Reintrepreting the cardiovascular system as a mechanical model

NASA Astrophysics Data System (ADS)

Lemos, Diogo; Machado, José; Minas, Graça; Soares, Filomena; Barros, Carla; Leão, Celina Pinto

2013-10-01

The simulation of the different physiological systems is very useful as a pedagogical tool, allowing a better understanding of the mechanisms and the functions of the processes. The observation of the physiological phenomena through mechanical simulators represents a great asset. Furthermore, the development of these simulators allows reinterpreting physiological systems, with the advantage of using the same transducers and sensors that are commonly used in diagnostic and therapeutic cardiovascular procedures for the monitoring of system' parameters. The cardiovascular system is one of the most important systems of the human body and has been the target of several biomedical studies. The present work describes a mechanical simulation of the cardiovascular system, in particularly, the systemic circulation, which can be described in terms of its hemodynamic variables. From the mechanical process and parameters, physiological system's behavior was reproduced, as accurately as possible.

Assessment of start-up mechanisms for anaerobic fluidized bed reactor in series based on mathematical simulation

NASA Astrophysics Data System (ADS)

Sudibyo, Hanifrahmawan; Guntama, Dody; Budhijanto, Wiratni

2017-05-01

Anaerobic digestion is associated with long hydraulic residence time and hence leads to huge reactor volume, especially for high rate input to the reactor. To overcome this major drawback, one of the possibilities is optimizing the schemes of reactor configuration and start-up mechanisms. This study aimed to determine the most promising start-up mechanism for anaerobic digestion reactors in series, with respect to the shortest hydraulic residence time to reach the highest biogas production rate. The reactor to be studied is anaerobic fluidized bed reactor (AFBR) which is known as the most efficient reactor for high organic loading rate. Case to be studied is landfill leachate digestion. Although reactor optimization can be conducted experimentally, it could be expensive and time consuming. This study proposed the utilization of mathematical modeling to screen the possibilities towards the best options to be verified experimentally. Kinetic study of landfill leachate anaerobic digestion was first conducted to depict the rate of microbial growth and the rate of substrate consumption. Kinetics constants obtained from this batch experiment were then used in the mathematical model representing AFBR. Several mechanisms were simulated in this study. In the first mechanism, all digesters were started simultaneously. In the second mechanism, each digester was started until it achieved steady-state condition before the next digester was started. The third mechanism was start-up scenario for single reactor as opposed to the previous two mechanisms. These all three mechanisms were simulated for either one-through stream and recycling a portion of the reactor effluent. The mathematical simulation result was used to evaluate each mechanism based on hydraulic residence time required for all digesters in series to reach the steady-state condition, the extent of pollutant removal, and the rate of biogas production. In the need of high sCOD removal, the second mechanism emerged as the best one.

Monoatomic layer removal mechanism in chemical mechanical polishing process: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Si, Lina; Guo, Dan; Luo, Jianbin; Lu, Xinchun

2010-03-01

Molecular dynamics simulations of nanoscratching processes were used to study the atomic-scale removal mechanism of single crystalline silicon in chemical mechanical polishing (CMP) process and particular attention was paid to the effect of scratching depth. The simulation results under a scratching depth of 1 nm showed that a thick layer of silicon material was removed by chip formation and an amorphous layer was formed on the silicon surface after nanoscratching. By contrast, the simulation results with a depth of 0.1 nm indicated that just one monoatomic layer of workpiece was removed and a well ordered crystalline surface was obtained, which is quite consistent with previous CMP experimental results. Therefore, monoatomic layer removal mechanism was presented, by which it is considered that during CMP process the material was removed by one monoatomic layer after another, and the mechanism could provide a reasonable understanding on how the high precision surface was obtained. Also, the effects of the silica particle size and scratching velocity on the removal mechanism were investigated; the wear regimes and interatomic forces between silica particle and workpiece were studied to account for the different removal mechanisms with indentation depths of 0.1 and 1 nm.

Gating Mechanisms of Mechanosensitive Channels of Large Conductance, I: A Continuum Mechanics-Based Hierarchical Framework

PubMed Central

Chen, Xi; Cui, Qiang; Tang, Yuye; Yoo, Jejoong; Yethiraj, Arun

2008-01-01

A hierarchical simulation framework that integrates information from molecular dynamics (MD) simulations into a continuum model is established to study the mechanical response of mechanosensitive channel of large-conductance (MscL) using the finite element method (FEM). The proposed MD-decorated FEM (MDeFEM) approach is used to explore the detailed gating mechanisms of the MscL in Escherichia coli embedded in a palmitoyloleoylphosphatidylethanolamine lipid bilayer. In Part I of this study, the framework of MDeFEM is established. The transmembrane and cytoplasmic helices are taken to be elastic rods, the loops are modeled as springs, and the lipid bilayer is approximated by a three-layer sheet. The mechanical properties of the continuum components, as well as their interactions, are derived from molecular simulations based on atomic force fields. In addition, analytical closed-form continuum model and elastic network model are established to complement the MDeFEM approach and to capture the most essential features of gating. In Part II of this study, the detailed gating mechanisms of E. coli-MscL under various types of loading are presented and compared with experiments, structural model, and all-atom simulations, as well as the analytical models established in Part I. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction. PMID:18390626

Numerical Study of Particle Damping Mechanism in Piston Vibration System via Particle Dynamics Simulation

NASA Astrophysics Data System (ADS)

Bai, Xian-Ming; Shah, Binoy; Keer, Leon; Wang, Jane; Snurr, Randall

2008-03-01

Mechanical damping systems with granular particles as the damping media have promising applications in extreme temperature conditions. In particle-based damping systems, the mechanical energy is dissipated through the inelastic collision and friction of particles. In the past, many experiments have been performed to investigate the particle damping problems. However, the detailed energy dissipation mechanism is still unclear due to the complex collision and flow behavior of dense particles. In this work, we use 3-D particle dynamics simulation to investigate the damping mechanism of an oscillating cylinder piston immerged in millimeter-size steel particles. The time evolution of the energy dissipation through the friction and inelastic collision is accurately monitored during the damping process. The contribution from the particle-particle interaction and particle-wall interaction is also separated for investigation. The effects of moisture, surface roughness, and density of particles are carefully investigated in the simulation. The comparison between the numerical simulation and experiment is also performed. The simulation results can help us understand the particle damping mechanism and design the new generation of particle damping devices.

Lung assist devices influence cardio-energetic parameters: Numerical simulation study.

PubMed

De Lazzari, C; Quatember, B; Recheis, W; Mayr, M; Demertzis, S; Allasia, G; De Rossi, A; Cavoretto, R; Venturino, E; Genuini, I

2015-08-01

We aim at an analysis of the effects mechanical ventilators (MVs) and thoracic artificial lungs (TALs) will have on the cardiovascular system, especially on important quantities, such as left and right ventricular external work (EW), pressure-volume area (PVA) and cardiac mechanical efficiency (CME). Our analyses are based on simulation studies which were carried out by using our CARDIOSIM(©) software simulator. At first, we carried out simulation studies of patients undergoing mechanical ventilation (MV) without a thoracic artificial lung (TAL). Subsequently, we conducted simulation studies of patients who had been provided with a TAL, but did not undergo MV. We aimed at describing the patient's physiological characteristics and their variations with time, such as EW, PVA, CME, cardiac output (CO) and mean pulmonary arterial/venous pressure (PAP/PVP). We were starting with a simulation run under well-defined initial conditions which was followed by simulation runs for a wide range of mean intrathoracic pressure settings. Our simulations of MV without TAL showed that for mean intrathoracic pressure settings from negative (-4 mmHg) to positive (+5 mmHg) values, the left and right ventricular EW and PVA, right ventricular CME and CO decreased, whereas left ventricular CME and the PAP increased. The simulation studies of patients with a TAL, comprised all the usual TAL arrangements, viz. configurations "in series" and in parallel with the natural lung and, moreover, hybrid configurations. The main objective of the simulation studies was, as before, the assessment of the hemodynamic response to the application of a TAL. We could for instance show that, in case of an "in series" configuration, a reduction (an increase) in left (right) ventricular EW and PVA values occurred, whereas the best performance in terms of CO can be achieved in the case of an in parallel configuration.

A Comparison of Two Chemical Mechanisms Using Data from the Southern Oxidant and Aerosol Study

NASA Astrophysics Data System (ADS)

Green, S. B.; Saylor, R. D.

2016-12-01

The Atmospheric Chemistry and Canopy Exchange Simulation System (ACCESS) is a 1-D column model of the physical and chemical processes occurring from the Earth's surface to the top of the planetary boundary layer (PBL). In this study, we couple ACCESS with environmental data from the Southern Oxidant and Aerosol Study (SOAS) intensive field measurement campaign to simulate the chemical evolution of biogenic hydrocarbons above a forest canopy over two time periods: a four-day period from June 29-July 2, 2013 and a three-day period from June 21-23, 2013. We quantify the efficacy of the model by calculating R2 values between SOAS chemical measurements and simulation results of isoprene, methyl vinyl ketone (MVK), methacrolein (MACR), α-pinene, and limonene. Two kinetic mechanisms, one from Browne et al. (2014) (RACM2+) and another from Schwantes et al. (2015) (CIT), were implemented in ACCESS and used in independent simulations to determine which mechanism better represents the SOAS data through daytime and nighttime periods. The results demonstrate that RACM2+ and CIT perform at comparable levels for simulating the evolution of isoprene, MVK, and MACR, but both differ substantially from measurements of α-pinene and limonene. The mechanisms perform equally well during both daytime and nighttime periods and thus, substantiated by our results, there is no strong justification for implementing one mechanism over the other.

Geochemical Reaction Mechanism Discovery from Molecular Simulation

DOE PAGES

Stack, Andrew G.; Kent, Paul R. C.

2014-11-10

Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less

Mechanical Deformation Mechanisms and Properties of Prion Fibrils Probed by Atomistic Simulations

NASA Astrophysics Data System (ADS)

Choi, Bumjoon; Kim, Taehee; Ahn, Eue Soo; Lee, Sang Woo; Eom, Kilho

2017-03-01

Prion fibrils, which are a hallmark for neurodegenerative diseases, have recently been found to exhibit the structural diversity that governs disease pathology. Despite our recent finding concerning the role of the disease-specific structure of prion fibrils in determining their elastic properties, the mechanical deformation mechanisms and fracture properties of prion fibrils depending on their structures have not been fully characterized. In this work, we have studied the tensile deformation mechanisms of prion and non-prion amyloid fibrils by using steered molecular dynamics simulations. Our simulation results show that the elastic modulus of prion fibril, which is formed based on left-handed β-helical structure, is larger than that of non-prion fibril constructed based on right-handed β-helix. However, the mechanical toughness of prion fibril is found to be less than that of non-prion fibril, which indicates that infectious prion fibril is more fragile than non-infectious (non-prion) fibril. Our study sheds light on the role of the helical structure of amyloid fibrils, which is related to prion infectivity, in determining their mechanical deformation mechanisms and properties.

Increase in the Random Dopant Induced Threshold Fluctuations and Lowering in Sub 100 nm MOSFETs Due to Quantum Effects: A 3-D Density-Gradient Simulation Study

NASA Technical Reports Server (NTRS)

Asenov, Asen; Slavcheva, G.; Brown, A. R.; Davies, J. H.; Saini, S.

2000-01-01

In this paper we present a detailed simulation study of the influence of quantum mechanical effects in the inversion layer on random dopant induced threshold voltage fluctuations and lowering in sub 100 nm MOSFETs. The simulations have been performed using a 3-D implementation of the density gradient (DG) formalism incorporated in our established 3-D atomistic simulation approach. This results in a self-consistent 3-D quantum mechanical picture, which implies not only the vertical inversion layer quantisation but also the lateral confinement effects related to current filamentation in the 'valleys' of the random potential fluctuations. We have shown that the net result of including quantum mechanical effects, while considering statistical dopant fluctuations, is an increase in both threshold voltage fluctuations and lowering. At the same time, the random dopant induced threshold voltage lowering partially compensates for the quantum mechanical threshold voltage shift in aggressively scaled MOSFETs with ultrathin gate oxides.

Elucidating the thermal, chemical, and mechanical mechanisms of ultraviolet ablation in poly(methyl methacrylate) via molecular dynamics simulations.

PubMed

Conforti, Patrick F; Prasad, Manish; Garrison, Barbara J

2008-08-01

[Figure: see text]. Laser ablation harnesses photon energy to remove material from a surface. Although applications such as laser-assisted in situ keratomileusis (LASIK) surgery, lithography, and nanoscale device fabrication take advantage of this process, a better understanding the underlying mechanism of ablation in polymeric materials remains much sought after. Molecular simulation is a particularly attractive technique to study the basic aspects of ablation because it allows control over specific process parameters and enables observation of microscopic mechanistic details. This Account describes a hybrid molecular dynamics-Monte Carlo technique to simulate laser ablation in poly(methyl methacrylate) (PMMA). It also discusses the impact of thermal and chemical excitation on the ensuing ejection processes. We used molecular dynamics simulation to study the molecular interactions in a coarse-grained PMMA substrate following photon absorption. To ascertain the role of chemistry in initiating ablation, we embedded a Monte Carlo protocol within the simulation framework. These calculations permit chemical reactions to occur probabilistically during the molecular dynamics calculation using predetermined reaction pathways and Arrhenius rates. With this hybrid scheme, we can examine thermal and chemical pathways of decomposition separately. In the simulations, we observed distinct mechanisms of ablation for each type of photoexcitation pathway. Ablation via thermal processes is governed by a critical number of bond breaks following the deposition of energy. For the case in which an absorbed photon directly causes a bond scission, ablation occurs following the rapid chemical decomposition of material. A detailed analysis of the processes shows that a critical energy for ablation can describe this complex series of events. The simulations show a decrease in the critical energy with a greater amount of photochemistry. Additionally, the simulations demonstrate the effects of the energy deposition rate on the ejection mechanism. When the energy is deposited rapidly, not allowing for mechanical relaxation of the sample, the formation of a pressure wave and subsequent tensile wave dominates the ejection process. This study provides insight into the influence of thermal, chemical, and mechanical processes in PMMA and facilitates greater understanding of the complex nature of polymer ablation. These simulations complement experiments that have used chemical design to harness the photochemical properties of materials to enhance laser ablation. We successfully fit the results of the simulations to established analytical models of both photothermal and photochemical ablation and demonstrate their relevance. Although the simulations are for PMMA, the mechanistic concepts are applicable to a large range of systems and provide a conceptual foundation for interpretation of experimental data.

A multiscale quantum mechanics/electromagnetics method for device simulations.

PubMed

Yam, ChiYung; Meng, Lingyi; Zhang, Yu; Chen, GuanHua

2015-04-07

Multiscale modeling has become a popular tool for research applying to different areas including materials science, microelectronics, biology, chemistry, etc. In this tutorial review, we describe a newly developed multiscale computational method, incorporating quantum mechanics into electronic device modeling with the electromagnetic environment included through classical electrodynamics. In the quantum mechanics/electromagnetics (QM/EM) method, the regions of the system where active electron scattering processes take place are treated quantum mechanically, while the surroundings are described by Maxwell's equations and a semiclassical drift-diffusion model. The QM model and the EM model are solved, respectively, in different regions of the system in a self-consistent manner. Potential distributions and current densities at the interface between QM and EM regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. The method is illustrated in the simulation of several realistic systems. In the case of junctionless field-effect transistors, transfer characteristics are obtained and a good agreement between experiments and simulations is achieved. Optical properties of a tandem photovoltaic cell are studied and the simulations demonstrate that multiple QM regions are coupled through the classical EM model. Finally, the study of a carbon nanotube-based molecular device shows the accuracy and efficiency of the QM/EM method.

A simulation tool to study high-frequency chest compression energy transfer mechanisms and waveforms for pulmonary disease applications.

PubMed

O'Clock, George D; Lee, Yong Wan; Lee, Jongwon; Warwick, Warren J

2010-07-01

High-frequency chest compression (HFCC) can be used as a therapeutic intervention to assist in the transport and clearance of mucus and enhance water secretion for cystic fibrosis patients. An HFCC pump-vest and half chest-lung simulation, with 23 lung generations, has been developed using inertance, compliance, viscous friction relationships, and Newton's second law. The simulation has proven to be useful in studying the effects of parameter variations and nonlinear effects on HFCC system performance and pulmonary system response. The simulation also reveals HFCC waveform structure and intensity changes in various segments of the pulmonary system. The HFCC system simulation results agree with measurements, indicating that the HFCC energy transport mechanism involves a mechanically induced pulsation or vibration waveform with average velocities in the lung that are dependent upon small air displacements over large areas associated with the vest-chest interface. In combination with information from lung physiology, autopsies and a variety of other lung modeling efforts, the results of the simulation can reveal a number of therapeutic implications.

Study of photo-oxidative reactivity of sunscreening agents based on photo-oxidation of uric acid by kinetic Monte Carlo simulation.

PubMed

Moradmand Jalali, Hamed; Bashiri, Hadis; Rasa, Hossein

2015-05-01

In the present study, the mechanism of free radical production by light-reflective agents in sunscreens (TiO2, ZnO and ZrO2) was obtained by applying kinetic Monte Carlo simulation. The values of the rate constants for each step of the suggested mechanism have been obtained by simulation. The effect of the initial concentration of mineral oxides and uric acid on the rate of uric acid photo-oxidation by irradiation of some sun care agents has been studied. The kinetic Monte Carlo simulation results agree qualitatively with the existing experimental data for the production of free radicals by sun care agents. Copyright © 2015 Elsevier B.V. All rights reserved.

Atomistic Simulations of Graphene Growth: From Kinetics to Mechanism.

PubMed

Qiu, Zongyang; Li, Pai; Li, Zhenyu; Yang, Jinlong

2018-03-20

Epitaxial growth is a promising strategy to produce high-quality graphene samples. At the same time, this method has great flexibility for industrial scale-up. To optimize growth protocols, it is essential to understand the underlying growth mechanisms. This is, however, very challenging, as the growth process is complicated and involves many elementary steps. Experimentally, atomic-scale in situ characterization methods are generally not feasible at the high temperature of graphene growth. Therefore, kinetics is the main experimental information to study growth mechanisms. Theoretically, first-principles calculations routinely provide atomic structures and energetics but have a stringent limit on the accessible spatial and time scales. Such gap between experiment and theory can be bridged by atomistic simulations using first-principles atomic details as input and providing the overall growth kinetics, which can be directly compared with experiment, as output. Typically, system-specific approximations should be applied to make such simulations computationally feasible. By feeding kinetic Monte Carlo (kMC) simulations with first-principles parameters, we can directly simulate the graphene growth process and thus understand the growth mechanisms. Our simulations suggest that the carbon dimer is the dominant feeding species in the epitaxial growth of graphene on both Cu(111) and Cu(100) surfaces, which enables us to understand why the reaction is diffusion limited on Cu(111) but attachment limited on Cu(100). When hydrogen is explicitly considered in the simulation, the central role hydrogen plays in graphene growth is revealed, which solves the long-standing puzzle into why H 2 should be fed in the chemical vapor deposition of graphene. The simulation results can be directly compared with the experimental kinetic data, if available. Our kMC simulations reproduce the experimentally observed quintic-like behavior of graphene growth on Ir(111). By checking the simulation results, we find that such nonlinearity is caused by lattice mismatch, and the induced growth front inhomogeneity can be universally used to predict growth behaviors in other heteroepitaxial systems. Notably, although experimental kinetics usually gives useful insight into atomic mechanisms, it can sometimes be misleading. Such pitfalls can be avoided via atomistic simulations, as demonstrated in our study of the graphene etching process. Growth protocols can be designed theoretically with computational kinetic and mechanistic information. By contrasting the different activation energies involved in an atom-exchange-based carbon penetration process for monolayer and bilayer graphene, we propose a three-step strategy to grow high-quality bilayer graphene. Based on first-principles parameters, a kinetic pathway toward the high-density, ordered N doping of epitaxial graphene on Cu(111) using a C 5 NCl 5 precursor is also identified. These studies demonstrate that atomistic simulations can unambiguously produce or reproduce the kinetic information on graphene growth, which is pivotal to understanding the growth mechanism and designing better growth protocols. A similar strategy can be used in growth mechanism studies of other two-dimensional atomic crystals.

Interaction of hydraulic and buckling mechanisms in blowout fractures.

PubMed

Nagasao, Tomohisa; Miyamoto, Junpei; Jiang, Hua; Tamaki, Tamotsu; Kaneko, Tsuyoshi

2010-04-01

The etiology of blowout fractures is generally attributed to 2 mechanisms--increase in the pressure of the orbital contents (the hydraulic mechanism) and direct transmission of impacts on the orbital walls (the buckling mechanism). The present study aims to elucidate whether or not an interaction exists between these 2 mechanisms. We performed a simulation experiment using 10 Computer-Aided-Design skull models. We applied destructive energy to the orbits of the 10 models in 3 different ways. First, to simulate pure hydraulic mechanism, energy was applied solely on the internal walls of the orbit. Second, to simulate pure buckling mechanism, energy was applied solely on the inferior rim of the orbit. Third, to simulate the combined effect of the hydraulic and buckling mechanisms, energy was applied both on the internal wall of the orbit and inferior rim of the orbit. After applying the energy, we calculated the areas of the regions where fracture occurred in the models. Thereafter, we compared the areas among the 3 energy application patterns. When the hydraulic and buckling mechanisms work simultaneously, fracture occurs on wider areas of the orbital walls than when each of these mechanisms works separately. The hydraulic and buckling mechanisms interact, enhancing each other's effect. This information should be taken into consideration when we examine patients in whom blowout fracture is suspected.

NUMERICAL SIMULATION OF NANOINDENTATION AND PATCH CLAMP EXPERIMENTS ON MECHANOSENSITIVE CHANNELS OF LARGE CONDUCTANCE IN ESCHERICHIA COLI

PubMed Central

Tang, Yuye; Chen, Xi; Yoo, Jejoong; Yethiraj, Arun; Cui, Qiang

2010-01-01

A hierarchical simulation framework that integrates information from all-atom simulations into a finite element model at the continuum level is established to study the mechanical response of a mechanosensitive channel of large conductance (MscL) in bacteria Escherichia Coli (E.coli) embedded in a vesicle formed by the dipalmitoylphosphatidycholine (DPPC) lipid bilayer. Sufficient structural details of the protein are built into the continuum model, with key parameters and material properties derived from molecular mechanics simulations. The multi-scale framework is used to analyze the gating of MscL when the lipid vesicle is subjective to nanoindentation and patch clamp experiments, and the detailed structural transitions of the protein are obtained explicitly as a function of external load; it is currently impossible to derive such information based solely on all-atom simulations. The gating pathways of E.coli-MscL qualitatively agree with results from previous patch clamp experiments. The gating mechanisms under complex indentation-induced deformation are also predicted. This versatile hierarchical multi-scale framework may be further extended to study the mechanical behaviors of cells and biomolecules, as well as to guide and stimulate biomechanics experiments. PMID:21874098

Analysis of hydraulic steering system of tracked all-terrain vehicles' articulated mechanism

NASA Astrophysics Data System (ADS)

Meng, Zhongliang; Zang, Hao

2018-04-01

As for the researches on the dynamic characteristics of tracked all-terrain vehicles' articulated mechanism, the hydraulic feature of their steering system needs researching more, apart from the study on mechanical models. According to the maximum pressure required by the steering system of tracked all-terrain vehicle and the principle of the steering system, this paper conducts an analysis of the hydraulic steering system of the articulated mechanism. Based on the structure principle of the steering gear, a simulation model of the tracked all-terrain vehicle turning left is built. When building the simulation model of the steering gear, it makes a simulation analysis, taking the tracked all-terrain vehicle turning left as an example.

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.

PubMed

Decherchi, Sergio; Berteotti, Anna; Bottegoni, Giovanni; Rocchia, Walter; Cavalli, Andrea

2015-01-27

The study of biomolecular interactions between a drug and its biological target is of paramount importance for the design of novel bioactive compounds. In this paper, we report on the use of molecular dynamics (MD) simulations and machine learning to study the binding mechanism of a transition state analogue (DADMe-immucillin-H) to the purine nucleoside phosphorylase (PNP) enzyme. Microsecond-long MD simulations allow us to observe several binding events, following different dynamical routes and reaching diverse binding configurations. These simulations are used to estimate kinetic and thermodynamic quantities, such as kon and binding free energy, obtaining a good agreement with available experimental data. In addition, we advance a hypothesis for the slow-onset inhibition mechanism of DADMe-immucillin-H against PNP. Combining extensive MD simulations with machine learning algorithms could therefore be a fruitful approach for capturing key aspects of drug-target recognition and binding.

Finite Element Analysis of Osteocytes Mechanosensitivity Under Simulated Microgravity

NASA Astrophysics Data System (ADS)

Yang, Xiao; Sun, Lian-Wen; Du, Cheng-Fei; Wu, Xin-Tong; Fan, Yu-Bo

2018-04-01

It was found that the mechanosensitivity of osteocytes could be altered under simulated microgravity. However, how the mechanical stimuli as the biomechanical origins cause the bioresponse in osteocytes under microgravity is unclear yet. Computational studies may help us to explore the mechanical deformation changes of osteocytes under microgravity. Here in this paper, we intend to use the computational simulation to investigate the mechanical behavior of osteocytes under simulated microgravity. In order to obtain the shape information of osteocytes, the biological experiment was conducted under simulated microgravity prior to the numerical simulation The cells were rotated by a clinostat for 6 hours or 5 days and fixed, the cytoskeleton and the nucleus were immunofluorescence stained and scanned, and the cell shape and the fluorescent intensity were measured from fluorescent images to get the dimension information of osteocytes The 3D finite element (FE) cell models were then established based on the scanned image stacks. Several components such as the actin cortex, the cytoplasm, the nucleus, the cytoskeleton of F-actin and microtubules were considered in the model. The cell models in both 6 hours and 5 days groups were then imposed by three magnitudes (0.5, 10 and 15 Pa) of simulating fluid shear stress, with cell total displacement and the internal discrete components deformation calculated. The results showed that under the simulated microgravity: (1) the nuclear area and height statistically significantly increased, which made the ratio of membrane-cortex height to nucleus height statistically significantly decreased; (2) the fluid shear stress-induced maximum displacements and average displacements in the whole cell decreased, with the deformation decreasing amplitude was largest when exposed to 1.5Pa of fluid shear stress; (3) the fluid shear stress-induced deformation of cell membrane-cortex and cytoskeleton decreased, while the fluid shear stress-induced deformation of nucleus increased. The results suggested the mechanical behavior of whole osteocyte cell body was suppressed by simulated microgravity, and this decrement was enlarged with either the increasing amplitude of fluid shear stress or the duration of simulated microgravity. What's more, the mechanical behavior of membrane-cortex and cytoskeleton was suppressed by the simulated microgravity, which indicated the mechanotransduction process in the cell body may be further inhibited. On the contrary, the cell nucleus deformation increased under simulated microgravity, which may be related to either the decreased amount of cytoskeleton or the increased volume occupied proportion of nucleus in whole cell under the simulated microgravity. The numerical results supported our previous biological experiments, and showed particularly affected cellular components under the simulated microgravity. The computational study here may help us to better understand the mechanism of mechanosensitivity changes in osteocytes under simulated microgravity, and further to explore the mechanism of the bone loss in space flight.

An Overview of the State of the Art in Atomistic and Multiscale Simulation of Fracture

NASA Technical Reports Server (NTRS)

Saether, Erik; Yamakov, Vesselin; Phillips, Dawn R.; Glaessgen, Edward H.

2009-01-01

The emerging field of nanomechanics is providing a new focus in the study of the mechanics of materials, particularly in simulating fundamental atomic mechanisms involved in the initiation and evolution of damage. Simulating fundamental material processes using first principles in physics strongly motivates the formulation of computational multiscale methods to link macroscopic failure to the underlying atomic processes from which all material behavior originates. This report gives an overview of the state of the art in applying concurrent and sequential multiscale methods to analyze damage and failure mechanisms across length scales.

Simulation study on dynamics model of two kinds of on-orbit soft-contact mechanism

NASA Astrophysics Data System (ADS)

Ye, X.; Dong, Z. H.; Yang, F.

2018-05-01

Aiming at the problem that the operating conditions of the space manipulator is harsh and the space manipulator could not bear the large collision momentum, this paper presents a new concept and technical method, namely soft contact technology. Based on ADAMS dynamics software, this paper compares and simulates the mechanism model of on-orbit soft-contact mechanism based on the bionic model and the integrated double joint model. The main purpose is to verify the path planning ability and the momentum buffering ability based on the different design concept mechanism. The simulation results show that both the two mechanism models have the path planning function before the space target contact, and also has the momentum buffer and controllability during the space target contact process.

QM/MM MD and Free Energy Simulation Study of Methyl Transfer Processes Catalyzed by PKMTs and PRMTs.

PubMed

Chu, Yuzhuo; Guo, Hong

2015-09-01

Methyl transfer processes catalyzed by protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs) control important biological events including transcriptional regulation and cell signaling. One important property of these enzymes is that different PKMTs and PRMTs catalyze the formation of different methylated product (product specificity). These different methylation states lead to different biological outcomes. Here, we review the results of quantum mechanics/molecular mechanics molecular dynamics and free energy simulations that have been performed to study the reaction mechanism of PKMTs and PRMTs and the mechanism underlying the product specificity of the methyl transfer processes.

QM/MM MD and free energy simulation study of methyl transfer processes catalyzed by PKMTs and PRMTs.

PubMed

Chu, Yuzhuo; Guo, Hong

2015-01-16

Methyl transfer processes catalyzed by protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs) control important biological events including transcriptional regulation and cell signaling. One important property of these enzymes is that different PKMTs and PRMTs catalyze the formation of different methylated product (product specificity). These different methylation states lead to different biological outcomes. Here we review the results of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) and free energy simulations that have been performed to study the reaction mechanism of PKMTs and PRMTs and the mechanism underlying the product specificity of the methyl transfer processes.

Simulation and Analysis of Mechanical Properties of Silica Aerogels: From Rationalization to Prediction

PubMed Central

Ma, Hao; Zheng, Xiaoyang; Luo, Xuan; Yang, Fan

2018-01-01

Silica aerogels are highly porous 3D nanostructures and have exhibited excellent physio-chemical properties. Although silica aerogels have broad potential in many fields, the poor mechanical properties greatly limit further applications. In this study, we have applied the finite volume method (FVM) method to calculate the mechanical properties of silica aerogels with different geometric properties such as particle size, pore size, ligament diameter, etc. The FVM simulation results show that a power law correlation existing between relative density and mechanical properties (elastic modulus and yield stress) of silica aerogels, which are consistent with experimental and literature studies. In addition, depending on the relative densities, different strategies are proposed in order to synthesize silica aerogels with better mechanical performance by adjusting the distribution of pore size and ligament diameter of aerogels. Finally, the results suggest that it is possible to synthesize silica aerogels with ultra-low density as well as high strength and stiffness as long as the textural features are well controlled. It is believed that the FVM simulation methodology could be a valuable tool to study mechanical performance of silica aerogel based materials in the future. PMID:29385745

Simulation and Analysis of Mechanical Properties of Silica Aerogels: From Rationalization to Prediction.

PubMed

Ma, Hao; Zheng, Xiaoyang; Luo, Xuan; Yi, Yong; Yang, Fan

2018-01-30

Silica aerogels are highly porous 3D nanostructures and have exhibited excellent physio-chemical properties. Although silica aerogels have broad potential in many fields, the poor mechanical properties greatly limit further applications. In this study, we have applied the finite volume method (FVM) method to calculate the mechanical properties of silica aerogels with different geometric properties such as particle size, pore size, ligament diameter, etc. The FVM simulation results show that a power law correlation existing between relative density and mechanical properties (elastic modulus and yield stress) of silica aerogels, which are consistent with experimental and literature studies. In addition, depending on the relative densities, different strategies are proposed in order to synthesize silica aerogels with better mechanical performance by adjusting the distribution of pore size and ligament diameter of aerogels. Finally, the results suggest that it is possible to synthesize silica aerogels with ultra-low density as well as high strength and stiffness as long as the textural features are well controlled. It is believed that the FVM simulation methodology could be a valuable tool to study mechanical performance of silica aerogel based materials in the future.

Mechanical ventilation and thoracic artificial lung assistance during mechanical circulatory support with PUCA pump: in silico study.

PubMed

De Lazzari, Claudio; Genuini, Igino; Quatember, Bernhard; Fedele, Francesco

2014-02-01

Patients assisted with left ventricular assist device (LVAD) may require prolonged mechanical ventilatory assistance secondary to postoperative respiratory failure. The goal of this work is the study of the interdependent effects LVAD like pulsatile catheter (PUCA) pump and mechanical ventilatory support or thoracic artificial lung (TAL), by the hemodynamic point of view, using a numerical simulator of the human cardiovascular system. In the simulator, different circulatory sections are described using lumped parameter models. Lumped parameter models have been designed to describe the hydrodynamic behavior of both PUCA pump and thoracic artificial lung. Ventricular behavior atrial and septum functions were reproduced using variable elastance model. Starting from simulated pathological conditions we studied the effects produced on some hemodynamic variables by simultaneous PUCA pump, thoracic artificial lung or mechanical ventilation assistance. Thoracic artificial lung was applied in parallel or in hybrid mode. The effects of mechanical ventilation have been simulated by changing mean intrathoracic pressure value from -4 mmHg to +5 mmHg. The hemodynamic variables observed during the simulations, in different assisted conditions, were: left and right ventricular end systolic (diastolic) volume, systolic/diastolic aortic pressure, mean pulmonary arterial pressure, left and right mean atrial pressure, mean systemic venous pressure and the total blood flow. Results show that the application of PUCA (without mechanical ventilatory assistance) increases the total blood flow, reduces the left ventricular end systolic volume and increases the diastolic aortic pressure. Parallel TAL assistance increases the right ventricular end diastolic (systolic) volume reduction both when PUCA is switched "ON" and both when PUCA is switched "OFF". By switching "OFF" the PUCA pump, it seems that parallel thoracic artificial lung assistance produces a greater cardiac output (respect to hybrid TAL assistance). Results concerning PUCA and TAL interaction produced by simulations cannot be compared with "in vivo" results since they are not presented in literature. But results concerning the effects produced by LVAD and mechanical ventilation have a trend consistent with those presented in literature. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation.

PubMed

Shokuhfar, Ali; Arab, Behrouz

2013-09-01

Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA) with diethylenetriamine (DETA) curing agent, and to study the behavior of resulted epoxy polymer with different conversion rates. The constant-strain (static) approach was then applied to calculate the mechanical properties (Bulk, shear and Young's moduli, elastic stiffness constants, and Poisson's ratio) of the uncured and cross-linked systems. Estimated material properties were found to be in good agreement with experimental observations. Moreover, the dependency of mechanical properties on the cross linking density was investigated and revealed improvements in the mechanical properties with increasing the cross linking density. The radial distribution function (RDF) was also used to study the evolution of local structures of the simulated systems as a function of cross linking density.

Melt-growth dynamics in CdTe crystals

DOE PAGES

Zhou, X. W.; Ward, D. K.; Wong, B. M.; ...

2012-06-01

We use a new, quantum-mechanics-based bond-order potential (BOP) to reveal melt growth dynamics and fine scale defect formation mechanisms in CdTe crystals. Previous molecular dynamics simulations of semiconductors have shown qualitatively incorrect behavior due to the lack of an interatomic potential capable of predicting both crystalline growth and property trends of many transitional structures encountered during the melt → crystal transformation. Here, we demonstrate successful molecular dynamics simulations of melt growth in CdTe using a BOP that significantly improves over other potentials on property trends of different phases. Our simulations result in a detailed understanding of defect formation during themore » melt growth process. Equally important, we show that the new BOP enables defect formation mechanisms to be studied at a scale level comparable to empirical molecular dynamics simulation methods with a fidelity level approaching quantum-mechanical methods.« less

A high-compression electron gun for C6+ production: concept, simulations and mechanical design

NASA Astrophysics Data System (ADS)

Mertzig, Robert; Breitenfeldt, M.; Mathot, S.; Pitters, J.; Shornikov, A.; Wenander, F.

2017-07-01

In this paper we report on simulations and the mechanical design of a high-compression electron gun for an Electron Beam Ion Source (EBIS) dedicated for production of high intensity and high repetition rate pulses of bare carbon ions for injection into linac-based hadron therapy facilities. The gun is presently under construction at CERN to be retrofitted into the TwinEBIS test bench for experimental studies. We describe the design constraints, show results of numeric simulations and report on the mechanical design featuring several novel ideas. The reported design makes use of combined-function units with reduced number of mechanical joints that were carefully controlled and tuned during the manufacturing phase. The simulations addressed a wide range of topics including the influence of thermal effects, focusing optics, symmetry-breaking misalignments and injection into a full 5 T field.

Mechanical simulators for training for laparoscopic surgery in urology.

PubMed

Rassweiler, Jens; Klein, Jan; Teber, Dogu; Schulze, Michael; Frede, Thomas

2007-03-01

The introduction of laparoscopic surgery into urology has led to new training concepts differing significantly from previous concepts of training for open surgery. This paper focuses on the type and importance of mechanical simulators in laparoscopic training. On the basis of our own studies and experience with the development of various concepts of laparoscopic training, including different modules (i.e., Pelvi-trainer, animal models, clinical mentoring) since 1991, we reviewed the current literature concerning all types of simulators. We focused on training for laparoscopic ablative and reconstructive surgery using mechanical simulators. The principle of a mechanical simulator (i.e., a box with the possibility of trocar insertion) has not changed during the last decade. However, the types of Pelvi-trainers and the models used inside have been improved significantly. According to the task of the simulator, various sophisticated models have been developed, including standardized phantoms, animal organs, and even perfused segments of porcine organs. For laparoscopic suturing, various step-by-step training concepts have been presented. These can be used for determination of the ability of a physician with an interest in laparoscopic surgery, but also to classify the training status of a laparosopic surgeon. Training in laparoscopic surgery has become an important topic, not only in learning a procedure, but also in maintaining skills and preparing for the management of complications. For these purposes, mechanical simulators will definitely play an important role in the future.

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul

2015-01-21

The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, whichmore » is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.« less

Numerical simulation of volume-controlled mechanical ventilated respiratory system with 2 different lungs.

PubMed

Shi, Yan; Zhang, Bolun; Cai, Maolin; Zhang, Xiaohua Douglas

2017-09-01

Mechanical ventilation is a key therapy for patients who cannot breathe adequately by themselves, and dynamics of mechanical ventilation system is of great significance for life support of patients. Recently, models of mechanical ventilated respiratory system with 1 lung are used to simulate the respiratory system of patients. However, humans have 2 lungs. When the respiratory characteristics of 2 lungs are different, a single-lung model cannot reflect real respiratory system. In this paper, to illustrate dynamic characteristics of mechanical ventilated respiratory system with 2 different lungs, we propose a mathematical model of mechanical ventilated respiratory system with 2 different lungs and conduct experiments to verify the model. Furthermore, we study the dynamics of mechanical ventilated respiratory system with 2 different lungs. This research study can be used for improving the efficiency and safety of volume-controlled mechanical ventilation system. Copyright © 2016 John Wiley & Sons, Ltd.

Numerical simulations of internal wave generation by convection in water.

PubMed

Lecoanet, Daniel; Le Bars, Michael; Burns, Keaton J; Vasil, Geoffrey M; Brown, Benjamin P; Quataert, Eliot; Oishi, Jeffrey S

2015-06-01

Water's density maximum at 4°C makes it well suited to study internal gravity wave excitation by convection: an increasing temperature profile is unstable to convection below 4°C, but stably stratified above 4°C. We present numerical simulations of a waterlike fluid near its density maximum in a two-dimensional domain. We successfully model the damping of waves in the simulations using linear theory, provided we do not take the weak damping limit typically used in the literature. To isolate the physical mechanism exciting internal waves, we use the spectral code dedalus to run several simplified model simulations of our more detailed simulation. We use data from the full simulation as source terms in two simplified models of internal-wave excitation by convection: bulk excitation by convective Reynolds stresses, and interface forcing via the mechanical oscillator effect. We find excellent agreement between the waves generated in the full simulation and the simplified simulation implementing the bulk excitation mechanism. The interface forcing simulations overexcite high-frequency waves because they assume the excitation is by the "impulsive" penetration of plumes, which spreads energy to high frequencies. However, we find that the real excitation is instead by the "sweeping" motion of plumes parallel to the interface. Our results imply that the bulk excitation mechanism is a very accurate heuristic for internal-wave generation by convection.

Simulation on the internal structure of three-dimensional proximal tibia under different mechanical environments.

PubMed

Fang, Juan; Gong, He; Kong, Lingyan; Zhu, Dong

2013-12-20

Bone can adjust its morphological structure to adapt to the changes of mechanical environment, i.e. the bone structure change is related to mechanical loading. This implies that osteoarthritis may be closely associated with knee joint deformity. The purposes of this paper were to simulate the internal bone mineral density (BMD) change in three-dimensional (3D) proximal tibia under different mechanical environments, as well as to explore the relationship between mechanical environment and bone morphological abnormity. The right proximal tibia was scanned with CT to reconstruct a 3D proximal tibia model in MIMICS, then it was imported to finite element software ANSYS to establish 3D finite element model. The internal structure of 3D proximal tibia of young normal people was simulated using quantitative bone remodeling theory in combination with finite element method, then based on the changing pattern of joint contact force on the tibial plateau in valgus knees, the mechanical loading was changed, and the simulated normal tibia structure was used as initial structure to simulate the internal structure of 3D proximal tibia for old people with 6° valgus deformity. Four regions of interest (ROIs) were selected in the proximal tibia to quantitatively analyze BMD and compare with the clinical measurements. The simulation results showed that the BMD distribution in 3D proximal tibia was consistent with clinical measurements in normal knees and that in valgus knees was consistent with the measurement of patients with osteoarthritis in clinics. It is shown that the change of mechanical environment is the main cause for the change of subchondral bone structure, and being under abnormal mechanical environment for a long time may lead to osteoarthritis. Besides, the simulation method adopted in this paper can more accurately simulate the internal structure of 3D proximal tibia under different mechanical environments. It helps to better understand the mechanism of osteoarthritis and provides theoretical basis and computational method for the prevention and treatment of osteoarthritis. It can also serve as basis for further study on periprosthetic BMD changes after total knee arthroplasty, and provide a theoretical basis for optimization design of prosthesis.

Simulation on the internal structure of three-dimensional proximal tibia under different mechanical environments

PubMed Central

2013-01-01

Background Bone can adjust its morphological structure to adapt to the changes of mechanical environment, i.e. the bone structure change is related to mechanical loading. This implies that osteoarthritis may be closely associated with knee joint deformity. The purposes of this paper were to simulate the internal bone mineral density (BMD) change in three-dimensional (3D) proximal tibia under different mechanical environments, as well as to explore the relationship between mechanical environment and bone morphological abnormity. Methods The right proximal tibia was scanned with CT to reconstruct a 3D proximal tibia model in MIMICS, then it was imported to finite element software ANSYS to establish 3D finite element model. The internal structure of 3D proximal tibia of young normal people was simulated using quantitative bone remodeling theory in combination with finite element method, then based on the changing pattern of joint contact force on the tibial plateau in valgus knees, the mechanical loading was changed, and the simulated normal tibia structure was used as initial structure to simulate the internal structure of 3D proximal tibia for old people with 6° valgus deformity. Four regions of interest (ROIs) were selected in the proximal tibia to quantitatively analyze BMD and compare with the clinical measurements. Results The simulation results showed that the BMD distribution in 3D proximal tibia was consistent with clinical measurements in normal knees and that in valgus knees was consistent with the measurement of patients with osteoarthritis in clinics. Conclusions It is shown that the change of mechanical environment is the main cause for the change of subchondral bone structure, and being under abnormal mechanical environment for a long time may lead to osteoarthritis. Besides, the simulation method adopted in this paper can more accurately simulate the internal structure of 3D proximal tibia under different mechanical environments. It helps to better understand the mechanism of osteoarthritis and provides theoretical basis and computational method for the prevention and treatment of osteoarthritis. It can also serve as basis for further study on periprosthetic BMD changes after total knee arthroplasty, and provide a theoretical basis for optimization design of prosthesis. PMID:24359345

Study of changes in properties of solar sail materials from radiation exposure

NASA Technical Reports Server (NTRS)

Smith, T.

1977-01-01

Techniques for monitoring changes in preparation of solar sail materials resulting from space radiation simulation, stressing (e.g., thermal, mechanical) and exposure to terrestrial environments are developed. The properties of interest are: metallic coating deterioration, polymeric film deterioration, interfacial debonding and possible metallic coating diffusion into the polymeric film. Four accelerated tests were devised to simulate the possible degradation processes mentioned above. These four tests are: a thermal shock test to simulate the wide variation of temperature expected in space (260 C to -100 C), a cyclic temperature test to stimulate the 6 minute temperature cycle anticipated in space, a mechanical vibration test to simulate mechanical bonding, folding and handling, and a humidity test to simulate terrestrial environment effects. The techniques for monitoring property changes are: visual and microscopic examination, ellipsometry, surface potential difference (SPD), photoelectron emission (PEE), and water contact angles.

Zero-gravity movement studies

NASA Technical Reports Server (NTRS)

Badler, N. I.; Fishwick, P.; Taft, N.; Agrawala, M.

1985-01-01

The use of computer graphics to simulate the movement of articulated animals and mechanisms has a number of uses ranging over many fields. Human motion simulation systems can be useful in education, medicine, anatomy, physiology, and dance. In biomechanics, computer displays help to understand and analyze performance. Simulations can be used to help understand the effect of external or internal forces. Similarly, zero-gravity simulation systems should provide a means of designing and exploring the capabilities of hypothetical zero-gravity situations before actually carrying out such actions. The advantage of using a simulation of the motion is that one can experiment with variations of a maneuver before attempting to teach it to an individual. The zero-gravity motion simulation problem can be divided into two broad areas: human movement and behavior in zero-gravity, and simulation of articulated mechanisms.

