-activating protein (SCAP) binds to Sterol Regulatory Element-binding Protein 2 (SREBP2) in order to transport the complex from the endoplasmic reticulum to the Golgi apparatus. Cholesterol is secreted out of the astrocytes by ATP-Binding Cassette A1 (ABCA1) transporter. Lipoprotein receptors such as triggering receptor expressed on myeloid cells 2 (TREM2) internalize cholesterol into the microglia, while lipoprotein receptors such as Low-density lipoprotein receptor-related protein 1 (LRP1) internalize cholesterol into the neuron. Cytochrome P450 Family 46 Subfamily A Member 1 (CYP46A1) converts excess cholesterol to 24S-hydroxycholesterol (24S-OHC). Cholesterol has been approved for its direct effect on the production of amyloid-beta and tau proteins. The addition of cholesterol to the brain promotes the activity of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1), secretase, and amyloid precursor protein (APP), which all aid in amyloid-beta production. The reduction of cholesterol esters in the brain have been found to reduce phosphorylated tau levels in mice. In this work, a computational pipeline was developed to identify the protein targets involved in cholesterol regulation in brain and further to identify chemical compounds as the inhibitors of a selected protein target. Since extensive evidence shows the strong correlation between brain cholesterol regulation and Alzheimer’s disease, a detailed literature review on genes or pathways related to the brain cholesterol synthesis and regulation was first conducted in this work. An interaction network was then built for those genes so that the top gene targets were identified. The involvement of these genes in Alzheimer’s disease progression was discussed, which was followed by the investigation of existing clinical trials for those targets. A ligand-protein docking program was finally developed to screen 1.5 million chemical compounds for the selected protein target. A machine learning program was developed to evaluate and predict the binding interaction between chemical compounds and the protein target. The results from this work pave the way for further drug discovery to regulate brain cholesterol to combat Alzheimer’s disease.

Keywords: Alzheimer’s disease, drug discovery, ligand-protein docking, gene-network analysis, cholesterol regulation

Procedia PDF Downloads 75

Authors: Rosario Rivera Rubite, Ching-I Peng, Che-Wei Lin, Mark Hughes, Yoshiko Kono, Kuo-Fang Chung

Abstract:

The flora of Panay Island is under-collected compared with the other islands of the Philippines. In a joint expedition to the island, botanists from Taiwan and the Philippines found three unknown Begonia and compared them with potentially allied species. The three species are clearly assignable to Begonia section Baryandra which is largely endemic to the Philippines. Studies of literature, herbarium specimens, and living plants support the recognition of the three new species: Begonia culasiensis, Begonia merrilliana, and Begonia sykakiengii. Somatic chromosomes at metaphase were determined to be 2n=30 for B. culasiensis and 2n=28 for both B. merrilliana and B. sykakiengii, which are congruent with those of most species in sect. Baryandra. Molecular phylogenetic evidence is consistent with B. culasiensis being a relict from the late Miocene, and with B. merrilliana and B. sykakiengii being younger species of Pleistocene origin. The continuing discovery of endemic Philippine species means the remaining fragments of both primary and secondary native vegetation in the archipelago are of increasing value in terms of natural capital. A secure future for the species could be realized through ex-situ conservation collections and raising awareness with community groups.

Keywords: conservation, endemic , herbarium , limestone, phylogenetics, taxonomy

Procedia PDF Downloads 217