Mechanical response of two polyimides through coarse-grained molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sudarkodi, V.; Sooraj, K.; Nair, Nisanth N.; Basu, Sumit; Parandekar, Priya V.; Sinha, Nishant K.; Prakash, Om; Tsotsis, Tom

2018-03-01

Coarse-grained molecular dynamics (MD) simulations allow us to predict the mechanical responses of polymers, starting merely with a description of their molecular architectures. It is interesting to ask whether, given two competing molecular architectures, coarse-grained MD simulations can predict the differences that can be expected in their mechanical responses. We have studied two crosslinked polyimides PMR15 and HFPE52—both used in high- temperature applications—to assess whether the subtle differences in their uniaxial stress-strain responses, revealed by experiments, can be reproduced by carefully coarse-grained MD models. The coarse graining procedure for PMR15 is outlined in this work, while the coarse grain forcefields for HFPE52 are borrowed from an earlier one (Pandiyan et al 2015 Macromol. Theory Simul. 24 513-20). We show that the stress-strain responses of both these polyimides are qualitatively reproduced, and important insights into their deformation and failure mechanisms are obtained. More importantly, the differences in the molecular architecture between the polyimides carry over to the differences in the stress-strain responses in a manner that parallels the experimental results. A critical assessment of the successes and shortcomings of predicting mechanical responses through coarse-grained MD simulations has been made.

Molecular dynamics simulations of classical sound absorption in a monatomic gas

NASA Astrophysics Data System (ADS)

Ayub, M.; Zander, A. C.; Huang, D. M.; Cazzolato, B. S.; Howard, C. Q.

2018-05-01

Sound wave propagation in argon gas is simulated using molecular dynamics (MD) in order to determine the attenuation of acoustic energy due to classical (viscous and thermal) losses at high frequencies. In addition, a method is described to estimate attenuation of acoustic energy using the thermodynamic concept of exergy. The results are compared against standing wave theory and the predictions of the theory of continuum mechanics. Acoustic energy losses are studied by evaluating various attenuation parameters and by comparing the changes in behavior at three different frequencies. This study demonstrates acoustic absorption effects in a gas simulated in a thermostatted molecular simulation and quantifies the classical losses in terms of the sound attenuation constant. The approach can be extended to further understanding of acoustic loss mechanisms in the presence of nanoscale porous materials in the simulation domain.

Molecular Dynamics of Dense Fluids: Simulation-Theory Symbiosis

NASA Astrophysics Data System (ADS)

Yip, Sidney

35 years ago Berni J. Alder showed the Boltzmann-Enskog kinetic theory failed to adequately account for the viscosity of fluids near solid density as determined by molecular dynamics simulation. This work, along with other notable simulation findings, provided great stimulus to the statistical mechanical studies of transport phenomena, particularly in dealing with collective effects in the time correlation functions of liquids. An extended theoretical challenge that remains partially resolved at best is the shear viscosity of supercooled liquids. How can one give a unified explanation of the so-called fragile and strong characteristic temperature behavior, with implications for the dynamics of glass transition? In this tribute on the occasion of his 90th birthday symposium, we recount a recent study where simulation, combined with heuristic (transition-state) and first principles (linear response) theories, identifies the molecular mechanisms governing glassy-state relaxation. Such an interplay between simulation and theory is progress from the early days; instead of simulation challenging theory, now simulation and theory complement each other.

Evaporation kinetics of Mg2SiO4 crystals and melts from molecular dynamics simulations

NASA Technical Reports Server (NTRS)

Kubicki, J. D.; Stolper, E. M.

1993-01-01

Computer simulations based on the molecular dynamics (MD) technique were used to study the mechanisms and kinetics of free evaporation from crystalline and molten forsterite (i.e., Mg2SiO4) on an atomic level. The interatomic potential employed for these simulations reproduces the energetics of bonding in forsterite and in gas-phase MgO and SiO2 reasonably accurately. Results of the simulation include predicted evaporation rates, diffusion rates, and reaction mechanisms for Mg2SiO4(s or l) yields 2Mg(g) + 20(g) + SiO2(g).

Investigation of the performances of PZT vs rare earth (BaLaTiO3) vibration based energy harvester

NASA Astrophysics Data System (ADS)

Pak, Nehemiah; Aris, Hasnizah; Nadia Taib, Bibi

2017-11-01

This study proposes the investigation of two piezoelectric material namely PZT and Lanthanum Doped Barium Titanate (BaLaTiO3) performance as a vibration based energy harvester. The piezoelectric material when applied mechanical stress or strain produces electricity through the piezoelectric effect. The vibration energy would exude mechanical energy and thus apply mechanical force on the energy harvester. The energy harvester would be designed and simulated using the piezoelectric material individually. The studied outputs are divided to frequency response, the load dependence, and the acceleration dependence whereby measurement are observed and taken at maximum power output. The simulation is done using the cantilevers design which employs d31 type of constants. Three different simulations to study the dependence of output power on the resonant frequency response, load and acceleration have found that material that exhibit highest power generation was the BaLaTiO3.

Tensile strength of Iß crystalline cellulose predicted by molecular dynamics simulation

Treesearch

Xiawa Wu; Robert J. Moon; Ashlie Martini

2014-01-01

The mechanical properties of Iß crystalline cellulose are studied using molecular dynamics simulation. A model Iß crystal is deformed in the three orthogonal directions at three different strain rates. The stress-strain behaviors for each case are analyzed and then used to calculate mechanical properties. The results show that the elastic modulus, Poisson's ratio...

On the Numerical Study of Heavy Rainfall in Taiwan

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo; Chen, Ching-Sen; Chen, Yi-Leng; Jou, Ben Jong-Dao; Lin, Pay-Liam; Starr, David OC. (Technical Monitor)

2001-01-01

Heavy rainfall events are frequently observed over the western side of the CMR (central mountain range), which runs through Taiwan in a north-south orientation, in a southwesterly flow regime and over the northeastern side of the CMR in a northeasterly flow regime. Previous studies have revealed the mechanisms by which the heavy rainfall events are formed. Some of them have examined characteristics of the heavy rainfall via numerical simulations. In this paper, some of the previous numerical studies on heavy rainfall events around Taiwan during the Mei-Yu season (May and June), summer (non-typhoon cases) and autumn will be reviewed. Associated mechanisms proposed from observational studies will be reviewed first, and then characteristics of numerically simulated heavy rainfall events will be presented. The formation mechanisms of heavy rainfall from simulated results and from observational analysis are then compared and discussed. Based on these previous modeling studies, we will also discuss what are the major observations and modeling processes which will be needed for understanding the heavy precipitation in the future.

Molecular-dynamics simulations of crosslinking and confinement effects on structure, segmental mobility and mechanics of filled elastomers

NASA Astrophysics Data System (ADS)

Davris, Theodoros; Lyulin, Alexey V.

2016-05-01

The significant drop of the storage modulus under uniaxial deformation (Payne effect) restrains the performance of the elastomer-based composites and the development of possible new applications. In this paper molecular-dynamics (MD) computer simulations using LAMMPS MD package have been performed to study the mechanical properties of a coarse-grained model of this family of nanocomposite materials. Our goal is to provide simulational insights into the viscoelastic properties of filled elastomers, and try to connect the macroscopic mechanics with composite microstructure, the strength of the polymer-filler interactions and the polymer mobility at different scales. To this end we simulate random copolymer films capped between two infinite solid (filler aggregate) walls. We systematically vary the strength of the polymer-substrate adhesion interactions, degree of polymer confinement (film thickness), polymer crosslinking density, and study their influence on the equilibrium and non-equilibrium structure, segmental dynamics, and the mechanical properties of the simulated systems. The glass-transition temperature increases once the mesh size became smaller than the chain radius of gyration; otherwise it remained invariant to mesh-size variations. This increase in the glass-transition temperature was accompanied by a monotonic slowing-down of segmental dynamics on all studied length scales. This observation is attributed to the correspondingly decreased width of the bulk density layer that was obtained in films whose thickness was larger than the end-to-end distance of the bulk polymer chains. To test this hypothesis additional simulations were performed in which the crystalline walls were replaced with amorphous or rough walls.

On the Origin of the Catalytic power of Caboxypetidase A and Other Metalloenzymes

PubMed Central

Kilshtain, Alexandra Vardi; Warshel, Arieh

2009-01-01

Zinc metalloenzymes play a major role in key biological processes and Carboxypeptidase-A (CPA) is a major prototype of such enzymes. The present work quantifies the energetics of the catalytic reaction of CPA and its mutants using the EVB approach. The simulations allow us to quantify the origin of the catalytic power of this enzyme and to examine different mechanistic alternatives. The first step of the analysis used experimental information to determine the activation energy of each assumed mechanism of the reference reaction without the enzyme. The next step of the analysis involved EVB simulations of the reference reaction and then a calibration of the simulations by forcing them to reproduce the energetics of the reference reaction, in each assumed mechanism. The calibrated EVB was then used in systematic simulations of the catalytic reaction in the protein environment, without changing any parameter. The simulations reproduced the observed rate enhancement in two feasible general acid-general base mechanisms (GAGB-1 and GAGB-2), although the calculations with the GAGB-2 mechanism underestimated the catalytic effect in some treatments. We also reproduced the catalytic effect in the R127A mutant. The mutation calculations indicate that the GAGB-2 mechanism is significantly less likely than the GAGB-1 mechanism. It is also found, that the enzyme loses all its catalytic effect without the metal. This and earlier studies show that the catalytic effect of the metal is not some constant electrostatic effect, that can be assessed from gas phase studies, but a reflection of the dielectric effect of the specific environment. PMID:19480013

Inactivation of TEM-1 by avibactam (NXL-104): insights from quantum mechanics/molecular mechanics metadynamics simulations.

PubMed

Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco; Colombo, Giorgio

2014-08-12

The fast and constant development of drug-resistant bacteria represents a serious medical emergence. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this context, avibactam represents a promising, innovative inhibitor of beta-lactamases with a novel molecular structure compared to previously developed inhibitors, showing a promising inhibitory activity toward a significant number of beta-lactamase enzymes. In this work, we studied, at the atomistic level, the mechanisms of formation of the covalent complex between avibactam and TEM-1, an experimentally well-characterized class A beta-lactamase, using classical and quantum mechanics/molecular mechanics (QM/MM) simulations combined with metadynamics. Our simulations provide a detailed structural and energetic picture of the molecular steps leading to the formation of the avibactam/TEM-1 covalent adduct. In particular, they support a mechanism in which the rate-determining step is the water-assisted Glu166 deprotonation by Ser70. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements. Additionally, our simulations highlight the important role of Lys73 in assisting the Ser70 and Ser130 deprotonations. While based on the specific case of the avibactam/TEM-1, the simple protocol we present here can be immediately extended and applied to the study of covalent complex formation in different enzyme-inhibitor pairs.

Differential transcriptional regulation by alternatively designed mechanisms: A mathematical modeling approach.

PubMed

Yildirim, Necmettin; Aktas, Mehmet Emin; Ozcan, Seyma Nur; Akbas, Esra; Ay, Ahmet

2017-01-01

Cells maintain cellular homeostasis employing different regulatory mechanisms to respond external stimuli. We study two groups of signal-dependent transcriptional regulatory mechanisms. In the first group, we assume that repressor and activator proteins compete for binding to the same regulatory site on DNA (competitive mechanisms). In the second group, they can bind to different regulatory regions in a noncompetitive fashion (noncompetitive mechanisms). For both competitive and noncompetitive mechanisms, we studied the gene expression dynamics by increasing the repressor or decreasing the activator abundance (inhibition mechanisms), or by decreasing the repressor or increasing the activator abundance (activation mechanisms). We employed delay differential equation models. Our simulation results show that the competitive and noncompetitive inhibition mechanisms exhibit comparable repression effectiveness. However, response time is fastest in the noncompetitive inhibition mechanism due to increased repressor abundance, and slowest in the competitive inhibition mechanism by increased repressor level. The competitive and noncompetitive inhibition mechanisms through decreased activator abundance show comparable and moderate response times, while the competitive and noncompetitive activation mechanisms by increased activator protein level display more effective and faster response. Our study exemplifies the importance of mathematical modeling and computer simulation in the analysis of gene expression dynamics.

Numerical modeling of the fracture process in a three-unit all-ceramic fixed partial denture.

PubMed

Kou, Wen; Kou, Shaoquan; Liu, Hongyuan; Sjögren, Göran

2007-08-01

The main objectives were to examine the fracture mechanism and process of a ceramic fixed partial denture (FPD) framework under simulated mechanical loading using a recently developed numerical modeling code, the R-T(2D) code, and also to evaluate the suitability of R-T(2D) code as a tool for this purpose. Using the recently developed R-T(2D) code the fracture mechanism and process of a 3U yttria-tetragonal zirconia polycrystal ceramic (Y-TZP) FPD framework was simulated under static loading. In addition, the fracture pattern obtained using the numerical simulation was compared with the fracture pattern obtained in a previous laboratory test. The result revealed that the framework fracture pattern obtained using the numerical simulation agreed with that observed in a previous laboratory test. Quasi-photoelastic stress fringe pattern and acoustic emission showed that the fracture mechanism was tensile failure and that the crack started at the lower boundary of the framework. The fracture process could be followed both in step-by-step and step-in-step. Based on the findings in the current study, the R-T(2D) code seems suitable for use as a complement to other tests and clinical observations in studying stress distribution, fracture mechanism and fracture processes in ceramic FPD frameworks.

A New Numerical Simulation technology of Multistage Fracturing in Horizontal Well

NASA Astrophysics Data System (ADS)

Cheng, Ning; Kang, Kaifeng; Li, Jianming; Liu, Tao; Ding, Kun

2017-11-01

Horizontal multi-stage fracturing is recognized the effective development technology of unconventional oil resources. Geological mechanics in the numerical simulation of hydraulic fracturing technology occupies very important position, compared with the conventional numerical simulation technology, because of considering the influence of geological mechanics. New numerical simulation of hydraulic fracturing can more effectively optimize the design of fracturing and evaluate the production after fracturing. This paper studies is based on the three-dimensional stress and rock physics parameters model, using the latest fluid-solid coupling numerical simulation technology to engrave the extension process of fracture and describes the change of stress field in fracturing process, finally predict the production situation.

Quantum Corrections to the 'Atomistic' MOSFET Simulations

NASA Technical Reports Server (NTRS)

Asenov, Asen; Slavcheva, G.; Kaya, S.; Balasubramaniam, R.

2000-01-01

We have introduced in a simple and efficient manner quantum mechanical corrections in our 3D 'atomistic' MOSFET simulator using the density gradient formalism. We have studied in comparison with classical simulations the effect of the quantum mechanical corrections on the simulation of random dopant induced threshold voltage fluctuations, the effect of the single charge trapping on interface states and the effect of the oxide thickness fluctuations in decanano MOSFETs with ultrathin gate oxides. The introduction of quantum corrections enhances the threshold voltage fluctuations but does not affect significantly the amplitude of the random telegraph noise associated with single carrier trapping. The importance of the quantum corrections for proper simulation of oxide thickness fluctuation effects has also been demonstrated.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sotomayor, Marcos

Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictionsmore » must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.« less

Simulations of neuromuscular control in lamprey swimming.

PubMed Central

Ekeberg, O; Grillner, S

1999-01-01

The neuronal generation of vertebrate locomotion has been extensively studied in the lamprey. Models at different levels of abstraction are being used to describe this system, from abstract nonlinear oscillators to interconnected model neurons comprising multiple compartments and a Hodgkin-Huxley representation of the most relevant ion channels. To study the role of sensory feedback by simulation, it eventually also becomes necessary to incorporate the mechanical movements in the models. By using simplifying models of muscle activation, body mechanics, counteracting water forces, and sensory feedback through stretch receptors and vestibular organs, we have been able to close the feedback loop to enable studies of the interaction between the neuronal and the mechanical systems. The neuromechanical simulations reveal that the currently known network is sufficient for generating a whole repertoire of swimming patterns. Swimming at different speeds and with different wavelengths, together with the performance of lateral turns can all be achieved by simply varying the brainstem input. The neuronal mechanisms behind pitch and roll manoeuvres are less clear. We have put forward a 'crossed-oscillators' hypothesis where partly separate dorsal and ventral circuits are postulated. Neuromechanical simulations of this system show that it is also capable of generating realistic pitch turns and rolls, and that vestibular signals can stabilize the posture during swimming. PMID:10382223

Mechanisms of Regulating Tissue Elongation in Drosophila Wing: Impact of Oriented Cell Divisions, Oriented Mechanical Forces, and Reduced Cell Size

PubMed Central

Li, Yingzi; Naveed, Hammad; Kachalo, Sema; Xu, Lisa X.; Liang, Jie

2014-01-01

Regulation of cell growth and cell division plays fundamental roles in tissue morphogenesis. However, the mechanisms of regulating tissue elongation through cell growth and cell division are still not well understood. The wing imaginal disc of Drosophila provides a model system that has been widely used to study tissue morphogenesis. Here we use a recently developed two-dimensional cellular model to study the mechanisms of regulating tissue elongation in Drosophila wing. We simulate the effects of directional cues on tissue elongation. We also computationally analyze the role of reduced cell size. Our simulation results indicate that oriented cell divisions, oriented mechanical forces, and reduced cell size can all mediate tissue elongation, but they function differently. We show that oriented cell divisions and oriented mechanical forces act as directional cues during tissue elongation. Between these two directional cues, oriented mechanical forces have a stronger influence than oriented cell divisions. In addition, we raise the novel hypothesis that reduced cell size may significantly promote tissue elongation. We find that reduced cell size alone cannot drive tissue elongation. However, when combined with directional cues, such as oriented cell divisions or oriented mechanical forces, reduced cell size can significantly enhance tissue elongation in Drosophila wing. Furthermore, our simulation results suggest that reduced cell size has a short-term effect on cell topology by decreasing the frequency of hexagonal cells, which is consistent with experimental observations. Our simulation results suggest that cell divisions without cell growth play essential roles in tissue elongation. PMID:24504016

Action simulation: time course and representational mechanisms

PubMed Central

Springer, Anne; Parkinson, Jim; Prinz, Wolfgang

2013-01-01

The notion of action simulation refers to the ability to re-enact foreign actions (i.e., actions observed in other individuals). Simulating others' actions implies a mirroring of their activities, based on one's own sensorimotor competencies. Here, we discuss theoretical and experimental approaches to action simulation and the study of its representational underpinnings. One focus of our discussion is on the timing of internal simulation and its relation to the timing of external action, and a paradigm that requires participants to predict the future course of actions that are temporarily occluded from view. We address transitions between perceptual mechanisms (referring to action representation before and after occlusion) and simulation mechanisms (referring to action representation during occlusion). Findings suggest that action simulation runs in real-time; acting on newly created action representations rather than relying on continuous visual extrapolations. A further focus of our discussion pertains to the functional characteristics of the mechanisms involved in predicting other people's actions. We propose that two processes are engaged, dynamic updating and static matching, which may draw on both semantic and motor information. In a concluding section, we discuss these findings in the context of broader theoretical issues related to action and event representation, arguing that a detailed functional analysis of action simulation in cognitive, neural, and computational terms may help to further advance our understanding of action cognition and motor control. PMID:23847563

Troubleshooting Instruction in Vocational-Technical Education Via Dynamic Simulation. Final Report.

ERIC Educational Resources Information Center

Finch, Curtis R.

This study was designed to examine the feasibility of using simulation as a means of teaching vocational-technical students to detect and identify malfunctions in selected electrical and mechanical systems. A dynamic simulator was employed which features interchangeable panels and logic that permits the simulation of electrical or mechanical…

Influence of hip joint simulator design and mechanics on the wear and creep of metal-on-polyethylene bearings

PubMed Central

Ali, Murat; Al-Hajjar, Mazen; Partridge, Susan; Williams, Sophie; Fisher, John; Jennings, Louise M

2016-01-01

Hip joint simulators are used extensively for preclinical testing of hip replacements. The variation in simulator design and test conditions used worldwide can affect the tribological performance of polyethylene. The aim of this study was to assess the effects of simulator mechanics and design on the wear and creep of ultra-high-molecular-weight polyethylene. In the first part of this study, an electromechanical simulator and pneumatic simulator were used to compare the wear and creep of metal-on-polyethylene components under the same standard gait conditions. In the second part of the study, the same electromechanical hip joint simulator was used to investigate the influence of kinematics on wear. Higher wear rates and penetration depths were observed from the electromechanical simulator compared with the pneumatic simulator. When adduction/abduction was introduced to the gait cycle, there was no significant difference in wear with that obtained under the gait cycle condition without adduction/abduction. This study confirmed the influence of hip simulator design and loading conditions on the wear of polyethylene, and therefore direct comparisons of absolute wear rates between different hip joint simulators should be avoided. This study also confirmed that the resulting wear path was the governing factor in obtaining clinically relevant wear rates, and this can be achieved with either two axes or three axes of rotations. However, three axes of rotation (with the inclusion of adduction/abduction) more closely replicate clinical conditions and should therefore be the design approach for newly developed hip joint simulators used for preclinical testing. PMID:27160559

Influence of hip joint simulator design and mechanics on the wear and creep of metal-on-polyethylene bearings.

PubMed

Ali, Murat; Al-Hajjar, Mazen; Partridge, Susan; Williams, Sophie; Fisher, John; Jennings, Louise M

2016-05-01

Hip joint simulators are used extensively for preclinical testing of hip replacements. The variation in simulator design and test conditions used worldwide can affect the tribological performance of polyethylene. The aim of this study was to assess the effects of simulator mechanics and design on the wear and creep of ultra-high-molecular-weight polyethylene. In the first part of this study, an electromechanical simulator and pneumatic simulator were used to compare the wear and creep of metal-on-polyethylene components under the same standard gait conditions. In the second part of the study, the same electromechanical hip joint simulator was used to investigate the influence of kinematics on wear. Higher wear rates and penetration depths were observed from the electromechanical simulator compared with the pneumatic simulator. When adduction/abduction was introduced to the gait cycle, there was no significant difference in wear with that obtained under the gait cycle condition without adduction/abduction. This study confirmed the influence of hip simulator design and loading conditions on the wear of polyethylene, and therefore direct comparisons of absolute wear rates between different hip joint simulators should be avoided. This study also confirmed that the resulting wear path was the governing factor in obtaining clinically relevant wear rates, and this can be achieved with either two axes or three axes of rotations. However, three axes of rotation (with the inclusion of adduction/abduction) more closely replicate clinical conditions and should therefore be the design approach for newly developed hip joint simulators used for preclinical testing. © IMechE 2016.

Using molecular dynamics simulations and finite element method to study the mechanical properties of nanotube reinforced polyethylene and polyketone

NASA Astrophysics Data System (ADS)

Rouhi, S.; Alizadeh, Y.; Ansari, R.; Aryayi, M.

2015-09-01

Molecular dynamics simulations are used to study the mechanical behavior of single-walled carbon nanotube reinforced composites. Polyethylene and polyketone are selected as the polymer matrices. The effects of nanotube atomic structure and diameter on the mechanical properties of polymer matrix nanocomposites are investigated. It is shown that although adding nanotube to the polymer matrix raises the longitudinal elastic modulus significantly, the transverse tensile and shear moduli do not experience important change. As the previous finite element models could not be used for polymer matrices with the atom types other than carbon, molecular dynamics simulations are used to propose a finite element model which can be used for any polymer matrices. It is shown that this model can predict Young’s modulus with an acceptable accuracy.

Continuum damage modeling and simulation of hierarchical dental enamel

NASA Astrophysics Data System (ADS)

Ma, Songyun; Scheider, Ingo; Bargmann, Swantje

2016-05-01

Dental enamel exhibits high fracture toughness and stiffness due to a complex hierarchical and graded microstructure, optimally organized from nano- to macro-scale. In this study, a 3D representative volume element (RVE) model is adopted to study the deformation and damage behavior of the fibrous microstructure. A continuum damage mechanics model coupled to hyperelasticity is developed for modeling the initiation and evolution of damage in the mineral fibers as well as protein matrix. Moreover, debonding of the interface between mineral fiber and protein is captured by employing a cohesive zone model. The dependence of the failure mechanism on the aspect ratio of the mineral fibers is investigated. In addition, the effect of the interface strength on the damage behavior is studied with respect to geometric features of enamel. Further, the effect of an initial flaw on the overall mechanical properties is analyzed to understand the superior damage tolerance of dental enamel. The simulation results are validated by comparison to experimental data from micro-cantilever beam testing at two hierarchical levels. The transition of the failure mechanism at different hierarchical levels is also well reproduced in the simulations.

Mechanical stability of propped hydraulic fractures: A numerical study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asgian, M.I.; Cundall, P.A.; Brady, B.H.

1995-03-01

Proppant is sometimes produced along with hydrocarbons in hydraulically fractured petroleum wells. Sometimes 10% to 20% of the proppant is backproduced, which can lead to damaged equipment and downtime. Furthermore, proppant flowback can lead to a substantial loss of fracture conductivity. A numerical study was conducted to help understand what conditions are likely to lead to proppant flowback. In the simulations, the mechanical interaction of a larger number (several thousand) individual proppant grains was modeled with a distinct-element-type code. The numerical simulations show that hydraulic fractures propped with cohesionless, unbonded proppant fail under closure stress at a critical ratio ofmore » mean grain diameter to fracture width. This is consistent with published laboratory studies. The simulations identify the mechanism (arch failure) that triggers the mechanical instability and also show that the primary way that drawdowns (less than {approx} 75 psi/ft) affect proppant flowback is to transport loose proppant grains in front of the stable arch to the wellbore. Drawdowns > 75 psi/ft are sufficient to destabilize the arch and to cause progressive failure of the propped fractures.« less

Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour.

PubMed

Land, Sander; Gurev, Viatcheslav; Arens, Sander; Augustin, Christoph M; Baron, Lukas; Blake, Robert; Bradley, Chris; Castro, Sebastian; Crozier, Andrew; Favino, Marco; Fastl, Thomas E; Fritz, Thomas; Gao, Hao; Gizzi, Alessio; Griffith, Boyce E; Hurtado, Daniel E; Krause, Rolf; Luo, Xiaoyu; Nash, Martyn P; Pezzuto, Simone; Plank, Gernot; Rossi, Simone; Ruprecht, Daniel; Seemann, Gunnar; Smith, Nicolas P; Sundnes, Joakim; Rice, J Jeremy; Trayanova, Natalia; Wang, Dafang; Jenny Wang, Zhinuo; Niederer, Steven A

2015-12-08

Models of cardiac mechanics are increasingly used to investigate cardiac physiology. These models are characterized by a high level of complexity, including the particular anisotropic material properties of biological tissue and the actively contracting material. A large number of independent simulation codes have been developed, but a consistent way of verifying the accuracy and replicability of simulations is lacking. To aid in the verification of current and future cardiac mechanics solvers, this study provides three benchmark problems for cardiac mechanics. These benchmark problems test the ability to accurately simulate pressure-type forces that depend on the deformed objects geometry, anisotropic and spatially varying material properties similar to those seen in the left ventricle and active contractile forces. The benchmark was solved by 11 different groups to generate consensus solutions, with typical differences in higher-resolution solutions at approximately 0.5%, and consistent results between linear, quadratic and cubic finite elements as well as different approaches to simulating incompressible materials. Online tools and solutions are made available to allow these tests to be effectively used in verification of future cardiac mechanics software.

The atomic-scale nucleation mechanism of NiTi metallic glasses upon isothermal annealing studied via molecular dynamics simulations.

PubMed

Li, Yang; Li, JiaHao; Liu, BaiXin

2015-10-28

Nucleation is one of the most essential transformation paths in phase transition and exerts a significant influence on the crystallization process. Molecular dynamics simulations were performed to investigate the atomic-scale nucleation mechanisms of NiTi metallic glasses upon devitrification at various temperatures (700 K, 750 K, 800 K, and 850 K). Our simulations reveal that at 700 K and 750 K, nucleation is polynuclear with high nucleation density, while at 800 K it is mononuclear. The underlying nucleation mechanisms have been clarified, manifesting that nucleation can be induced either by the initial ordered clusters (IOCs) or by the other precursors of nuclei evolved directly from the supercooled liquid. IOCs and other precursors stem from the thermal fluctuations of bond orientational order in supercooled liquids during the quenching process and during the annealing process, respectively. The simulation results not only elucidate the underlying nucleation mechanisms varied with temperature, but also unveil the origin of nucleation. These discoveries offer new insights into the devitrification mechanism of metallic glasses.

Reactive Molecular Dynamics Simulations to Understand Mechanical Response of Thaumasite under Temperature and Strain Rate Effects.

PubMed

Hajilar, Shahin; Shafei, Behrouz; Cheng, Tao; Jaramillo-Botero, Andres

2017-06-22

Understanding the structural, thermal, and mechanical properties of thaumasite is of great interest to the cement industry, mainly because it is the phase responsible for the aging and deterioration of civil infrastructures made of cementitious materials attacked by external sources of sulfate. Despite the importance, effects of temperature and strain rate on the mechanical response of thaumasite had remained unexplored prior to the current study, in which the mechanical properties of thaumasite are fully characterized using the reactive molecular dynamics (RMD) method. With employing a first-principles based reactive force field, the RMD simulations enable the description of bond dissociation and formation under realistic conditions. From the stress-strain curves of thaumasite generated in the x, y, and z directions, the tensile strength, Young's modulus, and fracture strain are determined for the three orthogonal directions. During the course of each simulation, the chemical bonds undergoing tensile deformations are monitored to reveal the bonds responsible for the mechanical strength of thaumasite. The temperature increase is found to accelerate the bond breaking rate and consequently the degradation of mechanical properties of thaumasite, while the strain rate only leads to a slight enhancement of them for the ranges considered in this study.

Excavator Design Validation

NASA Technical Reports Server (NTRS)

Pholsiri, Chalongrath; English, James; Seberino, Charles; Lim, Yi-Je

2010-01-01

The Excavator Design Validation tool verifies excavator designs by automatically generating control systems and modeling their performance in an accurate simulation of their expected environment. Part of this software design includes interfacing with human operations that can be included in simulation-based studies and validation. This is essential for assessing productivity, versatility, and reliability. This software combines automatic control system generation from CAD (computer-aided design) models, rapid validation of complex mechanism designs, and detailed models of the environment including soil, dust, temperature, remote supervision, and communication latency to create a system of high value. Unique algorithms have been created for controlling and simulating complex robotic mechanisms automatically from just a CAD description. These algorithms are implemented as a commercial cross-platform C++ software toolkit that is configurable using the Extensible Markup Language (XML). The algorithms work with virtually any mobile robotic mechanisms using module descriptions that adhere to the XML standard. In addition, high-fidelity, real-time physics-based simulation algorithms have also been developed that include models of internal forces and the forces produced when a mechanism interacts with the outside world. This capability is combined with an innovative organization for simulation algorithms, new regolith simulation methods, and a unique control and study architecture to make powerful tools with the potential to transform the way NASA verifies and compares excavator designs. Energid's Actin software has been leveraged for this design validation. The architecture includes parametric and Monte Carlo studies tailored for validation of excavator designs and their control by remote human operators. It also includes the ability to interface with third-party software and human-input devices. Two types of simulation models have been adapted: high-fidelity discrete element models and fast analytical models. By using the first to establish parameters for the second, a system has been created that can be executed in real time, or faster than real time, on a desktop PC. This allows Monte Carlo simulations to be performed on a computer platform available to all researchers, and it allows human interaction to be included in a real-time simulation process. Metrics on excavator performance are established that work with the simulation architecture. Both static and dynamic metrics are included.

A parametric study of surface roughness and bonding mechanisms of aluminum alloys with epoxies: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Timilsina, Rajendra; Termaath, Stephanie

The marine environment is highly aggressive towards most materials. However, aluminium-magnesium alloys (Al-Mg, specifically, 5xxx series) have exceptionally long service life in such aggressive marine environments. For instance, an Al-Mg alloy, AA5083, is extensively used in naval structures because of its good mechanical strength, formability, seawater corrosion resistance and weldability. However, bonding mechanisms of these alloys with epoxies in a rough surface environment are not fully understood yet. It requires a rigorous investigation at molecular or atomic levels. We performed a molecular dynamics simulation to study an adherend surface preparation and surface bonding mechanisms of Al-Mg alloy (AA5083) with different epoxies by developing several computer models. Various distributions of surface roughness are introduced in the models and performed molecular dynamics simulations. Formation of a beta phase (Al3Mg2) , microstructures, bonding energies at the interface, bonding strengths and durability are investigated. Office of Naval Research.

Simulation studies of nucleation of ferroelectric polarization reversal.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brennecka, Geoffrey L.; Winchester, Benjamin Michael

2014-08-01

Electric field-induced reversal of spontaneous polarization is the defining characteristic of a ferroelectric material, but the process(es) and mechanism(s) associated with the initial nucleation of reverse-polarity domains are poorly understood. This report describes studies carried out using phase field modeling of LiTaO 3, a relatively simple prototype ferroelectric material, in order to explore the effects of either mechanical deformation or optically-induced free charges on nucleation and resulting domain configuration during field-induced polarization reversal. Conditions were selected to approximate as closely as feasible those of accompanying experimental work in order to provide not only support for the experimental work but alsomore » ensure that additional experimental validation of the simulations could be carried out in the future. Phase field simulations strongly support surface mechanical damage/deformation as effective for dramatically reducing the overall coercive field (Ec) via local field enhancements. Further, optically-nucleated polarization reversal appears to occur via stabilization of latent nuclei via the charge screening effects of free charges.« less

A feasibility study on the design and walking operation of a biped locomotor via dynamic simulation

NASA Astrophysics Data System (ADS)

Wang, Mingfeng; Ceccarelli, Marco; Carbone, Giuseppe

2016-06-01

A feasibility study on the mechanical design and walking operation of a Cassino biped locomotor is presented in this paper. The biped locomotor consists of two identical 3 degrees-of-freedom tripod leg mechanisms with a parallel manipulator architecture. Planning of the biped walking gait is performed by coordinating the motions of the two leg mechanisms and waist. A threedimensional model is elaborated in SolidWorks® environment in order to characterize a feasible mechanical design. Dynamic simulation is carried out in MSC.ADAMS® environment with the aims of characterizing and evaluating the dynamic walking performance of the proposed design. Simulation results show that the proposed biped locomotor with proper input motions of linear actuators performs practical and feasible walking on flat surfaces with limited actuation and reaction forces between its feet and the ground. A preliminary prototype of the biped locomotor is built for the purpose of evaluating the operation performance of the biped walking gait of the proposed locomotor.

Study the bonding mechanism of binders on hydroxyapatite surface and mechanical properties for 3DP fabrication bone scaffolds.

PubMed

Wei, Qinghua; Wang, Yanen; Li, Xinpei; Yang, Mingming; Chai, Weihong; Wang, Kai; zhang, Yingfeng

2016-04-01

In 3DP fabricating artificial bone scaffolds process, the interaction mechanism between binder and bioceramics power determines the microstructure and macro mechanical properties of Hydroxyapatite (HA) bone scaffold. In this study, we applied Molecular Dynamics (MD) methods to investigating the bonding mechanism and essence of binders on the HA crystallographic planes for 3DP fabrication bone scaffolds. The cohesive energy densities of binders and the binding energies, PCFs g(r), mechanical properties of binder/HA interaction models were analyzed through the MD simulation. Additionally, we prepared the HA bone scaffold specimens with different glues by 3DP additive manufacturing, and tested their mechanical properties by the electronic universal testing machine. The simulation results revealed that the relationship of the binding energies between binders and HA surface is consistent with the cohesive energy densities of binders, which is PAM/HA>PVA/HA>PVP/HA. The PCFs g(r) indicated that their interfacial interactions mainly attribute to the ionic bonds and hydrogen bonds which formed between the polar atoms, functional groups in binder polymer and the Ca, -OH in HA. The results of mechanical experiments verified the relationship of Young׳s modulus for three interaction models in simulation, which is PVA/HA>PAM/HA>PVP/HA. But the trend of compressive strength is PAM/HA>PVA/HA>PVP/HA, this is consistent with the binding energies of simulation. Therefore, the Young׳s modulus of bone scaffolds are limited by the Young׳s modulus of binders, and the compressive strength is mainly decided by the viscosity of binder. Finally, the major reasons for differences in mechanical properties between simulation and experiment were found, the space among HA pellets and the incomplete infiltration of glue were the main reasons influencing the mechanical properties of 3DP fabrication HA bone scaffolds. These results provide useful information in choosing binder for 3DP fabrication bone scaffolds and understanding the interaction mechanism between binder and HA bioceramics power. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mechanical properties of a collagen fibril under simulated degradation.

PubMed

Malaspina, David C; Szleifer, Igal; Dhaher, Yasin

2017-11-01

Collagen fibrils are a very important component in most of the connective tissue in humans. An important process associated with several physiological and pathological states is the degradation of collagen. Collagen degradation is usually mediated by enzymatic and non-enzymatic processes. In this work we use molecular dynamics simulations to study the influence of simulated degradation on the mechanical properties of the collagen fibril. We applied tensile stress to the collagen fiber at different stages of degradation. We compared the difference in the fibril mechanical priorities due the removal of enzymatic crosslink, surface degradation and volumetric degradation. As anticipated, our results indicated that, regardless of the degradation scenario, fibril mechanical properties is reduced. The type of degradation mechanism (crosslink, surface or volumetric) expressed differential effect on the change in the fibril stiffness. Our simulation results showed dramatic change in the fibril stiffness with a small amount of degradation. This suggests that the hierarchical structure of the fibril is a key component for the toughness and is very sensitive to changes in the organization of the fibril. The overall results are intended to provide a theoretical framework for the understanding the mechanical behavior of collagen fibrils under degradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

AdapChem

NASA Technical Reports Server (NTRS)

Oluwole, Oluwayemisi O.; Wong, Hsi-Wu; Green, William

2012-01-01

AdapChem software enables high efficiency, low computational cost, and enhanced accuracy on computational fluid dynamics (CFD) numerical simulations used for combustion studies. The software dynamically allocates smaller, reduced chemical models instead of the larger, full chemistry models to evolve the calculation while ensuring the same accuracy to be obtained for steady-state CFD reacting flow simulations. The software enables detailed chemical kinetic modeling in combustion CFD simulations. AdapChem adapts the reaction mechanism used in the CFD to the local reaction conditions. Instead of a single, comprehensive reaction mechanism throughout the computation, a dynamic distribution of smaller, reduced models is used to capture accurately the chemical kinetics at a fraction of the cost of the traditional single-mechanism approach.

TOWARDS ICE FORMATION CLOSURE IN MIXED-PHASE BOUNDARY LAYER CLOUDS DURING ISDAC

NASA Astrophysics Data System (ADS)

Avramov, A.; Ackerman, A. S.; Fridlind, A. M.; van Diedenhoven, B.; Korolev, A. V.

2009-12-01

Mixed-phase stratus clouds are ubiquitous in the Arctic during the winter and transition seasons. Despite their important role in various climate feedback mechanisms they are not well understood and are difficult to represent faithfully in cloud models. In particular, models of all types experience difficulties reproducing observed ice concentrations and liquid/ice water partitioning in these clouds. Previous studies have demonstrated that simulated ice concentrations and ice water content are critically dependent on ice nucleation modes and ice crystal habit assumed in simulations. In this study we use large-eddy simulations with size-resolved microphysics to determine whether uncertainties in ice nucleus concentrations, ice nucleation mechanisms, ice crystal habits and large-scale forcing are sufficient to account for the difference between simulated and observed quantities. We present results of simulations of two case studies based on observations taken during the recent Indirect and Semi-Direct Aerosol Campaign (ISDAC) on April 8 and 26, 2008. The model simulations are evaluated through extensive comparison with in-situ observations and ground-based remote sensing measurements.

Simulated effect on the compressive and shear mechanical properties of bionic integrated honeycomb plates.

PubMed

He, Chenglin; Chen, Jinxiang; Wu, Zhishen; Xie, Juan; Zu, Qiao; Lu, Yun

2015-05-01

Honeycomb plates can be applied in many fields, including furniture manufacturing, mechanical engineering, civil engineering, transportation and aerospace. In the present study, we discuss the simulated effect on the mechanical properties of bionic integrated honeycomb plates by investigating the compressive and shear failure modes and the mechanical properties of trabeculae reinforced by long or short fibers. The results indicate that the simulated effect represents approximately 80% and 70% of the compressive and shear strengths, respectively. Compared with existing bionic samples, the mass-specific strength was significantly improved. Therefore, this integrated honeycomb technology remains the most effective method for the trial manufacturing of bionic integrated honeycomb plates. The simulated effect of the compressive rigidity is approximately 85%. The short-fiber trabeculae have an advantage over the long-fiber trabeculae in terms of shear rigidity, which provides new evidence for the application of integrated bionic honeycomb plates. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular dynamics simulations for mechanical properties of borophene: parameterization of valence force field model and Stillinger-Weber potential

PubMed Central

Zhou, Yu-Ping; Jiang, Jin-Wu

2017-01-01

While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983

Robotic simulation of identical athletic-task kinematics on cadaveric limbs exhibits a lack of differences in knee mechanics between contralateral pairs

PubMed Central

Bates, Nathaniel A.; McPherson, April L.; Nesbitt, Rebecca J.; Shearn, Jason T.; Myer, Gregory D.; Hewett, Timothy E.

2017-01-01

Limb asymmetry is a known factor for increased ACL injury risk. These asymmetries are normally observed during in vivo testing. Prior studies have developed in vitro testing methodologies driven by in vivo kinematics to investigate knee mechanics relative to ACL injury. The objective of this study was to determine if mechanical side-to-side asymmetries persist in contralateral pairs during in vitro simulation testing. In vivo kinematics were recorded for male and female drop vertical jump and sidestep cutting tasks. The recorded kinematics were used to robotically simulate the motions on 7 contralateral pairs of cadaveric lower extremities specimens. ACL and MCL force, torque, and strains were recorded and analyzed for differences between contralateral pairs. There was a general lack of mechanical differences between limb sides. Adduction peak torque for the male sidestep cut movement was significantly different between limb sides (p = 0.04). However, this is consistent with ACL injury mechanics in that movement in the frontal plane (abduction/adduction) increases injury risk and it is possible loading differences in this plane may have resulted from tolerances within the setup process. The findings of this study indicate that contralateral knee joints were representative of each other during biomechanical in vitro tests. In future cadaveric robotic simulations, contralateral limbs can be used interchangeably. In addition, direct comparisons of the structural behaviors of isolated conditions for contralateral knee joints can be performed. PMID:28062120

A qualitative analysis of bus simulator training on transit incidents : a case study in Florida. [Summary].

DOT National Transportation Integrated Search

2013-01-01

The simulator was once a very expensive, large-scale mechanical device for training military pilots or astronauts. Modern computers, linking sophisticated software and large-screen displays, have yielded simulators for the desktop or configured as sm...

Analysis of Decomposition for Structure I Methane Hydrate by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Wei, Na; Sun, Wan-Tong; Meng, Ying-Feng; Liu, An-Qi; Zhou, Shou-Wei; Guo, Ping; Fu, Qiang; Lv, Xin

2018-05-01

Under multi-nodes of temperatures and pressures, microscopic decomposition mechanisms of structure I methane hydrate in contact with bulk water molecules have been studied through LAMMPS software by molecular dynamics simulation. Simulation system consists of 482 methane molecules in hydrate and 3027 randomly distributed bulk water molecules. Through analyses of simulation results, decomposition number of hydrate cages, density of methane molecules, radial distribution function for oxygen atoms, mean square displacement and coefficient of diffusion of methane molecules have been studied. A significant result shows that structure I methane hydrate decomposes from hydrate-bulk water interface to hydrate interior. As temperature rises and pressure drops, the stabilization of hydrate will weaken, decomposition extent will go deep, and mean square displacement and coefficient of diffusion of methane molecules will increase. The studies can provide important meanings for the microscopic decomposition mechanisms analyses of methane hydrate.

Multi-scale simulations of apatite-collagen composites: from molecules to materials

NASA Astrophysics Data System (ADS)

Zahn, Dirk

2017-03-01

We review scale-bridging simulation studies for the exploration of atomicto-meso scale processes that account for the unique structure and mechanic properties of apatite-protein composites. As the atomic structure and composition of such complex biocomposites only partially is known, the first part (i) of our modelling studies is dedicated to realistic crystal nucleation scenarios of inorganic-organic composites. Starting from the association of single ions, recent insights range from the mechanisms of motif formation, ripening reactions and the self-organization of nanocrystals, including their interplay with growth-controlling molecular moieties. On this basis, (ii) reliable building rules for unprejudiced scale-up models can be derived to model bulk materials. This is exemplified for (enamel-like) apatite-protein composites, encompassing up to 106 atom models to provide a realistic account of the 10 nm length scale, whilst model coarsening is used to reach μm length scales. On this basis, a series of deformation and fracture simulation studies were performed and helped to rationalize biocomposite hardness, plasticity, toughness, self-healing and fracture mechanisms. Complementing experimental work, these modelling studies provide particularly detailed insights into the relation of hierarchical composite structure and favorable mechanical properties.

Multi-Region Boundary Element Analysis for Coupled Thermal-Fracturing Processes in Geomaterials

NASA Astrophysics Data System (ADS)

Shen, Baotang; Kim, Hyung-Mok; Park, Eui-Seob; Kim, Taek-Kon; Wuttke, Manfred W.; Rinne, Mikael; Backers, Tobias; Stephansson, Ove

2013-01-01

This paper describes a boundary element code development on coupled thermal-mechanical processes of rock fracture propagation. The code development was based on the fracture mechanics code FRACOD that has previously been developed by Shen and Stephansson (Int J Eng Fracture Mech 47:177-189, 1993) and FRACOM (A fracture propagation code—FRACOD, User's manual. FRACOM Ltd. 2002) and simulates complex fracture propagation in rocks governed by both tensile and shear mechanisms. For the coupled thermal-fracturing analysis, an indirect boundary element method, namely the fictitious heat source method, was implemented in FRACOD to simulate the temperature change and thermal stresses in rocks. This indirect method is particularly suitable for the thermal-fracturing coupling in FRACOD where the displacement discontinuity method is used for mechanical simulation. The coupled code was also extended to simulate multiple region problems in which rock mass, concrete linings and insulation layers with different thermal and mechanical properties were present. Both verification and application cases were presented where a point heat source in a 2D infinite medium and a pilot LNG underground cavern were solved and studied using the coupled code. Good agreement was observed between the simulation results, analytical solutions and in situ measurements which validates an applicability of the developed coupled code.

Simulation Studies of Mechanical Properties of Novel Silica Nano-structures

NASA Astrophysics Data System (ADS)

Muralidharan, Krishna; Torras Costa, Joan; Trickey, Samuel B.

2006-03-01

Advances in nanotechnology and the importance of silica as a technological material continue to stimulate computational study of the properties of possible novel silica nanostructures. Thus we have done classical molecular dynamics (MD) and multi-scale quantum mechanical (QM/MD) simulation studies of the mechanical properties of single-wall and multi-wall silica nano-rods of varying dimensions. Such nano-rods have been predicted by Mallik et al. to be unusually strong in tensile failure. Here we compare failure mechanisms of such nano-rods under tension, compression, and bending. The concurrent multi-scale QM/MD studies use the general PUPIL system (Torras et al.). In this case, PUPIL provides automated interoperation of the MNDO Transfer Hamiltonian QM code (Taylor et al.) and a locally written MD code. Embedding of the QM-forces domain is via the scheme of Mallik et al. Work supported by NSF ITR award DMR-0325553.

Compaction behavior and deformation mechanism of directly compressible textured mannitol in a rotary tablet press simulator.

PubMed

Tarlier, Nicolas; Soulairol, Ian; Bataille, Bernard; Baylac, Gilles; Ravel, Patrice; Nofrerias, Isaac; Lefèvre, Philippe; Sharkawi, Tahmer

2015-11-10

Textured mannitol powder is widely used as a pharmaceutical excipient for tablet compaction. In order to choose the right tableting parameters, it is necessary to understand its mechanical behavior during deformation under industrial tableting conditions. The aim of this study was to evaluate the mechanical behavior during deformation of a textured mannitol using a rotary tablet press simulator. Mean yield pressure (Py) obtained by Heckel modeling, Walker coefficients (W) and Stress Rate Sensitivity (SRS) were compared to reference excipients, known for either their plastic (microcrystalline cellulose) or fragmentary (lactose and dibasic calcium phosphate) deformation behavior. Py, W and SRS values showed that the studied textured mannitol has a fragmentary deformation mechanism. Furthermore, this mechanical behavior was not sensitive to lubrication, which is characteristic of fragmentary excipients. Copyright © 2015 Elsevier B.V. All rights reserved.

Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pratihar, Subha; Barnes, George L.; Laskin, Julia

In this Perspective mass spectrometry experiments and chemical dynamics simulations are described which have explored the atomistic dynamics of protonated peptide ions, peptide-H+, colliding with organic surfaces. These studies have investigated surface-induced dissociation (SID) for which peptide-H+ fragments upon collision with the surface, peptide-H+ physisorption on the surface, soft landing (SL), and peptide-H+ reaction with the surface, reactive landing (RL). The simulations include QM+MM and QM/MM direct dynamics. For collisions with self-assembled monolayer (SAM) surfaces there is quite good agreement between experiment and simulation in the efficiency of energy transfer to the peptide-H+ ion’s internal degrees of freedom. Both themore » experiments and simulations show two mechanisms for peptide-H+ fragmentation, i.e. shattering and statistical, RRKM dynamics. Mechanisms for SL are probed in simulations of collisions of protonated dialanine with a perfluorinated SAM surface. RL has been studied experimentally for a number of peptide-H+ + surface systems, and qualitative agreement between simulation and experiment is found for two similar systems.« less

Cluster growth mechanisms in Lennard-Jones fluids: A comparison between molecular dynamics and Brownian dynamics simulations

NASA Astrophysics Data System (ADS)

Jung, Jiyun; Lee, Jumin; Kim, Jun Soo

2015-03-01

We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.

Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical-Molecular Mechanical Simulations of Proton Transfer in DNA.

PubMed

Das, Susanta; Nam, Kwangho; Major, Dan Thomas

2018-03-13

In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. ±1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.

Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations

PubMed Central

Liu, Fei; Zhao, Yi-Lei; Wang, Xiaolei; Hu, Hongbo; Peng, Huasong; Wang, Wei; Wang, Jing-Fang; Zhang, Xuehong

2015-01-01

The phenazine biosynthetic pathway is of considerable importance for the pharmaceutical industry. The pathway produces two products: phenazine-1,6-dicarboxylic acid and phenazine-1-carboxylic acid. PhzF is an isomerase that catalyzes trans-2,3-dihydro-3-hydroxyanthranilic acid isomerization and plays an essential role in the phenazine biosynthetic pathway. Although the PhzF crystal structure has been determined recently, an understanding of the detailed catalytic mechanism and the roles of key catalytic residues are still lacking. In this study, a computational strategy using a combination of molecular modeling, molecular dynamics simulations, and quantum mechanics/molecular mechanics simulations was used to elucidate these important issues. The Apo enzyme, enzyme–substrate complexes with negatively charged Glu45, enzyme–transition state analog inhibitor complexes with neutral Glu45, and enzyme–product complexes with negatively charged Glu45 structures were optimized and modeled using a 200 ns molecular dynamics simulation. Residues such as Gly73, His74, Asp208, Gly212, Ser213, and water, which play important roles in ligand binding and the isomerization reaction, were comprehensively investigated. Our results suggest that the Glu45 residue at the active site of PhzF acts as a general base/acid catalyst during proton transfer. This study provides new insights into the detailed catalytic mechanism of PhzF and the results have important implications for PhzF modification. PMID:26414009

Effect of thermal and mechanical parameter’s damage numerical simulation cycling effects on defects in hot metal forming processes

NASA Astrophysics Data System (ADS)

El Amri, Abdelouahid; el yakhloufi Haddou, Mounir; Khamlichi, Abdellatif

2017-10-01

Damage mechanisms in hot metal forming processes are accelerated by mechanical stresses arising during Thermal and mechanical properties variations, because it consists of the materials with different thermal and mechanical loadings and swelling coefficients. In this work, 3D finite element models (FEM) are developed to simulate the effect of Temperature and the stresses on the model development, using a general purpose FE software ABAQUS. Explicit dynamic analysis with coupled Temperature displacement procedure is used for a model. The purpose of this research was to study the thermomechanical damage mechanics in hot forming processes. The important process variables and the main characteristics of various hot forming processes will also be discussed.

Computational Design of Graphene Nanoscrolls

NASA Astrophysics Data System (ADS)

Bejagam, Karteek; Singh, Samrendra; Deshmukh, Sanket; Deshmukh Group Team; Samrendra Group Collaboration

Graphene nanoscrolls have obtained a significant interest in recent years due to their potential applications in tribology, nanotechnology, and bioengineering. For example, recently it has been shown that graphene nanoscrolls can be used to experience superlubricity - almost zero friction state. In the present study we employ the metal/non-metal nanoparticles to facilitate the graphene nanoscroll formation. We have conducted reactive molecular dynamics (RMD) simulations of diamond, Nickel, and Gold nanoparticles placed on the 2D graphene sheet. RMD simulations reveal the mechanisms that facilitates or prohibits the graphene nanoscroll formation. Our simulations suggest that the surface chemistry and interactions between nanoparticles and graphene play a crucial in determining the mechanism of scroll formation and the nature of the nanoscroll. We also find that the type of a nanoparticle has strong influence on the elastic and mechanical properties of the nanoscroll. Our study provides a systematic pathway to design graphene nanoscrolls with a wide range of properties.

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;

Coupled thermal–hydrological–mechanical modeling of CO 2 -enhanced coalbed methane recovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Tianran; Rutqvist, Jonny; Oldenburg, Curtis M.

CO 2 -enhanced coalbed methane recovery, also known as CO 2 -ECBM, is a potential win-win approach for enhanced methane production while simultaneously sequestering injected anthropogenic CO 2 to decrease CO 2 emissions into the atmosphere. Here, CO 2 -ECBM is simulated using a coupled thermal–hydrological–mechanical (THM) numerical model that considers multiphase (gas and water) flow and solubility, multicomponent (CO 2 and CH 4 ) diffusion and adsorption, heat transfer and coal deformation. The coupled model is based on the TOUGH-FLAC simulator, which is applied here for the first time to model CO 2 -ECBM. The capacity of the simulatormore » for modeling methane production is verified by a code-to-code comparison with the general-purpose finite-element solver COMSOL. Then, the TOUGH-FLAC simulator is applied in an isothermal simulation to study the variations in permeability evolution during a CO 2 -ECBM operation while considering four different stress-dependent permeability models that have been implemented into the simulator. Finally, the TOUGH-FLAC simulator is applied in non-isothermal simulations to model THM responses during a CO 2 -ECBM operation.Our simulations show that the permeability evolution, mechanical stress, and deformation are all affected by changes in pressure, temperature and adsorption swelling, with adsorption swelling having the largest effect. The calculated stress changes do not induce any mechanical failure in the coal seam, except near the injection well in one case of a very unfavorable stress field.« less

Coupled thermal–hydrological–mechanical modeling of CO 2 -enhanced coalbed methane recovery

DOE PAGES

Ma, Tianran; Rutqvist, Jonny; Oldenburg, Curtis M.; ...

2017-05-22

CO 2 -enhanced coalbed methane recovery, also known as CO 2 -ECBM, is a potential win-win approach for enhanced methane production while simultaneously sequestering injected anthropogenic CO 2 to decrease CO 2 emissions into the atmosphere. Here, CO 2 -ECBM is simulated using a coupled thermal–hydrological–mechanical (THM) numerical model that considers multiphase (gas and water) flow and solubility, multicomponent (CO 2 and CH 4 ) diffusion and adsorption, heat transfer and coal deformation. The coupled model is based on the TOUGH-FLAC simulator, which is applied here for the first time to model CO 2 -ECBM. The capacity of the simulatormore » for modeling methane production is verified by a code-to-code comparison with the general-purpose finite-element solver COMSOL. Then, the TOUGH-FLAC simulator is applied in an isothermal simulation to study the variations in permeability evolution during a CO 2 -ECBM operation while considering four different stress-dependent permeability models that have been implemented into the simulator. Finally, the TOUGH-FLAC simulator is applied in non-isothermal simulations to model THM responses during a CO 2 -ECBM operation.Our simulations show that the permeability evolution, mechanical stress, and deformation are all affected by changes in pressure, temperature and adsorption swelling, with adsorption swelling having the largest effect. The calculated stress changes do not induce any mechanical failure in the coal seam, except near the injection well in one case of a very unfavorable stress field.« less

Development of a parallel FE simulator for modeling the whole trans-scale failure process of rock from meso- to engineering-scale

NASA Astrophysics Data System (ADS)

Li, Gen; Tang, Chun-An; Liang, Zheng-Zhao

2017-01-01

Multi-scale high-resolution modeling of rock failure process is a powerful means in modern rock mechanics studies to reveal the complex failure mechanism and to evaluate engineering risks. However, multi-scale continuous modeling of rock, from deformation, damage to failure, has raised high requirements on the design, implementation scheme and computation capacity of the numerical software system. This study is aimed at developing the parallel finite element procedure, a parallel rock failure process analysis (RFPA) simulator that is capable of modeling the whole trans-scale failure process of rock. Based on the statistical meso-damage mechanical method, the RFPA simulator is able to construct heterogeneous rock models with multiple mechanical properties, deal with and represent the trans-scale propagation of cracks, in which the stress and strain fields are solved for the damage evolution analysis of representative volume element by the parallel finite element method (FEM) solver. This paper describes the theoretical basis of the approach and provides the details of the parallel implementation on a Windows - Linux interactive platform. A numerical model is built to test the parallel performance of FEM solver. Numerical simulations are then carried out on a laboratory-scale uniaxial compression test, and field-scale net fracture spacing and engineering-scale rock slope examples, respectively. The simulation results indicate that relatively high speedup and computation efficiency can be achieved by the parallel FEM solver with a reasonable boot process. In laboratory-scale simulation, the well-known physical phenomena, such as the macroscopic fracture pattern and stress-strain responses, can be reproduced. In field-scale simulation, the formation process of net fracture spacing from initiation, propagation to saturation can be revealed completely. In engineering-scale simulation, the whole progressive failure process of the rock slope can be well modeled. It is shown that the parallel FE simulator developed in this study is an efficient tool for modeling the whole trans-scale failure process of rock from meso- to engineering-scale.

An Experimental Study of the Reputation Mechanism in a Business Game

ERIC Educational Resources Information Center

Greco, Marco; Branca, Antonio Maurizio; Morena, Gianfranco

2011-01-01

Reputation enables different parties to establish a trusting and cooperative relationship, a key factor in integrative negotiations referred to as "win-win" negotiations. Thus, a good reputation mechanism can bring simulations closer to reality. In this study, the authors review the reputation mechanisms applied to the online business game WIN WIN…

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

NASA Astrophysics Data System (ADS)

Zhang, Zhiwei; Chen, Pei; Qin, Fei; An, Tong; Yu, Huiping

2018-05-01

Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD) layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young's modulus, ultimate tensile strength (UTS), and strain at fracture is observed.

Operation analysis of a Chebyshev-Pantograph leg mechanism for a single DOF biped robot

NASA Astrophysics Data System (ADS)

Liang, Conghui; Ceccarelli, Marco; Takeda, Yukio

2012-12-01

In this paper, operation analysis of a Chebyshev-Pantograph leg mechanism is presented for a single degree of freedom (DOF) biped robot. The proposed leg mechanism is composed of a Chebyshev four-bar linkage and a pantograph mechanism. In contrast to general fully actuated anthropomorphic leg mechanisms, the proposed leg mechanism has peculiar features like compactness, low-cost, and easy-operation. Kinematic equations of the proposed leg mechanism are formulated for a computer oriented simulation. Simulation results show the operation performance of the proposed leg mechanism with suitable characteristics. A parametric study has been carried out to evaluate the operation performance as function of design parameters. A prototype of a single DOF biped robot equipped with two proposed leg mechanisms has been built at LARM (Laboratory of Robotics and Mechatronics). Experimental test shows practical feasible walking ability of the prototype, as well as drawbacks are discussed for the mechanical design.

Quantum mechanical study of solvent effects in a prototype S{sub N}2 reaction in solution: Cl{sup −} attack on CH{sub 3}Cl

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuechler, Erich R.; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431; York, Darrin M., E-mail: york@biomaps.rutgers.edu

2014-02-07

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype S{sub N}2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resultingmore » free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.« less

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.; York, Darrin M.

2014-02-01

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl.

PubMed

Kuechler, Erich R; York, Darrin M

2014-02-07

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

Diffusion-coupled cohesive interface simulations of stress corrosion intergranular cracking in polycrystalline materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pu, Chao; Gao, Yanfei; Wang, Yanli

To study the stress corrosion intergranular cracking mechanism, a diffusion-coupled cohesive zone model (CZM) is proposed for the simulation of the stress-assisted diffusional process along grain boundaries and the mechanical response of grain boundary sliding and separation. This simulation methodology considers the synergistic effects of impurity diffusion driven by pressure gradient and degradation of grain boundary strength by impurity concentration. The diffusion-coupled CZM is combined with crystal plasticity finite element model (CPFEM) to simulate intergranular fracture of polycrystalline material under corrosive environment. Significant heterogeneity of the stress field and extensive impurity accumulation is observed at grain boundaries and junction points.more » Deformation mechanism maps are constructed with respect to the grain boundary degradation factor and applied strain rate, which dictate the transition from internal to near-surface intergranular fracture modes under various strain amplitudes and grain sizes.« less

Finite Element Simulation of Compression Molding of Woven Fabric Carbon Fiber/Epoxy Composites: Part I Material Model Development

DOE PAGES

Li, Yang; Zhao, Qiangsheng; Mirdamadi, Mansour; ...

2016-01-06

Woven fabric carbon fiber/epoxy composites made through compression molding are one of the promising choices of material for the vehicle light-weighting strategy. Previous studies have shown that the processing conditions can have substantial influence on the performance of this type of the material. Therefore the optimization of the compression molding process is of great importance to the manufacturing practice. An efficient way to achieve the optimized design of this process would be through conducting finite element (FE) simulations of compression molding for woven fabric carbon fiber/epoxy composites. However, performing such simulation remains a challenging task for FE as multiple typesmore » of physics are involved during the compression molding process, including the epoxy resin curing and the complex mechanical behavior of woven fabric structure. In the present study, the FE simulation of the compression molding process of resin based woven fabric composites at continuum level is conducted, which is enabled by the implementation of an integrated material modeling methodology in LS-Dyna. Specifically, the chemo-thermo-mechanical problem of compression molding is solved through the coupling of three material models, i.e., one thermal model for temperature history in the resin, one mechanical model to update the curing-dependent properties of the resin and another mechanical model to simulate the behavior of the woven fabric composites. Preliminary simulations of the carbon fiber/epoxy woven fabric composites in LS-Dyna are presented as a demonstration, while validations and models with real part geometry are planned in the future work.« less

FE Simulation Models for Hot Stamping an Automobile Component with Tailor-Welded High-Strength Steels

NASA Astrophysics Data System (ADS)

Tang, Bingtao; Wang, Qiaoling; Wei, Zhaohui; Meng, Xianju; Yuan, Zhengjun

2016-05-01

Ultra-high-strength in sheet metal parts can be achieved with hot stamping process. To improve the crash performance and save vehicle weight, it is necessary to produce components with tailored properties. The use of tailor-welded high-strength steel is a relatively new hot stamping process for saving weight and obtaining desired local stiffness and crash performance. The simulation of hot stamping boron steel, especially tailor-welded blanks (TWBs) stamping, is more complex and challenging. Information about thermal/mechanical properties of tools and sheet materials, heat transfer, and friction between the deforming material and the tools is required in detail. In this study, the boron-manganese steel B1500HS and high-strength low-alloy steel B340LA are tailor welded and hot stamped. In order to precisely simulate the hot stamping process, modeling and simulation of hot stamping tailor-welded high-strength steels, including phase transformation modeling, thermal modeling, and thermal-mechanical modeling, is investigated. Meanwhile, the welding zone of tailor-welded blanks should be sufficiently accurate to describe thermal, mechanical, and metallurgical parameters. FE simulation model using TWBs with the thickness combination of 1.6 mm boron steel and 1.2 mm low-alloy steel is established. In order to evaluate the mechanical properties of the hot stamped automotive component (mini b-pillar), hardness and microstructure at each region are investigated. The comparisons between simulated results and experimental observations show the reliability of thermo-mechanical and metallurgical modeling strategies of TWBs hot stamping process.

Advances in quantum simulations of ATPase catalysis in the myosin motor.

PubMed

Kiani, Farooq Ahmad; Fischer, Stefan

2015-04-01

During its contraction cycle, the myosin motor catalyzes the hydrolysis of ATP. Several combined quantum/classical mechanics (QM/MM) studies of this step have been published, which substantially contributed to our thinking about the catalytic mechanism. The methodological difficulties encountered over the years in the simulation of this complex reaction are now understood: (a) Polarization of the protein peptide groups surrounding the highly charged ATP(4-) cannot be neglected. (b) Some unsuspected protein groups need to be treated QM. (c) Interactions with the γ-phosphate versus the β-phosphate favor a concurrent versus a sequential mechanism, respectively. Thus, these practical aspects strongly influence the computed mechanism, and should be considered when studying other catalyzed phosphor-ester hydrolysis reactions, such as in ATPases or GTPases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Influence of circumferential notch and fatigue crack on the mechanical integrity of biodegradable magnesium-based alloy in simulated body fluid.

PubMed

Bobby Kannan, M; Singh Raman, R K; Witte, F; Blawert, C; Dietzel, W

2011-02-01

Applications of magnesium alloys as biodegradable orthopaedic implants are critically dependent on the mechanical integrity of the implant during service. In this study, the mechanical integrity of an AZ91 magnesium alloy was studied using a constant extension rate tensile (CERT) method. The samples in two different geometries that is, circumferentially notched (CN), and circumferentially notched and fatigue cracked (CNFC), were tested in air and in simulated body fluid (SBF). The test results show that the mechanical integrity of the AZ91 magnesium alloy decreased substantially (∼50%) in both the CN and CNFC samples exposed to SBF. Fracture surface analysis revealed secondary cracks suggesting stress corrosion cracking susceptibility of the alloy in SBF. Copyright © 2010 Wiley Periodicals, Inc.

Development of automation and robotics for space via computer graphic simulation methods

NASA Technical Reports Server (NTRS)

Fernandez, Ken

1988-01-01

A robot simulation system, has been developed to perform automation and robotics system design studies. The system uses a procedure-oriented solid modeling language to produce a model of the robotic mechanism. The simulator generates the kinematics, inverse kinematics, dynamics, control, and real-time graphic simulations needed to evaluate the performance of the model. Simulation examples are presented, including simulation of the Space Station and the design of telerobotics for the Orbital Maneuvering Vehicle.

Berthing simulator for space station and orbiter

NASA Technical Reports Server (NTRS)

Veerasamy, Sam

1991-01-01

The development of a real-time man-in-the-loop berthing simulator is in progress at NASA Lyndon B. Johnson Space Center (JSC) to conduct a parametric study and to measure forces during contact conditions of the actual docking mechanisms for the Space Station Freedom and the orbiter. In berthing, the docking ports of the Space Station and the orbiter are brought together using the orbiter robotic arm to control the relative motion of the vehicles. The berthing simulator consists of a dynamics docking test system (DDTS), computer system, simulator software, and workstations. In the DDTS, the Space Station, and the orbiter docking mechanisms are mounted on a six-degree-of-freedom (6 DOF) table and a fixed platform above the table. Six load cells are used on the fixed platform to measure forces during contact conditions of the docking mechanisms. Two Encore Concept 32/9780 computers are used to simulate the orbiter robotic arm and to operate the berthing simulator. A systematic procedure for a real-time dynamic initialization is being developed to synchronize the Space Station docking port trajectory with the 6 DOF table movement. The berthing test can be conducted manually or automatically and can be extended for any two orbiting vehicles using a simulated robotic arm. The real-time operation of the berthing simulator is briefly described.

Multiaxial mechanical properties and constitutive modeling of human adipose tissue: a basis for preoperative simulations in plastic and reconstructive surgery.

PubMed

Sommer, Gerhard; Eder, Maximilian; Kovacs, Laszlo; Pathak, Heramb; Bonitz, Lars; Mueller, Christoph; Regitnig, Peter; Holzapfel, Gerhard A

2013-11-01

A preoperative simulation of soft tissue deformations during plastic and reconstructive surgery is desirable to support the surgeon's planning and to improve surgical outcomes. The current development of constitutive adipose tissue models, for the implementation in multilayer computational frameworks for the simulation of human soft tissue deformations, has proved difficult because knowledge of the required mechanical parameters of fat tissue is limited. Therefore, for the first time, human abdominal adipose tissues were mechanically investigated by biaxial tensile and triaxial shear tests. The results of this study suggest that human abdominal adipose tissues under quasi-static and dynamic multiaxial loadings can be characterized as a nonlinear, anisotropic and viscoelastic soft biological material. The nonlinear and anisotropic features are consequences of the material's collagenous microstructure. The aligned collagenous septa observed in histological investigations causes the anisotropy of the tissue. A hyperelastic model used in this study was appropriate to represent the quasi-static multiaxial mechanical behavior of fat tissue. The constitutive parameters are intended to serve as a basis for soft tissue simulations using the finite element method, which is an apparent method for obtaining promising results in the field of plastic and reconstructive surgery. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Simulation and experimental analysis of nanoindentation and mechanical properties of amorphous NiAl alloys.

PubMed

Wang, Chih-Hao; Fang, Te-Hua; Cheng, Po-Chien; Chiang, Chia-Chin; Chao, Kuan-Chi

2015-06-01

This paper used numerical and experimental methods to investigate the mechanical properties of amorphous NiAl alloys during the nanoindentation process. A simulation was performed using the many-body tight-binding potential method. Temperature, plastic deformation, elastic recovery, and hardness were evaluated. The experimental method was based on nanoindentation measurements, allowing a precise prediction of Young's modulus and hardness values for comparison with the simulation results. The indentation simulation results showed a significant increase of NiAl hardness and elastic recovery with increasing Ni content. Furthermore, the results showed that hardness and Young's modulus increase with increasing Ni content. The simulation results are in good agreement with the experimental results. Adhesion test of amorphous NiAl alloys at room temperature is also described in this study.

Simulated airplane headache: a proxy towards identification of underlying mechanisms.

PubMed

Bui, Sebastian Bao Dinh; Petersen, Torben; Poulsen, Jeppe Nørgaard; Gazerani, Parisa

2017-12-01

Airplane Headache (AH) occurs during flights and often appears as an intense, short lasting headache during take-off or landing. Reports are limited on pathological mechanisms underlying the occurrence of this headache. Proper diagnosis and treatments would benefit from identification of potential pathways involved in AH pathogenesis. This study aimed at providing a simulated airplane headache condition as a proxy towards identification of its underlying mechanisms. Fourteen participants including 7 volunteers suffering from AH and 7 healthy matched controls were recruited after meeting the diagnostic and safety criteria based on an approved study protocol. Simulation of AH was achieved by entering a pressure chamber with similar characteristics of an airplane flight. Selected potential biomarkers including salivary prostaglandin E 2 (PGE 2 ), cortisol, facial thermo-images, blood pressure, pulse, and saturation pulse oxygen (SPO) were defined and values were collected before, during and after flight simulation in the pressure chamber. Salivary samples were analyzed with ELISA techniques, while data analysis and statistical tests were handled with SPSS version 22.0. All participants in the AH-group experienced a headache attack similar to AH experience during flight. The non-AH-group did not experience any headaches. Our data showed that the values for PGE 2 , cortisol and SPO were significantly different in the AH-group in comparison with the non-AH-group during the flight simulation in the pressure chamber. The pressure chamber proved useful not only to provoke AH-like attack but also to study potential biomarkers for AH in this study. PGE 2 , and cortisol levels together with SPO presented dysregulation during the simulated AH-attack in affected individuals compared with healthy controls. Based on these findings we propose to use pressure chamber as a model to induce AH, and thus assess new potential biomarkers for AH in future studies.

Mechanism of the αβ Conformational Change in F1-ATPase after ATP Hydrolysis: Free-Energy Simulations

PubMed Central

Ito, Yuko; Ikeguchi, Mitsunori

2015-01-01

One of the motive forces for F1-ATPase rotation is the conformational change of the catalytically active β subunit due to closing and opening motions caused by ATP binding and hydrolysis, respectively. The closing motion is accomplished in two steps: the hydrogen-bond network around ATP changes and then the entire structure changes via B-helix sliding, as shown in our previous study. Here, we investigated the opening motion induced by ATP hydrolysis using all-atom free-energy simulations, combining the nudged elastic band method and umbrella sampling molecular-dynamics simulations. Because hydrolysis requires residues in the α subunit, the simulations were performed with the αβ dimer. The results indicate that the large-scale opening motion is also achieved by the B-helix sliding (in the reverse direction). However, the sliding mechanism is different from that of ATP binding because sliding is triggered by separation of the hydrolysis products ADP and Pi. We also addressed several important issues: 1), the timing of the product Pi release; 2), the unresolved half-closed β structure; and 3), the ADP release mechanism. These issues are fundamental for motor function; thus, the rotational mechanism of the entire F1-ATPase is also elucidated through this αβ study. During the conformational change, conserved residues among the ATPase proteins play important roles, suggesting that the obtained mechanism may be shared with other ATPase proteins. When combined with our previous studies, these results provide a comprehensive view of the β-subunit conformational change that drives the ATPase. PMID:25564855

Mechanisms of elevation-dependent warming over complex terrain in high-resolution simulations of regional climate change

NASA Astrophysics Data System (ADS)

Minder, J. R.; Letcher, T.; Liu, C.

2016-12-01

Numerous observational and modeling studies have suggested that over mountainous terrain certain elevations can experience systematically enhanced rates of near-surface climate warming relative to the surrounding region, a phenomenon referred to as elevation-dependent warming (EDW). In many of these studies high-elevation locations were found to experience the fastest warming rates. A variety of physical mechanisms for EDW have been proposed but there is no consensus as to the dominant cause. We examine EDW in regional climate model (RCM) simulations with very high horizontal resolution (4-km horizontal grid). The simulation domain centers on the Rocky Mountains and intermountain west of the United States. Climate change simulations are conducted using the "pseudo global warming" framework to focus on the regional response to large-scale thermodynamic and radiative climate changes representative of mid-century anthropogenic global climate change. Substantial EDW is found in these simulations. Warming varies with elevation by up to 1°C depending on the season considered. The structure of EDW is only weakly sensitive to variations in horizontal grid spacing ranging from 4 to 36 km. The snow-albedo feedback (SAF) plays a major role in causing the simulated EDW. The elevation band of maximum warming varies seasonally, mostly following the margin of the seasonal snowpack where snow cover and albedo reductions are maximized under climate warming. Additional simulations where the SAF is artificially suppressed demonstrate that EDW variations of up to 0.6°C can be attributed to the SAF. Simulations with a suppressed SAF still exhibit EDW variations up to 0.8°C that must be explained by other mechanisms. This remaining EDW shows a near linear increase in warming with elevation in most months and does not appear to be inherited from the profile of large-scale free-tropospheric warming. Simple theoretical calculations suggest that the non-linear dependence of surface emission on temperature offers one promising mechanism. The role of water vapor and cloud feedbacks are also considered as alternative mechanisms.

Validation of Noncontact Anterior Cruciate Ligament Tears Produced by a Mechanical Impact Simulator Against the Clinical Presentation of Injury.

PubMed

Bates, Nathaniel A; Schilaty, Nathan D; Nagelli, Christopher V; Krych, Aaron J; Hewett, Timothy E

2018-06-01

Anterior cruciate ligament (ACL) injuries are catastrophic events that affect athletic careers and lead to long-term degenerative knee changes. As injuries are believed to occur within the first 50 milliseconds after initial contact during a rapid deceleration task, impact simulators that rapidly deliver impulse loads to cadaveric specimens have been developed. However, no impactor has reproducibly and reliably created ACL injures in a distribution that mimics clinical observation. To better understand ACL injury patterns through a cadaveric investigation that applied in vivo-measured external loads to the knee during simulated landings. Controlled laboratory study. A novel mechanical impact simulator reproduced kinetics from in vivo-recorded drop landing tasks on 45 cadaveric knees. Specimens were exposed to a randomized order of variable knee abduction moment, anterior tibial shear, and internal tibial rotation loads before the introduction of an impulse load at the foot. This process was repeated until a hard or soft tissue injury was induced on the joint. Injuries were assessed by an orthopaedic surgeon, and ligament strain was recorded by implanted strain gauges. The mechanical impact simulator induced ACL injuries in 87% of specimens, with medial collateral ligament (MCL) injuries in 31%. ACL tear locations were 71% femoral side, 21% midsubstance, and 9% tibial side. Peak strain before failure for ACL-injured specimens was 15.3% ± 8.7% for the ACL and 5.1% ± 5.6% for the MCL ( P < .001). The ACL injuries induced by the mechanical impact simulator in the present study have provided clinically relevant in vitro representations of in vivo ACL injury patterns as cited in the literature. Additionally, current ligament strains corroborate the literature to support disproportionate loading of the ACL relative to the MCL during athletic tasks. These findings indicate that the mechanical impact simulator is an appropriate model for examining independent mechanical variables, treatment techniques, and preventive interventions during athletic tasks leading up to and including an ACL injury. Accordingly, this system can be utilized to further parse out contributing factors to an ACL injury as well as assess the shortcomings of ACL reconstruction techniques in a dynamic, simulated environment that is better representative of in vivo injury scenarios.

MSFC Three Point Docking Mechanism design review

NASA Technical Reports Server (NTRS)

Schaefer, Otto; Ambrosio, Anthony

1992-01-01

In the next few decades, we will be launching expensive satellites and space platforms that will require recovery for economic reasons, because of initial malfunction, servicing, repairs, or out of a concern for post lifetime debris removal. The planned availability of a Three Point Docking Mechanism (TPDM) is a positive step towards an operational satellite retrieval infrastructure. This study effort supports NASA/MSFC engineering work in developing an automated docking capability. The work was performed by the Grumman Space & Electronics Group as a concept evaluation/test for the Tumbling Satellite Retrieval Kit. Simulation of a TPDM capture was performed in Grumman's Large Amplitude Space Simulator (LASS) using mockups of both parts (the mechanism and payload). Similar TPDM simulation activities and more extensive hardware testing was performed at NASA/MSFC in the Flight Robotics Laboratory and Space Station/Space Operations Mechanism Test Bed (6-DOF Facility).

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

An integrated modeling method for wind turbines

NASA Astrophysics Data System (ADS)

Fadaeinedjad, Roohollah

To study the interaction of the electrical, mechanical, and aerodynamic aspects of a wind turbine, a detailed model that considers all these aspects must be used. A drawback of many studies in the area of wind turbine simulation is that either a very simple mechanical model is used with a detailed electrical model, or vice versa. Hence the interactions between electrical and mechanical aspects of wind turbine operation are not accurately taken into account. In this research, it will be shown that a combination of different simulation packages, namely TurbSim, FAST, and Simulink can be used to model the aerodynamic, mechanical, and electrical aspects of a wind turbine in detail. In this thesis, after a review of some wind turbine concepts and software tools, a simulation structure is proposed for studying wind turbines that integrates the mechanical and electrical components of a wind energy conversion device. Based on the simulation structure, a comprehensive model for a three-bladed variable speed wind turbine with doubly-fed induction generator is developed. Using the model, the impact of a voltage sag on the wind turbine tower vibration is investigated under various operating conditions such as power system short circuit level, mechanical parameters, and wind turbine operating conditions. It is shown how an electrical disturbance can cause more sustainable tower vibrations under high speed and turbulent wind conditions, which may disrupt the operation of pitch control system. A similar simulation structure is used to model a two-bladed fixed speed wind turbine with an induction generator. An extension of the concept is introduced by adding a diesel generator system. The model is utilized to study the impact of the aeroelastic aspects of wind turbine (i.e. tower shadow, wind shears, yaw error, turbulence, and mechanical vibrations) on the power quality of a stand-alone wind-diesel system. Furthermore, an IEEE standard flickermeter model is implemented in a Simulink environment to study the flicker contribution of the wind turbine in the wind-diesel system. By using a new wind power plant representation method, a large wind farm (consisting of 96 fixed speed wind turbines) is modelled to study the power quality of wind power system. The flicker contribution of wind farm is also studied with different wind turbine numbers, using the flickermeter model. Keywords. Simulink, FAST, TurbSim, AreoDyn, wind energy, doubly-fed induction generator, variable speed wind turbine, voltage sag, tower vibration, power quality, flicker, fixed speed wind turbine, wind shear, tower shadow, and yaw error.

Experiments and Simulations of Fully Hydro-Mechanically Coupled Response of Rough Fractures Exposed to High-Pressure Fluid Injection

NASA Astrophysics Data System (ADS)

Vogler, D.; Settgast, R. R.; Annavarapu, C.; Madonna, C.; Bayer, P.; Amann, F.

2018-02-01

In this work, we present the application of a fully coupled hydro-mechanical method to investigate the effect of fracture heterogeneity on fluid flow through fractures at the laboratory scale. Experimental and numerical studies of fracture closure behavior in the presence of heterogeneous mechanical and hydraulic properties are presented. We compare the results of two sets of laboratory experiments on granodiorite specimens against numerical simulations in order to investigate the mechanical fracture closure and the hydro-mechanical effects, respectively. The model captures fracture closure behavior and predicts a nonlinear increase in fluid injection pressure with loading. Results from this study indicate that the heterogeneous aperture distributions measured for experiment specimens can be used as model input for a local cubic law model in a heterogeneous fracture to capture fracture closure behavior and corresponding fluid pressure response.

Study of the influence of volume fraction of ceramic inclusions in NiCr-TiC composite with columnar structure on its mechanical behavior

NASA Astrophysics Data System (ADS)

Eremina, Galina M.; Smolin, Alexey Yu.; Shilko, Evgeny V.

2017-12-01

Metal-ceramic materials are characterized by high mechanical and tribological properties. The surface treatment of the composite by an electron beam in inert gas plasma leads to a qualitative and quantitative change in its microstructure as well as to a change in mechanical properties of the components: a columnar structure forms in the modified layer. Different treatment regimes result in different concentrations of inclusions in the surface layer. In this paper, the effect of the volume concentration of inclusions on the integral mechanical properties of a dispersion-strengthened NiCr-TiC composite is studied on the basis of 3D numerical simulation. The results of computer simulation show that the change in concentration significantly affects the integral mechanical characteristics of the composite material as well as the nature of the nucleation and development of damages in it.

Numeric simulation model for long-term orthodontic tooth movement with contact boundary conditions using the finite element method.

PubMed

Hamanaka, Ryo; Yamaoka, Satoshi; Anh, Tuan Nguyen; Tominaga, Jun-Ya; Koga, Yoshiyuki; Yoshida, Noriaki

2017-11-01

Although many attempts have been made to simulate orthodontic tooth movement using the finite element method, most were limited to analyses of the initial displacement in the periodontal ligament and were insufficient to evaluate the effect of orthodontic appliances on long-term tooth movement. Numeric simulation of long-term tooth movement was performed in some studies; however, neither the play between the brackets and archwire nor the interproximal contact forces were considered. The objectives of this study were to simulate long-term orthodontic tooth movement with the edgewise appliance by incorporating those contact conditions into the finite element model and to determine the force system when the space is closed with sliding mechanics. We constructed a 3-dimensional model of maxillary dentition with 0.022-in brackets and 0.019 × 0.025-in archwire. Forces of 100 cN simulating sliding mechanics were applied. The simulation was accomplished on the assumption that bone remodeling correlates with the initial tooth displacement. This method could successfully represent the changes in the moment-to-force ratio: the tooth movement pattern during space closure. We developed a novel method that could simulate the long-term orthodontic tooth movement and accurately determine the force system in the course of time by incorporating contact boundary conditions into finite element analysis. It was also suggested that friction is progressively increased during space closure in sliding mechanics. Copyright © 2017. Published by Elsevier Inc.

Effects of Geomechanical Mechanism on the Gas Production Behavior: A Simulation Study of Class-3 Type Four-Way-Closure Ridge Hydrate Deposit Offshore Southwestern Taiwan

NASA Astrophysics Data System (ADS)

Wu, Cheng-Yueh; Chiu, Yung-Cheng; Huang, Yi-Jyun; Hsieh, Bieng-Zih

2017-04-01

The future energy police of Taiwan will heavily rely on the clean energy, including renewable energy and low-carbon energy, to meet the target of mitigating CO2 emission. In addition to developing the renewable energies like solar and wind resources, Taiwan will increase the natural gas consumption to obtain enough electrical power with low-carbon emission. The vast resources of gas hydrates recognized in southwestern offshore Taiwan makes a great opportunity for Taiwan to have own energy resources in the future. Therefore, Taiwan put significant efforts on the evaluation of gas hydrate reserves recently. Production behavior of natural gas dissociated from gas hydrate deposits is an important issue to the hydrate reserves evaluation. The depressurization method is a useful engineering recovery method for gas production from a class-3 type hydrate deposit. The dissociation efficiency will be affected by the pressure drawdown disturbance. However, when the pore pressure of hydrate deposits is depressurized for gas production, the rock matrix will surfer more stresses and the formation deformation might be occurred. The purpose of this study was to investigate the effects of geomechanical mechanism on the gas production from a class-3 hydrate deposit using depressurization method. The case of a class-3 type hydrate deposit of Four-Way-Closure Ridge was studied. In this study a reservoir simulator, STARS, was used. STARS is a multiphase flow, heat transfer, geo-chemical and geo-mechanical mechanisms coupling simulator which is capable to simulate the dissociation/reformation of gas hydrate and the deformation of hydrate reservoirs and overburdens. The simulating ability of STARTS simulator was validated by duplicating the hydrate comparison projects of National Energy Technology Lab. The study target, Four-Way-Closure (FWC) Ridge hydrate deposit, was discovered by the bottom simulating reflectors (BSRs). The geological parameters were collected from the geological and geophysical studies and the geo-mechanical data were analogized from Japan's hydrate production case. The first step for the geological modelling was to digitize the structure map of FWC Ridge and built a grid system for the reservoir. The formation parameters, such as formation thickness, porosity and permeability, the phase behavior parameters, rock-fluid parameters, initial conditions (including formation pressure, temperature and hydrate saturation), geo-mechanical parameters were assigned into each grid. In this case we used a horizontal well with specific operating conditions to produce water and dissociated gas from the reservoir. The sensitivity analyses on geological and geo-mechanical parameters were conducted in this study. The case of different pressure drop showed that the recovery factor (RF) was 2.50%, 13.50% and 20.47% when the pressure drop of 60%, 70% and 75% from the initial reservoir pressure was used respectively. Based on the case of pressure drop of 75% (from the initial reservoir pressure), the RF was 35.13%, 25.9%, 20.47% and 16.65% when the initial hydrate saturation of 30%, 40%, 50% and 60% was assumed respectively. The greater formation permeability, the better gas recovery. The capillary pressure had a minor affection on the gas production in this case study. The best well location was at the upper layer because of the gravity effect. For the effects of the geo-mechanics, we observed that the rock mechanisms had impacts on the final cumulative gas production. The larger the Young's Modulus and the smaller the Poisson's Ratio, the smaller the subsidence on the seabed. Our simulation results showed that the seabed subsidence in FWC Ridge was about 1 meter during the production period.

Adiabatic shear mechanisms for the hard cutting process

NASA Astrophysics Data System (ADS)

Yue, Caixu; Wang, Bo; Liu, Xianli; Feng, Huize; Cai, Chunbin

2015-05-01

The most important consequence of adiabatic shear phenomenon is formation of sawtooth chip. Lots of scholars focused on the formation mechanism of sawtooth, and the research often depended on experimental approach. For the present, the mechanism of sawtooth chip formation still remains some ambiguous aspects. This study develops a combined numerical and experimental approach to get deeper understanding of sawtooth chip formation mechanism for Polycrystalline Cubic Boron Nitride (PCBN) tools orthogonal cutting hard steel GCr15. By adopting the Johnson-Cook material constitutive equations, the FEM simulation model established in this research effectively overcomes serious element distortions and cell singularity in high strain domain caused by large material deformation, and the adiabatic shear phenomenon is simulated successfully. Both the formation mechanism and process of sawtooth are simulated. Also, the change features regarding the cutting force as well as its effects on temperature are studied. More specifically, the contact of sawtooth formation frequency with cutting force fluctuation frequency is established. The cutting force and effect of cutting temperature on mechanism of adiabatic shear are investigated. Furthermore, the effects of the cutting condition on sawtooth chip formation are researched. The researching results show that cutting feed has the most important effect on sawtooth chip formation compared with cutting depth and speed. This research contributes a better understanding of mechanism, feature of chip formation in hard turning process, and supplies theoretical basis for the optimization of hard cutting process parameters.

Computer simulations of transport through membranes: passive diffusion, pores, channels and transporters.

PubMed

Tieleman, D Peter

2006-10-01

A key function of biological membranes is to provide mechanisms for the controlled transport of ions, nutrients, metabolites, peptides and proteins between a cell and its environment. We are using computer simulations to study several processes involved in transport. In model membranes, the distribution of small molecules can be accurately calculated; we are making progress towards understanding the factors that determine the partitioning behaviour in the inhomogeneous lipid environment, with implications for drug distribution, membrane protein folding and the energetics of voltage gating. Lipid bilayers can be simulated at a scale that is sufficiently large to study significant defects, such as those caused by electroporation. Computer simulations of complex membrane proteins, such as potassium channels and ATP-binding cassette (ABC) transporters, can give detailed information about the atomistic dynamics that form the basis of ion transport, selectivity, conformational change and the molecular mechanism of ATP-driven transport. This is illustrated in the present review with recent simulation studies of the voltage-gated potassium channel KvAP and the ABC transporter BtuCD.

Molecular dynamics modeling and simulation of void growth in two dimensions

NASA Astrophysics Data System (ADS)

Chang, H.-J.; Segurado, J.; Rodríguez de la Fuente, O.; Pabón, B. M.; LLorca, J.

2013-10-01

The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yang; Zhao, Qiangsheng; Mirdamadi, Mansour

Woven fabric carbon fiber/epoxy composites made through compression molding are one of the promising choices of material for the vehicle light-weighting strategy. Previous studies have shown that the processing conditions can have substantial influence on the performance of this type of the material. Therefore the optimization of the compression molding process is of great importance to the manufacturing practice. An efficient way to achieve the optimized design of this process would be through conducting finite element (FE) simulations of compression molding for woven fabric carbon fiber/epoxy composites. However, performing such simulation remains a challenging task for FE as multiple typesmore » of physics are involved during the compression molding process, including the epoxy resin curing and the complex mechanical behavior of woven fabric structure. In the present study, the FE simulation of the compression molding process of resin based woven fabric composites at continuum level is conducted, which is enabled by the implementation of an integrated material modeling methodology in LS-Dyna. Specifically, the chemo-thermo-mechanical problem of compression molding is solved through the coupling of three material models, i.e., one thermal model for temperature history in the resin, one mechanical model to update the curing-dependent properties of the resin and another mechanical model to simulate the behavior of the woven fabric composites. Preliminary simulations of the carbon fiber/epoxy woven fabric composites in LS-Dyna are presented as a demonstration, while validations and models with real part geometry are planned in the future work.« less

Numerical simulation analysis of four-stage mutation of solid-liquid two-phase grinding

NASA Astrophysics Data System (ADS)

Li, Junye; Liu, Yang; Hou, Jikun; Hu, Jinglei; Zhang, Hengfu; Wu, Guiling

2018-03-01

In order to explore the numerical simulation of solid-liquid two-phase abrasive grain polishing and abrupt change tube, in this paper, the fourth order abrupt change tube was selected as the research object, using the fluid mechanics software to simulate,based on the theory of solid-liquid two-phase flow dynamics, study on the mechanism of AFM micromachining a workpiece during polishing.Analysis at different inlet pressures, the dynamic pressure distribution pipe mutant fourth order abrasive flow field, turbulence intensity, discuss the influence of the inlet pressure of different abrasive flow polishing effect.

Studies on thermal decomposition behaviors of polypropylene using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Huang, Jinbao; He, Chao; Tong, Hong; Pan, Guiying

2017-11-01

Polypropylene (PP) is one of the main components of waste plastics. In order to understand the mechanism of PP thermal decomposition, the pyrolysis behaviour of PP has been simulated from 300 to 1000 K in periodic boundary conditions by molecular dynamic method, based on AMBER force field. The simulation results show that the pyrolysis process of PP can mostly be divided into three stages: low temperature pyrolysis stage, intermediate temperature stage and high temperature pyrolysis stage. PP pyrolysis is typical of random main-chain scission, and the possible formation mechanism of major pyrolysis products was analyzed.

Dynamic adaptive chemistry for turbulent flame simulations

NASA Astrophysics Data System (ADS)

Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.

2013-02-01

The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.

Smoothed particle hydrodynamics method for simulating waterfall flow

NASA Astrophysics Data System (ADS)

Suwardi, M. G.; Jondri; Tarwidi, D.

2018-03-01

The existence of waterfall in many nations, such as Indonesia has a potential to develop and to fulfill the electricity demand in the nation. By utilizing mechanical flow energy of the waterfall, it would be able to generate electricity. The study of mechanical energy could be done by simulating waterfall flow using 2-D smoothed particle hydrodynamics (SPH) method. The SPH method is suitable to simulate the flow of the waterfall, because it has an advantage which could form particles movement that mimic the characteristics of fluid. In this paper, the SPH method is used to solve Navier-Stokes and continuity equation which are the main cores of fluid motion. The governing equations of fluid flow are used to obtain the acceleration, velocity, density, and position of the SPH particles as well as the completion of Leapfrog time-stepping method. With these equations, simulating a waterfall flow would be more attractive and able to complete the analysis of mechanical energy as desired. The mechanical energy that generated from the waterfall flow is calculated and analyzed based on the mass, height, and velocity of each SPH particle.

Comparisons of Kinematics and Dynamics Simulation Software Tools

NASA Technical Reports Server (NTRS)

Shiue, Yeu-Sheng Paul

2002-01-01

Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.

Collaborative simulation method with spatiotemporal synchronization process control

NASA Astrophysics Data System (ADS)

Zou, Yisheng; Ding, Guofu; Zhang, Weihua; Zhang, Jian; Qin, Shengfeng; Tan, John Kian

2016-10-01

When designing a complex mechatronics system, such as high speed trains, it is relatively difficult to effectively simulate the entire system's dynamic behaviors because it involves multi-disciplinary subsystems. Currently,a most practical approach for multi-disciplinary simulation is interface based coupling simulation method, but it faces a twofold challenge: spatial and time unsynchronizations among multi-directional coupling simulation of subsystems. A new collaborative simulation method with spatiotemporal synchronization process control is proposed for coupling simulating a given complex mechatronics system across multiple subsystems on different platforms. The method consists of 1) a coupler-based coupling mechanisms to define the interfacing and interaction mechanisms among subsystems, and 2) a simulation process control algorithm to realize the coupling simulation in a spatiotemporal synchronized manner. The test results from a case study show that the proposed method 1) can certainly be used to simulate the sub-systems interactions under different simulation conditions in an engineering system, and 2) effectively supports multi-directional coupling simulation among multi-disciplinary subsystems. This method has been successfully applied in China high speed train design and development processes, demonstrating that it can be applied in a wide range of engineering systems design and simulation with improved efficiency and effectiveness.

Trajectory control of robot manipulators with closed-kinematic chain mechanism

NASA Technical Reports Server (NTRS)

Nguyen, Charles C.; Pooran, Farhad J.; Premack, Timothy

1987-01-01

The problem of Cartesian trajectory control of a closed-kinematic chain mechanism robot manipulator, recently built at CAIR to study the assembly of NASA hardware for the future Space Station, is considered. The study is performed by both computer simulation and experimentation for tracking of three different paths: a straight line, a sinusoid, and a circle. Linearization and pole placement methods are employed to design controller gains. Results show that the controllers are robust and there are good agreements between simulation and experimentation. The results also show excellent tracking quality and small overshoots.

Mechanical model for simulating the conditioning of air in the respiratory tract.

PubMed

Bergonse Neto, Nelson; Von Bahten, Luiz Carlos; Moura, Luís Mauro; Coelho, Marlos de Souza; Stori Junior, Wilson de Souza; Bergonse, Gilberto da Fontoura Rey

2007-01-01

To create a mechanical model that could be regulated to simulate the conditioning of inspired and expired air with the same normal values of temperature, pressure, and relative humidity as those of the respiratory system of a healthy young man on mechanical ventilation. Using several types of materials, a mechanical device was built and regulated using normal values of vital capacity, tidal volume, maximal inspiratory pressure, positive end-expiratory pressure, and gas temperature in the system. The device was submitted to mechanical ventilation for a period of 29.8 min. The changes in the temperature of the air circulating in the system were recorded every two seconds. The statistical analysis of the data collected revealed that the device was approximately as efficient in the conditioning of air as is the respiratory system of a human being. By the study endpoint, we had developed a mechanical device capable of simulating the conditioning of air in the respiratory tract. The device mimics the conditions of temperature, pressure, and relative humidity seen in the respiratory system of healthy individuals.

Situating Computer Simulation Professional Development: Does It Promote Inquiry-Based Simulation Use?

ERIC Educational Resources Information Center

Gonczi, Amanda L.; Maeng, Jennifer L.; Bell, Randy L.; Whitworth, Brooke A.

2016-01-01

This mixed-methods study sought to identify professional development implementation variables that may influence participant (a) adoption of simulations, and (b) use for inquiry-based science instruction. Two groups (Cohort 1, N = 52; Cohort 2, N = 104) received different professional development. Cohort 1 was focused on Web site use mechanics.…

Ab Initio Modeling of Structure and Properties of Single and Mixed Alkali Silicate Glasses.

PubMed

Baral, Khagendra; Li, Aize; Ching, Wai-Yim

2017-10-12

A density functional theory (DFT)-based ab initio molecular dynamics (AIMD) has been applied to simulate models of single and mixed alkali silicate glasses with two different molar concentrations of alkali oxides. The structural environments and spatial distributions of alkali ions in the 10 simulated models with 20% and 30% of Li, Na, K and equal proportions of Li-Na and Na-K are studied in detail for subtle variations among the models. Quantum mechanical calculations of electronic structures, interatomic bonding, and mechanical and optical properties are carried out for each of the models, and the results are compared with available experimental observation and other simulations. The calculated results are in good agreement with the experimental data. We have used the novel concept of using the total bond order density (TBOD), a quantum mechanical metric, to characterize internal cohesion in these glass models. The mixed alkali effect (MAE) is visible in the bulk mechanical properties but not obvious in other physical properties studied in this paper. We show that Li doping deviates from expected trend due to the much stronger Li-O bonding than those of Na and K doping. The approach used in this study is in contrast with current studies in alkali-doped silicate glasses based only on geometric characterizations.

The effects and mechanisms of clinorotation on proliferation and differentiation in bone marrow mesenchymal stem cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Ming; Wang, Yongchun; Yang, Min

Data from human and rodent studies have demonstrated that microgravity induces observed bone loss in real spaceflight or simulated experiments. The decrease of bone formation and block of maturation may play important roles in bone loss induced by microgravity. The aim of this study was to investigate the changes of proliferation and differentiation in bone marrow mesenchymal stem cells (BMSCs) induced by simulated microgravity and the mechanisms underlying it. We report here that clinorotation, a simulated model of microgravity, decreased proliferation and differentiation in BMSCs after exposure to 48 h simulated microgravity. The inhibited proliferation are related with blocking the cellmore » cycle in G2/M and enhancing the apoptosis. While alterations of the osteoblast differentiation due to the decreased SATB2 expression induced by simulated microgravity in BMSCs. - Highlights: • Simulated microgravity inhibited proliferation and differentiation in BMSCs. • The decreased proliferation due to blocked cell cycle and enhanced the apoptosis. • The inhibited differentiation accounts for alteration of SATB2, Hoxa2 and Cbfa1.« less

Impact of Gas-Phase Mechanisms on Weather Research Forecasting Model with Chemistry (WRF/Chem) Predictions: Mechanism Implementation and Comparative Evaluation

EPA Science Inventory

Gas-phase mechanisms provide important oxidant and gaseous precursors for secondary aerosol formation. Different gas-phase mechanisms may lead to different predictions of gases, aerosols, and aerosol direct and indirect effects. In this study, WRF/Chem-MADRID simulations are cond...

Simulation study of solar plasma eruptions caused by interactions between emerging flux and coronal arcade fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaneko, Takafumi; Yokoyama, Takaaki, E-mail: kaneko@eps.s.u-tokyo.ac.jp

2014-11-20

We investigate the triggering mechanisms of plasma eruptions in the solar atmosphere due to interactions between emerging flux and coronal arcade fields by using two-dimensional MHD simulations. We perform parameter surveys with respect to arcade field height, magnetic field strength, and emerging flux location. Our results show that two possible mechanisms exist, and which mechanism is dominant depends mostly on emerging flux location. One mechanism appears when the location of emerging flux is close to the polarity inversion line (PIL) of an arcade field. This mechanism requires reconnection between the emerging flux and the arcade field, as pointed out bymore » previous studies. The other mechanism appears when the location of emerging flux is around the edge of an arcade field. This mechanism does not require reconnection between the emerging flux and the arcade field but does demand reconnection in the arcade field above the PIL. Furthermore, we found that the eruptive condition for this mechanism can be represented by a simple formula.« less

Direct Simulation of Magnetic Resonance Relaxation Rates and Line Shapes from Molecular Trajectories

PubMed Central

Rangel, David P.; Baveye, Philippe C.; Robinson, Bruce H.

2012-01-01

We simulate spin relaxation processes, which may be measured by either continuous wave or pulsed magnetic resonance techniques, using trajectory-based simulation methodologies. The spin–lattice relaxation rates are extracted numerically from the relaxation simulations. The rates obtained from the numerical fitting of the relaxation curves are compared to those obtained by direct simulation from the relaxation Bloch–Wangsness–Abragam– Redfield theory (BWART). We have restricted our study to anisotropic rigid-body rotational processes, and to the chemical shift anisotropy (CSA) and a single spin–spin dipolar (END) coupling mechanisms. Examples using electron paramagnetic resonance (EPR) nitroxide and nuclear magnetic resonance (NMR) deuterium quadrupolar systems are provided. The objective is to compare those rates obtained by numerical simulations with the rates obtained by BWART. There is excellent agreement between the simulated and BWART rates for a Hamiltonian describing a single spin (an electron) interacting with the bath through the chemical shift anisotropy (CSA) mechanism undergoing anisotropic rotational diffusion. In contrast, when the Hamiltonian contains both the chemical shift anisotropy (CSA) and the spin–spin dipolar (END) mechanisms, the decay rate of a single exponential fit of the simulated spin–lattice relaxation rate is up to a factor of 0.2 smaller than that predicted by BWART. When the relaxation curves are fit to a double exponential, the slow and fast rates extracted from the decay curves bound the BWART prediction. An extended BWART theory, in the literature, includes the need for multiple relaxation rates and indicates that the multiexponential decay is due to the combined effects of direct and cross-relaxation mechanisms. PMID:22540276

Application of a BOSS – Gaussian Interface for QM/MM Simulations of Henry and Methyl Transfer Reactions

PubMed Central

Vilseck, Jonah Z.; Kostal, Jakub; Tirado-Rives, Julian; Jorgensen, William L.

2015-01-01

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with quantum mechanics alone. For several decades, semi-empirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the inter-program communication. The BOSS–Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS–Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations employing semiempirical methods. PMID:26311531

In silico prediction of drug therapy in catecholaminergic polymorphic ventricular tachycardia

PubMed Central

Yang, Pei‐Chi; Moreno, Jonathan D.; Miyake, Christina Y.; Vaughn‐Behrens, Steven B.; Jeng, Mao‐Tsuen; Grandi, Eleonora; Wehrens, Xander H. T.; Noskov, Sergei Y.

2016-01-01

Key points The mechanism of therapeutic efficacy of flecainide for catecholaminergic polymorphic ventricular tachycardia (CPVT) is unclear.Model predictions suggest that Na+ channel effects are insufficient to explain flecainide efficacy in CPVT.This study represents a first step toward predicting therapeutic mechanisms of drug efficacy in the setting of CPVT and then using these mechanisms to guide modelling and simulation to predict alternative drug therapies. Abstract Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited arrhythmia syndrome characterized by fatal ventricular arrhythmias in structurally normal hearts during β‐adrenergic stimulation. Current treatment strategies include β‐blockade, flecainide and ICD implementation – none of which is fully effective and each comes with associated risk. Recently, flecainide has gained considerable interest in CPVT treatment, but its mechanism of action for therapeutic efficacy is unclear. In this study, we performed in silico mutagenesis to construct a CPVT model and then used a computational modelling and simulation approach to make predictions of drug mechanisms and efficacy in the setting of CPVT. Experiments were carried out to validate model results. Our simulations revealed that Na+ channel effects are insufficient to explain flecainide efficacy in CPVT. The pure Na+ channel blocker lidocaine and the antianginal ranolazine were additionally tested and also found to be ineffective. When we tested lower dose combination therapy with flecainide, β‐blockade and CaMKII inhibition, our model predicted superior therapeutic efficacy than with flecainide monotherapy. Simulations indicate a polytherapeutic approach may mitigate side‐effects and proarrhythmic potential plaguing CPVT pharmacological management today. Importantly, our prediction of a novel polytherapy for CPVT was confirmed experimentally. Our simulations suggest that flecainide therapeutic efficacy in CPVT is unlikely to derive from primary interactions with the Na+ channel, and benefit may be gained from an alternative multi‐drug regimen. PMID:26515697

Mesoscale mechanics of twisting carbon nanotube yarns.

PubMed

Mirzaeifar, Reza; Qin, Zhao; Buehler, Markus J

2015-03-12

Fabricating continuous macroscopic carbon nanotube (CNT) yarns with mechanical properties close to individual CNTs remains a major challenge. Spinning CNT fibers and ribbons for enhancing the weak interactions between the nanotubes is a simple and efficient method for fabricating high-strength and tough continuous yarns. Here we investigate the mesoscale mechanics of twisting CNT yarns using full atomistic and coarse grained molecular dynamics simulations, considering concurrent mechanisms at multiple length-scales. To investigate the mechanical response of such a complex structure without losing insights into the molecular mechanism, we applied a multiscale strategy. The full atomistic results are used for training a coarse grained model for studying larger systems consisting of several CNTs. The mesoscopic model parameters are updated as a function of the twist angle, based on the full atomistic results, in order to incorporate the atomistic scale deformation mechanisms in larger scale simulations. By bridging across two length scales, our model is capable of accurately predicting the mechanical behavior of twisted yarns while the atomistic level deformations in individual nanotubes are integrated into the model by updating the parameters. Our results focused on studying a bundle of close packed nanotubes provide novel mechanistic insights into the spinning of CNTs. Our simulations reveal how twisting a bundle of CNTs improves the shear interaction between the nanotubes up to a certain level due to increasing the interaction surface. Furthermore, twisting the bundle weakens the intertube interactions due to excessive deformation in the cross sections of individual CNTs in the bundle.

MECHANISMS OF NITROUS OXIDE FORMATION IN COAL FLAMES

EPA Science Inventory

The paper gives results of a study, using both detailed kinetic modeling and plug-flow simulator experiments, to investigate an unknown mechanism by which N2O is formed in coal flames. This mechanism has considerable importance in determining the influence of common and advanced ...

Effects of Solid Fraction on Droplet Wetting and Vapor Condensation: A Molecular Dynamic Simulation Study.

PubMed

Gao, Shan; Liao, Quanwen; Liu, Wei; Liu, Zhichun

2017-10-31

Recently, numerous studies focused on the wetting process of droplets on various surfaces at a microscale level. However, there are a limited number of studies about the mechanism of condensation on patterned surfaces. The present study performed the dynamic wetting behavior of water droplets and condensation process of water molecules on substrates with different pillar structure parameters, through molecular dynamic simulation. The dynamic wetting results indicated that droplets exhibit Cassie state, PW state, and Wenzel state successively on textured surfaces with decreasing solid fraction. The droplets possess a higher static contact angle and a smaller spreading exponent on textured surfaces than those on smooth surfaces. The condensation processes, including the formation, growth, and coalescence of a nanodroplet, are simulated and quantitatively recorded, which are difficult to be observed by experiments. In addition, a wetting transition and a dewetting transition were observed and analyzed in condensation on textured surfaces. Combining these simulation results with previous theoretical and experimental studies will guide us to understand the hypostasis and mechanism of the condensation more clearly.

Skylab fluid mechanics simulations: Oscillation, rotation, collision and coalescence of water droplets under low-gravity environment

NASA Technical Reports Server (NTRS)

Vaughan, O. H., Jr.; Hung, R. J.

1975-01-01

Skylab 4 crew members performed a series of demonstrations showing the oscillations, rotations, as well as collision coalescence of water droplets which simulate various physical models of fluids under low gravity environment. The results from Skylab demonstrations provide information and illustrate the potential of an orbiting space-oriented research laboratory for the study of more sophisticated fluid mechanic experiments. Experiments and results are discussed.

Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

PubMed

van der Vaart, Arjan

2015-05-01

Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

An electrical circuit model for simulation of indoor radon concentration.

PubMed

Musavi Nasab, S M; Negarestani, A

2013-01-01

In this study, a new model based on electric circuit theory was introduced to simulate the behaviour of indoor radon concentration. In this model, a voltage source simulates radon generation in walls, conductivity simulates migration through walls and voltage across a capacitor simulates radon concentration in a room. This simulation considers migration of radon through walls by diffusion mechanism in one-dimensional geometry. Data reported in a typical Greek house were employed to examine the application of this technique of simulation to the behaviour of radon.

What has finite element analysis taught us about diabetic foot disease and its management? A systematic review.

PubMed

Telfer, Scott; Erdemir, Ahmet; Woodburn, James; Cavanagh, Peter R

2014-01-01

Over the past two decades finite element (FE) analysis has become a popular tool for researchers seeking to simulate the biomechanics of the healthy and diabetic foot. The primary aims of these simulations have been to improve our understanding of the foot's complicated mechanical loading in health and disease and to inform interventions designed to prevent plantar ulceration, a major complication of diabetes. This article provides a systematic review and summary of the findings from FE analysis-based computational simulations of the diabetic foot. A systematic literature search was carried out and 31 relevant articles were identified covering three primary themes: methodological aspects relevant to modelling the diabetic foot; investigations of the pathomechanics of the diabetic foot; and simulation-based design of interventions to reduce ulceration risk. Methodological studies illustrated appropriate use of FE analysis for simulation of foot mechanics, incorporating nonlinear tissue mechanics, contact and rigid body movements. FE studies of pathomechanics have provided estimates of internal soft tissue stresses, and suggest that such stresses may often be considerably larger than those measured at the plantar surface and are proportionally greater in the diabetic foot compared to controls. FE analysis allowed evaluation of insole performance and development of new insole designs, footwear and corrective surgery to effectively provide intervention strategies. The technique also presents the opportunity to simulate the effect of changes associated with the diabetic foot on non-mechanical factors such as blood supply to local tissues. While significant advancement in diabetic foot research has been made possible by the use of FE analysis, translational utility of this powerful tool for routine clinical care at the patient level requires adoption of cost-effective (both in terms of labour and computation) and reliable approaches with clear clinical validity for decision making.

Influences of chemical sympathectomy and simulated weightlessness on male and female rats

NASA Technical Reports Server (NTRS)

Woodman, Christopher R.; Stump, Craig S.; Stump, Jane A.; Sebastian, Lisa A.; Rahman, Z.; Tipton, Charles M.

1991-01-01

Consideration is given to a study aimed at determining whether the sympathetic nervous system is associated with the changes in maximum oxygen consumption (VO2max), run time, and mechanical efficiency observed during simulated weightlessness in male and female rats. Female and male rats were compared for food consumption, body mass, and body composition in conditions of simulated weightlessness to provide an insight into how these parameters may influence aerobic capacity and exercise performance. It is concluded that chemical sympathectomy and/or a weight-bearing stimulus will attenuate the loss in VO2max associated with simulated weightlessness in rats despite similar changes in body mass and composition. It is noted that the mechanisms remain unclear at this time.

Measured and Simulated Dark J-V Characteristics of a-Si:H Single Junction p-i-n Solar Cells Irradiated with 40 keV Electrons

NASA Technical Reports Server (NTRS)

Lord, Kenneth; Woodyard, James R.

2002-01-01

The effect of 40 keV electron irradiation on a-Si:H p-i-n single-junction solar cells was investigated using measured and simulated dark J-V characteristics. EPRI-AMPS and PC-1D simulators were explored for use in the studies. The EPRI-AMPS simulator was employed and simulator parameters selected to produce agreement with measured J-V characteristics. Three current mechanisms were evident in the measured dark J-V characteristics after electron irradiation, namely, injection, shunting and a term of the form CV(sup m). Using a single discrete defect state level at the center of the band gap, good agreement was achieved between measured and simulated J-V characteristics in the forward-bias voltage region where the dark current density was dominated by injection. The current mechanism of the form CV(sup m) was removed by annealing for two hours at 140 C. Subsequent irradiation restored the CV(sup m) current mechanism and it was removed by a second anneal. Some evidence of the CV(sup m) term is present in device simulations with a higher level of discrete density of states located at the center of the bandgap.

Modeling and simulation of protein-surface interactions: achievements and challenges.

PubMed

Ozboyaci, Musa; Kokh, Daria B; Corni, Stefano; Wade, Rebecca C

2016-01-01

Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

Design of an air traffic computer simulation system to support investigation of civil tiltrotor aircraft operations

NASA Technical Reports Server (NTRS)

Rogers, Ralph V.

1992-01-01

This research project addresses the need to provide an efficient and safe mechanism to investigate the effects and requirements of the tiltrotor aircraft's commercial operations on air transportation infrastructures, particularly air traffic control. The mechanism of choice is computer simulation. Unfortunately, the fundamental paradigms of the current air traffic control simulation models do not directly support the broad range of operational options and environments necessary to study tiltrotor operations. Modification of current air traffic simulation models to meet these requirements does not appear viable given the range and complexity of issues needing resolution. As a result, the investigation of systemic, infrastructure issues surrounding the effects of tiltrotor commercial operations requires new approaches to simulation modeling. These models should be based on perspectives and ideas closer to those associated with tiltrotor air traffic operations.

Exploring molecular insights into the interaction mechanism of cholesterol derivatives with the Mce4A: A combined spectroscopic and molecular dynamic simulation studies.

PubMed

Khan, Shagufta; Khan, Faez Iqbal; Mohammad, Taj; Khan, Parvez; Hasan, Gulam Mustafa; Lobb, Kevin A; Islam, Asimul; Ahmad, Faizan; Imtaiyaz Hassan, Md

2018-05-01

Mammalian cell entry protein (Mce4A) is a member of MCE-family, and is being considered as a potential drug target of Mycobacterium tuberculosis infection because it is required for invasion and latent survival of pathogen by utilizing host's cholesterol. In the present study, we performed molecular docking followed by 100 ns MD simulation studies to understand the mechanism of interaction of Mce4A to the cholesterol derivatives and probucol. The selected ligands, cholesterol, 25-hydroxycholesterol, 5-cholesten-3β-ol-7-one and probucol bind to the predicted active site cavity of Mce4A, and complexes remain stable during entire simulation of 100 ns. In silico studies were further validated by fluorescence-binding studies to calculate actual binding affinity and number of binding site(s). The non-toxicity of all ligands was confirmed on human monocytic cell (THP1) by MTT assay. This work provides a deeper insight into the mechanism of interaction of Mce4A to cholesterol derivatives, which may be further exploited to design potential and specific inhibitors to ameliorate the Mycobacterium pathogenesis. Copyright © 2018 Elsevier B.V. All rights reserved.

Theoretical studies on the selective mechanisms of GSK3β and CDK2 by molecular dynamics simulations and free energy calculations.

PubMed

Zhao, Sufang; Zhu, Jingyu; Xu, Lei; Jin, Jian

2017-06-01

Glycogen synthase kinase 3 (GSK3) is a serine/threonine protein kinase which is widely involved in cell signaling and controls a broad number of cellular functions. GSK3 contains α and β isoforms, and GSK3β has received more attention and becomes an attractive drug target for the treatment of several diseases. The binding pocket of cyclin-dependent kinase 2 (CDK2) shares high sequence identity to that of GSK3β, and therefore, the design of highly selective inhibitors toward GSK3β remains a big challenge. In this study, a computational strategy, which combines molecular docking, molecular dynamics simulations, free energy calculations, and umbrella sampling simulations, was employed to explore the binding mechanisms of two selective inhibitors to GSK3β and CDK2. The simulation results highlighted the key residues critical for GSK3β selectivity. It was observed that although GSK3β and CDK2 share the conserved ATP-binding pockets, some different residues have significant contributions to protein selectivity. This study provides valuable information for understanding the GSK3β-selective binding mechanisms and the rational design of selective GSK3β inhibitors. © 2016 John Wiley & Sons A/S.

Crew interface definition study, phase 1

NASA Technical Reports Server (NTRS)

Callihan, J. C.; Kraemer, J. W.; Alles, J. A.

1971-01-01

The timeline analysis of the Shuttle orbiter missions which was conducted in the Phase I Crew Interface Definition Study and the requirements for the man-in-the-loop simulation study are presented. Mission definitions and objectives are presented as they relate to various Shuttle Orbiter missions. The requirements for crew participation and the information required by the crew are discussed, and finally the rationale behind the display concept and calling procedures is given. The simulation objectives, the simulation mechanization, including a detailed presentation of the display and control concept, the simulator test plan and the results are discussed.

Mechanical characterization of atherosclerotic arteries using finite-element modeling: feasibility study on mock arteries.

PubMed

Pazos, Valérie; Mongrain, Rosaire; Tardif, Jean-Claude

2010-06-01

Clinical studies on lipid-lowering therapy have shown that changing the composition of lipid pools reduced significantly the risk of cardiac events associated with plaque rupture. It has been shown also that changing the composition of the lipid pool affects its mechanical properties. However, knowledge about the mechanical properties of human atherosclerotic lesions remains limited due to the difficulty of the experiments. This paper aims to assess the feasibility of characterizing a lipid pool embedded in the wall of a pressurized vessel using finite-element simulations and an optimization algorithm. Finite-element simulations of inflation experiments were used together with nonlinear least squares algorithm to estimate the material model parameters of the wall and of the inclusion. An optimal fit of the simulated experiment and the real experiment was sought with the parameter estimation algorithm. The method was first tested on a single-layer polyvinyl alcohol (PVA) cryogel stenotic vessel, and then, applied on a double-layered PVA cryogel stenotic vessel with a lipid inclusion.

Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study

NASA Astrophysics Data System (ADS)

Lee, Vannajan Sanghiran; Kodchakorn, Kanchanok; Jitonnom, Jitrayut; Nimmanpipug, Piyarat; Kongtawelert, Prachya; Premanode, Bhusana

2010-10-01

The reaction mechanism of creatinine-creatininase binding to form creatine as a final product has been investigated by using a combined ab initio quantum mechanical/molecular mechanical approach and classical molecular dynamics (MD) simulations. In MD simulations, an X-ray crystal structure of the creatininase/creatinine was modified for creatininase/creatinine complexes and the MD simulations were run for free creatininase and creatinine in water. MD results reveal that two X-ray water molecules can be retained in the active site as catalytic water. The binding free energy from Molecular Mechanics Poisson-Boltzmann Surface Area calculation predicted the strong binding of creatinine with Zn2+, Asp45 and Glu183. Two step mechanisms via Mn2+/Zn2+ (as in X-ray structure) and Zn2+/Zn2+ were proposed for water adding step and ring opening step with two catalytic waters. The pathway using synchronous transit methods with local density approximations with PWC functional for the fragment in the active region were obtained. Preferable pathway Zn2+/Zn2+ was observed due to lower activation energy in water adding step. The calculated energy in the second step for both systems were comparable with the barrier of 26.03 and 24.44 kcal/mol for Mn2+/Zn2+ and Zn2+/Zn2+, respectively.

Simulation based estimation of dynamic mechanical properties for viscoelastic materials used for vocal fold models

NASA Astrophysics Data System (ADS)

Rupitsch, Stefan J.; Ilg, Jürgen; Sutor, Alexander; Lerch, Reinhard; Döllinger, Michael

2011-08-01

In order to obtain a deeper understanding of the human phonation process and the mechanisms generating sound, realistic setups are built up containing artificial vocal folds. Usually, these vocal folds consist of viscoelastic materials (e.g., polyurethane mixtures). Reliable simulation based studies on the setups require the mechanical properties of the utilized viscoelastic materials. The aim of this work is the identification of mechanical material parameters (Young's modulus, Poisson's ratio, and loss factor) for those materials. Therefore, we suggest a low-cost measurement setup, the so-called vibration transmission analyzer (VTA) enabling to analyze the transfer behavior of viscoelastic materials for propagating mechanical waves. With the aid of a mathematical Inverse Method, the material parameters are adjusted in a convenient way so that the simulation results coincide with the measurement results for the transfer behavior. Contrary to other works, we determine frequency dependent functions for the mechanical properties characterizing the viscoelastic material in the frequency range of human speech (100-250 Hz). The results for three different materials clearly show that the Poisson's ratio is close to 0.5 and that the Young's modulus increases with higher frequencies. For a frequency of 400 Hz, the Young's modulus of the investigated viscoelastic materials is approximately 80% higher than for the static case (0 Hz). We verify the identified mechanical properties with experiments on fabricated vocal fold models. Thereby, only small deviations between measurements and simulations occur.

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of reaction dynamics, which provides a useful tool to study chemical or biochemical systems in solution or enzymes.

Effect of orientation on deformation behavior of Fe nanowires: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Sainath, G.; Srinivasan, V. S.; Choudhary, B. K.; Mathew, M. D.; Jayakumar, T.

2014-04-01

Molecular dynamics simulations have been carried out to study the effect of crystal orientation on tensile deformation behaviour of single crystal BCC Fe nanowires at 10 K. Two nanowires with an initial orientation of <100>/{100} and <110>/{111} have been chosen for this study. The simulation results show that the deformation mechanisms varied with crystal orientation. The nanowire with an initial orientation of <100>/{100} deforms predominantly by twinning mechanism, whereas the nanowire oriented in <110>/{111}, deforms by dislocation plasticity. In addition, the single crystal oriented in <110>/{111} shows higher strength and elastic modulus than <100>/{100} oriented nanowire.

Identifying Structure-Property Relationships Through DREAM.3D Representative Volume Elements and DAMASK Crystal Plasticity Simulations: An Integrated Computational Materials Engineering Approach

NASA Astrophysics Data System (ADS)

Diehl, Martin; Groeber, Michael; Haase, Christian; Molodov, Dmitri A.; Roters, Franz; Raabe, Dierk

2017-05-01

Predicting, understanding, and controlling the mechanical behavior is the most important task when designing structural materials. Modern alloy systems—in which multiple deformation mechanisms, phases, and defects are introduced to overcome the inverse strength-ductility relationship—give raise to multiple possibilities for modifying the deformation behavior, rendering traditional, exclusively experimentally-based alloy development workflows inappropriate. For fast and efficient alloy design, it is therefore desirable to predict the mechanical performance of candidate alloys by simulation studies to replace time- and resource-consuming mechanical tests. Simulation tools suitable for this task need to correctly predict the mechanical behavior in dependence of alloy composition, microstructure, texture, phase fractions, and processing history. Here, an integrated computational materials engineering approach based on the open source software packages DREAM.3D and DAMASK (Düsseldorf Advanced Materials Simulation Kit) that enables such virtual material development is presented. More specific, our approach consists of the following three steps: (1) acquire statistical quantities that describe a microstructure, (2) build a representative volume element based on these quantities employing DREAM.3D, and (3) evaluate the representative volume using a predictive crystal plasticity material model provided by DAMASK. Exemplarily, these steps are here conducted for a high-manganese steel.

Mixing Layer Formation near the Tropopause Due to Gravity Wave Critical Level Interactions in a Cloud-Resolving Model.

NASA Astrophysics Data System (ADS)

Moustaoui, Mohamed; Joseph, Binson; Teitelbaum, Hector

2004-12-01

A plausible mechanism for the formation of mixing layers in the lower stratosphere above regions of tropical convection is demonstrated numerically using high-resolution, two-dimensional (2D), anelastic, nonlinear, cloud-resolving simulations. One noteworthy point is that the mixing layer simulated in this study is free of anvil clouds and well above the cloud anvil top located in the upper troposphere. Hence, the present mechanism is complementary to the well-known process by which overshooting cloud turrets causes mixing within stratospheric anvil clouds. The paper is organized as a case study verifying the proposed mechanism using atmospheric soundings obtained during the Central Equatorial Pacific Experiment (CEPEX), when several such mixing layers, devoid of anvil clouds, had been observed. The basic dynamical ingredient of the present mechanism is (quasi stationary) gravity wave critical level interactions, occurring in association with a reversal of stratospheric westerlies to easterlies below the tropopause region. The robustness of the results is shown through simulations at different resolutions. The insensitivity of the qualitative results to the details of the subgrid scheme is also evinced through further simulations with and without subgrid mixing terms. From Lagrangian reconstruction of (passive) ozone fields, it is shown that the mixing layer is formed kinematically through advection by the resolved-scale (nonlinear) velocity field.

Gravity, an Regulation Factor in BMSCs Differentiation to osteoblasts

NASA Astrophysics Data System (ADS)

Yan, Huang; Yinghui, Li; Fen, Yang; Zhongquan, Dai

PURPOSE Most studies of regulatory mechanisms of adult stem cell differentiation are concentrated in chemical factors but few efforts are put into physical factors Recent space life science studies indicate mechanical factors participate in the differentiation of cells The aim of this study is to investigate the effects of simulated microgravity or hypergravity on the osteogenic differentiation of rat bone marrow mesenchymal stem cells BMSCs METHODOLOGY The BMSCs at day 7 were added osteogenic inducer 10nM dexamethasone 10mM beta -glycerophosphate and 50 mu M asorbic acid-2-phosphate for 7 days and cultured under simulated microgravity or hypergravity 2g for 1 day 3 days 5 days or 7 days RESULTS After treating BMSCs with osteogenic inducer and hypergravity the cells expressed more ColIA1 Cbfa1 and ALP than in single steogenic inducer treatment Reversely the cells treated with osteogenic inducer and simulated microgravity expressed less ColIA1 Cbfa1 and ALP CONCLUSIONS Our study suggests that hypergravity promotes the osteogenic differentiation of BMSCs and simulated microgravity inhibits this process Gravity is an important regulation factor in BMSCs differentiation to osteoblasts

Multiscale Mechanics of Articular Cartilage: Potentials and Challenges of Coupling Musculoskeletal, Joint, and Microscale Computational Models

PubMed Central

Halloran, J. P.; Sibole, S.; van Donkelaar, C. C.; van Turnhout, M. C.; Oomens, C. W. J.; Weiss, J. A.; Guilak, F.; Erdemir, A.

2012-01-01

Articular cartilage experiences significant mechanical loads during daily activities. Healthy cartilage provides the capacity for load bearing and regulates the mechanobiological processes for tissue development, maintenance, and repair. Experimental studies at multiple scales have provided a fundamental understanding of macroscopic mechanical function, evaluation of the micromechanical environment of chondrocytes, and the foundations for mechanobiological response. In addition, computational models of cartilage have offered a concise description of experimental data at many spatial levels under healthy and diseased conditions, and have served to generate hypotheses for the mechanical and biological function. Further, modeling and simulation provides a platform for predictive risk assessment, management of dysfunction, as well as a means to relate multiple spatial scales. Simulation-based investigation of cartilage comes with many challenges including both the computational burden and often insufficient availability of data for model development and validation. This review outlines recent modeling and simulation approaches to understand cartilage function from a mechanical systems perspective, and illustrates pathways to associate mechanics with biological function. Computational representations at single scales are provided from the body down to the microstructure, along with attempts to explore multiscale mechanisms of load sharing that dictate the mechanical environment of the cartilage and chondrocytes. PMID:22648577

Modeling and Proposed Molecular Mechanism of Hydroxyurea Through Docking and Molecular Dynamic Simulation to Curtail the Action of Ribonucleotide Reductase.

PubMed

Iman, Maryam; Khansefid, Zeynab; Davood, Asghar

2016-01-01

Ribonucleotide Reductase (RNR) is an important anticancer chemotherapy target. It has main key role in DNA synthesis and cell growth. Therefore several RNR inhibitors, such as hydroxyurea, have entered the clinical trials. Based on our proposed mechanism, radical site of RNR protein reacts with hydroxyurea in which hydroxyurea is converted into its oxidized form compound III, and whereby the tyrosyl radical is converted into a normal tyrosine residue. In this study, docking and molecular dynamics simulations were used for proposed molecular mechanism of hydroxyurea in RNR inhibition as anticancer agent. The binding affinity of hydroxyurea and compound III to RNR was studied by docking method. The docking study was performed for the crystal structure of human RNR with the radical scavenger Hydroxyurea and its oxidized form to inhibit the human RNR. hydroxyurea and compound III bind at the active site with Tyr-176, which are essential for free radical formation. This helps to understand the functional aspects and also aids in the development of novel inhibitors for the human RNR2. To confirm the binding mode of inhibitors, the molecular dynamics (MD) simulations were performed using GROMACS 4.5.5, based upon the docked conformation of inhibitors. Both of the studied compounds stayed in the active site. The results of MD simulations confirmed the binding mode of ligands, accuracy of docking and the reliability of active conformations which were obtained by AutoDock. MD studies confirm our proposed mechanism in which compound III reacts with the active site residues specially Tyr-176, and inhibits the radical generation and subsequently inhibits the RNR enzyme.

Improved simulation method of automotive spot weld failure with an account of the mechanical properties of spot welds

NASA Astrophysics Data System (ADS)

Wu, H.; Meng, X. M.; Fang, R.; Huang, Y. F.; Zhan, S.

2017-12-01

In this paper, the microstructure and mechanical properties of spot weld were studied, the hardness of nugget and heat affected zone (HAZ) were also tested by metallographic microscope and microhardness tester. The strength of the spot weld with the different parts' area has been characterized. According to the experiments result, CAE model of spot weld with HAZ structure was established, and simulation results of different lap-shear CAE models were analyzed. The results show that the spot weld model which contained the HAZ has good performance and more suitable for engineering application in spot weld simulation.

Mechanical impact of dynamic phenomena in Francis turbines at off design conditions

NASA Astrophysics Data System (ADS)

Duparchy, F.; Brammer, J.; Thibaud, M.; Favrel, A.; Lowys, P. Y.; Avellan, F.

2017-04-01

At partial load and overload conditions, Francis turbines are subjected to hydraulic instabilities that can potentially result in high dynamic solicitations of the turbine components and significantly reduce their lifetime. This study presents both experimental data and numerical simulations that were used as complementary approaches to study these dynamic solicitations. Measurements performed on a reduced scale physical model, including a special runner instrumented with on-board strain gauges and pressure sensors, were used to investigate the dynamic phenomena experienced by the runner. They were also taken as reference to validate the numerical simulation results. After validation, advantage was taken from the numerical simulations to highlight the mechanical response of the structure to the unsteady hydraulic phenomena, as well as their impact on the fatigue damage of the runner.

MEchatronic REspiratory System SImulator for Neonatal Applications (MERESSINA) project: a novel bioengineering goal

PubMed Central

Scaramuzzo, Rosa T; Ciantelli, Massimiliano; Baldoli, Ilaria; Bellanti, Lisa; Gentile, Marzia; Cecchi, Francesca; Sigali, Emilio; Tognarelli, Selene; Ghirri, Paolo; Mazzoleni, Stefano; Menciassi, Arianna; Cuttano, Armando; Boldrini, Antonio; Laschi, Cecilia; Dario, Paolo

2013-01-01

Respiratory function is mandatory for extrauterine life, but is sometimes impaired in newborns due to prematurity, congenital malformations, or acquired pathologies. Mechanical ventilation is standard care, but long-term complications, such as bronchopulmonary dysplasia, are still largely reported. Therefore, continuous medical education is mandatory to correctly manage devices for assistance. Commercially available breathing function simulators are rarely suitable for the anatomical and physiological realities. The aim of this study is to develop a high-fidelity mechatronic simulator of neonatal airways and lungs for staff training and mechanical ventilator testing. The project is divided into three different phases: (1) a review study on respiratory physiology and pathophysiology and on already available single and multi-compartment models; (2) the prototyping phase; and (3) the on-field system validation. PMID:23966804

Computational study of 3-D hot-spot initiation in shocked insensitive high-explosive

NASA Astrophysics Data System (ADS)

Najjar, F. M.; Howard, W. M.; Fried, L. E.; Manaa, M. R.; Nichols, A., III; Levesque, G.

2012-03-01

High-explosive (HE) material consists of large-sized grains with micron-sized embedded impurities and pores. Under various mechanical/thermal insults, these pores collapse generating hightemperature regions leading to ignition. A hydrodynamic study has been performed to investigate the mechanisms of pore collapse and hot spot initiation in TATB crystals, employing a multiphysics code, ALE3D, coupled to the chemistry module, Cheetah. This computational study includes reactive dynamics. Two-dimensional high-resolution large-scale meso-scale simulations have been performed. The parameter space is systematically studied by considering various shock strengths, pore diameters and multiple pore configurations. Preliminary 3-D simulations are undertaken to quantify the 3-D dynamics.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

PubMed

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

A representative-sandwich model for simultaneously coupled mechanical-electrical-thermal simulation of a lithium-ion cell under quasi-static indentation tests

DOE PAGES

Zhang, Chao; Santhanagopalan, Shriram; Sprague, Michael A.; ...

2015-08-29

The safety behavior of lithium-ion batteries under external mechanical crush is a critical concern, especially during large scale deployment. We previously presented a sequentially coupled mechanical-electrical-thermal modeling approach for studying mechanical abuse induced short circuit. Here in this work, we study different mechanical test conditions and examine the interaction between mechanical failure and electrical-thermal responses, by developing a simultaneous coupled mechanical-electrical-thermal model. The present work utilizes a single representative-sandwich (RS) to model the full pouch cell with explicit representations for each individual component such as the active material, current collector, separator, etc. Anisotropic constitutive material models are presented to describemore » the mechanical properties of active materials and separator. The model predicts accurately the force-strain response and fracture of battery structure, simulates the local failure of separator layer, and captures the onset of short circuit for lithium-ion battery cell under sphere indentation tests with three different diameters. Electrical-thermal responses to the three different indentation tests are elaborated and discussed. Lastly, numerical studies are presented to show the potential impact of test conditions on the electrical-thermal behavior of the cell after the occurrence of short circuit.« less

A representative-sandwich model for simultaneously coupled mechanical-electrical-thermal simulation of a lithium-ion cell under quasi-static indentation tests

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chao; Santhanagopalan, Shriram; Sprague, Michael A.

The safety behavior of lithium-ion batteries under external mechanical crush is a critical concern, especially during large scale deployment. We previously presented a sequentially coupled mechanical-electrical-thermal modeling approach for studying mechanical abuse induced short circuit. Here in this work, we study different mechanical test conditions and examine the interaction between mechanical failure and electrical-thermal responses, by developing a simultaneous coupled mechanical-electrical-thermal model. The present work utilizes a single representative-sandwich (RS) to model the full pouch cell with explicit representations for each individual component such as the active material, current collector, separator, etc. Anisotropic constitutive material models are presented to describemore » the mechanical properties of active materials and separator. The model predicts accurately the force-strain response and fracture of battery structure, simulates the local failure of separator layer, and captures the onset of short circuit for lithium-ion battery cell under sphere indentation tests with three different diameters. Electrical-thermal responses to the three different indentation tests are elaborated and discussed. Lastly, numerical studies are presented to show the potential impact of test conditions on the electrical-thermal behavior of the cell after the occurrence of short circuit.« less

Expansion of flight simulator capability for study and solution of aircraft directional control problems on runways

NASA Technical Reports Server (NTRS)

Kibbee, G. W.

1978-01-01

The development, evaluation, and evaluation results of a DC-9-10 runway directional control simulator are described. An existing wide bodied flight simulator was modified to this aircraft configuration. The simulator was structured to use either two of antiskid simulations; (1) an analog mechanization that used aircraft hardware; or (2) a digital software simulation. After the simulation was developed it was evaluated by 14 pilots who made 818 simulated flights. These evaluations involved landings, rejected takeoffs, and various ground maneuvers. Qualitatively most pilots evaluated the simulator as realistic with good potential especially for pilot training for adverse runway conditions.

Drape simulation and subjective assessment of virtual drape

NASA Astrophysics Data System (ADS)

Buyukaslan, E.; Kalaoglu, F.; Jevsnik, S.

2017-10-01

In this study, a commercial 3D virtual garment simulation software (Optitex) is used to simulate drape behaviours of five different fabrics. Mechanical properties of selected fabrics are measured by Fabric Assurance by Simple Testing (FAST) method. Measured bending, shear and extension properties of fabrics are inserted to the simulation software to achieve more realistic simulations. Simulation images of fabrics are shown to 27 people and they are asked to match real drape images of fabrics with simulated drape images. Fabric simulations of two fabrics were correctly matched by the majority of the test group. However, the other three fabrics’ simulations were mismatched by most of the people.

Mechanical property studies of human gallstones.

PubMed

Stranne, S K; Cocks, F H; Gettliffe, R

1990-08-01

The recent development of gallstone fragmentation methods has increased the significance of the study of the mechanical properties of human gallstones. In the present work, fracture strength data and microhardness values of gallstones of various chemical compositions are presented as tested in both dry and simulated bile environments. Generally, both gallstone hardness and fracture strength values were significantly less than kidney stone values found in previous studies. However, a single calcium carbonate stone was found to have an outer shell hardness exceeding those values found for kidney stones. Diametral compression measurements in simulated bile conclusively demonstrated low gallstone fracture strength as well as brittle fracture in the stones tested. Based on the results of this study, one may conclude that the wide range of gallstone microhardnesses found may explain the reported difficulties previous investigators have experienced using various fragmentation techniques on specific gallstones. Moreover, gallstone mechanical properties may be relatively sensitive to bile-environment composition.

First-principles investigation of mechanical properties of silicene, germanene and stanene

NASA Astrophysics Data System (ADS)

Mortazavi, Bohayra; Rahaman, Obaidur; Makaremi, Meysam; Dianat, Arezoo; Cuniberti, Gianaurelio; Rabczuk, Timon

2017-03-01

Two-dimensional allotropes of group-IV substrates including silicene, germanene and stanene have recently attracted considerable attention in nanodevice fabrication industry. These materials involving the buckled structure have been experimentally fabricated lately. In this study, first-principles density functional theory calculations were utilized to investigate the mechanical properties of single-layer and free-standing silicene, germanene and stanene. Uniaxial tensile and compressive simulations were carried out to probe and compare stress-strain properties; such as the Young's modulus, Poisson's ratio and ultimate strength. We evaluated the chirality effect on the mechanical response and bond structure of the 2D substrates. Our first-principles simulations suggest that in all studied samples application of uniaxial loading can alter the electronic nature of the buckled structures into the metallic character. Our investigation provides a general but also useful viewpoint with respect to the mechanical properties of silicene, germanene and stanene.

Scanning electron microscope fine tuning using four-bar piezoelectric actuated mechanism

NASA Astrophysics Data System (ADS)

Hatamleh, Khaled S.; Khasawneh, Qais A.; Al-Ghasem, Adnan; Jaradat, Mohammad A.; Sawaqed, Laith; Al-Shabi, Mohammad

2018-01-01

Scanning Electron Microscopes are extensively used for accurate micro/nano images exploring. Several strategies have been proposed to fine tune those microscopes in the past few years. This work presents a new fine tuning strategy of a scanning electron microscope sample table using four bar piezoelectric actuated mechanisms. The introduced paper presents an algorithm to find all possible inverse kinematics solutions of the proposed mechanism. In addition, another algorithm is presented to search for the optimal inverse kinematic solution. Both algorithms are used simultaneously by means of a simulation study to fine tune a scanning electron microscope sample table through a pre-specified circular or linear path of motion. Results of the study shows that, proposed algorithms were able to minimize the power required to drive the piezoelectric actuated mechanism by a ratio of 97.5% for all simulated paths of motion when compared to general non-optimized solution.

Blast and the Consequences on Traumatic Brain Injury-Multiscale Mechanical Modeling of Brain

DTIC Science & Technology

2011-02-17

blast simulation. LS-DYNA as an explicit FE code has been employed to simulate this multi- material fluid –structure interaction problem. The 3-D head...formulation is implemented to model the air-blast simulation. LS-DYNA as an explicit FE code has been employed to simulate this multi-material fluid ...Biomechanics Study of Influencing Parameters for brain under Impact ............................... 12 5.1 The Impact of Cerebrospinal Fluid

Computational studies of physical properties of Nb-Si based alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ouyang, Lizhi

2015-04-16

The overall goal is to provide physical properties data supplementing experiments for thermodynamic modeling and other simulations such as phase filed simulation for microstructure and continuum simulations for mechanical properties. These predictive computational modeling and simulations may yield insights that can be used to guide materials design, processing, and manufacture. Ultimately, they may lead to usable Nb-Si based alloy which could play an important role in current plight towards greener energy. The main objectives of the proposed projects are: (1) developing a first principles method based supercell approach for calculating thermodynamic and mechanic properties of ordered crystals and disordered latticesmore » including solid solution; (2) application of the supercell approach to Nb-Si base alloy to compute physical properties data that can be used for thermodynamic modeling and other simulations to guide the optimal design of Nb-Si based alloy.« less

A ReaxFF-based molecular dynamics study of the mechanisms of interactions between reactive oxygen plasma species and the Candida albicans cell wall

NASA Astrophysics Data System (ADS)

Zhao, T.; Shi, L.; Zhang, Y. T.; Zou, L.; Zhang, L.

2017-10-01

Atmospheric pressure non-equilibrium plasmas have attracted significant attention and have been widely used to inactivate pathogens, yet the mechanisms underlying the interactions between plasma-generated species and bio-organisms have not been elucidated clearly. In this paper, reactive molecular dynamics simulations are employed to investigate the mechanisms of interactions between reactive oxygen plasma species (O, OH, and O2) and β-1,6-glucan (a model for the C. albicans cell wall) from a microscopic point of view. Our simulations show that O and OH species can break structurally important C-C and C-O bonds, while O2 molecules exhibit only weak, non-bonded interactions with β-1,6-glucan. Hydrogen abstraction from hydroxyl or CH groups occurs first in all bond cleavage mechanisms. This is followed by a cascade of bond cleavage and double bond formation events. These lead to the destruction of the fungal cell wall. O and OH have similar effects related to their bond cleavage mechanisms. Our simulation results provide fundamental insights into the mechanisms underlying the interactions between reactive oxygen plasma species and the fungal cell wall of C. albicans at the atomic level.

Simulation with quantum mechanics/molecular mechanics for drug discovery.

PubMed

Barbault, Florent; Maurel, François

2015-10-01

Biological macromolecules, such as proteins or nucleic acids, are (still) molecules and thus they follow the same chemical rules that any simple molecule follows, even if their size generally renders accurate studies unhelpful. However, in the context of drug discovery, a detailed analysis of ligand association is required for understanding or predicting their interactions and hybrid quantum mechanics/molecular mechanics (QM/MM) computations are relevant tools to help elucidate this process. In this review, the authors explore the use of QM/MM for drug discovery. After a brief description of the molecular mechanics (MM) technique, the authors describe the subtractive and additive techniques for QM/MM computations. The authors then present several application cases in topics involved in drug discovery. QM/MM have been widely employed during the last decades to study chemical processes such as enzyme-inhibitor interactions. However, despite the enthusiasm around this area, plain MM simulations may be more meaningful than QM/MM. To obtain reliable results, the authors suggest fixing several keystone parameters according to the underlying chemistry of each studied system.

Simulation with quantum mechanics/molecular mechanics for drug discovery.

PubMed

Barbault, Florent; Maurel, François

2015-08-08

Biological macromolecules, such as proteins or nucleic acids, are (still) molecules and thus they follow the same chemical rules that any simple molecule follows, even if their size generally renders accurate studies unhelpful. However, in the context of drug discovery, a detailed analysis of ligand association is required for understanding or predicting their interactions and hybrid quantum mechanics/molecular mechanics (QM/MM) computations are relevant tools to help elucidate this process. Areas covered: In this review, the authors explore the use of QM/MM for drug discovery. After a brief description of the molecular mechanics (MM) technique, the authors describe the subtractive and additive techniques for QM/MM computations. The authors then present several application cases in topics involved in drug discovery. Expert opinion: QM/MM have been widely employed during the last decades to study chemical processes such as enzyme-inhibitor interactions. However, despite the enthusiasm around this area, plain MM simulations may be more meaningful than QM/MM. To obtain reliable results, the authors suggest fixing several keystone parameters according to the underlying chemistry of each studied system.

Force decay of elastomeric chains - a mechanical design and product comparison study.

PubMed

Balhoff, David A; Shuldberg, Matthew; Hagan, Joseph L; Ballard, Richard W; Armbruster, Paul C

2011-03-01

To evaluate the percentage force decay of elastomeric chain products utilizing three different design mechanisms simulating canine retraction; and to evaluate the percentage force decay of elastomeric chain products from four different companies. In vitro, laboratory study. LSUHSC Dental School, New Orleans, LA, USA. Closed (non-spaced), grey elastomeric chains from four companies were selected for the study. Three acrylic resin jigs were constructed to provide a framework for three simulated space closure mechanisms. The 6-5-3, the chain loop, and the 6-3 were the configuration mechanisms used in the study. An electronic force gauge was used to measure the percentage force decay associated with each elastomeric chain over 28 days at preselected times. There was a significant difference in the mean percentage force decay for the three different mechanisms (P < 0·001). For all four companies, the 6-3 mechanical design had the smallest mean percentage force decay. There was a significant difference in the mean percentage force decay for the different companies (P < 0·001). For all three mechanisms, Ormco had the smallest percentage force decay while Unitek had the highest percentage force decay. The significant difference in the mean percentage force decay for the different mechanisms suggests that the 6-3 design is a more efficient means of closing extraction spaces utilizing elastomeric chains.

Climate Modeling and Causal Identification for Sea Ice Predictability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunke, Elizabeth Clare; Urrego Blanco, Jorge Rolando; Urban, Nathan Mark

This project aims to better understand causes of ongoing changes in the Arctic climate system, particularly as decreasing sea ice trends have been observed in recent decades and are expected to continue in the future. As part of the Sea Ice Prediction Network, a multi-agency effort to improve sea ice prediction products on seasonal-to-interannual time scales, our team is studying sensitivity of sea ice to a collection of physical process and feedback mechanism in the coupled climate system. During 2017 we completed a set of climate model simulations using the fully coupled ACME-HiLAT model. The simulations consisted of experiments inmore » which cloud, sea ice, and air-ocean turbulent exchange parameters previously identified as important for driving output uncertainty in climate models were perturbed to account for parameter uncertainty in simulated climate variables. We conducted a sensitivity study to these parameters, which built upon a previous study we made for standalone simulations (Urrego-Blanco et al., 2016, 2017). Using the results from the ensemble of coupled simulations, we are examining robust relationships between climate variables that emerge across the experiments. We are also using causal discovery techniques to identify interaction pathways among climate variables which can help identify physical mechanisms and provide guidance in predictability studies. This work further builds on and leverages the large ensemble of standalone sea ice simulations produced in our previous w14_seaice project.« less

A Selection of Composites Simulation Practices at NASA Langley Research Center

NASA Technical Reports Server (NTRS)

Ratcliffe, James G.

2007-01-01

One of the major areas of study at NASA Langley Research Center is the development of technologies that support the use of advanced composite materials in aerospace applications. Amongst the supporting technologies are analysis tools used to simulate the behavior of these materials. This presentation will discuss a number of examples of analysis tools and simulation practices conducted at NASA Langley. The presentation will include examples of damage tolerance analyses for both interlaminar and intralaminar failure modes. Tools for modeling interlaminar failure modes include fracture mechanics and cohesive methods, whilst tools for modeling intralaminar failure involve the development of various progressive failure analyses. Other examples of analyses developed at NASA Langley include a thermo-mechanical model of an orthotropic material and the simulation of delamination growth in z-pin reinforced laminates.

Electro-Thermal-Mechanical Simulation Capability Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, D

This is the Final Report for LDRD 04-ERD-086, 'Electro-Thermal-Mechanical Simulation Capability'. The accomplishments are well documented in five peer-reviewed publications and six conference presentations and hence will not be detailed here. The purpose of this LDRD was to research and develop numerical algorithms for three-dimensional (3D) Electro-Thermal-Mechanical simulations. LLNL has long been a world leader in the area of computational mechanics, and recently several mechanics codes have become 'multiphysics' codes with the addition of fluid dynamics, heat transfer, and chemistry. However, these multiphysics codes do not incorporate the electromagnetics that is required for a coupled Electro-Thermal-Mechanical (ETM) simulation. There aremore » numerous applications for an ETM simulation capability, such as explosively-driven magnetic flux compressors, electromagnetic launchers, inductive heating and mixing of metals, and MEMS. A robust ETM simulation capability will enable LLNL physicists and engineers to better support current DOE programs, and will prepare LLNL for some very exciting long-term DoD opportunities. We define a coupled Electro-Thermal-Mechanical (ETM) simulation as a simulation that solves, in a self-consistent manner, the equations of electromagnetics (primarily statics and diffusion), heat transfer (primarily conduction), and non-linear mechanics (elastic-plastic deformation, and contact with friction). There is no existing parallel 3D code for simulating ETM systems at LLNL or elsewhere. While there are numerous magnetohydrodynamic codes, these codes are designed for astrophysics, magnetic fusion energy, laser-plasma interaction, etc. and do not attempt to accurately model electromagnetically driven solid mechanics. This project responds to the Engineering R&D Focus Areas of Simulation and Energy Manipulation, and addresses the specific problem of Electro-Thermal-Mechanical simulation for design and analysis of energy manipulation systems such as magnetic flux compression generators and railguns. This project compliments ongoing DNT projects that have an experimental emphasis. Our research efforts have been encapsulated in the Diablo and ALE3D simulation codes. This new ETM capability already has both internal and external users, and has spawned additional research in plasma railgun technology. By developing this capability Engineering has become a world-leader in ETM design, analysis, and simulation. This research has positioned LLNL to be able to compete for new business opportunities with the DoD in the area of railgun design. We currently have a three-year $1.5M project with the Office of Naval Research to apply our ETM simulation capability to railgun bore life issues and we expect to be a key player in the railgun community.« less

Evolution of mechanical response of sodium montmorillonite interlayer with increasing hydration by molecular dynamics.

PubMed

Schmidt, Steven R; Katti, Dinesh R; Ghosh, Pijush; Katti, Kalpana S

2005-08-16

The mechanical response of the interlayer of hydrated montmorillonite was evaluated using steered molecular dynamics. An atomic model of the sodium montmorillonite was previously constructed. In the current study, the interlayer of the model was hydrated with multiple layers of water. Using steered molecular dynamics, external forces were applied to individual atoms of the clay surface, and the response of the model was studied. The displacement versus applied stress and stress versus strain relationships of various parts of the interlayer were studied. The paper describes the construction of the model, the simulation procedure, and results of the simulations. Some results of the previous work are further interpreted in the light of the current research. The simulations provide quantitative stress deformation relationships as well as an insight into the molecular interactions taking place between the clay surface and interlayer water and cations.

Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein.

PubMed

Sharma, Monika; Anirudh, C R

2017-10-03

STAR proteins are evolutionary conserved mRNA-binding proteins that post-transcriptionally regulate gene expression at all stages of RNA metabolism. These proteins possess conserved STAR domain that recognizes identical RNA regulatory elements as YUAAY. Recently reported crystal structures show that STAR domain is composed of N-terminal QUA1, K-homology domain (KH) and C-terminal QUA2, and mRNA binding is mediated by KH-QUA2 domain. Here, we present simulation studies done to investigate binding of mRNA to STAR protein, mammalian Quaking protein (QKI). We carried out conventional MD simulations of STAR domain in presence and absence of mRNA, and studied the impact of mRNA on the stability, dynamics and underlying allosteric mechanism of STAR domain. Our unbiased simulations results show that presence of mRNA stabilizes the overall STAR domain by reducing the structural deviations, correlating the 'within-domain' motions, and maintaining the native contacts information. Absence of mRNA not only influenced the essential modes of motion of STAR domain, but also affected the connectivity of networks within STAR domain. We further explored the dissociation of mRNA from STAR domain using umbrella sampling simulations, and the results suggest that mRNA binding to STAR domain occurs in multi-step: first conformational selection of mRNA backbone conformations, followed by induced fit mechanism as nucleobases interact with STAR domain.

Characterization of three-dimensional anisotropic heart valve tissue mechanical properties using inverse finite element analysis.

PubMed

Abbasi, Mostafa; Barakat, Mohammed S; Vahidkhah, Koohyar; Azadani, Ali N

2016-09-01

Computational modeling has an important role in design and assessment of medical devices. In computational simulations, considering accurate constitutive models is of the utmost importance to capture mechanical response of soft tissue and biomedical materials under physiological loading conditions. Lack of comprehensive three-dimensional constitutive models for soft tissue limits the effectiveness of computational modeling in research and development of medical devices. The aim of this study was to use inverse finite element (FE) analysis to determine three-dimensional mechanical properties of bovine pericardial leaflets of a surgical bioprosthesis under dynamic loading condition. Using inverse parameter estimation, 3D anisotropic Fung model parameters were estimated for the leaflets. The FE simulations were validated using experimental in-vitro measurements, and the impact of different constitutive material models was investigated on leaflet stress distribution. The results of this study showed that the anisotropic Fung model accurately simulated the leaflet deformation and coaptation during valve opening and closing. During systole, the peak stress reached to 3.17MPa at the leaflet boundary while during diastole high stress regions were primarily observed in the commissures with the peak stress of 1.17MPa. In addition, the Rayleigh damping coefficient that was introduced to FE simulations to simulate viscous damping effects of surrounding fluid was determined. Copyright © 2016 Elsevier Ltd. All rights reserved.

Autoignition of hydrogen and air using direct numerical simulation

NASA Astrophysics Data System (ADS)

Doom, Jeffrey; Mahesh, Krishnan

2008-11-01

Direct numerical simulation (DNS) is used to study to auto--ignition in laminar vortex rings and turbulent diffusion flames. A novel, all--Mach number algorithm developed by Doom et al (J. Comput. Phys. 2007) is used. The chemical mechanism is a nine species, nineteen reaction mechanism for H2 and Air from Mueller at el (Int. J. Chem. Kinet. 1999). The vortex ring simulations inject diluted H2 at ambient temperature into hot air, and study the effects of stroke ratio, air to fuel ratio and Lewis number. At smaller stroke ratios, ignition occurs in the wake of the vortex ring and propagates into the vortex core. At larger stroke ratios, ignition occurs along the edges of the trailing column before propagating towards the vortex core. The turbulent diffusion flame simulations are three--dimensional and consider the interaction of initially isotropic turbulence with an unstrained diffusion flame. The simulations examine the nature of distinct ignition kernels, the relative roles of chemical reactions, and the relation between the observed behavior and laminar flames and the perfectly stirred reactor problem. These results will be discussed.

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

PubMed

Hertig, Samuel; Latorraca, Naomi R; Dror, Ron O

2016-06-01

Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

Effect of irradiation on mechanical properties of symmetrical grain boundaries investigated by atomic simulations

NASA Astrophysics Data System (ADS)

Wang, X. Y.; Gao, N.; Setyawan, W.; Xu, B.; Liu, W.; Wang, Z. G.

2017-08-01

Tensile response of irradiated symmetric grain boundaries to the externally applied strain has been studied using atomic simulation methods. The absorption of irradiation induced defects by grain boundaries has been confirmed to degrade the mechanical properties of grain boundaries through the change of its undertaken deformation mechanism. Atomic rearrangement, the formations of a stress accumulation region and vacancy-rich zone and the nucleation and movement of dislocations under stress effect have been observed after the displacement cascades in grain boundaries, which are considered as main reasons to induce above degradation. These results suggest the necessity of considering both trapping efficiency to defects and the mechanical property change of irradiated grain boundaries for further development of radiation resistant materials.

Numerical Simulation of the Motion of Aerosol Particles in Open Cell Foam Materials

NASA Astrophysics Data System (ADS)

Solovev, S. A.; Soloveva, O. V.; Popkova, O. S.

2018-03-01

The motion of aerosol particles in open cell foam material is studied. The porous medium is investigated for a three-dimensional case with detailed simulation of cellular structures within an ordered geometry. Numerical calculations of the motion of particles and their deposition due to inertial and gravitational mechanisms are performed. Deposition efficiency curves for a broad range of particle sizes are constructed. The effect deposition mechanisms have on the efficiency of the porous material as a filter is analyzed.

Protein's electronic polarization contributes significantly to its catalytic function

NASA Astrophysics Data System (ADS)

Xiang, Yun; Duan, Lili; Zhang, John Z. H.

2011-05-01

Ab initio quantum mechanical/molecular mechanical method is combined with the polarized protein-specific charge to study the chemical reactions catalyzed by protein enzymes. Significant improvement in the accuracy and efficiency of free-energy simulation is demonstrated by calculating the free-energy profile of the primary proton transfer reaction in triosephosphate isomerase. Quantitative agreement with experimental results is achieved. Our simulation results indicate that electronic polarization makes important contribution to enzyme catalysis by lowering the energy barrier by as much as 3 kcal/mol.

Coherent microscopic picture for urea-induced denaturation of proteins.

PubMed

Yang, Zaixing; Xiu, Peng; Shi, Biyun; Hua, Lan; Zhou, Ruhong

2012-08-02

In a previous study, we explored the mechanism of urea-induced denaturation of proteins by performing molecular dynamics (MD) simulations of hen lysozyme in 8 M urea and supported the "direct interaction mechanism" whereby urea denatures protein via dispersion interaction (Hua, L.; Zhou, R. H.; Thirumalai, D.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 16928). Here we perform large scale MD simulations of five representative protein/peptide systems in aqueous urea to investigate if the above mechanism is common to other proteins. In all cases, accumulations of urea around proteins/peptide are observed, suggesting that urea denatures proteins by directly attacking protein backbones and side chains rather than indirectly disrupting water structure as a "water breaker". Consistent with our previous case study of lysozyme, the current energetic analyses with five protein/peptide systems reveal that urea's preferential binding to proteins mainly comes from urea's stronger dispersion interactions with proteins than with bulk solution, whereas the electrostatic (hydrogen-bonded) interactions only play a relatively minor (even negative) role during this denaturation process. Furthermore, the simulations of the peptide system at different urea concentrations (8 and 4.5 M), and with different force fields (CHARMM and OPLSAA) suggest that the above mechanism is robust, independent of the urea concentration and force field used. Last, we emphasize the importance of periodic boundary conditions in pairwise energetic analyses. This article provides a comprehensive study on the physical mechanism of urea-induced protein denaturation and suggests that the "dispersion-interaction-driven" mechanism should be general.

Investigation of Mechanisms of Viscoelastic Behavior of Collagen Molecule

PubMed Central

Ghodsi, Hossein; Darvish, Kurosh

2015-01-01

Unique mechanical properties of collagen molecule make it one of the most important and abundant proteins in animals. Many tissues such as connective tissues rely on these properties to function properly. In the past decade, molecular dynamics (MD) simulations have been used extensively to study the mechanical behavior of molecules. For collagen, MD simulations were primarily used to determine its elastic properties. In this study, constant force steered MD simulations were used to perform creep tests on collagen molecule segments. The mechanical behavior of the segments, with lengths of approximately 20 (1X), 38 (2X), 74 (4X), and 290 nm (16X), was characterized using a quasi-linear model to describe the observed viscoelastic responses. To investigate the mechanisms of the viscoelastic behavior, hydrogen bonds (H-bonds) rupture/formation time history of the segments were analyzed and it was shown that the formation growth rate of H-bonds in the system is correlated with the creep growth rate of the segment ( β = 2.41 βH). In addition, a linear relationship between H-bonds formation growth rate and the length of the segment was quantified. Based on these findings, a general viscoelastic model was developed and verified where, using the smallest segment as a building block, the viscoelastic properties of larger segments could be predicted. In addition, the effect of temperature control methods on the mechanical properties were studied, and it was shown that application of Langevin Dynamics had adverse effect on these properties while the Lowe-Anderson method was shown to be more appropriate for this application. This study provides information that is essential for multi-scale modeling of collagen fibrils using a bottom-up approach. PMID:26256473

Investigation of mechanisms of viscoelastic behavior of collagen molecule.

PubMed

Ghodsi, Hossein; Darvish, Kurosh

2015-11-01

Unique mechanical properties of collagen molecule make it one of the most important and abundant proteins in animals. Many tissues such as connective tissues rely on these properties to function properly. In the past decade, molecular dynamics (MD) simulations have been used extensively to study the mechanical behavior of molecules. For collagen, MD simulations were primarily used to determine its elastic properties. In this study, constant force steered MD simulations were used to perform creep tests on collagen molecule segments. The mechanical behavior of the segments, with lengths of approximately 20 (1X), 38 (2X), 74 (4X), and 290 nm (16X), was characterized using a quasi-linear model to describe the observed viscoelastic responses. To investigate the mechanisms of the viscoelastic behavior, hydrogen bonds (H-bonds) rupture/formation time history of the segments were analyzed and it was shown that the formation growth rate of H-bonds in the system is correlated with the creep growth rate of the segment (β=2.41βH). In addition, a linear relationship between H-bonds formation growth rate and the length of the segment was quantified. Based on these findings, a general viscoelastic model was developed and verified here, using the smallest segment as a building block, the viscoelastic properties of larger segments could be predicted. In addition, the effect of temperature control methods on the mechanical properties were studied, and it was shown that application of Langevin Dynamics had adverse effect on these properties while the Lowe-Anderson method was shown to be more appropriate for this application. This study provides information that is essential for multi-scale modeling of collagen fibrils using a bottom-up approach. Copyright © 2015 Elsevier Ltd. All rights reserved.

Low-frequency repetitive transcranial magnetic simulation prevents chronic epileptic seizure

PubMed Central

Wang, Yinxu; Wang, Xiaoming; Ke, Sha; Tan, Juan; Hu, Litian; Zhang, Yaodan; Cui, Wenjuan

2013-01-01

Although low-frequency repetitive transcranial magnetic simulation can potentially treat epilepsy, its underlying mechanism remains unclear. This study investigated the influence of low-frequency re-petitive transcranial magnetic simulation on changes in several nonlinear dynamic electroence-phalographic parameters in rats with chronic epilepsy and explored the mechanism underlying petitive transcranial magnetic simulation-induced antiepileptic effects. An epilepsy model was es-tablished using lithium-pilocarpine intraperitoneal injection into adult Sprague-Dawley rats, which were then treated with repetitive transcranial magnetic simulation for 7 consecutive days. Nonlinear electroencephalographic parameters were obtained from the rats at 7, 14, and 28 days post-stimulation. Results showed significantly lower mean correlation-dimension and Kolmogo-rov-entropy values for stimulated rats than for non-stimulated rats. At 28 days, the complexity and point-wise correlation dimensional values were lower in stimulated rats. Low-frequency repetitive transcranial magnetic simulation has suppressive effects on electrical activity in epileptic rats, thus explaining its effectiveness in treating epilepsy. PMID:25206567

A simple polymeric model describes cell nuclear mechanical response

NASA Astrophysics Data System (ADS)

Banigan, Edward; Stephens, Andrew; Marko, John

The cell nucleus must continually resist inter- and intracellular mechanical forces, and proper mechanical response is essential to basic cell biological functions as diverse as migration, differentiation, and gene regulation. Experiments probing nuclear mechanics reveal that the nucleus stiffens under strain, leading to two characteristic regimes of force response. This behavior depends sensitively on the intermediate filament protein lamin A, which comprises the outer layer of the nucleus, and the properties of the chromatin interior. To understand these mechanics, we study a simulation model of a polymeric shell encapsulating a semiflexible polymer. This minimalistic model qualitatively captures the typical experimental nuclear force-extension relation and observed nuclear morphologies. Using a Flory-like theory, we explain the simulation results and mathematically estimate the force-extension relation. The model and experiments suggest that chromatin organization is a dominant contributor to nuclear mechanics, while the lamina protects cell nuclei from large deformations.

Three-Dimensional Direct Numerical Simulation of Methane-Air Turbulent Premixed Flames with Reduced Kinetic Mechanism

NASA Astrophysics Data System (ADS)

Tanahashi, Mamoru; Kikuta, Satoshi; Miyauchi, Toshio

2004-11-01

Three-dimensional DNS of methane-air turbulent premixed flames have been conducted to investigate local extinction mechanism of turbulent premixed flames. A reduced kinetic mechanism (MeCH-19), which is created from GRI-Mech. 2.11 and includes 23 reactive species and 19 step reactions, are used to simulate CH_4-O_2-N2 reaction in turbulence. The effectiveness of this reduced kinetic mechanism has been conformed by preliminary two-dimensional DNS with the reduced kinetic mechanism and two detailed kinetic mechanisms; GRI-Mech. 2.11 and Miller & Bowman. Flame structures of methane-air turbulent premixed flames are compared with those of hydrogen-air turbulent premixed flames which have been obtained by 3D-DNS with a detailed kinetic mechanism in our previous study. Local extinctions occur in methane-air turbulent premixed flames, whereas no extinction is observed for hydrogen-air flames in nearly same turbulence condition. The local extinction mechanism is discussed based on eddy/flame interaction in small scales.

On the Generation and Use of TCP Acknowledgments

NASA Technical Reports Server (NTRS)

Allman, Mark

1998-01-01

This paper presents a simulation study of various TCP acknowledgment generation and utilization techniques. We investigate the standard version of TCP and the two standard acknowledgment strategies employed by receivers: those that acknowledge each incoming segment and those that implement delayed acknowledgments. We show the delayed acknowledgment mechanism hurts TCP performance, especially during slow start. Next we examine three alternate mechanisms for generating and using acknowledgments designed to mitigate the negative impact of delayed acknowledgments. The first method is to generate delayed ACKs only when the sender is not using the slow start algorithm. The second mechanism, called byte counting, allows TCP senders to increase the amount of data being injected into the network based on the amount of data acknowledged rather than on the number of acknowledgments received. The last mechanism is a limited form of byte counting. Each of these mechanisms is evaluated in a simulated network with no competing traffic, as well as a dynamic environment with a varying amount of competing traffic. We study the costs and benefits of the alternate mechanisms when compared to the standard algorithm with delayed ACKs.

Study on the Depth, Rate, Shape, and Strength of Pulse with Cardiovascular Simulator.

PubMed

Lee, Ju-Yeon; Jang, Min; Shin, Sang-Hoon

2017-01-01

Pulse diagnosis is important in oriental medicine. The purpose of this study is explaining the mechanisms of pulse with a cardiovascular simulator. The simulator is comprised of the pulse generating part, the vessel part, and the measurement part. The pulse generating part was composed of motor, slider-crank mechanism, and piston pump. The vessel part, which was composed with the aorta and a radial artery, was fabricated with silicon to implement pulse wave propagation. The pulse parameters, such as the depth, rate, shape, and strength, were simulated. With changing the mean pressure, the floating pulse and the sunken pulse were generated. The change of heart rate generated the slow pulse and the rapid pulse. The control of the superposition time of the reflected wave generated the string-like pulse and the slippery pulse. With changing the pulse pressure, the vacuous pulse and the replete pulse were generated. The generated pulses showed good agreements with the typical pulses.

Elastic plastic self-consistent (EPSC) modeling of plastic deformation in fayalite olivine

DOE PAGES

Burnley, Pamela C

2015-07-01

Elastic plastic self-consistent (EPSC) simulations are used to model synchrotron X-ray diffraction observations from deformation experiments on fayalite olivine using the deformation DIA apparatus. Consistent with results from other in situ diffraction studies of monomineralic polycrystals, the results show substantial variations in stress levels among grain populations. Rather than averaging the lattice reflection stresses or choosing a single reflection to determine the macroscopic stress supported by the specimen, an EPSC simulation is used to forward model diffraction data and determine a macroscopic stress that is consistent with lattice strains of all measured diffraction lines. The EPSC simulation presented here includesmore » kink band formation among the plastic deformation mechanisms in the simulation. The inclusion of kink band formation is critical to the success of the models. This study demonstrates the importance of kink band formation as an accommodation mechanism during plastic deformation of olivine as well as the utility of using EPSC models to interpret diffraction from in situ deformation experiments.« less

Predicting the Macroscopic Fracture Energy of Epoxy Resins from Atomistic Molecular Simulations

DOE PAGES

Meng, Zhaoxu; Bessa, Miguel A.; Xia, Wenjie; ...

2016-12-06

Predicting the macroscopic fracture energy of highly crosslinked glassy polymers from atomistic simulations is challenging due to the size of the process zone being large in these systems. Here, we present a scale-bridging approach that links atomistic molecular dynamics simulations to macroscopic fracture properties on the basis of a continuum fracture mechanics model for two different epoxy materials. Our approach reveals that the fracture energy of epoxy resins strongly depends on the functionality of epoxy resin and the component ratio between the curing agent (amine) and epoxide. The most intriguing part of our study is that we demonstrate that themore » fracture energy exhibits a maximum value within the range of conversion degrees considered (from 65% to 95%), which can be attributed to the combined effects of structural rigidity and post-yield deformability. Our study provides physical insight into the molecular mechanisms that govern the fracture characteristics of epoxy resins and demonstrates the success of utilizing atomistic molecular simulations towards predicting macroscopic material properties.« less

Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

PubMed Central

Zhan, Minzhong; Guo, Ming; Jiang, Yanke; Wang, Xiaomeng

2015-01-01

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA. PMID:26140374

Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy.

PubMed

Zhan, Minzhong; Guo, Ming; Jiang, Yanke; Wang, Xiaomeng

2015-07-01

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.

Molecular origin of differences in hole and electron mobility in amorphous Alq3--a multiscale simulation study.

PubMed

Fuchs, Andreas; Steinbrecher, Thomas; Mommer, Mario S; Nagata, Yuki; Elstner, Marcus; Lennartz, Christian

2012-03-28

In order to determine the molecular origin of the difference in electron and hole mobilities of amorphous thin films of Alq(3) (meridional Alq(3) (tris(8-hydroxyquinoline) aluminium)) we performed multiscale simulations covering quantum mechanics, molecular mechanics and lattice models. The study includes realistic disordered morphologies, polarized site energies to describe diagonal disorder, quantum chemically calculated transfer integrals for the off-diagonal disorder, inner sphere reorganization energies and an approximative scheme for outer sphere reorganization energies. Intermolecular transfer rates were calculated via Marcus-theory and mobilities were simulated via kinetic Monte Carlo simulations and by a Master Equation approach. The difference in electron and hole mobility originates from the different localization of charge density in the radical anion (more delocalized) compared to the radical cation (more confined). This results in higher diagonal disorder for holes and less favourable overlap properties for the hole transfer integrals leading to an overall higher electron mobility.

Predicting the Macroscopic Fracture Energy of Epoxy Resins from Atomistic Molecular Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Zhaoxu; Bessa, Miguel A.; Xia, Wenjie

Predicting the macroscopic fracture energy of highly crosslinked glassy polymers from atomistic simulations is challenging due to the size of the process zone being large in these systems. Here, we present a scale-bridging approach that links atomistic molecular dynamics simulations to macroscopic fracture properties on the basis of a continuum fracture mechanics model for two different epoxy materials. Our approach reveals that the fracture energy of epoxy resins strongly depends on the functionality of epoxy resin and the component ratio between the curing agent (amine) and epoxide. The most intriguing part of our study is that we demonstrate that themore » fracture energy exhibits a maximum value within the range of conversion degrees considered (from 65% to 95%), which can be attributed to the combined effects of structural rigidity and post-yield deformability. Our study provides physical insight into the molecular mechanisms that govern the fracture characteristics of epoxy resins and demonstrates the success of utilizing atomistic molecular simulations towards predicting macroscopic material properties.« less

Tribological Properties of AlCrCuFeNi2 High-Entropy Alloy in Different Conditions

NASA Astrophysics Data System (ADS)

Liu, Yong; Ma, Shengguo; Gao, Michael C.; Zhang, Chuan; Zhang, Teng; Yang, Huijun; Wang, Zhihua; Qiao, Junwei

2016-07-01

In order to understand the environmental effect on the mechanical behavior of high-entropy alloys, the tribological properties of AlCrCuFeNi2 are studied systematically in dry, simulated rainwater, and deionized water conditions against the Si3N4 ceramic ball at a series of different normal loads. The present study shows that both the friction and wear rate in simulated rainwater are the lowest. The simulated rainwater plays a significant role in the tribological behavior with the effect of forming passive film, lubricating, cooling, cleaning, and corrosion. The wear mechanism in simulated rainwater is mainly adhesive wear accompanied by abrasive wear as well as corrosive wear. In contrast, those in dry condition and deionized water are abrasive wear, adhesive wear, and surface plastic deformation. Oxidation contributes to the wear behavior in dry condition but is prevented in liquid condition. In addition, the phase diagram of Al x CrCuFeNi2 is predicted using CALPHAD modeling, which is in good agreement with the literature report and the present study.

A Computational Study of a Circular Interface Richtmyer-Meshkov Instability in MHD

NASA Astrophysics Data System (ADS)

Maxon, William; Black, Wolfgang; Denissen, Nicholas; McFarland, Jacob; Los Alamos National Laboratory Collaboration; University of Missouri Shock Tube Laboratory Team

2017-11-01

The Richtmyer-Meshkov instability (RMI) is a hydrodynamic instability that appears in several high energy density applications such as inertial confinement fusion (ICF). In ICF, as the thermonuclear fuel is being compressed it begins to mix due to fluid instabilities including the RMI. This mixing greatly decreases the energy output. The RMI occurs when two fluids of different densities are impulsively accelerated and the pressure and density gradients are misaligned. In magnetohydrodynamics (MHD), the RMI may be suppressed by introducing a magnetic field in an electrically conducting fluid, such as a plasma. This suppression has been studied as a possible mechanism for improving confinement in ICF targets. In this study,ideal MHD simulations are performed with a circular interface impulsively accelerated by a shock wave in the presence of a magnetic field. These simulations are executed with the research code FLAG, a multiphysics, arbitrary Lagrangian/Eulerian, hydrocode developed and utilized at Los Alamos National Laboratory. The simulation results will be assessed both quantitatively and qualitatively to examine the stabilization mechanism. These simulations will guide ongoing MHD experiments at the University of Missouri Shock Tube Facility.

Monte Carlo Simulation of a Segmented Detector for Low-Energy Electron Antineutrinos

NASA Astrophysics Data System (ADS)

Qomi, H. Akhtari; Safari, M. J.; Davani, F. Abbasi

2017-11-01

Detection of low-energy electron antineutrinos is of importance for several purposes, such as ex-vessel reactor monitoring, neutrino oscillation studies, etc. The inverse beta decay (IBD) is the interaction that is responsible for detection mechanism in (organic) plastic scintillation detectors. Here, a detailed study will be presented dealing with the radiation and optical transport simulation of a typical segmented antineutrino detector withMonte Carlo method using MCNPX and FLUKA codes. This study shows different aspects of the detector, benefiting from inherent capabilities of the Monte Carlo simulation codes.

Interactive Simulations to Support Quantum Mechanics Instruction for Chemistry Students

ERIC Educational Resources Information Center

Kohnle, Antje; Benfield, Cory; Hahner, Georg; Paetkau, Mark

2017-01-01

The QuVis Quantum Mechanics Visualization Project provides freely available research-based interactive simulations with accompanying activities for the teaching and learning of quantum mechanics across a wide range of topics and levels. This article gives an overview of some of the simulations and describes their use in an introductory physical…

Shock wave energy dissipation behavior (SWED) in Network forming ionic liquids (NILs): A Molecular dynamics study

NASA Astrophysics Data System (ADS)

Guda Vishnu, Karthik; Strachan, Alejandro

2017-06-01

SWED materials play a crucial role in protecting both personnel and structures in close proximity to blasts or ballistic impact. Exposure to shock waves with intensities as low as 1 MPa can cause brain injury in personnel and, hence, it is extremely important to understand the mechanisms operating in SWED materials and help design improved formulations. Recent experimental studies show that NILs containing di-ammonium cations and citrate anions with glass transition temperatures (Tg) below room temperature exhibit shockwave absorption characteristics that outperform polyurea (PU), a benchmark SWED assessment material. The experimentalists further hypothesized that the increased SWED ability in NILs with longer side chains (in di-ammonium cation) is due to a permanent structural ordering and nano-scale segregation. We use molecular dynamics simulations with the Dreiding force field to study shock propagation mechanisms in NILs. Shock propagation mechanisms in these materials are explored by performing both Hugoniostat and large scale non-equilibrium molecular dynamics (NEMD) simulations at 300 K. The simulation results show that the NIL 5-6 (5 C atoms (back bone) and 6 C atoms (side chain)) attenuates shocks better than NIL 5-3 (3 C atoms (side chain) and higher Tg) and PMMA in agreement with experimental observation. The simulations show that under shock loading the structures lose long range order; we find no evidence of nano-segregation nor or permanent structural changes.

Turbulence simulation mechanization for Space Shuttle Orbiter dynamics and control studies

NASA Technical Reports Server (NTRS)

Tatom, F. B.; King, R. L.

1977-01-01

The current version of the NASA turbulent simulation model in the form of a digital computer program, TBMOD, is described. The logic of the program is discussed and all inputs and outputs are defined. An alternate method of shear simulation suitable for incorporation into the model is presented. The simulation is based on a von Karman spectrum and the assumption of isotropy. The resulting spectral density functions for the shear model are included.

Communication in red fox dyads: a computer simulation study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montgomery, Gerald Gene

1973-06-01

For any two animals, three major factors limit communication. These are (1) whether appropriate signal mechanisms are available to them, (2) whether the animals are motivated to communicate, and (3) whether their movements and locations are such that signal can pass between them. In this study, signal mechanisms and motivation were not considered as variables, but the role of animal movement in limiting communication was. A computer simulation study of amounts of communication which occur in red fox (Vulpes vulpes) dyads when various means of signalling are used, and when. the animals move about and signal with - various emissionmore » intensities and at various time intervals is reported.« less

Predictive role of computer simulation in assessing signaling pathways of crizotinib-treated A549 lung cancer cells.

PubMed

Xia, Pu; Mou, Fei-Fei; Wang, Li-Wei

2012-01-01

Non-small-cell lung cancer (NSCLC) is a leading cause of cancer deaths worldwide. Crizotinib has been approved by the U.S. Food and Drug Administration for the treatment of patients with advanced NSCLC. However, understanding of mechanisms of action is still limited. In our studies, we confirmed crizotinib-induced apoptosis in A549 lung cancer cells. In order to assess mechanisms, small molecular docking technology was used as a preliminary simulation of signaling pathways. Interesting, our results of experiments were consistent with the results of computer simulation. This indicates that small molecular docking technology should find wide use for its reliability and convenience.

The Effects of Time Advance Mechanism on Simple Agent Behaviors in Combat Simulations

DTIC Science & Technology

2011-12-01

modeling packages that illustrate the differences between discrete-time simulation (DTS) and discrete-event simulation ( DES ) methodologies. Many combat... DES ) models , often referred to as “next-event” (Law and Kelton 2000) or discrete time simulation (DTS), commonly referred to as “time-step.” DTS...discrete-time simulation (DTS) and discrete-event simulation ( DES ) methodologies. Many combat models use DTS as their simulation time advance mechanism

A continuum dislocation dynamics framework for plasticity of polycrystalline materials

NASA Astrophysics Data System (ADS)

Askari, Hesam Aldin

The objective of this research is to investigate the mechanical response of polycrystals in different settings to identify the mechanisms that give rise to specific response observed in the deformation process. Particularly the large deformation of magnesium alloys and yield properties of copper in small scales are investigated. We develop a continuum dislocation dynamics framework based on dislocation mechanisms and interaction laws and implement this formulation in a viscoplastic self-consistent scheme to obtain the mechanical response in a polycrystalline system. The versatility of this method allows various applications in the study of problems involving large deformation, study of microstructure and its evolution, superplasticity, study of size effect in polycrystals and stochastic plasticity. The findings from the numerical solution are compared to the experimental results to validate the simulation results. We apply this framework to study the deformation mechanisms in magnesium alloys at moderate to fast strain rates and room temperature to 450 °C. Experiments for the same range of strain rates and temperatures were carried out to obtain the mechanical and material properties, and to compare with the numerical results. The numerical approach for magnesium is divided into four main steps; 1) room temperature unidirectional loading 2) high temperature deformation without grain boundary sliding 3) high temperature with grain boundary sliding mechanism 4) room temperature cyclic loading. We demonstrate the capability of our modeling approach in prediction of mechanical properties and texture evolution and discuss the improvement obtained by using the continuum dislocation dynamics method. The framework was also applied to nano-sized copper polycrystals to study the yield properties at small scales and address the observed yield scatter. By combining our developed method with a Monte Carlo simulation approach, the stochastic plasticity at small length scales was studied and the sources of the uncertainty in the polycrystalline structure are discussed. Our results suggest that the stochastic response is mainly because of a) stochastic plasticity due to dislocation substructure inside crystals and b) the microstructure of the polycrystalline material. The extent of the uncertainty is correlated to the "effective cell length" in the sampling procedure whether using simulations and experimental approach.

Effect of Annealing Treatment on Mechanical Properties of Nanocrystalline α-iron: an Atomistic Study

PubMed Central

Tong, Xuhang; Zhang, Hao; Li, D. Y.

2015-01-01

Claims are often found in the literature that metallic materials can be nanocrystallized by severe plastic deformation (SPD). However, SPD does not generate a well-defined nanocrystalline (NC) material, which can be achieved by subsequent annealing/recovery treatment. In this study, molecular dynamics (MD) simulation is employed to study the effect of annealing on structure and mechanical properties of cyclic deformed NC α-iron, which simulates SPD-processed α-iron. It is demonstrated that grain boundaries in the deformed NC α-iron evolve to a more equilibrium state during annealing, eliminating or minimizing the residual stress. The annealing treatment increases the system's strength by reducing dislocation emission sources, and improves material ductility through strengthening grain boundaries' resistance to intergranular cracks. The results indicate that the annealing treatment is an essential process for obtaining a well-defined NC structure with superior mechanical properties. PMID:25675978

TOUGH2Biot - A simulator for coupled thermal-hydrodynamic-mechanical processes in subsurface flow systems: Application to CO2 geological storage and geothermal development

NASA Astrophysics Data System (ADS)

Lei, Hongwu; Xu, Tianfu; Jin, Guangrong

2015-04-01

Coupled thermal-hydrodynamic-mechanical processes have become increasingly important in studying the issues affecting subsurface flow systems, such as CO2 sequestration in deep saline aquifers and geothermal development. In this study, a mechanical module based on the extended Biot consolidation model was developed and incorporated into the well-established thermal-hydrodynamic simulator TOUGH2, resulting in an integrated numerical THM simulation program TOUGH2Biot. A finite element method was employed to discretize space for rock mechanical calculation and the Mohr-Coulomb failure criterion was used to determine if the rock undergoes shear-slip failure. Mechanics is partly coupled with the thermal-hydrodynamic processes and gives feedback to flow through stress-dependent porosity and permeability. TOUGH2Biot was verified against analytical solutions for the 1D Terzaghi consolidation and cooling-induced subsidence. TOUGH2Biot was applied to evaluate the thermal, hydrodynamic, and mechanical responses of CO2 geological sequestration at the Ordos CCS Demonstration Project, China and geothermal exploitation at the Geysers geothermal field, California. The results demonstrate that TOUGH2Biot is capable of analyzing change in pressure and temperature, displacement, stress, and potential shear-slip failure caused by large scale underground man-made activity in subsurface flow systems. TOUGH2Biot can also be easily extended for complex coupled process problems in fractured media and be conveniently updated to parallel versions on different platforms to take advantage of high-performance computing.

Advances in cardiovascular fluid mechanics: bench to bedside.

PubMed

Dasi, Lakshmi P; Sucosky, Philippe; de Zelicourt, Diane; Sundareswaran, Kartik; Jimenez, Jorge; Yoganathan, Ajit P

2009-04-01

This paper presents recent advances in cardiovascular fluid mechanics that define the current state of the art. These studies include complex multimodal investigations with advanced measurement and simulation techniques. We first discuss the complex flows within the total cavopulmonary connection in Fontan patients. We emphasize the quantification of energy losses by studying the importance of caval offsets as well as the differences among various Fontan surgical protocols. In our studies of the fluid mechanics of prosthetic heart valves, we reveal for the first time the full three-dimensional complexity of flow fields in the vicinity of bileaflet and trileaflet valves and the microscopic hinge flow dynamics. We also present results of these valves functioning in a patient-specific native aorta geometry. Our in vitro mitral valve studies show the complex mechanism of the native mitral valve apparatus. We demonstrate that the different components of the mitral valve have independent and synergistically complex functions that allow the valve to operate efficiently. We also show how valve mechanics change under pathological and repair conditions associated with enlarged ventricles. Finally, our ex vivo studies on the interactions between the aortic valve and its surrounding hemodynamic environment are aimed at providing insights into normal valve function and valve pathology. We describe the development of organ- and tissue-culture systems and the biological response of the tissue subjected to their respective simulated mechanical environment. The studies noted above have enhanced our understanding of the complex fluid mechanics associated with the cardiovascular system and have led to new translational technologies.

Mechanical characterization of metallic nanowires by using a customized atomic microscope

NASA Astrophysics Data System (ADS)

Celik, Emrah

A new experimental method to characterize the mechanical properties of metallic nanowires is introduced. An accurate and fast mechanical characterization of nanowires requires simultaneous imaging and testing of nanowires. However, there exists no practical experimental procedure in the literature that provides a quantitative mechanical analysis and imaging of the nanowire specimens during mechanical testing. In this study, a customized atomic force microscope (AFM) is placed inside a scanning electron microscope (SEM) in order to locate the position of the nanowires. The tip of the atomic force microscope cantilever is utilized to bend and break the nanowires. The nanowires are prepared by electroplating of nickel ions into the nanoscale pores of the alumina membranes. Force versus bending displacement responses of these nanowires are measured experimentally and then compared against those of the finite element analysis and peridynamic simulations to extract their mechanical properties through an inverse approach. The average elastic modulus of nickel nanowires, which are extracted using finite element analysis and peridynamic simulations, varies between 220 GPa and 225 GPa. The elastic modulus of bulk nickel published in the literature is comparable to that of nickel nanowires. This observation agrees well with the previous findings on nanowires stating that the elastic modulus of nanowires with diameters over 100nm is similar to that of bulk counterparts. The average yield stress of nickel nanowires, which are extracted using finite element analysis and peridynamic simulations, is found to be between 3.6 GPa to 4.1 GPa. The average value of yield stress of nickel nanowires with 250nm diameter is significantly higher than that of bulk nickel. Higher yield stress of nickel nanowires observed in this study can be explained by the lower defect density of nickel nanowires when compared to their bulk counterparts. Deviation in the extracted mechanical properties is investigated by analyzing the major sources of uncertainty in the experimental procedure. The effects of the nanowire orientation, the loading position and the nanowire diameter on the mechanical test results are quantified using ANSYS simulations. Among all of these three sources of uncertainty investigated, the nanowire diameter has been found to have the most significant effect on the extracted mechanical properties.

Molecular dynamics simulations for the examination of mechanical properties of hydroxyapatite/ poly α-n-butyl cyanoacrylate under additive manufacturing.

PubMed

Wang, Yanen; Wei, Qinghua; Pan, Feilong; Yang, Mingming; Wei, Shengmin

2014-01-01

Molecular dynamics (MD) simulations emerged to be a helpful tool in the field of material science. In rapid prototyping artificial bone scaffolds process, the binder spraying volume and mechanism are very important for bone scaffolds mechanical properties. In this study, we applied MD simulations to investigating the binding energy of α-n-butyl cyanoacrylate (NBCA) on Hydroxyapatite (HA) crystallographic planes (001, 100 and 110), and to calculating and analyzing the mechanical properties and radial distribution function of the HA(110)/NBCA mixed system. The simulation results suggested that HA (110) has the highest binding energy with NBCA owing to the high planar atom density, and the mechanical properties of HA(110)/NBCA mixed system is stronger than pure HA system. Therefore, the multi-grade strength bone scaffold could be fabricated through spraying various volume NBCA binders during 3D printing process. By calculating the radial distribution function of HA(110)/NBCA, the essence of the interface interaction were successfully elucidated. The forming situation parameters can be referred to calculation results. There exists a strong interaction between HA crystallographic plane (110) and NBCA, it is mainly derived from the hydrogen bonds between O atoms which connect with C atoms of NBCA and H atoms in HA crystal. Furthermore, a strong adsorption effect can be demonstrated between HA and NBCA.

2D Quantum Simulation of MOSFET Using the Non Equilibrium Green's Function Method

NASA Technical Reports Server (NTRS)

Svizhenko, Alexel; Anantram, M. P.; Govindan, T. R.; Yan, Jerry (Technical Monitor)

2000-01-01

The objectives this viewgraph presentation summarizes include: (1) the development of a quantum mechanical simulator for ultra short channel MOSFET simulation, including theory, physical approximations, and computer code; (2) explore physics that is not accessible by semiclassical methods; (3) benchmarking of semiclassical and classical methods; and (4) study other two-dimensional devices and molecular structure, from discretized Hamiltonian to tight-binding Hamiltonian.

Muscle-tendon mechanics explain unexpected effects of exoskeleton assistance on metabolic rate during walking.

PubMed

Jackson, Rachel W; Dembia, Christopher L; Delp, Scott L; Collins, Steven H

2017-06-01

The goal of this study was to gain insight into how ankle exoskeletons affect the behavior of the plantarflexor muscles during walking. Using data from previous experiments, we performed electromyography-driven simulations of musculoskeletal dynamics to explore how changes in exoskeleton assistance affected plantarflexor muscle-tendon mechanics, particularly for the soleus. We used a model of muscle energy consumption to estimate individual muscle metabolic rate. As average exoskeleton torque was increased, while no net exoskeleton work was provided, a reduction in tendon recoil led to an increase in positive mechanical work performed by the soleus muscle fibers. As net exoskeleton work was increased, both soleus muscle fiber force and positive mechanical work decreased. Trends in the sum of the metabolic rates of the simulated muscles correlated well with trends in experimentally observed whole-body metabolic rate ( R 2 =0.9), providing confidence in our model estimates. Our simulation results suggest that different exoskeleton behaviors can alter the functioning of the muscles and tendons acting at the assisted joint. Furthermore, our results support the idea that the series tendon helps reduce positive work done by the muscle fibers by storing and returning energy elastically. We expect the results from this study to promote the use of electromyography-driven simulations to gain insight into the operation of muscle-tendon units and to guide the design and control of assistive devices. © 2017. Published by The Company of Biologists Ltd.

Machine-Thermal Coupling Stresses Analysis of the Fin-Type Structural Thermoelectric Generator

NASA Astrophysics Data System (ADS)

Zhang, Zheng; Yue, Hao; Chen, Dongbo; Qin, Delei; Chen, Zijian

2017-05-01

The design structure and heat-transfer mechanism of a thermoelectric generator (TEG) determine its body temperature state. Thermal stress and thermal deformation generated by the temperature variation directly affect the stress state of thermoelectric modules (TEMs). Therefore, the rated temperature and pressing force of TEMs are important parameters in TEG design. Here, the relationships between structural of a fin-type TEG (FTEG) and these parameters are studied by modeling and "machine-thermal" coupling simulation. An indirect calculation method is adopted in the coupling simulation. First, numerical heat transfer calculations of a three-dimensional FTEG model are conducted according to an orthogonal simulation table. The influences of structural parameters for heat transfer in the channel and outer fin temperature distribution are analyzed. The optimal structural parameters are obtained and used to simulate temperature field of the outer fins. Second, taking the thermal calculation results as the initial condition, the thermal-solid coupling calculation is adopted. The thermal stresses of outer fin, mechanical force of spring-angle pressing mechanism, and clamping force on a TEM are analyzed. The simulation results show that the heat transfer area of the inner fin and the physical parameters of the metal materials are the keys to determining the FTEG temperature field. The pressing mechanism's mechanical force can be reduced by reducing the outer fin angle. In addition, a corrugated cooling water pipe, which has cooling and spring functionality, is conducive to establishing an adaptable clamping force to avoid the TEMs being crushed by the thermal stresses in the body.

Coupled simulation of CFD-flight-mechanics with a two-species-gas-model for the hot rocket staging

NASA Astrophysics Data System (ADS)

Li, Yi; Reimann, Bodo; Eggers, Thino

2016-11-01

The hot rocket staging is to separate the lowest stage by directly ignite the continuing-stage-motor. During the hot staging, the rocket stages move in a harsh dynamic environment. In this work, the hot staging dynamics of a multistage rocket is studied using the coupled simulation of Computational Fluid Dynamics and Flight Mechanics. Plume modeling is crucial for a coupled simulation with high fidelity. A 2-species-gas model is proposed to simulate the flow system of the rocket during the staging: the free-stream is modeled as "cold air" and the exhausted plume from the continuing-stage-motor is modeled with an equivalent calorically-perfect-gas that approximates the properties of the plume at the nozzle exit. This gas model can well comprise between the computation accuracy and efficiency. In the coupled simulations, the Navier-Stokes equations are time-accurately solved in moving system, with which the Flight Mechanics equations can be fully coupled. The Chimera mesh technique is utilized to deal with the relative motions of the separated stages. A few representative staging cases with different initial flight conditions of the rocket are studied with the coupled simulation. The torque led by the plume-induced-flow-separation at the aft-wall of the continuing-stage is captured during the staging, which can assist the design of the controller of the rocket. With the increasing of the initial angle-of-attack of the rocket, the staging quality becomes evidently poorer, but the separated stages are generally stable when the initial angle-of-attack of the rocket is small.

Modelling and simulating the forming of new dry automated lay-up reinforcements for primary structures

NASA Astrophysics Data System (ADS)

Bouquerel, Laure; Moulin, Nicolas; Drapier, Sylvain; Boisse, Philippe; Beraud, Jean-Marc

2017-10-01

While weight has been so far the main driver for the development of prepreg based-composites solutions for aeronautics, a new weight-cost trade-off tends to drive choices for next-generation aircrafts. As a response, Hexcel has designed a new dry reinforcement type for aircraft primary structures, which combines the benefits of automation, out-of-autoclave process cost-effectiveness, and mechanical performances competitive to prepreg solutions: HiTape® is a unidirectional (UD) dry carbon reinforcement with thermoplastic veil on each side designed for aircraft primary structures [1-3]. One privileged process route for HiTape® in high volume automated processes consists in forming initially flat dry reinforcement stacks, before resin infusion [4] or injection. Simulation of the forming step aims at predicting the geometry and mechanical properties of the formed stack (so-called preform) for process optimisation. Extensive work has been carried out on prepreg and dry woven fabrics forming behaviour and simulation, but the interest for dry non-woven reinforcements has emerged more recently. Some work has been achieved on non crimp fabrics but studies on the forming behaviour of UDs are seldom and deal with UD prepregs only. Tension and bending in the fibre direction, along with inter-ply friction have been identified as the main mechanisms controlling the HiTape® response during forming. Bending has been characterised using a modified Peirce's flexometer [5] and inter-ply friction study is under development. Anisotropic hyperelastic constitutive models have been selected to represent the assumed decoupled deformation mechanisms. Model parameters are then identified from associated experimental results. For forming simulation, a continuous approach at the macroscopic scale has been selected first, and simulation is carried out in the Zset framework [6] using proper shell finite elements.

Ab Initio QM/MM Study Shows a Highly Dissociated SN2 Hydrolysis Mechanism for the cGMP-Specific Phosphodiesterase-5.

PubMed

Li, Zhe; Wu, Yinuo; Feng, Ling-Jun; Wu, Ruibo; Luo, Hai-Bin

2014-12-09

Phosphodiesterases (PDEs) are the sole enzymes hydrolyzing the important second messengers cGMP and cAMP and have been identified as therapeutic targets for several diseases. The most successful examples are PDE5 inhibitors (i.e., sildenafil and tadalafil), which have been approved for the treatment of male erectile dysfunction and pulmonary hypertension. However, the side effects mostly due to nonselective inhibition toward other PDE isoforms, set back the clinical usage of PDE5 inhibitors. Until now, the exact catalytic mechanism of the substrate cGMP by PDE5 is still unclear. Herein, the first computational study on the catalytic hydrolysis mechanism of cGMP for PDE5 (catalytic domain) is performed by employing the state-of-the-art ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Our simulations show a SN2 type reaction procedure via a highly dissociated transition state with a reaction barrier of 8.88 kcal/mol, which is quite different from the previously suggested hydrolysis mechanism of cAMP for PDE4. Furthermore, the subsequent ligand exchange and the release of the product GMP have also been investigated by binding energy analysis and MD simulations. It is deduced that ligand exchange would be the rate-determining step of the whole reaction, which is consistent with many previous experimental results. The obtained mechanistic insights should be valuable for not only the rational design of more specific inhibitors toward PDE5 but also understanding the general hydrolysis mechanism of cGMP-specific PDEs.

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of {sup 64}Cu and {sup 67}Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nasrabadi, M. N., E-mail: mnnasrabadi@ast.ui.ac.ir; Sepiani, M.

2015-03-30

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE and LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Effect of Hydraulic Pressure on Warm Hydro Mechanical Deep Drawing of Magnesium Alloy Sheet

NASA Astrophysics Data System (ADS)

Liu, Wei; Wu, Linzhi; Yuan, Shijian

The uniaxial tensile test and hydraulic bulging test of AZ31 magnesium alloy sheets were applied to study the influence of temperature on the material properties and obtain the forming limit curves at different temperatures. Numerical simulations of warm hydro mechanical deep drawing were carried out to investigate the effect of hydraulic pressure on the formability of a cylindrical cup, and the simplified hydraulic pressure profiles were used to simulate the loading procedure of hydraulic pressure. The optimal hydraulic pressure at different temperatures were given and verified by experimental studies at temperature 100°C and 170V.

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of 64Cu and 67Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

NASA Astrophysics Data System (ADS)

Nasrabadi, M. N.; Sepiani, M.

2015-03-01

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE & LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Final Report for DE-FG02-99ER45795

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, John Warren

The research supported by this grant focuses on atomistic studies of defects, phase transitions, electronic and magnetic properties, and mechanical behaviors of materials. We have been studying novel properties of various emerging nanoscale materials on multiple levels of length and time scales, and have made accurate predictions on many technologically important properties. A significant part of our research has been devoted to exploring properties of novel nano-scale materials by pushing the limit of quantum mechanical simulations, and development of a rigorous scheme to design accurate classical inter-atomic potentials for larger scale atomistic simulations for many technologically important metals and metalmore » alloys.« less

A Dynamic Simulation of Musculoskeletal Function in the Mouse Hindlimb During Trotting Locomotion

PubMed Central

Charles, James P.; Cappellari, Ornella; Hutchinson, John R.

2018-01-01

Mice are often used as animal models of various human neuromuscular diseases, and analysis of these models often requires detailed gait analysis. However, little is known of the dynamics of the mouse musculoskeletal system during locomotion. In this study, we used computer optimization procedures to create a simulation of trotting in a mouse, using a previously developed mouse hindlimb musculoskeletal model in conjunction with new experimental data, allowing muscle forces, activation patterns, and levels of mechanical work to be estimated. Analyzing musculotendon unit (MTU) mechanical work throughout the stride allowed a deeper understanding of their respective functions, with the rectus femoris MTU dominating the generation of positive and negative mechanical work during the swing and stance phases. This analysis also tested previous functional inferences of the mouse hindlimb made from anatomical data alone, such as the existence of a proximo-distal gradient of muscle function, thought to reflect adaptations for energy-efficient locomotion. The results do not strongly support the presence of this gradient within the mouse musculoskeletal system, particularly given relatively high negative net work output from the ankle plantarflexor MTUs, although more detailed simulations could test this further. This modeling analysis lays a foundation for future studies of the control of vertebrate movement through the development of neuromechanical simulations. PMID:29868576

Effect of Shock-Induced Cavitation Bubble Collapse on the damage in the Simulated Perineuronal Net of the Brain.

PubMed

Wu, Yuan-Ting; Adnan, Ashfaq

2017-07-13

The purpose of this study is to conduct modeling and simulation to understand the effect of shock-induced mechanical loading, in the form of cavitation bubble collapse, on damage to the brain's perineuronal nets (PNNs). It is known that high-energy implosion due to cavitation collapse is responsible for corrosion or surface damage in many mechanical devices. In this case, cavitation refers to the bubble created by pressure drop. The presence of a similar damage mechanism in biophysical systems has long being suspected but not well-explored. In this paper, we use reactive molecular dynamics (MD) to simulate the scenario of a shock wave induced cavitation collapse within the perineuronal net (PNN), which is the near-neuron domain of a brain's extracellular matrix (ECM). Our model is focused on the damage in hyaluronan (HA), which is the main structural component of PNN. We have investigated the roles of cavitation bubble location, shockwave intensity and the size of a cavitation bubble on the structural evolution of PNN. Simulation results show that the localized supersonic water hammer created by an asymmetrical bubble collapse may break the hyaluronan. As such, the current study advances current knowledge and understanding of the connection between PNN damage and neurodegenerative disorders.

Dynamic modelling and experimental study of cantilever beam with clearance

NASA Astrophysics Data System (ADS)

Li, B.; Jin, W.; Han, L.; He, Z.

2012-05-01

Clearances occur in almost all mechanical systems, typically such as the clearance between slide plate of gun barrel and guide. Therefore, to study the clearances of mechanisms can be very important to increase the working performance and lifetime of mechanisms. In this paper, rigid dynamic modelling of cantilever with clearance was done according to the subject investigated. In the rigid dynamic modelling, clearance is equivalent to the spring-dashpot model, the impact of beam and boundary face was also taken into consideration. In ADAMS software, the dynamic simulation was carried out according to the model above. The software simulated the movement of cantilever with clearance under external excitation. Research found: When the clearance is larger, the force of impact will become larger. In order to study how the stiffness of the cantilever's supporting part influences natural frequency of the system, A Euler beam which is restricted by a draught spring and a torsion spring at its end was raised. Through numerical calculation, the relationship between natural frequency and stiffness was found. When the value of the stiffness is close to the limit value, the corresponding boundary condition is illustrated. An ADAMS experiment was carried out to check the theory and the simulation.

The framework for simulation of bioinspired security mechanisms against network infrastructure attacks.

PubMed

Shorov, Andrey; Kotenko, Igor

2014-01-01

The paper outlines a bioinspired approach named "network nervous system" and methods of simulation of infrastructure attacks and protection mechanisms based on this approach. The protection mechanisms based on this approach consist of distributed procedures of information collection and processing, which coordinate the activities of the main devices of a computer network, identify attacks, and determine necessary countermeasures. Attacks and protection mechanisms are specified as structural models using a set-theoretic approach. An environment for simulation of protection mechanisms based on the biological metaphor is considered; the experiments demonstrating the effectiveness of the protection mechanisms are described.

Insights into Lithium-ion battery degradation and safety mechanisms from mesoscale simulations using experimentally reconstructed mesostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roberts, Scott A.; Mendoza, Hector; Brunini, Victor E.

Battery performance, while observed at the macroscale, is primarily governed by the bicontinuous mesoscale network of the active particles and a polymeric conductive binder in its electrodes. Manufacturing processes affect this mesostructure, and therefore battery performance, in ways that are not always clear outside of empirical relationships. Directly studying the role of the mesostructure is difficult due to the small particle sizes (a few microns) and large mesoscale structures. Mesoscale simulation, however, is an emerging technique that allows the investigation into how particle-scale phenomena affect electrode behavior. In this manuscript, we discuss our computational approach for modeling electrochemical, mechanical, andmore » thermal phenomena of lithium-ion batteries at the mesoscale. Here, we review our recent and ongoing simulation investigations and discuss a path forward for additional simulation insights.« less

Insights into Lithium-ion battery degradation and safety mechanisms from mesoscale simulations using experimentally reconstructed mesostructures

DOE PAGES

Roberts, Scott A.; Mendoza, Hector; Brunini, Victor E.; ...

2016-10-20

Battery performance, while observed at the macroscale, is primarily governed by the bicontinuous mesoscale network of the active particles and a polymeric conductive binder in its electrodes. Manufacturing processes affect this mesostructure, and therefore battery performance, in ways that are not always clear outside of empirical relationships. Directly studying the role of the mesostructure is difficult due to the small particle sizes (a few microns) and large mesoscale structures. Mesoscale simulation, however, is an emerging technique that allows the investigation into how particle-scale phenomena affect electrode behavior. In this manuscript, we discuss our computational approach for modeling electrochemical, mechanical, andmore » thermal phenomena of lithium-ion batteries at the mesoscale. Here, we review our recent and ongoing simulation investigations and discuss a path forward for additional simulation insights.« less

Hyper-X Stage Separation Trajectory Validation Studies

NASA Technical Reports Server (NTRS)

Tartabini, Paul V.; Bose, David M.; McMinn, John D.; Martin, John G.; Strovers, Brian K.

2003-01-01

An independent twelve degree-of-freedom simulation of the X-43A separation trajectory was created with the Program to Optimize Simulated trajectories (POST II). This simulation modeled the multi-body dynamics of the X-43A and its booster and included the effect of two pyrotechnically actuated pistons used to push the vehicles apart as well as aerodynamic interaction forces and moments between the two vehicles. The simulation was developed to validate trajectory studies conducted with a 14 degree-of-freedom simulation created early in the program using the Automatic Dynamic Analysis of Mechanics Systems (ADAMS) simulation software. The POST simulation was less detailed than the official ADAMS-based simulation used by the Project, but was simpler, more concise and ran faster, while providing similar results. The increase in speed provided by the POST simulation provided the Project with an alternate analysis tool. This tool was ideal for performing separation control logic trade studies that required the running of numerous Monte Carlo trajectories.

Kinetic and radiative power from optically thin accretion flows

NASA Astrophysics Data System (ADS)

Sądowski, Aleksander; Gaspari, Massimo

2017-06-01

We perform a set of general relativistic, radiative, magneto-hydrodynamical simulations (GR-RMHD) to study the transition from radiatively inefficient to efficient state of accretion on a non-rotating black hole. We study ion to electron temperature ratios ranging from TI/Te = 10 to 100, and simulate flows corresponding to accretion rates as low as 10^{-6}\\dot{M}_Edd, and as high as 10^{-2}\\dot{M}_Edd. We have found that the radiative output of accretion flows increases with accretion rate, and that the transition occurs earlier for hotter electrons (lower TI/Te ratio). At the same time, the mechanical efficiency hardly changes and accounts to ≈3 per cent of the accreted rest mass energy flux, even at the highest simulated accretion rates. This is particularly important for the mechanical active galactic nuclei (AGN) feedback regulating massive galaxies, groups and clusters. Comparison with recent observations of radiative and mechanical AGN luminosities suggests that the ion to electron temperature ratio in the inner, collisionless accretion flow should fall within 10 < TI/Te < 30, I.e. the electron temperature should be several percent of the ion temperature.

Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Lu, Yan; Salsbury, Freddie R.

2015-01-01

ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.

QuVis interactive simulations: tools to support quantum mechanics instruction

NASA Astrophysics Data System (ADS)

Kohnle, Antje

2015-04-01

Quantum mechanics holds a fascination for many students, but its mathematical complexity and counterintuitive results can present major barriers. The QuVis Quantum Mechanics Visualization Project (www.st-andrews.ac.uk/physics/quvis) aims to overcome these issues through the development and evaluation of interactive simulations with accompanying activities for the learning and teaching of quantum mechanics. Over 90 simulations are now available on the QuVis website. One collection of simulations is embedded in the Institute of Physics Quantum Physics website (quantumphysics.iop.org), which consists of freely available resources for an introductory course in quantum mechanics starting from two-level systems. Simulations support model-building by reducing complexity, focusing on fundamental ideas and making the invisible visible. They promote engaged exploration, sense-making and linking of multiple representations, and include high levels of interactivity and direct feedback. Simulations are research-based and evaluation with students informs all stages of the development process. Simulations are iteratively refined using student feedback in individual observation sessions and in-class trials. Evaluation has shown that the simulations can help students learn quantum mechanics concepts at both the introductory and advanced undergraduate level and that students perceive simulations to be beneficial to their learning. Recent activity includes the launch of a new collection of HTML5 simulations that run on both desktop and tablet-based devices and the introduction of a goal and reward structure in simulations through the inclusion of challenges. This presentation will give an overview of the QuVis resources, highlight recent work and outline future plans. QuVis is supported by the UK Institute of Physics, the UK Higher Education Academy and the University of St Andrews.

High Performance Simulations of Accretion Disk Dynamics and Jet Formations Around Kerr Black Holes

NASA Technical Reports Server (NTRS)

Nishikawa, Ken-Ichi; Mizuno, Yosuke; Watson, Michael

2007-01-01

We investigate jet formation in black-hole systems using 3-D General Relativistic Particle-In-Cell (GRPIC) and 3-D GRMHD simulations. GRPIC simulations, which allow charge separations in a collisionless plasma, do not need to invoke the frozen condition as in GRMHD simulations. 3-D GRPIC simulations show that jets are launched from Kerr black holes as in 3-D GRMHD simulations, but jet formation in the two cases may not be identical. Comparative study of black hole systems with GRPIC and GRMHD simulations with the inclusion of radiate transfer will further clarify the mechanisms that drive the evolution of disk-jet systems.

[Research progress on mechanical performance evaluation of artificial intervertebral disc].

PubMed

Li, Rui; Wang, Song; Liao, Zhenhua; Liu, Weiqiang

2018-03-01

The mechanical properties of artificial intervertebral disc (AID) are related to long-term reliability of prosthesis. There are three testing methods involved in the mechanical performance evaluation of AID based on different tools: the testing method using mechanical simulator, in vitro specimen testing method and finite element analysis method. In this study, the testing standard, testing equipment and materials of AID were firstly introduced. Then, the present status of AID static mechanical properties test (static axial compression, static axial compression-shear), dynamic mechanical properties test (dynamic axial compression, dynamic axial compression-shear), creep and stress relaxation test, device pushout test, core pushout test, subsidence test, etc. were focused on. The experimental techniques using in vitro specimen testing method and testing results of available artificial discs were summarized. The experimental methods and research status of finite element analysis were also summarized. Finally, the research trends of AID mechanical performance evaluation were forecasted. The simulator, load, dynamic cycle, motion mode, specimen and test standard would be important research fields in the future.

Plasma and radio waves from Neptune: Source mechanisms and propagation

NASA Astrophysics Data System (ADS)

Wong, H. K.

1994-03-01

This report summarizes results obtained through the support of NASA Grant NAGW-2412. The objective of this project is to conduct a comprehensive investigation of the radio wave emission observed by the planetary radio astronomy (PRA) instrument on board Voyager 2 as if flew by Neptune. This study has included data analysis, theoretical and numerical calculations, ray tracing, and modeling to determine the possible source mechanism(s) and locations of the Neptune radio emissions. We have completed four papers, which are included in the appendix. The paper 'Modeling of Whistler Ray Paths in the Magnetosphere of Neptune' investigated the propagation and dispersion of lighting-generated whistler in the magnetosphere of Neptune by using three dimensional ray tracing. The two papers 'Numerical Simulations of Bursty Radio Emissions from Planetary Magnetospheres' and 'Numerical Simulations of Bursty Planetary Radio Emissions' employed numerical simulations to investigate an alternate source mechanism of bursty radio emissions in addition to the cyclotron maser instability. We have also studied the possible generation of Z and whistler mode waves by the temperature anisotropic beam instability and the result was published in 'Electron Cyclotron Wave Generation by Relativistic Electrons.' Besides the aforementioned studies, we have also collaborated with members of the PRA team to investigate various aspects of the radio wave data. Two papers have been submitted for publication and the abstracts of these papers are also listed in the appendix.

Efficiency of five chemical protective clothing materials against nano and submicron aerosols when submitted to mechanical deformations.

PubMed

Ben Salah, Mehdi; Hallé, Stéphane; Tuduri, Ludovic

2016-01-01

Due to their potential toxicity, the use of nanoparticles in the workplace is a growing concern. Some studies indicate that nanoparticles can penetrate the skin and lead to adverse health effects. Since chemical protective clothing is the last barrier to protect the skin, this study aims to better understand nanoparticle penetration behaviour in dermal protective clothing under mechanical deformation. For this purpose, five of the most common types of fabrics used in protective clothing, one woven and four nonwoven, were chosen and submitted to different simulated exposure conditions. They were tested against polydispersed NaCl aerosols having an electrical-mobility diameter between 14 and 400 nm. A bench-scale exposure setup and a sampling protocol was developed to measure the level of penetration of the aerosols through the material samples of disposable coveralls and lab coat, while subjecting them to mechanical deformations to simulate the conditions of usage in the workplace. Particle size distribution of the aerosol was determined upstream and downstream using a scanning mobility particle sizer (SMPS). The measured efficiencies demonstrated that the performances of nonwoven materials were similar. Three nonwovens had efficiencies above 99%, while the woven fabric was by far, the least effective. Moreover, the results established that mechanical deformations, as simulated for this study, did not have a significant effect on the fabrics' efficiencies.

Plasma and radio waves from Neptune: Source mechanisms and propagation

NASA Technical Reports Server (NTRS)

Wong, H. K.

1994-01-01

This report summarizes results obtained through the support of NASA Grant NAGW-2412. The objective of this project is to conduct a comprehensive investigation of the radio wave emission observed by the planetary radio astronomy (PRA) instrument on board Voyager 2 as if flew by Neptune. This study has included data analysis, theoretical and numerical calculations, ray tracing, and modeling to determine the possible source mechanism(s) and locations of the Neptune radio emissions. We have completed four papers, which are included in the appendix. The paper 'Modeling of Whistler Ray Paths in the Magnetosphere of Neptune' investigated the propagation and dispersion of lighting-generated whistler in the magnetosphere of Neptune by using three dimensional ray tracing. The two papers 'Numerical Simulations of Bursty Radio Emissions from Planetary Magnetospheres' and 'Numerical Simulations of Bursty Planetary Radio Emissions' employed numerical simulations to investigate an alternate source mechanism of bursty radio emissions in addition to the cyclotron maser instability. We have also studied the possible generation of Z and whistler mode waves by the temperature anisotropic beam instability and the result was published in 'Electron Cyclotron Wave Generation by Relativistic Electrons.' Besides the aforementioned studies, we have also collaborated with members of the PRA team to investigate various aspects of the radio wave data. Two papers have been submitted for publication and the abstracts of these papers are also listed in the appendix.

A Framework for Simulating Turbine-Based Combined-Cycle Inlet Mode-Transition

NASA Technical Reports Server (NTRS)

Le, Dzu K.; Vrnak, Daniel R.; Slater, John W.; Hessel, Emil O.

2012-01-01

A simulation framework based on the Memory-Mapped-Files technique was created to operate multiple numerical processes in locked time-steps and send I/O data synchronously across to one-another to simulate system-dynamics. This simulation scheme is currently used to study the complex interactions between inlet flow-dynamics, variable-geometry actuation mechanisms, and flow-controls in the transition from the supersonic to hypersonic conditions and vice-versa. A study of Mode-Transition Control for a high-speed inlet wind-tunnel model with this MMF-based framework is presented to illustrate this scheme and demonstrate its usefulness in simulating supersonic and hypersonic inlet dynamics and controls or other types of complex systems.

Quantitative computer simulations of extraterrestrial processing operations

NASA Technical Reports Server (NTRS)

Vincent, T. L.; Nikravesh, P. E.

1989-01-01

The automation of a small, solid propellant mixer was studied. Temperature control is under investigation. A numerical simulation of the system is under development and will be tested using different control options. Control system hardware is currently being put into place. The construction of mathematical models and simulation techniques for understanding various engineering processes is also studied. Computer graphics packages were utilized for better visualization of the simulation results. The mechanical mixing of propellants is examined. Simulation of the mixing process is being done to study how one can control for chaotic behavior to meet specified mixing requirements. An experimental mixing chamber is also being built. It will allow visual tracking of particles under mixing. The experimental unit will be used to test ideas from chaos theory, as well as to verify simulation results. This project has applications to extraterrestrial propellant quality and reliability.

Handsheet formation and mechanical testing via fiber-level simulations

Treesearch

Leonard H. Switzer; Daniel J. Klingenberg; C. Tim Scott

2004-01-01

A fiber model and simulation method are employed to investigate the mechanical response of planar fiber networks subjected to elongational deformation. The simulated responses agree qualitatively with numerous experimental observations. suggesting that such simulation methods may be useful for probing the relationships between fiber properties and interactions and the...

Effect of irradiation on mechanical properties of symmetrical grain boundaries investigated by atomic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, X. Y.; Gao, N.; Setyawan, W.

Tensile response of irradiated symmetric grain boundaries to externally applied strain has been studied using atomic simulation methods. The absorption of irradiation induced defects by grain boundaries has been confirmed to degrade the mechanical properties of grain boundaries through the change of its under- taken deformation mechanism. Atomic rearrangement, the formations of a stress accumulation region and vacancy-rich zone and the nucleation and movement of dislocations under stress effect have been observed after the displacement cascades in grain boundaries, which are considered as main reasons to induce above degradation. These results suggest the necessity of considering both trap- ping efficiencymore » to defects and the mechanical property change of irradiated grain boundaries for further development of radiation resistant materials.« less

“Impact of CB6 and CB05TU chemical mechanisms on air quality”

EPA Science Inventory

“Impacts of CB6 and CB05TU chemical mechanisms on air quality”In this study, we incorporate the newly developed Carbon Bond chemical mechanism (CB6) into the Community Multiscale Air Quality modeling system (CMAQv5.0.1) and perform air quality model simulations with the CB6 and t...

REDBACK: an Open-Source Highly Scalable Simulation Tool for Rock Mechanics with Dissipative Feedbacks

NASA Astrophysics Data System (ADS)

Poulet, T.; Veveakis, M.; Paesold, M.; Regenauer-Lieb, K.

2014-12-01

Multiphysics modelling has become an indispensable tool for geoscientists to simulate the complex behaviours observed in their various fields of study where multiple processes are involved, including thermal, hydraulic, mechanical and chemical (THMC) laws. This modelling activity involves simulations that are computationally expensive and its soaring uptake is tightly linked to the increasing availability of supercomputing power and easy access to powerful nonlinear solvers such as PETSc (http://www.mcs.anl.gov/petsc/). The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework (http://mooseframework.org) that can harness such computational power and allow scientists to develop easily some tightly-coupled fully implicit multiphysics simulations that run automatically in parallel on large clusters. This open-source framework provides a powerful tool to collaborate on numerical modelling activities and we are contributing to its development with REDBACK (https://github.com/pou036/redback), a module for Rock mEchanics with Dissipative feedBACKs. REDBACK builds on the tensor mechanics finite strain implementation available in MOOSE to provide a THMC simulator where the energetic formulation highlights the importance of all dissipative terms in the coupled system of equations. We show first applications of fully coupled dehydration reactions triggering episodic fluid transfer through shear zones (Alevizos et al, 2014). The dimensionless approach used allows focusing on the critical underlying variables which are driving the resulting behaviours observed and this tool is specifically designed to study material instabilities underpinning geological features like faulting, folding, boudinage, shearing, fracturing, etc. REDBACK provides a collaborative and educational tool which captures the physical and mathematical understanding of such material instabilities and provides an easy way to apply this knowledge to realistic scenarios, where the size and complexity of the geometries considered, along with the material parameters distributions, add as many sources of different instabilities. References: Alevizos, S., T. Poulet, and E. Veveakis (2014), J. Geophys. Res., 119, 4558-4582, doi:10.1002/2013JB010070.

What Has Finite Element Analysis Taught Us about Diabetic Foot Disease and Its Management? A Systematic Review

PubMed Central

Telfer, Scott; Erdemir, Ahmet; Woodburn, James; Cavanagh, Peter R.

2014-01-01

Background Over the past two decades finite element (FE) analysis has become a popular tool for researchers seeking to simulate the biomechanics of the healthy and diabetic foot. The primary aims of these simulations have been to improve our understanding of the foot’s complicated mechanical loading in health and disease and to inform interventions designed to prevent plantar ulceration, a major complication of diabetes. This article provides a systematic review and summary of the findings from FE analysis-based computational simulations of the diabetic foot. Methods A systematic literature search was carried out and 31 relevant articles were identified covering three primary themes: methodological aspects relevant to modelling the diabetic foot; investigations of the pathomechanics of the diabetic foot; and simulation-based design of interventions to reduce ulceration risk. Results Methodological studies illustrated appropriate use of FE analysis for simulation of foot mechanics, incorporating nonlinear tissue mechanics, contact and rigid body movements. FE studies of pathomechanics have provided estimates of internal soft tissue stresses, and suggest that such stresses may often be considerably larger than those measured at the plantar surface and are proportionally greater in the diabetic foot compared to controls. FE analysis allowed evaluation of insole performance and development of new insole designs, footwear and corrective surgery to effectively provide intervention strategies. The technique also presents the opportunity to simulate the effect of changes associated with the diabetic foot on non-mechanical factors such as blood supply to local tissues. Discussion While significant advancement in diabetic foot research has been made possible by the use of FE analysis, translational utility of this powerful tool for routine clinical care at the patient level requires adoption of cost-effective (both in terms of labour and computation) and reliable approaches with clear clinical validity for decision making. PMID:25290098

Simulation Studies for Inspection of the Benchmark Test with PATRASH

NASA Astrophysics Data System (ADS)

Shimosaki, Y.; Igarashi, S.; Machida, S.; Shirakata, M.; Takayama, K.; Noda, F.; Shigaki, K.

2002-12-01

In order to delineate the halo-formation mechanisms in a typical FODO lattice, a 2-D simulation code PATRASH (PArticle TRAcking in a Synchrotron for Halo analysis) has been developed. The electric field originating from the space charge is calculated by the Hybrid Tree code method. Benchmark tests utilizing three simulation codes of ACCSIM, PATRASH and SIMPSONS were carried out. These results have been confirmed to be fairly in agreement with each other. The details of PATRASH simulation are discussed with some examples.

Open Knee: Open Source Modeling & Simulation to Enable Scientific Discovery and Clinical Care in Knee Biomechanics

PubMed Central

Erdemir, Ahmet

2016-01-01

Virtual representations of the knee joint can provide clinicians, scientists, and engineers the tools to explore mechanical function of the knee and its tissue structures in health and disease. Modeling and simulation approaches such as finite element analysis also provide the possibility to understand the influence of surgical procedures and implants on joint stresses and tissue deformations. A large number of knee joint models are described in the biomechanics literature. However, freely accessible, customizable, and easy-to-use models are scarce. Availability of such models can accelerate clinical translation of simulations, where labor intensive reproduction of model development steps can be avoided. The interested parties can immediately utilize readily available models for scientific discovery and for clinical care. Motivated by this gap, this study aims to describe an open source and freely available finite element representation of the tibiofemoral joint, namely Open Knee, which includes detailed anatomical representation of the joint's major tissue structures, their nonlinear mechanical properties and interactions. Three use cases illustrate customization potential of the model, its predictive capacity, and its scientific and clinical utility: prediction of joint movements during passive flexion, examining the role of meniscectomy on contact mechanics and joint movements, and understanding anterior cruciate ligament mechanics. A summary of scientific and clinically directed studies conducted by other investigators are also provided. The utilization of this open source model by groups other than its developers emphasizes the premise of model sharing as an accelerator of simulation-based medicine. Finally, the imminent need to develop next generation knee models are noted. These are anticipated to incorporate individualized anatomy and tissue properties supported by specimen-specific joint mechanics data for evaluation, all acquired in vitro from varying age groups and pathological states. PMID:26444849

Open Knee: Open Source Modeling and Simulation in Knee Biomechanics.

PubMed

Erdemir, Ahmet

2016-02-01

Virtual representations of the knee joint can provide clinicians, scientists, and engineers the tools to explore mechanical functions of the knee and its tissue structures in health and disease. Modeling and simulation approaches such as finite element analysis also provide the possibility to understand the influence of surgical procedures and implants on joint stresses and tissue deformations. A large number of knee joint models are described in the biomechanics literature. However, freely accessible, customizable, and easy-to-use models are scarce. Availability of such models can accelerate clinical translation of simulations, where labor-intensive reproduction of model development steps can be avoided. Interested parties can immediately utilize readily available models for scientific discovery and clinical care. Motivated by this gap, this study aims to describe an open source and freely available finite element representation of the tibiofemoral joint, namely Open Knee, which includes the detailed anatomical representation of the joint's major tissue structures and their nonlinear mechanical properties and interactions. Three use cases illustrate customization potential of the model, its predictive capacity, and its scientific and clinical utility: prediction of joint movements during passive flexion, examining the role of meniscectomy on contact mechanics and joint movements, and understanding anterior cruciate ligament mechanics. A summary of scientific and clinically directed studies conducted by other investigators are also provided. The utilization of this open source model by groups other than its developers emphasizes the premise of model sharing as an accelerator of simulation-based medicine. Finally, the imminent need to develop next-generation knee models is noted. These are anticipated to incorporate individualized anatomy and tissue properties supported by specimen-specific joint mechanics data for evaluation, all acquired in vitro from varying age groups and pathological states. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

A modified social force model for crowd dynamics

NASA Astrophysics Data System (ADS)

Hassan, Ummi Nurmasyitah; Zainuddin, Zarita; Abu-Sulyman, Ibtesam M.

2017-08-01

The Social Force Model (SFM) is one of the most successful models in microscopic pedestrian studies that is used to study the movement of pedestrians. Many modifications have been done to improvise the SFM by earlier researchers such as the incorporation of a constant respect factor into the self-stopping mechanism. Before the new mechanism is introduced, the researchers found out that a pedestrian will immediately come to a halt if other pedestrians are near to him, which seems to be an unrealistic behavior. Therefore, researchers introduce a self-slowing mechanism to gradually stop a pedestrian when he is approaching other pedestrians. Subsequently, the dynamic respect factor is introduced into the self-slowing mechanism based on the density of the pedestrians to make the model even more realistic. In real life situations, the respect factor of the pedestrians should be dynamic values instead of a constant value. However, when we reproduce the simulation of the dynamic respect factor, we found that the movement of the pedestrians are unrealistic because the pedestrians are lacking perception of the pedestrians in front of him. In this paper, we adopted both dynamic respect factor and dynamic angular parameter, called modified dynamic respect factor, which is dependent on the density of the pedestrians. Simulations are performed in a normal unidirectional walkway to compare the simulated pedestrians' movements produced by both models. The results obtained showed that the modified dynamic respect factor produces more realistic movement of the pedestrians which conform to the real situation. Moreover, we also found that the simulations endow the pedestrian with a self-slowing mechanism and a perception of other pedestrians in front of him.

Eta-CMAQ Air Quality Forecasts for O3 and Related Species Using Three Different Photochemical Mechanisms (CB4, CB05, SAPRC-99): Comparisons with Measurements During the 2004 ICARTT Study

EPA Science Inventory

In this study, we compare the CB4, CB05 and SAPRC-99 mechanisms by examining the impact of these different chemical mechanisms on the Eta-CMAQ air quality forecast model simulations for O₃ and its related precursors over the eastern US through comparisons with the inte...

An imaged-based inverse finite element method to determine in-vivo mechanical properties of the human trabecular meshwork.

PubMed

Pant, Anup D; Kagemann, Larry; Schuman, Joel S; Sigal, Ian A; Amini, Rouzbeh

2017-01-01

Previous studies have shown that the trabecular meshwork (TM) is mechanically stiffer in glaucomatous eyes as compared to normal eyes. It is believed that elevated TM stiffness increases resistance to the aqueous humor outflow, producing increased intraocular pressure (IOP). It would be advantageous to measure TM mechanical properties in vivo , as these properties are believed to play an important role in the pathophysiology of glaucoma and could be useful for identifying potential risk factors. The purpose of this study was to develop a method to estimate in-vivo TM mechanical properties using clinically available exams and computer simulations. Inverse finite element simulation. A finite element model of the TM was constructed from optical coherence tomography (OCT) images of a healthy volunteer before and during IOP elevation. An axisymmetric model of the TM was then constructed. Images of the TM at a baseline IOP level of 11, and elevated level of 23 mmHg were treated as the undeformed and deformed configurations, respectively. An inverse modeling technique was subsequently used to estimate the TM shear modulus ( G ). An optimization technique was used to find the shear modulus that minimized the difference between Schlemm's canal area in the in-vivo images and simulations. Upon completion of inverse finite element modeling, the simulated area of the Schlemm's canal changed from 8,889 µm 2 to 2,088 µm 2 , similar to the experimentally measured areal change of the canal (from 8,889 µm 2 to 2,100 µm 2 ). The calculated value of shear modulus was found to be 1.93 kPa, (implying an approximate Young's modulus of 5.75 kPa), which is consistent with previous ex-vivo measurements. The combined imaging and computational simulation technique provides a unique approach to calculate the mechanical properties of the TM in vivo without any surgical intervention. Quantification of such mechanical properties will help us examine the mechanistic role of TM biomechanics in the regulation of IOP in healthy and glaucomatous eyes.

Modeling of damage driven fracture failure of fiber post-restored teeth.

PubMed

Xu, Binting; Wang, Yining; Li, Qing

2015-09-01

Mechanical failure of biomaterials, which can be initiated by either violent force, or progressive stress fatigue, is a serious issue. Great efforts have been made to improve the mechanical performances of dental restorations. Virtual simulation is a promising approach for biomechanical investigations, which presents significant advantages in improving efficiency than traditional in vivo/in vitro studies. Over the past few decades, a number of virtual studies have been conducted to investigate the biomechanical issues concerning dental biomaterials, but only with limited incorporation of brittle failure phenomena. Motivated by the contradictory findings between several finite element analyses and common clinical observations on the fracture resistance of post-restored teeth, this study aimed to provide an approach using numerical simulations for investigating the fracture failure process through a non-linear fracture mechanics model. The ability of this approach to predict fracture initiation and propagation in a complex biomechanical status based on the intrinsic material properties was investigated. Results of the virtual simulations matched the findings of experimental tests, in terms of the ultimate fracture failure strengths and predictive areas under risk of clinical failure. This study revealed that the failure of dental post-restored restorations is a typical damage-driven continuum-to-discrete process. This approach is anticipated to have ramifications not only for modeling fracture events, but also for the design and optimization of the mechanical properties of biomaterials for specific clinically determined requirements. Copyright © 2015 Elsevier Ltd. All rights reserved.

Simulation of Weld Mechanical Behavior to Include Welding-Induced Residual Stress and Distortion: Coupling of SYSWELD and Abaqus Codes

DTIC Science & Technology

2015-11-01

Memorandum Simulation of Weld Mechanical Behavior to Include Welding -Induced Residual Stress and Distortion: Coupling of SYSWELD and Abaqus Codes... Weld Mechanical Behavior to Include Welding -Induced Residual Stress and Distortion: Coupling of SYSWELD and Abaqus Codes by Charles R. Fisher...TYPE Technical Report 3. DATES COVERED (From - To) Dec 2013 – July 2015 4. TITLE AND SUBTITLE Simulation of Weld Mechanical Behavior to Include

Simulation of Weld Mechanical Behavior to Include Welding Induced Residual Stress and Distortion: Coupling of SYSWELD and Abaqus Codes

DTIC Science & Technology

2015-11-01

Memorandum Simulation of Weld Mechanical Behavior to Include Welding -Induced Residual Stress and Distortion: Coupling of SYSWELD and Abaqus Codes... Weld Mechanical Behavior to Include Welding -Induced Residual Stress and Distortion: Coupling of SYSWELD and Abaqus Codes by Charles R. Fisher...TYPE Technical Report 3. DATES COVERED (From - To) Dec 2013 – July 2015 4. TITLE AND SUBTITLE Simulation of Weld Mechanical Behavior to Include

Cyclic Voltammetry Simulations with DigiSim Software: An Upper-Level Undergraduate Experiment

ERIC Educational Resources Information Center

Messersmith, Stephania J.

2014-01-01

An upper-division undergraduate chemistry experiment is described which utilizes DigiSim software to simulate cyclic voltammetry (CV). Four mechanisms were studied: a reversible electron transfer with no subsequent or proceeding chemical reactions, a reversible electron transfer followed by a reversible chemical reaction, a reversible chemical…

Mechanical discrete simulator of the electro-mechanical lift with n:1 roping

NASA Astrophysics Data System (ADS)

Alonso, F. J.; Herrera, I.

2016-05-01

The design process of new products in lift engineering is a difficult task due to, mainly, the complexity and slenderness of the lift system, demanding a predictive tool for the lift mechanics. A mechanical ad-hoc discrete simulator, as an alternative to ‘general purpose’ mechanical simulators is proposed. Firstly, the synthesis and experimentation process that has led to establish a suitable model capable of simulating accurately the response of the electromechanical lift is discussed. Then, the equations of motion are derived. The model comprises a discrete system of 5 vertically displaceable masses (car, counterweight, car frame, passengers/loads and lift drive), an inertial mass of the assembly tension pulley-rotor shaft which can rotate about the machine axis and 6 mechanical connectors with 1:1 suspension layout. The model is extended to any n:1 roping lift by setting 6 equivalent mechanical components (suspension systems for car and counterweight, lift drive silent blocks, tension pulley-lift drive stator and passengers/load equivalent spring-damper) by inductive inference from 1:1 and generalized 2:1 roping system. The application to simulate real elevator systems is proposed by numeric time integration of the governing equations using the Kutta-Meden algorithm and implemented in a computer program for ad-hoc elevator simulation called ElevaCAD.

The influence of temperature on ozone production under varying NOx conditions - a modelling study

NASA Astrophysics Data System (ADS)

Coates, Jane; Mar, Kathleen A.; Ojha, Narendra; Butler, Tim M.

2016-09-01

Surface ozone is a secondary air pollutant produced during the atmospheric photochemical degradation of emitted volatile organic compounds (VOCs) in the presence of sunlight and nitrogen oxides (NOx). Temperature directly influences ozone production through speeding up the rates of chemical reactions and increasing the emissions of VOCs, such as isoprene, from vegetation. In this study, we used an idealised box model with different chemical mechanisms (Master Chemical Mechanism, MCMv3.2; Common Representative Intermediates, CRIv2; Model for OZone and Related Chemical Tracers, MOZART-4; Regional Acid Deposition Model, RADM2; Carbon Bond Mechanism, CB05) to examine the non-linear relationship between ozone, NOx and temperature, and we compared this to previous observational studies. Under high-NOx conditions, an increase in ozone from 20 to 40 °C of up to 20 ppbv was due to faster reaction rates, while increased isoprene emissions added up to a further 11 ppbv of ozone. The largest inter-mechanism differences were obtained at high temperatures and high-NOx emissions. CB05 and RADM2 simulated more NOx-sensitive chemistry than MCMv3.2, CRIv2 and MOZART-4, which could lead to different mitigation strategies being proposed depending on the chemical mechanism. The increased oxidation rate of emitted VOC with temperature controlled the rate of Ox production; the net influence of peroxy nitrates increased net Ox production per molecule of emitted VOC oxidised. The rate of increase in ozone mixing ratios with temperature from our box model simulations was about half the rate of increase in ozone with temperature observed over central Europe or simulated by a regional chemistry transport model. Modifying the box model set-up to approximate stagnant meteorological conditions increased the rate of increase of ozone with temperature as the accumulation of oxidants enhanced ozone production through the increased production of peroxy radicals from the secondary degradation of emitted VOCs. The box model simulations approximating stagnant conditions and the maximal ozone production chemical regime reproduced the 2 ppbv increase in ozone per degree Celsius from the observational and regional model data over central Europe. The simulated ozone-temperature relationship was more sensitive to mixing than the choice of chemical mechanism. Our analysis suggests that reductions in NOx emissions would be required to offset the additional ozone production due to an increase in temperature in the future.

Utility of a novel error-stepping method to improve gradient-based parameter identification by increasing the smoothness of the local objective surface: a case-study of pulmonary mechanics.

PubMed

Docherty, Paul D; Schranz, Christoph; Chase, J Geoffrey; Chiew, Yeong Shiong; Möller, Knut

2014-05-01

Accurate model parameter identification relies on accurate forward model simulations to guide convergence. However, some forward simulation methodologies lack the precision required to properly define the local objective surface and can cause failed parameter identification. The role of objective surface smoothness in identification of a pulmonary mechanics model was assessed using forward simulation from a novel error-stepping method and a proprietary Runge-Kutta method. The objective surfaces were compared via the identified parameter discrepancy generated in a Monte Carlo simulation and the local smoothness of the objective surfaces they generate. The error-stepping method generated significantly smoother error surfaces in each of the cases tested (p<0.0001) and more accurate model parameter estimates than the Runge-Kutta method in three of the four cases tested (p<0.0001) despite a 75% reduction in computational cost. Of note, parameter discrepancy in most cases was limited to a particular oblique plane, indicating a non-intuitive multi-parameter trade-off was occurring. The error-stepping method consistently improved or equalled the outcomes of the Runge-Kutta time-integration method for forward simulations of the pulmonary mechanics model. This study indicates that accurate parameter identification relies on accurate definition of the local objective function, and that parameter trade-off can occur on oblique planes resulting prematurely halted parameter convergence. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Computational Study of Symmetric Methylation on Histone Arginine Catalyzed by Protein Arginine Methyltransferase PRMT5 through QM/MM MD and Free Energy Simulations

DOE PAGES

Yue, Yufei; CHu, Yuzhuo; Guo, Hong

2015-01-01

Protein arginine methyltransferases (PRMTs) catalyze the transfer of the methyl group from S-adenosyl-l-methionine (AdoMet) to arginine residues. There are three types of PRMTs (I, II and III) that produce different methylation products, including asymmetric dimethylarginine (ADMA), symmetric dimethylarginine (SDMA) and monomethylarginine (MMA). Since these different methylations can lead to different biological consequences, understanding the origin of product specificity of PRMTs is of considerable interest. In this article, the quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations are performed to study SDMA catalyzed by the Type II PRMT5 on the basis of experimental observation that the dimethylated productmore » is generated through a distributive fashion. The simulations have identified some important interactions and proton transfers during the catalysis. Similar to the cases involving Type I PRMTs, a conserved Glu residue (Glu435) in PRMT5 is suggested to function as general base catalyst based on the result of the simulations. Moreover, our results show that PRMT5 has an energetic preference for the first methylation on N-1 followed by the second methylation on a different -guanidino nitrogen of arginine (N-2).The first and second methyl transfers are estimated to have free energy barriers of 19-20 and 18-19 kcal/mol respectively. The computer simulations suggest a distinctive catalytic mechanism of symmetric dimethylation that seems to be different from asymmetric dimethylation.« less

Simulating a Thin Accretion Disk Using PLUTO

NASA Astrophysics Data System (ADS)

Phillipson, Rebecca; Vogeley, Michael S.; Boyd, Patricia T.

2017-08-01

Accreting black hole systems such as X-ray binaries and active galactic nuclei exhibit variability in their luminosity on many timescales ranging from milliseconds to tens of days, and even hundreds of days. The mechanism(s) driving this variability and the relationship between short- and long-term variability is poorly understood. Current studies on accretion disks seek to determine how the changes in black hole mass, the rate at which mass accretes onto the central black hole, and the external environment affect the variability on scales ranging from stellar-mass black holes to supermassive black holes. Traditionally, the fluid mechanics equations governing accretion disks have been simplified by considering only the kinematics of the disk, and perhaps magnetic fields, in order for their phenomenological behavior to be predicted analytically. We seek to employ numerical techniques to study accretion disks including more complicated physics traditionally ignored in order to more accurately understand their behavior over time. We present a proof-of-concept three dimensional, global simulation using the astrophysical hydrodynamic code PLUTO of a simplified thin disk model about a central black hole which will serve as the basis for development of more complicated models including external effects such as radiation and magnetic fields. We also develop a tool to generate a synthetic light curve that displays the variability in luminosity of the simulation over time. The preliminary simulation and accompanying synthetic light curve demonstrate that PLUTO is a reliable code to perform sophisticated simulations of accretion disk systems which can then be compared to observational results.

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations.

PubMed

Kuzmanic, Antonija; Sutto, Ludovico; Saladino, Giorgio; Nebreda, Angel R; Gervasio, Francesco L; Orozco, Modesto

2017-04-26

p38α is a Ser/Thr protein kinase involved in a variety of cellular processes and pathological conditions, which makes it a promising pharmacological target. Although the activity of the enzyme is highly regulated, its molecular mechanism of activation remains largely unexplained, even after decades of research. By using state-of-the-art molecular dynamics simulations, we decipher the key elements of the complex molecular mechanism refined by evolution to allow for a fine tuning of p38α kinase activity. Our study describes for the first time the molecular effects of different regulators of the enzymatic activity, and provides an integrative picture of the activation mechanism that explains the seemingly contradictory X-ray and NMR data.

Comparison of mechanical behavior between implant-simulated bone tissue and implant-jaw bone tissue interfaces based on Pull Out testing

NASA Astrophysics Data System (ADS)

Lopez, C.; Muñoz, J. C.; Pinillos, J. C.

2013-11-01

The main purpose of this research was to achieve a better understanding of the relationship within the mechanical properties of human cadaver jaw bone with kind D2 density regarding a substitute polymer to simulate bone tissue, proposed by the ASTM, to evaluate orthopedic implants. However, despite the existence of several densities of foams and his mechanical characterization has been classified into different degrees of tissue densities to simulate cancellous and cortical bone, the value of the densities are different contrasted with the densities of bone tissue, making difficult to establish direct relationship about mechanical behavior between the polymer and the bone material, and therefore no clear criteria known for choosing the polymeric foam which describes the mechanical behavior of tissue for a specific or particular study. To understand such behavior from bone tissue regarding the polymer samples, on this research was a dental implant inserted into the samples, and subjected to destructive Pull Out test according to ASTM F543The Pull Out strength was compared between implant-jawbone and implant-rigid polyurethane foam interfaces. Thus, the test pieces with mechanical behavior similar to bone tissue, enabling an approximation to choose degree appropriate of polymer to replace the bone tissue in future trials biomechanical.

Lattice Boltzmann Simulation of Seismic Mobilization of Residual Oil in Sandstone

NASA Astrophysics Data System (ADS)

Guo, R.; Jiang, F.; Deng, W.

2017-12-01

Seismic stimulation is a promising technology for enhanced oil recovery. However, current mechanism studies are mainly in the single constricted tubes or idealized porous media, and no study has been conducted in real reservoir porous media. We have developed a numerical simulation which uses the lattice Boltzmann method to directly calculate the characteristics of residual oil clusters to quantify seismic mobilization of residual oil in real Berea sandstone in a scale of 400μm x 400μm x 400μm. The residual oil clusters will be firstly obtained by applying the water flooding scheme to the oil-saturated sandstone. Then, we will apply the seismic stimulation to the sandstone by converting the seismic effect to oscillatory inertial force and add to the pore fluids. This oscillatory inertial force causes the mobilization of residual oil by overcoming the capillary force. The response of water and oil to the seismic stimulation will be observed in our simulations. Two seismic oil mobilization mechanisms will be investigated: (1) the passive response of residual oil clusters to the seismic stimulation, and (2) the resonance of oil clusters subject to low frequency seismic stimulation. We will then discuss which mechanism should be the dominant mechanism for the seismic stimulation oil recovery for practical applications.

Early Dynamics and Stabilization Mechanisms of Oil-in-Water Emulsions Containing Colloidal Particles Modified with Short Amphiphiles: A Numerical Study.

PubMed

Cerbelaud, Manuella; Videcoq, Arnaud; Alison, Lauriane; Tervoort, Elena; Studart, André R

2017-12-19

Emulsions stabilized by mixtures of particles and amphiphilic molecules are relevant for a wide range of applications, but their dynamics and stabilization mechanisms on the colloidal level are poorly understood. Given the challenges to experimentally probe the early dynamics and mechanisms of droplet stabilization, Brownian dynamics simulations are developed here to study the behavior of oil-in-water emulsions stabilized by colloidal particles modified with short amphiphiles. Simulation parameters are based on an experimental system that consists of emulsions obtained with octane as the oil phase and a suspension of alumina colloidal particles modified with short carboxylic acids as the continuous aqueous medium. The numerical results show that attractive forces between the colloidal particles favor the formation of closely packed clusters on the droplet surface or of a percolating network of particles throughout the continuous phase, depending on the amphiphile concentration. Simulations also reveal the importance of a strong adsorption of particles at the liquid interface to prevent their depletion from the droplet surface when another droplet approaches. Strongly adsorbed particles remain immobile on the droplet surface, generating an effective steric barrier against droplet coalescence. These findings provide new insights into the early dynamics and mechanisms of stabilization of emulsions using particles and amphiphilic molecules.

An adaptive quantum mechanics/molecular mechanics method for the infrared spectrum of water: incorporation of the quantum effect between solute and solvent.

PubMed

Watanabe, Hiroshi C; Banno, Misa; Sakurai, Minoru

2016-03-14

Quantum effects in solute-solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase. For accurate spectrum evaluation, the surrounding solvent molecules, in addition to the solute of interest, should be treated using a quantum mechanical method. However, conventional quantum mechanics/molecular mechanics (QM/MM) methods cannot handle free QM solvent molecules during molecular dynamics (MD) simulation because of the diffusion problem. To deal with this problem, we have previously proposed an adaptive QM/MM "size-consistent multipartitioning (SCMP) method". In the present study, as the first application of the SCMP method, we demonstrate the reproduction of the infrared spectrum of liquid-phase water, and evaluate the quantum effect in comparison with conventional QM/MM simulations.

Mechanisms for Robust Cognition.

PubMed

Walsh, Matthew M; Gluck, Kevin A

2015-08-01

To function well in an unpredictable environment using unreliable components, a system must have a high degree of robustness. Robustness is fundamental to biological systems and is an objective in the design of engineered systems such as airplane engines and buildings. Cognitive systems, like biological and engineered systems, exist within variable environments. This raises the question, how do cognitive systems achieve similarly high degrees of robustness? The aim of this study was to identify a set of mechanisms that enhance robustness in cognitive systems. We identify three mechanisms that enhance robustness in biological and engineered systems: system control, redundancy, and adaptability. After surveying the psychological literature for evidence of these mechanisms, we provide simulations illustrating how each contributes to robust cognition in a different psychological domain: psychomotor vigilance, semantic memory, and strategy selection. These simulations highlight features of a mathematical approach for quantifying robustness, and they provide concrete examples of mechanisms for robust cognition. © 2014 Cognitive Science Society, Inc.

Influence of particle shape on the microstructure evolution and the mechanical properties of granular materials

NASA Astrophysics Data System (ADS)

Tian, Jianqiu; Liu, Enlong; Jiang, Lian; Jiang, Xiaoqiong; Sun, Yi; Xu, Ran

2018-06-01

In order to study the influence of particle shape on the microstructure evolution and the mechanical properties of granular materials, a two-dimensional DEM analysis of samples with three particle shapes, including circular particles, triangular particles, and elongated particles, is proposed here to simulate the direct shear tests of coarse-grained soils. For the numerical test results, analyses are conducted in terms of particle rotations, fabric evolution, and average path length evolution. A modified Rowe's stress-dilatancy equation is also proposed and successfully fitted onto simulation data.

Modeling and performance improvement of the constant power regulator systems in variable displacement axial piston pump.

PubMed

Park, Sung Hwan; Lee, Ji Min; Kim, Jong Shik

2013-01-01

An irregular performance of a mechanical-type constant power regulator is considered. In order to find the cause of an irregular discharge flow at the cut-off pressure area, modeling and numerical simulations are performed to observe dynamic behavior of internal parts of the constant power regulator system for a swashplate-type axial piston pump. The commercial numerical simulation software AMESim is applied to model the mechanical-type regulator with hydraulic pump and simulate the performance of it. The validity of the simulation model of the constant power regulator system is verified by comparing simulation results with experiments. In order to find the cause of the irregular performance of the mechanical-type constant power regulator system, the behavior of main components such as the spool, sleeve, and counterbalance piston is investigated using computer simulation. The shape modification of the counterbalance piston is proposed to improve the undesirable performance of the mechanical-type constant power regulator. The performance improvement is verified by computer simulation using AMESim software.

Foam Delivery of Hydrogen for Enhanced Aquifer Contacting and Anaerobic Bioremediation of Chlorinated Solvents

DTIC Science & Technology

2005-11-01

101 Task 6 - Incorporation of the heterogeneity enhanced mechanisms in the UTCHEM numerical simulator...hydrogen sparging in a bench scale three-dimensional sand pack model. (6) Incorporation of the heterogeneity enhanced mechanisms in the UTCHEM ...Incorporation of the heterogeneity enhanced mechanisms in the UTCHEM numerical simulator. Simulation model for foam in porous media and

Multi-Scale Simulation of High Energy Density Ionic Liquids

DTIC Science & Technology

2007-06-19

and simulation of ionic liquids (ILs). A polarizable model was developed to simulate ILs more accurately at the atomistic level. A multiscale coarse...propellant, 1- hydroxyethyl-4-amino-1, 2, 4-triazolium nitrate (HEATN), were studied with the all-atom polarizable model. The mechanism suggested for HEATN...with this AFOSR-supported project, a polarizable forcefield for the ionic liquids such as 1-ethyl-3-methylimidazolium nitrate (EMIM*/NO3-) was

Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

PubMed

Ramya, L; Ramakrishnan, Vigneshwar

2016-07-01

Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cyclic Mechanical Loading Enhances Transport of Antibodies Into Articular Cartilage.

PubMed

DiDomenico, Chris D; Xiang Wang, Zhen; Bonassar, Lawrence J

2017-01-01

The goal of this study was to characterize antibody penetration through cartilage tissue under mechanical loading. Mechanical stimulation aids in the penetration of some proteins, but this effect has not characterized molecules such as antibodies (>100 kDa), which may hold some clinical value for treating osteoarthritis (OA). For each experiment, fresh articular cartilage plugs were obtained and exposed to fluorescently labeled antibodies while under cyclic mechanical load in unconfined compression for several hours. Penetration of these antibodies was quantified using confocal microscopy, and finite element (FE) simulations were conducted to predict fluid flow patterns within loaded samples. Transport enhancement followed a linear trend with strain amplitude (0.25-5%) and a nonlinear trend with frequency (0.25-2.60 Hz), with maximum enhancement found to be at 5% cyclic strain and 1 Hz, respectively. Regions of highest enhancement of transport within the tissue were associated with the regions of highest interstitial fluid velocity, as predicted from finite-element simulations. Overall, cyclic compression-enhanced antibody transport by twofold to threefold. To our knowledge, this is the first study to test how mechanical stimulation affects the diffusion of antibodies in cartilage and suggest further study into other important factors regarding macromolecular transport.

Ground Reaction Forces During Locomotion in Simulated Microgravity

NASA Technical Reports Server (NTRS)

Davis, B. L.; Cavanagh, Peter R.; Sommer, H. J., III; Wu, G.

1996-01-01

Significant losses in bone density and mineral, primarily in the lower extremities have been reported following exposure to weightlessness. Recent investigations suggest that mechanical influences such as bone deformation and strain rate may be critically important in stimulating new bone formation. It was hypothesized that velocity, cadence and harness design would significantly affect lower limb impact forces during treadmill exercise in simulated zero gravity (0G). A ground-based hypogravity simulator was used to investigate which factors affect limb loading during tethered treadmill exercise. A fractional factorial design was used and 12 subjects were studied. The results showed that running on active and passive treadmills in the simulator with a tethering force close to the maximum comfortable level produced similar magnitudes for the peak ground reaction force. It was also found that these maximum forces were significantly lower than those obtained during overground trials, even when the speeds of locomotion in the simulator were 66 % greater than those in 1 G. Cadence had no effect on any of the response variables. The maximum rate of force application (DFDT-Max) was similar for overground running and exercise in simulated 0G, provided that the "weightless subjects ran on a motorized treadmill. These findings have implications for the use of treadmill exercise as a countermeasure for hypokinetic osteoporosis. As the relationship between mechanical factors and osteogenesis becomes better understood, results from human experiments in 0G simulators will help to design in-flight exercise programs that are more closely targeted to generate appropriate mechanical stimuli.

Mechanisms of passive ion permeation through lipid bilayers: insights from simulations.

PubMed

Tepper, Harald L; Voth, Gregory A

2006-10-26

Multistate empirical valence bond and classical molecular dynamics simulations were used to explore mechanisms for passive ion leakage through a dimyristoyl phosphatidylcholine lipid bilayer. In accordance with a previous study on proton leakage (Biophys. J. 2005, 88, 3095), it was found that the permeation mechanism must be a highly concerted one, in which ion, solvent, and membrane coordinates are coupled. The presence of the ion itself significantly alters the response of those coordinates, suggesting that simulations of transmembrane water structures without explicit inclusion of the ionic solute are insufficient for elucidating transition mechanisms. The properties of H(+), Na(+), OH(-), and bare water molecules in the membrane interior were compared, both by biased sampling techniques and by constructing complete and unbiased transition paths. It was found that the anomalous difference in leakage rates between protons and other cations can be largely explained by charge delocalization effects rather than the usual kinetic picture (Grotthuss hopping of the proton). Permeability differences between anions and cations through phosphatidylcholine bilayers are correlated with suppression of favorable membrane breathing modes by cations.

The plastic response of Tantalum in Quasi-Isentropic Compression Ramp and Release

NASA Astrophysics Data System (ADS)

Moore, Alexander; Brown, Justin; Lim, Hojun; Lane, J. Matthew D.

2017-06-01

The mechanical response of various forms of tantalum under extreme pressures and strain rates is studied using dynamic quasi-isentropic compression loading conditions in atomistic simulations. Ramp compression in bcc metals under these conditions tend to show a significant strengthening effect with increasing pressure; however, due to limitations of experimental methods in such regimes, the underlying physics for this phenomenon is not well understood. Molecular dynamics simulations provide important information about the plasticity mechanisms and can be used to investigate this strengthening. MD simulations are performed on nanocrystalline Ta and single crystal defective Ta with dislocations and point defects to uncover how the material responds and the underlying plasticity mechanisms. The different systems of solid Ta are seen to plastically deform through different mechanisms. Fundamental understanding of tantalum plasticity in these high pressure and strain rate regimes is needed to model and fully understand experimental results. Sandia National Labs is a multi program laboratory managed and operated by Sandia Corp., a wholly owned subsidiary of Lockheed Martin Corp., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Interactive simulations for quantum key distribution

NASA Astrophysics Data System (ADS)

Kohnle, Antje; Rizzoli, Aluna

2017-05-01

Secure communication protocols are becoming increasingly important, e.g. for internet-based communication. Quantum key distribution (QKD) allows two parties, commonly called Alice and Bob, to generate a secret sequence of 0s and 1s called a key that is only known to themselves. Classically, Alice and Bob could never be certain that their communication was not compromised by a malicious eavesdropper. Quantum mechanics however makes secure communication possible. The fundamental principle of quantum mechanics that taking a measurement perturbs the system (unless the measurement is compatible with the quantum state) also applies to an eavesdropper. Using appropriate protocols to create the key, Alice and Bob can detect the presence of an eavesdropper by errors in their measurements. As part of the QuVis Quantum Mechanics Visualisation Project, we have developed a suite of four interactive simulations that demonstrate the basic principles of three different QKD protocols. The simulations use either polarised photons or spin 1/2 particles as physical realisations. The simulations and accompanying activities are freely available for use online or download, and run on a wide range of devices including tablets and PCs. Evaluation with students over three years was used to refine the simulations and activities. Preliminary studies show that the refined simulations and activities help students learn the basic principles of QKD at both the introductory and advanced undergraduate levels.

Production of anti-amoxicillin ScFv antibody and simulation studying its molecular recognition mechanism for penicillins.

PubMed

Liu, Jing; Zhang, Hui C; Duan, Chang F; Dong, Jun; Zhao, Guo X; Wang, Jian P; Li, Nan; Liu, Jin Z; Li, Yu W

2016-11-01

The molecular recognition mechanism of an antibody for its hapten is very interesting. The objective of this research was to study the intermolecular interactions of an anti-amoxicillin antibody with penicillin drugs. The single chain variable fragment (ScFv) antibody was generated from a hybridoma cell strain excreting the monoclonal antibody for amoxicillin. The recombinant ScFv antibody showed similar recognition ability for penicillins to its parental monoclonal antibody: simultaneous recognizing 11 penicillins with cross-reactivities of 18-107%. The three-dimensional structure of the ScFv antibody was simulated by using homology modeling, and its intermolecular interactions with 11 penicillins were studied by using molecular docking. Results showed that three CDRs are involved in antibody recognition; CDR L3 Arg 100, CDR H3 Tyr226, and CDR H3 Arg 228 were the key contact amino acid residues; hydrogen bonding was the main antibody-drug intermolecular force; and the core structure of penicillin drugs was the main antibody binding position. These results could explain the recognition mechanism of anti-amoxicillin antibody for amoxicillin and its analogs. This is the first study reporting the production of ScFv antibody for penicillins and stimulation studying its recognition mechanism.

The Framework for Simulation of Bioinspired Security Mechanisms against Network Infrastructure Attacks

PubMed Central

Kotenko, Igor

2014-01-01

The paper outlines a bioinspired approach named “network nervous system" and methods of simulation of infrastructure attacks and protection mechanisms based on this approach. The protection mechanisms based on this approach consist of distributed prosedures of information collection and processing, which coordinate the activities of the main devices of a computer network, identify attacks, and determine nessesary countermeasures. Attacks and protection mechanisms are specified as structural models using a set-theoretic approach. An environment for simulation of protection mechanisms based on the biological metaphor is considered; the experiments demonstrating the effectiveness of the protection mechanisms are described. PMID:25254229

Synthesis, QSAR, and Molecular Dynamics Simulation of Amidino-substituted Benzimidazoles as Dipeptidyl Peptidase III Inhibitors.

PubMed

Rastija, Vesna; Agić, Dejan; Tomiš, Sanja; Nikolič, Sonja; Hranjec, Marijana; Grace, Karminski-Zamola; Abramić, Marija

2015-01-01

A molecular modeling study is performed on series of benzimidazol-based inhibitors of human dipeptidyl peptidase III (DPP III). An eight novel compounds were synthesized in excellent yields using green chemistry approach. This study is aimed to elucidate the structural features of benzimidazole derivatives required for antagonism of human DPP III activity using Quantitative Structure-Activity Relationship (QSAR) analysis, and to understand the mechanism of one of the most potent inhibitor binding into the active site of this enzyme, by molecular dynamics (MD) simulations. The best model obtained includes S3K and RDF045m descriptors which have explained 89.4 % of inhibitory activity. Depicted moiety for strong inhibition activity matches to the structure of most potent compound. MD simulation has revealed importance of imidazolinyl and phenyl groups in the mechanism of binding into the active site of human DPP III.

The co-development of looking dynamics and discrimination performance

PubMed Central

Perone, Sammy; Spencer, John P.

2015-01-01

The study of looking dynamics and discrimination form the backbone of developmental science and are central processes in theories of infant cognition. Looking dynamics and discrimination change dramatically across the first year of life. Surprisingly, developmental changes in looking and discrimination have not been studied together. Recent simulations of a dynamic neural field (DNF) model of infant looking and memory suggest that looking and discrimination do change together over development and arise from a single neurodevelopmental mechanism. We probe this claim by measuring looking dynamics and discrimination along continuous, metrically organized dimensions in 5-, 7, and 10-month-old infants (N = 119). The results showed that looking dynamics and discrimination changed together over development and are linked within individuals. Quantitative simulations of a DNF model provide insights into the processes that underlie developmental change in looking dynamics and discrimination. Simulation results support the view that these changes might arise from a single neurodevelopmental mechanism. PMID:23957821

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin

PubMed Central

2018-01-01

Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD) simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM) to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins. PMID:29698481

Instrumented Architectural Simulation System

NASA Technical Reports Server (NTRS)

Delagi, B. A.; Saraiya, N.; Nishimura, S.; Byrd, G.

1987-01-01

Simulation of systems at an architectural level can offer an effective way to study critical design choices if (1) the performance of the simulator is adequate to examine designs executing significant code bodies, not just toy problems or small application fragements, (2) the details of the simulation include the critical details of the design, (3) the view of the design presented by the simulator instrumentation leads to useful insights on the problems with the design, and (4) there is enough flexibility in the simulation system so that the asking of unplanned questions is not suppressed by the weight of the mechanics involved in making changes either in the design or its measurement. A simulation system with these goals is described together with the approach to its implementation. Its application to the study of a particular class of multiprocessor hardware system architectures is illustrated.

Challenge toward the prediction of typhoon behaviour and down pour

NASA Astrophysics Data System (ADS)

Takahashi, K.; Onishi, R.; Baba, Y.; Kida, S.; Matsuda, K.; Goto, K.; Fuchigami, H.

2013-08-01

Mechanisms of interactions among different scale phenomena play important roles for forecasting of weather and climate. Multi-scale Simulator for the Geoenvironment (MSSG), which deals with multi-scale multi-physics phenomena, is a coupled non-hydrostatic atmosphere-ocean model designed to be run efficiently on the Earth Simulator. We present simulation results with the world-highest 1.9km horizontal resolution for the entire globe and regional heavy rain with 1km horizontal resolution and 5m horizontal/vertical resolution for urban area simulation. To gain high performance by exploiting the system capabilities, we propose novel performance evaluation metrics introduced in previous studies that incorporate the effects of the data caching mechanism between CPU and memory. With a useful code optimization guideline based on such metrics, we demonstrate that MSSG can achieve an excellent peak performance ratio of 32.2% on the Earth Simulator with the single-core performance found to be a key to a reduced time-to-solution.

Computational structural mechanics engine structures computational simulator

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1989-01-01

The Computational Structural Mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures.

An Insilico Design of Nanoclay Based Nanocomposites and Scaffolds in Bone Tissue Engineering

NASA Astrophysics Data System (ADS)

Sharma, Anurag

A multiscale in silico approach to design polymer nanocomposites and scaffolds for bone tissue engineering applications is described in this study. This study focuses on the role of biomaterials design and selection, structural integrity and mechanical properties evolution during degradation and tissue regeneration in the successful design of polymer nanocomposite scaffolds. Polymer nanocomposite scaffolds are synthesized using aminoacid modified montmorillonite nanoclay with biomineralized hydroxyapatite and polycaprolactone (PCL/in situ HAPclay). Representative molecular models of polymer nanocomposite system are systematically developed using molecular dynamics (MD) technique and successfully validated using material characterization techniques. The constant force steered molecular dynamics (fSMD) simulation results indicate a two-phase nanomechanical behavior of the polymer nanocomposite. The MD and fSMD simulations results provide quantitative contributions of molecular interactions between different constituents of representative models and their effect on nanomechanical responses of nanoclay based polymer nanocomposite system. A finite element (FE) model of PCL/in situ HAPclay scaffold is built using micro-computed tomography images and bridging the nanomechanical properties obtained from fSMD simulations into the FE model. A new reduction factor, K is introduced into modeling results to consider the effect of wall porosity of the polymer scaffold. The effect of accelerated degradation under alkaline conditions and human osteoblast cells culture on the evolution of mechanical properties of scaffolds are studied and the damage mechanics based analytical models are developed. Finally, the novel multiscale models are developed that incorporate the complex molecular and microstructural properties, mechanical properties at nanoscale and structural levels and mechanical properties evolution during degradation and tissue formation in the polymer nanocomposite scaffold. Overall, this study provides a leap into methodologies for in silico design of biomaterials for bone tissue engineering applications. Furthermore, as a part of this work, a molecular dynamics study of rice DNA in the presence of single walled carbon nanotube is carried out to understand the role played by molecular interactions in the conformation changes of rice DNA. The simulations results showed wrapping of DNA onto SWCNT, breaking and forming of hydrogen bonds due to unzipping of Watson-Crick (WC) nucleobase pairs and forming of new non-WC nucleobase pairs in DNA.

Computational Methods for Structural Mechanics and Dynamics

NASA Technical Reports Server (NTRS)

Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)

1989-01-01

Topics addressed include: transient dynamics; transient finite element method; transient analysis in impact and crash dynamic studies; multibody computer codes; dynamic analysis of space structures; multibody mechanics and manipulators; spatial and coplanar linkage systems; flexible body simulation; multibody dynamics; dynamical systems; and nonlinear characteristics of joints.

Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube.

PubMed

Duster, Adam W; Lin, Hai

2017-09-14

Recently, a collective variable "proton indicator" was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore. This is consistent with an earlier study that employed a multistate empirical valence bond potential and a different representation (center of excess charge) of the proton. We attribute this water recruitment to the delocalized nature of the solvated proton, which prefers to be in high-dielectric bulk solvent. While water recruitment into the pore is considered an artifact in the present simulations (because of the artificially imposed restraint on the proton), if the proton were naturally restrained, it could assist in building water wires prior to proton transfer through the pore. The potential of mean force for a proton translocation through the water-filled pore was computed by umbrella sampling, where the bias potentials were applied to the proton indicator. The free energy curve and barrier heights agree reasonably with those in the literature. The results suggest that the proton indicator can be used as a reaction coordinate in simulations of proton transport in confined environments.

Blocking Mechanism Study of Self-Compacting Concrete Based on Discrete Element Method

NASA Astrophysics Data System (ADS)

Zhang, Xuan; Li, Zhida; Zhang, Zhihua

2017-11-01

In order to study the influence factors of blocking mechanism of Self-Compaction Concrete (SCC), Roussel’s granular blocking model was verified and extended by establishing the discrete element model of SCC. The influence of different parameters on the filling capacity and blocking mechanism of SCC were also investigated. The results showed that: it was feasible to simulate the blocking mechanism of SCC by using Discrete Element Method (DEM). The passing ability of pebble aggregate was superior to the gravel aggregate and the passing ability of hexahedron particles was bigger than tetrahedron particles, while the tetrahedron particle simulation results were closer to the actual situation. The flow of SCC as another significant factor affected the passing ability that with the flow increased, the passing ability increased. The correction coefficient λ of the steel arrangement (channel section shape) and flow rate γ in the block model were introduced that the value of λ was 0.90-0.95 and the maximum casting rate was 7.8 L/min.

Nanoscale deicing by molecular dynamics simulation.

PubMed

Xiao, Senbo; He, Jianying; Zhang, Zhiliang

2016-08-14

Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.

Grasping synergies: A motor-control approach to the mirror neuron mechanism

NASA Astrophysics Data System (ADS)

D'Ausilio, Alessandro; Bartoli, Eleonora; Maffongelli, Laura

2015-03-01

The discovery of mirror neurons revived interest in motor theories of perception, fostering a number of new studies as well as controversies. In particular, the degree of motor specificity with which others' actions are simulated is highly debated. Human corticospinal excitability studies support the conjecture that a mirror mechanism encodes object-directed goals or low-level kinematic features of others' reaching and grasping actions. These interpretations lead to different experimental predictions and implications for the functional role of the simulation of others' actions. We propose that the representational granularity of the mirror mechanism cannot be any different from that of the motor system during action execution. Hence, drawing from motor control models, we propose that the building blocks of the mirror mechanism are the relatively few motor synergies explaining the variety of hand functions. The recognition of these synergies, from action observation, can be potentially very robust to visual noise and thus demonstrate a clear advantage of using motor knowledge for classifying others' action.

Shock-induced poration, cholesterol flip-flop and small interfering RNA transfection in a phospholipid membrane: Multimillion atom, microsecond molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Choubey, Amit

Biological cell membranes provide mechanical stability to cells and understanding their structure, dynamics and mechanics are important biophysics problems. Experiments coupled with computational methods such as molecular dynamics (MD) have provided insight into the physics of membranes. We use long-time and large-scale MD simulations to study the structure, dynamics and mechanical behavior of membranes. We investigate shock-induced collapse of nanobubbles in water using MD simulations based on a reactive force field. We observe a focused jet at the onset of bubble shrinkage and a secondary shock wave upon bubble collapse. The jet length scales linearly with the nanobubble radius, as observed in experiments on micron-to-millimeter size bubbles. Shock induces dramatic structural changes, including an ice-VII-like structural motif at a particle velocity of 1 km/s. The incipient ice VII formation and the calculated Hugoniot curve are in good agreement with experimental results. We also investigate molecular mechanisms of poration in lipid bilayers due to shock-induced collapse of nanobubbles. Our multimillion-atom MD simulations reveal that the jet impact generates shear flow of water on bilayer leaflets and pressure gradients across them. This transiently enhances the bilayer permeability by creating nanopores through which water molecules translocate rapidly across the bilayer. Effects of nanobubble size and temperature on the porosity of lipid bilayers are examined. The second research project focuses on cholesterol (CHOL) dynamics in phospholipid bilayers. Several experimental and computational studies have been performed on lipid bilayers consisting of dipalmitoylphosphatidylcholine (DPPC) and CHOL molecules. CHOL interleaflet transport (flip-flop) plays an important role in interleaflet coupling and determining CHOL flip-flop rate has been elusive. Various studies report that the rate ranges between milliseconds to seconds. We calculate CHOL flip-flop rates by performing a 15 mus all-atom MD simulation of a DPPC-CHOL bilayer. We find that the CHOL flip-flop rates are on the sub microsecond timescale. These results are verified by performing various independent parallel replica (PR) simulations. Our PR simulations provide significant boost in sampling of the flip-flop events. We observe that the CHOL flip-flop can induce membrane order, regulate membrane-bending energy, and facilitate membrane relaxation. The rapid flip-flop rates reported here have important implications for the role of CHOL in mechanical properties of cell membranes, formation of domains, and maintaining CHOL concentration asymmetry in plasma membrane. Our PR approach can reach submillisecond time scales and bridge the gap between MD simulations and Nuclear Magnetic Resonance (NMR) experiments on CHOL flip-flop dynamics in membranes. The last project deals with transfection barriers encountered by a bare small interfering RNA (siRNA) in a phospholipid bilayer. SiRNA molecules play a pivotal role in therapeutic applications. A key limitation to the widespread implementation of siRNA-based therapeutics is the difficulty of delivering siRNA-based drugs to cells. We have examined structural and mechanical barriers to siRNA passage across a phospholipid bilayer using all-atom MD simulations. We find that the electrostatic interaction between the anionic siRNA and head groups of phospholipid molecules induces a phase transformation from the liquid crystalline to ripple phase. Steered MD simulations reveal that the siRNA transfection through the ripple phase requires a force of ˜ 1.5 nN.

Numerical simulation of particle jet formation induced by shock wave acceleration in a Hele-Shaw cell

NASA Astrophysics Data System (ADS)

Osnes, A. N.; Vartdal, M.; Pettersson Reif, B. A.

2018-05-01

The formation of jets from a shock-accelerated cylindrical shell of particles, confined in a Hele-Shaw cell, is studied by means of numerical simulation. A number of simulations have been performed, systematically varying the coupling between the gas and solid phases in an effort to identify the primary mechanism(s) responsible for jet formation. We find that coupling through drag is sufficient for the formation of jets. Including the effect of particle volume fraction and particle collisions did not alter the general behaviour, but had some influence on the length, spacing and number of jets. Furthermore, we find that the jet selection process starts early in the dispersal process, during the initial expansion of the particle layer.

Finite element analysis of pedestrian lower limb fractures by direct force: the result of being run over or impact?

PubMed

Li, Zhengdong; Zou, Donghua; Liu, Ningguo; Zhong, Liangwei; Shao, Yu; Wan, Lei; Huang, Ping; Chen, Yijiu

2013-06-10

The elucidation and prediction of the biomechanics of lower limb fractures could serve as a useful tool in forensic practices. Finite element (FE) analysis could potentially help in the understanding of the fracture mechanisms of lower limb fractures frequently caused by car-pedestrian accidents. Our aim was (1) to develop and validate a FE model of the human lower limb, (2) to assess the biomechanics of specific injuries concerning run-over and impact loading conditions, and (3) to reconstruct one real car-pedestrian collision case using the model created in this study. We developed a novel lower limb FE model and simulated three different loading scenarios. The geometry of the model was reconstructed using Mimics 13.0 based on computed tomography (CT) scans from an actual traffic accident. The material properties were based upon a synthesis of data found in published literature. The FE model validation and injury reconstruction were conducted using the LS-DYNA code. The FE model was validated by a comparison of the simulation results of three-point bending, overall lateral impact tests and published postmortem human surrogate (PMHS) results. Simulated loading scenarios of running-over the thigh with a wheel, the impact on the upper leg, and impact on the lower thigh were conducted with velocities of 10 m/s, 20 m/s, and 40 m/s, respectively. We compared the injuries resulting from one actual case with the simulated results in order to explore the possible fracture bio-mechanism. The peak fracture forces, maximum bending moments, and energy lost ratio exhibited no significant differences between the FE simulations and the literature data. Under simulated run-over conditions, the segmental fracture pattern was formed and the femur fracture patterns and mechanisms were consistent with the actual injury features of the case. Our study demonstrated that this simulation method could potentially be effective in identifying forensic cases and exploring of the injury mechanisms of lower limb fractures encountered due to inflicted lesions. This model can also help to distinguish between possible and impossible scenarios. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter

NASA Astrophysics Data System (ADS)

Wang, Li-Ying; Ravi, Vidhya M.; Leblanc, Gérard; Padrós, Esteve; Cladera, Josep; Perálvarez-Marín, Alex

2016-09-01

Molecular dynamics simulations have been used to study the alternate access mechanism of the melibiose transporter from Escherichia coli. Starting from the outward-facing partially occluded form, 2 out of 12 simulations produced an outward full open form and one partially open, whereas the rest yielded fully or partially occluded forms. The shape of the outward-open form resembles other outward-open conformations of secondary transporters. During the transporter opening, conformational changes in some loops are followed by changes in the periplasm region of transmembrane helix 7. Helical curvature relaxation and unlocking of hydrophobic and ionic locks promote the outward opening of the transporter making accessible the substrate binding site. In particular, FRET studies on mutants of conserved aromatic residues of extracellular loop 4 showed lack of substrate binding, emphasizing the importance of this loop for making crucial interactions that control the opening of the periplasmic side. This study indicates that the alternate access mechanism for the melibiose transporter fits better into a flexible gating mechanism rather than the archetypical helical rigid-body rocker-switch mechanism.

Constraining physical parameters of ultra-fast outflows in PDS 456 with Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Hagino, K.; Odaka, H.; Done, C.; Gandhi, P.; Takahashi, T.

2014-07-01

Deep absorption lines with extremely high velocity of ˜0.3c observed in PDS 456 spectra strongly indicate the existence of ultra-fast outflows (UFOs). However, the launching and acceleration mechanisms of UFOs are still uncertain. One possible way to solve this is to constrain physical parameters as a function of distance from the source. In order to study the spatial dependence of parameters, it is essential to adopt 3-dimensional Monte Carlo simulations that treat radiation transfer in arbitrary geometry. We have developed a new simulation code of X-ray radiation reprocessed in AGN outflow. Our code implements radiative transfer in 3-dimensional biconical disk wind geometry, based on Monte Carlo simulation framework called MONACO (Watanabe et al. 2006, Odaka et al. 2011). Our simulations reproduce FeXXV and FeXXVI absorption features seen in the spectra. Also, broad Fe emission lines, which reflects the geometry and viewing angle, is successfully reproduced. By comparing the simulated spectra with Suzaku data, we obtained constraints on physical parameters. We discuss launching and acceleration mechanisms of UFOs in PDS 456 based on our analysis.

Effect of Particle Shape on Mechanical Behaviors of Rocks: A Numerical Study Using Clumped Particle Model

PubMed Central

Rong, Guan; Liu, Guang; Zhou, Chuang-bing

2013-01-01

Since rocks are aggregates of mineral particles, the effect of mineral microstructure on macroscopic mechanical behaviors of rocks is inneglectable. Rock samples of four different particle shapes are established in this study based on clumped particle model, and a sphericity index is used to quantify particle shape. Model parameters for simulation in PFC are obtained by triaxial compression test of quartz sandstone, and simulation of triaxial compression test is then conducted on four rock samples with different particle shapes. It is seen from the results that stress thresholds of rock samples such as crack initiation stress, crack damage stress, and peak stress decrease with the increasing of the sphericity index. The increase of sphericity leads to a drop of elastic modulus and a rise in Poisson ratio, while the decreasing sphericity usually results in the increase of cohesion and internal friction angle. Based on volume change of rock samples during simulation of triaxial compression test, variation of dilation angle with plastic strain is also studied. PMID:23997677

Effect of particle shape on mechanical behaviors of rocks: a numerical study using clumped particle model.

PubMed

Rong, Guan; Liu, Guang; Hou, Di; Zhou, Chuang-Bing

2013-01-01

Since rocks are aggregates of mineral particles, the effect of mineral microstructure on macroscopic mechanical behaviors of rocks is inneglectable. Rock samples of four different particle shapes are established in this study based on clumped particle model, and a sphericity index is used to quantify particle shape. Model parameters for simulation in PFC are obtained by triaxial compression test of quartz sandstone, and simulation of triaxial compression test is then conducted on four rock samples with different particle shapes. It is seen from the results that stress thresholds of rock samples such as crack initiation stress, crack damage stress, and peak stress decrease with the increasing of the sphericity index. The increase of sphericity leads to a drop of elastic modulus and a rise in Poisson ratio, while the decreasing sphericity usually results in the increase of cohesion and internal friction angle. Based on volume change of rock samples during simulation of triaxial compression test, variation of dilation angle with plastic strain is also studied.

An atomic finite element model for biodegradable polymers. Part 2. A model for change in Young's modulus due to polymer chain scission.

PubMed

Gleadall, Andrew; Pan, Jingzhe; Kruft, Marc-Anton

2015-11-01

Atomic simulations were undertaken to analyse the effect of polymer chain scission on amorphous poly(lactide) during degradation. Many experimental studies have analysed mechanical properties degradation but relatively few computation studies have been conducted. Such studies are valuable for supporting the design of bioresorbable medical devices. Hence in this paper, an Effective Cavity Theory for the degradation of Young's modulus was developed. Atomic simulations indicated that a volume of reduced-stiffness polymer may exist around chain scissions. In the Effective Cavity Theory, each chain scission is considered to instantiate an effective cavity. Finite Element Analysis simulations were conducted to model the effect of the cavities on Young's modulus. Since polymer crystallinity affects mechanical properties, the effect of increases in crystallinity during degradation on Young's modulus is also considered. To demonstrate the ability of the Effective Cavity Theory, it was fitted to several sets of experimental data for Young's modulus in the literature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Summer Work Experience: Determining Methane Combustion Mechanisms and Sub-Scale Diffuser Properties for Space Transporation System Engine Testing

NASA Technical Reports Server (NTRS)

Williams, Powtawche N.

1998-01-01

To assess engine performance during the testing of Space Shuttle Main Engines (SSMEs), the design of an optimal altitude diffuser is studied for future Space Transportation Systems (STS). For other Space Transportation Systems, rocket propellant using kerosene is also studied. Methane and dodecane have similar reaction schemes as kerosene, and are used to simulate kerosene combustion processes at various temperatures. The equations for the methane combustion mechanism at high temperature are given, and engine combustion is simulated on the General Aerodynamic Simulation Program (GASP). The successful design of an altitude diffuser depends on the study of a sub-scaled diffuser model tested through two-dimensional (2-D) flow-techniques. Subroutines given calculate the static temperature and pressure at each Mach number within the diffuser flow. Implementing these subroutines into program code for the properties of 2-D compressible fluid flow determines all fluid characteristics, and will be used in the development of an optimal diffuser design.

Photochemical modeling in California with two chemical mechanisms: model intercomparison and response to emission reductions.

PubMed

Cai, Chenxia; Kelly, James T; Avise, Jeremy C; Kaduwela, Ajith P; Stockwell, William R

2011-05-01

An updated version of the Statewide Air Pollution Research Center (SAPRC) chemical mechanism (SAPRC07C) was implemented into the Community Multiscale Air Quality (CMAQ) version 4.6. CMAQ simulations using SAPRC07C and the previously released version, SAPRC99, were performed and compared for an episode during July-August, 2000. Ozone (O3) predictions of the SAPRC07C simulation are generally lower than those of the SAPRC99 simulation in the key areas of central and southern California, especially in areas where modeled concentrations are greater than the federal 8-hr O3 standard of 75 parts per billion (ppb) and/or when the volatile organic compound (VOC)/nitrogen oxides (NOx) ratio is less than 13. The relative changes of ozone production efficiency (OPE) against the VOC/NOx ratio at 46 sites indicate that the OPE is reduced in SAPRC07C compared with SAPRC99 at most sites by as much as approximately 22%. The SAPRC99 and SAPRC07C mechanisms respond similarly to 20% reductions in anthropogenic VOC emissions. The response of the mechanisms to 20% NOx emissions reductions can be grouped into three cases. In case 1, in which both mechanisms show a decrease in daily maximum 8-hr O3 concentration with decreasing NOx emissions, the O3 decrease in SAPRC07C is smaller. In case 2, in which both mechanisms show an increase in O3 with decreasing NOx emissions, the O3 increase is larger in SAPRC07C. In case 3, SAPRC07C simulates an increase in O3 in response to reduced NOx emissions whereas SAPRC99 simulates a decrease in O3 for the same region. As a result, the areas where NOx controls would be disbeneficial are spatially expanded in SAPRC07C. Although the results presented here are valuable for understanding differences in predictions and model response for SAPRC99 and SAPRC07C, the study did not evaluate the impact of mechanism differences in the context of the U.S. Environmental Protection Agency's guidance for using numerical models in demonstrating air quality attainment. Therefore, additional study is required to evaluate the full regulatory implications of upgrading air quality models to SAPRC07.

Elucidating the Activation Mechanism of the Insulin-Family Proteins with Molecular Dynamics Simulations.

PubMed

Papaioannou, Anastasios; Kuyucak, Serdar; Kuncic, Zdenka

2016-01-01

The insulin-family proteins bind to their own receptors, but insulin-like growth factor II (IGF-II) can also bind to the A isoform of the insulin receptor (IR-A), activating unique and alternative signaling pathways from those of insulin. Although extensive studies of insulin have revealed that its activation is associated with the opening of the B chain-C terminal (BC-CT), the activation mechanism of the insulin-like growth factors (IGFs) still remains unknown. Here, we present the first comprehensive study of the insulin-family proteins comparing their activation process and mechanism using molecular dynamics simulations to reveal new insights into their specificity to the insulin receptor. We have found that all the proteins appear to exhibit similar stochastic dynamics in their conformational change to an active state. For the IGFs, our simulations show that activation involves two opening locations: the opening of the BC-CT section away from the core, similar to insulin; and the additional opening of the BC-CT section away from the C domain. Furthermore, we have found that these two openings occur simultaneously in IGF-I, but not in IGF-II, where they can occur independently. This suggests that the BC-CT section and the C domain behave as a unified domain in IGF-I, but as two independent domains in IGF-II during the activation process, implying that the IGFs undergo different activation mechanisms for receptor binding. The probabilities of the active and inactive states of the proteins suggest that IGF-II is hyperactive compared to IGF-I. The hinge residue and the hydrophobic interactions in the core are found to play a critical role in the stability and activity of IGFs. Overall, our simulations have elucidated the crucial differences and similarities in the activation mechanisms of the insulin-family proteins, providing new insights into the molecular mechanisms responsible for the observed differences between IGF-I and IGF-II in receptor binding.

Acceleration of the chemistry solver for modeling DI engine combustion using dynamic adaptive chemistry (DAC) schemes

NASA Astrophysics Data System (ADS)

Shi, Yu; Liang, Long; Ge, Hai-Wen; Reitz, Rolf D.

2010-03-01

Acceleration of the chemistry solver for engine combustion is of much interest due to the fact that in practical engine simulations extensive computational time is spent solving the fuel oxidation and emission formation chemistry. A dynamic adaptive chemistry (DAC) scheme based on a directed relation graph error propagation (DRGEP) method has been applied to study homogeneous charge compression ignition (HCCI) engine combustion with detailed chemistry (over 500 species) previously using an R-value-based breadth-first search (RBFS) algorithm, which significantly reduced computational times (by as much as 30-fold). The present paper extends the use of this on-the-fly kinetic mechanism reduction scheme to model combustion in direct-injection (DI) engines. It was found that the DAC scheme becomes less efficient when applied to DI engine simulations using a kinetic mechanism of relatively small size and the accuracy of the original DAC scheme decreases for conventional non-premixed combustion engine. The present study also focuses on determination of search-initiating species, involvement of the NOx chemistry, selection of a proper error tolerance, as well as treatment of the interaction of chemical heat release and the fuel spray. Both the DAC schemes were integrated into the ERC KIVA-3v2 code, and simulations were conducted to compare the two schemes. In general, the present DAC scheme has better efficiency and similar accuracy compared to the previous DAC scheme. The efficiency depends on the size of the chemical kinetics mechanism used and the engine operating conditions. For cases using a small n-heptane kinetic mechanism of 34 species, 30% of the computational time is saved, and 50% for a larger n-heptane kinetic mechanism of 61 species. The paper also demonstrates that by combining the present DAC scheme with an adaptive multi-grid chemistry (AMC) solver, it is feasible to simulate a direct-injection engine using a detailed n-heptane mechanism with 543 species with practical computer time.

Finite element analysis (FEA) analysis of the preflex beam

NASA Astrophysics Data System (ADS)

Wan, Lijuan; Gao, Qilang

2017-10-01

The development of finite element analysis (FEA) has been relatively mature, and is one of the important means of structural analysis. This method changes the problem that the research of complex structure in the past needs to be done by a large number of experiments. Through the finite element method, the numerical simulation of the structure can be used to achieve a variety of static and dynamic simulation analysis of the mechanical problems, it is also convenient to study the parameters of the structural parameters. Combined with a certain number of experiments to verify the simulation model can be completed in the past all the needs of experimental research. The nonlinear finite element method is used to simulate the flexural behavior of the prestressed composite beams with corrugated steel webs. The finite element analysis is used to understand the mechanical properties of the structure under the action of bending load.

Numerical Simulation and Mechanical Design for TPS Electron Beam Position Monitors

NASA Astrophysics Data System (ADS)

Hsueh, H. P.; Kuan, C. K.; Ueng, T. S.; Hsiung, G. Y.; Chen, J. R.

2007-01-01

Comprehensive study on the mechanical design and numerical simulation for the high resolution electron beam position monitors are key steps to build the newly proposed 3rd generation synchrotron radiation research facility, Taiwan Photon Source (TPS). With more advanced electromagnetic simulation tool like MAFIA tailored specifically for particle accelerator, the design for the high resolution electron beam position monitors can be tested in such environment before they are experimentally tested. The design goal of our high resolution electron beam position monitors is to get the best resolution through sensitivity and signal optimization. The definitions and differences between resolution and sensitivity of electron beam position monitors will be explained. The design consideration is also explained. Prototype deign has been carried out and the related simulations were also carried out with MAFIA. The results are presented here. Sensitivity as high as 200 in x direction has been achieved in x direction at 500 MHz.

Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling.

PubMed

Martins-Costa, Marilia T C; Ruiz-López, Manuel F

2017-04-15

We report an enhanced sampling technique that allows to reach the multi-nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid-vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall-clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Classical Molecular Dynamics Simulation of Nuclear Fuel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

2015-10-10

Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a varietymore » of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.« less

Dynamic simulation of road vehicle door window regulator mechanism of cross arm type

NASA Astrophysics Data System (ADS)

Miklos, I. Zs; Miklos, C.; Alic, C.

2017-01-01

The paper presents issues related to the dynamic simulation of a motor-drive operating mechanism of cross arm type, for the manipulation of road vehicle door windows, using Autodesk Inventor Professional software. The dynamic simulation of the mechanism involves a 3D modelling, kinematic coupling, drive motion parameters and external loads, as well as the graphically view of the kinematic and kinetostatic results for the various elements and kinematic couplings of the mechanism, under real operating conditions. Also, based on the results, the analysis of the mechanism components has been carried out using the finite element method.

Discovering mechanisms relevant for radiation damage evolution

DOE PAGES

Uberuaga, Blas Pedro; Martinez, Enrique Saez; Perez, Danny; ...

2018-02-22

he response of a material to irradiation is a consequence of the kinetic evolution of defects produced during energetic damage events. Thus, accurate predictions of radiation damage evolution require knowing the atomic scale mechanisms associated with those defects. Atomistic simulations are a key tool in providing insight into the types of mechanisms possible. Further, by extending the time scale beyond what is achievable with conventional molecular dynamics, even greater insight can be obtained. Here, we provide examples in which such simulations have revealed new kinetic mechanisms that were not obvious before performing the simulations. We also demonstrate, through the couplingmore » with higher level models, how those mechanisms impact experimental observables in irradiated materials. Lastly, we discuss the importance of these types of simulations in the context of predicting material behavior.« less

Discovering mechanisms relevant for radiation damage evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uberuaga, Blas Pedro; Martinez, Enrique Saez; Perez, Danny

he response of a material to irradiation is a consequence of the kinetic evolution of defects produced during energetic damage events. Thus, accurate predictions of radiation damage evolution require knowing the atomic scale mechanisms associated with those defects. Atomistic simulations are a key tool in providing insight into the types of mechanisms possible. Further, by extending the time scale beyond what is achievable with conventional molecular dynamics, even greater insight can be obtained. Here, we provide examples in which such simulations have revealed new kinetic mechanisms that were not obvious before performing the simulations. We also demonstrate, through the couplingmore » with higher level models, how those mechanisms impact experimental observables in irradiated materials. Lastly, we discuss the importance of these types of simulations in the context of predicting material behavior.« less

Advances in helical stent design and fabrication thermal treatment and structural interaction studies of the simulated plaque-laden artery

NASA Astrophysics Data System (ADS)

Welch, Tre Raymond

Advancements in processing biomaterials have lead to the development of bioresorbable PLLA drug-loaded stents with different geometric configurations. To further advance the technology, systematic studies have been carried out. This dissertation consists of five specific aims: (1) To characterize the effects of thermal annealing on the mechanical characteristics of PLLA helical stent, (2) To characterize the mechanical characteristics of a PLLA double helix stent, (3) To characterize the physical and chemical properties of PLLA films impregnated with niacin and curcumin, (4) To characterize the mechanical interaction of expanded stent and vascular wall with both model simulation and experimental studies using PDMS phantom arteries, (5) To simulate the stent-plaque-artery interactions using computer models. Results and their significances in bioresorbable PLLA drug-loaded stents technology as well as clinical prospects will be presented. For Aim1, thermal annealing is shown to improve mechanical characteristics of the helical stent, including pressure-diameter response curves, incremental stiffness, and collapse pressure. Differential scanning calorimetric analysis of stent fiber reveals that thermal annealing contribute to increased percent crystallinity, thus enhanced mechanical characteristics of the stent. For Aim 2, the new double helix design was shown to leads to improved mechanical characteristics of stent, including pressure-diameter response curves, incremental stiffness, and collapse pressure. Further, it was found to lead to an increased percent crystallinity and reduced degradation rate. For Aim 3, the changes in mechanical properties, crystallinity in PLLA polymer loaded with curcumin, or niacin, or both from that of control are clearly delineated. Results from Aim 4 shed lights on the mechanical disturbance in the vicinity of deployed stent and vascular wall as well as the abnormal shear stresses on the vascular endothelium. Their implications in triggering thrombi formation are discussed. Results from Aim 5 provided insights on the stent-plaque-artery mechanical interaction and how the altered mechanical environment after stent deployment could affect vascular remodeling and factors lead to re-stenosis. The significances of this work in advancing the bioresorbable PLLA drug-loaded stents technology as well as its clinical prospects are presented.

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement.

PubMed

Jiang, Hanlun; Sheong, Fu Kit; Zhu, Lizhe; Gao, Xin; Bernauer, Julie; Huang, Xuhui

2015-07-01

Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. In this study, we propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Our model is based on the results of a combination of Markov State Models (MSMs), large-scale protein-RNA docking, and molecular dynamics (MD) simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are distinguished by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure. Our results provide novel insights in Ago-miRNA recognition mechanisms and our methodology holds great potential to be widely applied in the studies of other important molecular recognition systems.

A design of hardware haptic interface for gastrointestinal endoscopy simulation.

PubMed

Gu, Yunjin; Lee, Doo Yong

2011-01-01

Gastrointestinal endoscopy simulations have been developed to train endoscopic procedures which require hundreds of practices to be competent in the skills. Even though realistic haptic feedback is important to provide realistic sensation to the user, most of previous simulations including commercialized simulation have mainly focused on providing realistic visual feedback. In this paper, we propose a novel design of portable haptic interface, which provides 2DOF force feedback, for the gastrointestinal endoscopy simulation. The haptic interface consists of translational and rotational force feedback mechanism which are completely decoupled, and gripping mechanism for controlling connection between the endoscope and the force feedback mechanism.

An electromechanical based deformable model for soft tissue simulation.

PubMed

Zhong, Yongmin; Shirinzadeh, Bijan; Smith, Julian; Gu, Chengfan

2009-11-01

Soft tissue deformation is of great importance to surgery simulation. Although a significant amount of research efforts have been dedicated to simulating the behaviours of soft tissues, modelling of soft tissue deformation is still a challenging problem. This paper presents a new deformable model for simulation of soft tissue deformation from the electromechanical viewpoint of soft tissues. Soft tissue deformation is formulated as a reaction-diffusion process coupled with a mechanical load. The mechanical load applied to a soft tissue to cause a deformation is incorporated into the reaction-diffusion system, and consequently distributed among mass points of the soft tissue. Reaction-diffusion of mechanical load and non-rigid mechanics of motion are combined to govern the simulation dynamics of soft tissue deformation. An improved reaction-diffusion model is developed to describe the distribution of the mechanical load in soft tissues. A three-layer artificial cellular neural network is constructed to solve the reaction-diffusion model for real-time simulation of soft tissue deformation. A gradient based method is established to derive internal forces from the distribution of the mechanical load. Integration with a haptic device has also been achieved to simulate soft tissue deformation with haptic feedback. The proposed methodology does not only predict the typical behaviours of living tissues, but it also accepts both local and large-range deformations. It also accommodates isotropic, anisotropic and inhomogeneous deformations by simple modification of diffusion coefficients.

Math modeling and computer mechanization for real time simulation of rotary-wing aircraft

NASA Technical Reports Server (NTRS)

Howe, R. M.

1979-01-01

Mathematical modeling and computer mechanization for real time simulation of rotary wing aircraft is discussed. Error analysis in the digital simulation of dynamic systems, such as rotary wing aircraft is described. The method for digital simulation of nonlinearities with discontinuities, such as exist in typical flight control systems and rotor blade hinges, is discussed.

Simulation Using Novel Equipment Designed to Explain Spirometric Abnormalities in Respiratory Disease Enhances Learning in Higher Cognitive Domains

ERIC Educational Resources Information Center

Jamison, J. P.; Stewart, M. T.

2015-01-01

Simulation of disorders of respiratory mechanics shown by spirometry provides insight into the pathophysiology of disease but some clinically important disorders have not been simulated and none have been formally evaluated for education. We have designed simple mechanical devices which, along with existing simulators, enable all the main…

Mechanism change in a simulation of peer review: from junk support to elitism.

PubMed

Paolucci, Mario; Grimaldo, Francisco

2014-01-01

Peer review works as the hinge of the scientific process, mediating between research and the awareness/acceptance of its results. While it might seem obvious that science would regulate itself scientifically, the consensus on peer review is eroding; a deeper understanding of its workings and potential alternatives is sorely needed. Employing a theoretical approach supported by agent-based simulation, we examined computational models of peer review, performing what we propose to call redesign , that is, the replication of simulations using different mechanisms . Here, we show that we are able to obtain the high sensitivity to rational cheating that is present in literature. In addition, we also show how this result appears to be fragile against small variations in mechanisms. Therefore, we argue that exploration of the parameter space is not enough if we want to support theoretical statements with simulation, and that exploration at the level of mechanisms is needed. These findings also support prudence in the application of simulation results based on single mechanisms, and endorse the use of complex agent platforms that encourage experimentation of diverse mechanisms.

Nuclear quantum effects and kinetic isotope effects in enzyme reactions.

PubMed

Vardi-Kilshtain, Alexandra; Nitoker, Neta; Major, Dan Thomas

2015-09-15

Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly specific chemical transformations. Studying the nature of rate enhancements and the mechanistic strategies in enzymes is very important, both from a basic scientific point of view, as well as in order to improve rational design of biomimetics. Kinetic isotope effect (KIE) is a very important tool in the study of chemical reactions and has been used extensively in the field of enzymology. Theoretically, the prediction of KIEs in condensed phase environments such as enzymes is challenging due to the need to include nuclear quantum effects (NQEs). Herein we describe recent progress in our group in the development of multi-scale simulation methods for the calculation of NQEs and accurate computation of KIEs. We also describe their application to several enzyme systems. In particular we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path-integral methods is reviewed. These methods are tailor suited to enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum-classical simulation approach to three case studies is presented. The first case involves the proton transfer in alanine racemase. The second case presented involves orotidine 5'-monophosphate decarboxylase where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine-tuning tool. Copyright © 2015 Elsevier Inc. All rights reserved.

The Simulation of Precipitation Evolutions and Mechanical Properties in Friction Stir Welding with Post-Weld Heat Treatments

NASA Astrophysics Data System (ADS)

Zhang, Z.; Wan, Z. Y.; Lindgren, L.-E.; Tan, Z. J.; Zhou, X.

2017-12-01

A finite element model of friction stir welding capable of re-meshing is used to simulate the temperature variations. Re-meshing of the finite element model is used to maintain a fine mesh resolving the gradients of the solution. The Kampmann-Wagner numerical model for precipitation is then used to study the relation between friction stir welds with post-weld heat treatment (PWHT) and the changes in mechanical properties. Results indicate that the PWHT holding time and PWHT holding temperature need to be optimally designed to obtain FSW with better mechanical properties. Higher precipitate number with lower precipitate sizes gives higher strength in the stirring zone after PWHT. The coarsening of precipitates in HAZ are the main reason to hinder the improvement of mechanical property when PWHT is used.

Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.

PubMed

Mendieta-Moreno, Jesús I; Trabada, Daniel G; Mendieta, Jesús; Lewis, James P; Gómez-Puertas, Paulino; Ortega, José

2016-11-03

The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

Systematic simulations of modified gravity: chameleon models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brax, Philippe; Davis, Anne-Christine; Li, Baojiu

2013-04-01

In this work we systematically study the linear and nonlinear structure formation in chameleon theories of modified gravity, using a generic parameterisation which describes a large class of models using only 4 parameters. For this we have modified the N-body simulation code ecosmog to perform a total of 65 simulations for different models and parameter values, including the default ΛCDM. These simulations enable us to explore a significant portion of the parameter space. We have studied the effects of modified gravity on the matter power spectrum and mass function, and found a rich and interesting phenomenology where the difference withmore » the ΛCDM paradigm cannot be reproduced by a linear analysis even on scales as large as k ∼ 0.05 hMpc{sup −1}, since the latter incorrectly assumes that the modification of gravity depends only on the background matter density. Our results show that the chameleon screening mechanism is significantly more efficient than other mechanisms such as the dilaton and symmetron, especially in high-density regions and at early times, and can serve as a guidance to determine the parts of the chameleon parameter space which are cosmologically interesting and thus merit further studies in the future.« less

Investigations of Tissue-Level Mechanisms of Primary Blast Injury Through Modeling, Simulation, Neuroimaging and Neuropathological Studies

DTIC Science & Technology

2012-07-10

materials used, the complexity of the human anatomy , manufacturing limitations, and analysis capability prohibits exactly matching surrogate material...upper and lower bounds for possible loading behaviour. Although it is impossible to exactly match the human anatomy according to mechanical

A mechanical adapter for installing mission equipment on large space structures

NASA Technical Reports Server (NTRS)

Lefever, A. E.; Totah, R. S.

1980-01-01

A mechanical attachment adapter was designed, constructed, and tested. The adapter was was included in a simulation program that investigated techniques for assembling erectable structures under simulated zero-g conditions by pressure-suited subjects in a simulated EVA mode. The adapter was utilized as an interface attachment between a simulated equipment module and one node point of a tetrahedral structural cell. The mating performance of the adapter, a self-energized mechanism, was easily and quickly demonstrated and required little effort on the part of the test subjects.

Lunar soil properties and soil mechanics

NASA Technical Reports Server (NTRS)

Mitchell, J. K.; Houston, W. N.; Hovland, H. J.

1972-01-01

The study to identify and define recognizable fabrics in lunar soil in order to determine the history of the lunar regolith in different locations is reported. The fabric of simulated lunar soil, and lunar soil samples are discussed along with the behavior of simulated lunar soil under dynamic and static loading. The planned research is also included.

Investigation of blast-induced traumatic brain injury.

PubMed

Taylor, Paul A; Ludwigsen, John S; Ford, Corey C

2014-01-01

Many troops deployed in Iraq and Afghanistan have sustained blast-related, closed-head injuries from being within non-lethal distance of detonated explosive devices. Little is known, however, about the mechanisms associated with blast exposure that give rise to traumatic brain injury (TBI). This study attempts to identify the precise conditions of focused stress wave energy within the brain, resulting from blast exposure, which will correlate with a threshold for persistent brain injury. This study developed and validated a set of modelling tools to simulate blast loading to the human head. Using these tools, the blast-induced, early-time intracranial wave motions that lead to focal brain damage were simulated. The simulations predict the deposition of three distinct wave energy components, two of which can be related to injury-inducing mechanisms, namely cavitation and shear. Furthermore, the results suggest that the spatial distributions of these damaging energy components are independent of blast direction. The predictions reported herein will simplify efforts to correlate simulation predictions with clinical measures of TBI and aid in the development of protective headwear.

Investigation of blast-induced traumatic brain injury

PubMed Central

Ludwigsen, John S.; Ford, Corey C.

2014-01-01

Objective Many troops deployed in Iraq and Afghanistan have sustained blast-related, closed-head injuries from being within non-lethal distance of detonated explosive devices. Little is known, however, about the mechanisms associated with blast exposure that give rise to traumatic brain injury (TBI). This study attempts to identify the precise conditions of focused stress wave energy within the brain, resulting from blast exposure, which will correlate with a threshold for persistent brain injury. Methods This study developed and validated a set of modelling tools to simulate blast loading to the human head. Using these tools, the blast-induced, early-time intracranial wave motions that lead to focal brain damage were simulated. Results The simulations predict the deposition of three distinct wave energy components, two of which can be related to injury-inducing mechanisms, namely cavitation and shear. Furthermore, the results suggest that the spatial distributions of these damaging energy components are independent of blast direction. Conclusions The predictions reported herein will simplify efforts to correlate simulation predictions with clinical measures of TBI and aid in the development of protective headwear. PMID:24766453

Researcher and Mechanic with Solar Collector in Solar Simulator Cell

NASA Image and Video Library

1976-08-21

Researcher Susan Johnson and a mechanic examine a flat-plate solar collector in the Solar Simulator Cell in the High Temperature Composites Laboratory at the National Aeronautics and Space Administration (NASA) Lewis Research Center. The Solar Simulator Cell allowed the researchers to control the radiation levels, air temperature, airflow, and fluid flow. The flat-plate collector, seen in a horizontal position here, was directed at the solar simulator, seen above Johnson, during the tests. Lewis researchers were studying the efficiency of various flat- plate solar collector designs in the 1970s for temperature control systems in buildings. The collectors consisted of a cover material, absorber plate, and parallel flow configuration. The collector’s absorber material and coating, covers, honeycomb material, mirrors, vacuum, and tube attachment could all be modified. Johnson’s study analyzed 35 collectors. Johnson, a lifelong pilot, joined NASA Lewis in 1974. The flat-plate solar collectors, seen here, were her first research project. Johnson also investigated advanced heat engines for general aviation and evaluated variable geometry combustors and liners. Johnson earned the Cleveland Technical Society’s Technical Achievement Award in 1984.

Molecular dynamics simulations of methane hydrate decomposition.

PubMed

Myshakin, Evgeniy M; Jiang, Hao; Warzinski, Robert P; Jordan, Kenneth D

2009-03-12

Molecular dynamics simulations have been carried out to study decomposition of methane hydrate at different cage occupancies. The decomposition rate is found to depend sensitively on the hydration number. The rate of the destruction of the cages displays Arrhenius behavior, consistent with an activated mechanism. During the simulations, reversible formation of partial water cages around methane molecules in the liquid was observed at the interface at temperatures above the computed hydrate decomposition temperature.

Mechanical versus kinematical shortening reconstructions of the Zagros High Folded Zone (Kurdistan Region of Iraq)

NASA Astrophysics Data System (ADS)

Frehner, M.; Reif, D.; Grasemann, B.

2012-04-01

Our study compares kinematical and mechanical techniques for the palinspastic reconstruction of folded cross-sections in collision orogens. The studied area and the reconstructed NE-SW-trending, 55.5 km long cross-section is located in the High Folded Zone of the Zagros fold-and-thrust belt in the Kurdistan Region of Iraq. The present-day geometry of the cross-section has been constructed from field, as well as remote sensing data. In a first step, the structures and the stratigraphy are simplified and summarized in eight units trying to identify the main geometric and mechanical parameters. In a second step, the shortening is kinematically estimated using the dip-domain method to 11%-15%. Then the same cross-section is used in a numerical finite-element model to perform dynamical unfolding simulations taking various rheological parameters into account. The main factor allowing for an efficient dynamic unfolding is the presence of interfacial slip conditions between the mechanically strong units. Other factors, such as Newtonian vs. power-law viscous rheology or the presence of a basement affect the numerical simulations much less strongly. If interfacial slip is accounted for, fold amplitudes are reduced efficiently during the dynamical unfolding simulations, while welded layer interfaces lead to unrealistic shortening estimates. It is suggested that interfacial slip and decoupling of the deformation along detachment horizons is an important mechanical parameter that controlled the folding processes in the Zagros High Folded Zone.

Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path–Force Matching QM/MM Method

PubMed Central

Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; Pu, J.

2016-01-01

Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are ubiquitous ATP-dependent membrane proteins involved in translocations of a wide variety of substrates across cellular membranes. To understand the chemomechanical coupling mechanism as well as functional asymmetry in these systems, a quantitative description of how ABC transporters hydrolyze ATP is needed. Complementary to experimental approaches, computer simulations based on combined quantum mechanical and molecular mechanical (QM/MM) potentials have provided new insights into the catalytic mechanism in ABC transporters. Quantitatively reliable determination of the free energy requirement for enzymatic ATP hydrolysis, however, requires substantial statistical sampling on QM/MM potential. A case study shows that brute force sampling of ab initio QM/MM (AI/MM) potential energy surfaces is computationally impractical for enzyme simulations of ABC transporters. On the other hand, existing semiempirical QM/MM (SE/MM) methods, although affordable for free energy sampling, are unreliable for studying ATP hydrolysis. To close this gap, a multiscale QM/MM approach named reaction path–force matching (RP–FM) has been developed. In RP–FM, specific reaction parameters for a selected SE method are optimized against AI reference data along reaction paths by employing the force matching technique. The feasibility of the method is demonstrated for a proton transfer reaction in the gas phase and in solution. The RP–FM method may offer a general tool for simulating complex enzyme systems such as ABC transporters. PMID:27498639

The effect of electronically steering a phased array ultrasound transducer on near-field tissue heating.

PubMed

Payne, Allison; Vyas, Urvi; Todd, Nick; de Bever, Joshua; Christensen, Douglas A; Parker, Dennis L

2011-09-01

This study presents the results obtained from both simulation and experimental techniques that show the effect of mechanically or electronically steering a phased array transducer on proximal tissue heating. The thermal response of a nine-position raster and a 16-mm diameter circle scanning trajectory executed through both electronic and mechanical scanning was evaluated in computer simulations and experimentally in a homogeneous tissue-mimicking phantom. Simulations were performed using power deposition maps obtained from the hybrid angular spectrum (HAS) method and applying a finite-difference approximation of the Pennes' bioheat transfer equation for the experimentally used transducer and also for a fully sampled transducer to demonstrate the effect of acoustic window, ultrasound beam overlap and grating lobe clutter on near-field heating. Both simulation and experimental results show that electronically steering the ultrasound beam for the two trajectories using the 256-element phased array significantly increases the thermal dose deposited in the near-field tissues when compared with the same treatment executed through mechanical steering only. In addition, the individual contributions of both beam overlap and grating lobe clutter to the near-field thermal effects were determined through comparing the simulated ultrasound beam patterns and resulting temperature fields from mechanically and electronically steered trajectories using the 256-randomized element phased array transducer to an electronically steered trajectory using a fully sampled transducer with 40 401 phase-adjusted sample points. Three distinctly different three distinctly different transducers were simulated to analyze the tradeoffs of selected transducer design parameters on near-field heating. Careful consideration of design tradeoffs and accurate patient treatment planning combined with thorough monitoring of the near-field tissue temperature will help to ensure patient safety during an MRgHIFU treatment.

Floating gastroretentive drug delivery systems: Comparison of experimental and simulated dissolution profiles and floatation behavior.

PubMed

Eberle, Veronika A; Schoelkopf, Joachim; Gane, Patrick A C; Alles, Rainer; Huwyler, Jörg; Puchkov, Maxim

2014-07-16

Gastroretentive drug delivery systems (GRDDS) play an important role in the delivery of drug substances to the upper part of the gastrointestinal tract; they offer a possibility to overcome the limited gastric residence time of conventional dosage forms. The aim of the study was to understand drug-release and floatation mechanisms of a floating GRDDS based on functionalized calcium carbonate (FCC). The inherently low apparent density of the excipient (approx. 0.6 g/cm(3)) enabled a mechanism of floatation. The higher specific surface of FCC (approx. 70 m(2)) allowed sufficient hardness of resulting compacts. The floating mechanism of GRDDS was simulated in silico under simulated acidic and neutral conditions, and the results were compared to those obtained in vitro. United States Pharmacopeia (USP) dissolution methods are of limited usefulness for evaluating floating behavior and drug release of floating dosage forms. Therefore, we developed a custom-built stomach model to simultaneously analyze floating characteristics and drug release. In silico dissolution and floatation profiles of the FCC-based tablet were simulated using a three-dimensional cellular automata-based model. In simulated gastric fluid, the FCC-based tablets showed instant floatation. The compacts stayed afloat during the measurement in 0.1 N HCl and eroded completely while releasing the model drug substance. When water was used as dissolution medium, the tablets had no floating lag time and sank down during the measurement, resulting in a change of release kinetics. Floating dosage forms based on FCC appear promising. It was possible to manufacture floating tablets featuring a density of less than unity and sufficient hardness for further processing. In silico dissolution simulation offered a possibility to understand floating behavior and drug-release mechanism. Copyright © 2014 Elsevier B.V. All rights reserved.

Hydro-mechanical model for wetting/drying and fracture development in geomaterials

DOE PAGES

Asahina, D.; Houseworth, J. E.; Birkholzer, J. T.; ...

2013-12-28

This study presents a modeling approach for studying hydro-mechanical coupled processes, including fracture development, within geological formations. This is accomplished through the novel linking of two codes: TOUGH2, which is a widely used simulator of subsurface multiphase flow based on the finite volume method; and an implementation of the Rigid-Body-Spring Network (RBSN) method, which provides a discrete (lattice) representation of material elasticity and fracture development. The modeling approach is facilitated by a Voronoi-based discretization technique, capable of representing discrete fracture networks. The TOUGH–RBSN simulator is intended to predict fracture evolution, as well as mass transport through permeable media, under dynamicallymore » changing hydrologic and mechanical conditions. Numerical results are compared with those of two independent studies involving hydro-mechanical coupling: (1) numerical modeling of swelling stress development in bentonite; and (2) experimental study of desiccation cracking in a mining waste. The comparisons show good agreement with respect to moisture content, stress development with changes in pore pressure, and time to crack initiation. Finally, the observed relationship between material thickness and crack patterns (e.g., mean spacing of cracks) is captured by the proposed modeling approach.« less

Numerical Study on Alternating Current Breakdown Mechanism Between Sphere-Sphere Electrodes in Transformer Oil-Based Magnetic Nanofluids.

PubMed

Lee, Won-Ho; Lee, Jong-Chul

2018-09-01

A numerical simulation was developed for magnetic nanoparticles in a liquid dielectric to investigate the AC breakdown voltage of the magnetic nanofluids according to the volume concentration of the magnetic nanoparticles. In prior research, we found that the dielectric breakdown voltage of the transformer oil-based magnetic nanofluids was positively or negatively affected according to the amount of magnetic nanoparticles under a testing condition of dielectric fluids, and the trajectory of the magnetic nanoparticles in a fabricated chip was visualized to verify the related phenomena via measurements and computations. In this study, a numerical simulation of magnetic nanoparticles in an insulating fluid was developed to model particle tracing for AC breakdown mechanisms happened to a sphere-sphere electrode configuration and to propose a possible mechanism regarding the change in the breakdown strength due to the behavior of the magnetic nanoparticles with different applied voltages.

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

PubMed Central

Kuzmanic, Antonija; Sutto, Ludovico; Saladino, Giorgio; Nebreda, Angel R; Gervasio, Francesco L; Orozco, Modesto

2017-01-01

p38α is a Ser/Thr protein kinase involved in a variety of cellular processes and pathological conditions, which makes it a promising pharmacological target. Although the activity of the enzyme is highly regulated, its molecular mechanism of activation remains largely unexplained, even after decades of research. By using state-of-the-art molecular dynamics simulations, we decipher the key elements of the complex molecular mechanism refined by evolution to allow for a fine tuning of p38α kinase activity. Our study describes for the first time the molecular effects of different regulators of the enzymatic activity, and provides an integrative picture of the activation mechanism that explains the seemingly contradictory X-ray and NMR data. DOI: http://dx.doi.org/10.7554/eLife.22175.001 PMID:28445123

Process simulation and dynamic control for marine oily wastewater treatment using UV irradiation.

PubMed

Jing, Liang; Chen, Bing; Zhang, Baiyu; Li, Pu

2015-09-15

UV irradiation and advanced oxidation processes have been recently regarded as promising solutions in removing polycyclic aromatic hydrocarbons (PAHs) from marine oily wastewater. However, such treatment methods are generally not sufficiently understood in terms of reaction mechanisms, process simulation and process control. These deficiencies can drastically hinder their application in shipping and offshore petroleum industries which produce bilge/ballast water and produced water as the main streams of marine oily wastewater. In this study, the factorial design of experiment was carried out to investigate the degradation mechanism of a typical PAH, namely naphthalene, under UV irradiation in seawater. Based on the experimental results, a three-layer feed-forward artificial neural network simulation model was developed to simulate the treatment process and to forecast the removal performance. A simulation-based dynamic mixed integer nonlinear programming (SDMINP) approach was then proposed to intelligently control the treatment process by integrating the developed simulation model, genetic algorithm and multi-stage programming. The applicability and effectiveness of the developed approach were further tested though a case study. The experimental results showed that the influences of fluence rate and temperature on the removal of naphthalene were greater than those of salinity and initial concentration. The developed simulation model could well predict the UV-induced removal process under varying conditions. The case study suggested that the SDMINP approach, with the aid of the multi-stage control strategy, was able to significantly reduce treatment cost when comparing to the traditional single-stage process optimization. The developed approach and its concept/framework have high potential of applicability in other environmental fields where a treatment process is involved and experimentation and modeling are used for process simulation and control. Copyright © 2015 Elsevier Ltd. All rights reserved.

The mechanisms of labor division from the perspective of individual optimization

NASA Astrophysics Data System (ADS)

Zhu, Lirong; Chen, Jiawei; Di, Zengru; Chen, Liujun; Liu, Yan; Stanley, H. Eugene

2017-12-01

Although the tools of complexity research have been applied to the phenomenon of labor division, its underlying mechanisms are still unclear. Researchers have used evolutionary models to study labor division in terms of global optimization, but focusing on individual optimization is a more realistic, real-world approach. We do this by first developing a multi-agent model that takes into account information-sharing and learning-by-doing and by using simulations to demonstrate the emergence of labor division. We then use a master equation method and find that the computational results are consistent with the results of the simulation. Finally we find that the core underlying mechanisms that cause labor division are learning-by-doing, information cost, and random fluctuation.

Thermo-Mechanical Analyses of Dynamically Loaded Rubber Cylinders

NASA Technical Reports Server (NTRS)

Johnson, Arthur R.; Chen, Tzi-Kang

2002-01-01

Thick rubber components are employed by the Army to carry large loads. In tanks, rubber covers road wheels and track systems to protect roadways. It is difficult for design engineers to simulate the details of the hysteretic heating for large strain viscoelastic deformations. In this study, an approximation to the viscoelastic energy dissipated per unit time is investigated for use in estimating mechanically induced viscoelastic heating. Coupled thermo-mechanical simulations of large cyclic deformations of rubber cylinders are presented. The cylinders are first compressed axially and then cyclically loaded about the compressed state. Details of the algorithm and some computational issues are discussed. The coupled analyses are conducted for tall and short rubber cylinders both with and without imbedded metal disks.

Simulation in production of open rotor propellers: from optimal surface geometry to automated control of mechanical treatment

NASA Astrophysics Data System (ADS)

Grinyok, A.; Boychuk, I.; Perelygin, D.; Dantsevich, I.

2018-03-01

A complex method of the simulation and production design of open rotor propellers was studied. An end-to-end diagram was proposed for the evaluating, designing and experimental testing the optimal geometry of the propeller surface, for the machine control path generation as well as for simulating the cutting zone force condition and its relationship with the treatment accuracy which was defined by the propeller elastic deformation. The simulation data provided the realization of the combined automated path control of the cutting tool.

Investigations in mechanisms and strategies to enhance hearing with cochlear implants

NASA Astrophysics Data System (ADS)

Churchill, Tyler H.

Cochlear implants (CIs) produce hearing sensations by stimulating the auditory nerve (AN) with current pulses whose amplitudes are modulated by filtered acoustic temporal envelopes. While this technology has provided hearing for multitudinous CI recipients, even bilaterally-implanted listeners have more difficulty understanding speech in noise and localizing sounds than normal hearing (NH) listeners. Three studies reported here have explored ways to improve electric hearing abilities. Vocoders are often used to simulate CIs for NH listeners. Study 1 was a psychoacoustic vocoder study examining the effects of harmonic carrier phase dispersion and simulated CI current spread on speech intelligibility in noise. Results showed that simulated current spread was detrimental to speech understanding and that speech vocoded with carriers whose components' starting phases were equal was the least intelligible. Cross-correlogram analyses of AN model simulations confirmed that carrier component phase dispersion resulted in better neural envelope representation. Localization abilities rely on binaural processing mechanisms in the brainstem and mid-brain that are not fully understood. In Study 2, several potential mechanisms were evaluated based on the ability of metrics extracted from stereo AN simulations to predict azimuthal locations. Results suggest that unique across-frequency patterns of binaural cross-correlation may provide a strong cue set for lateralization and that interaural level differences alone cannot explain NH sensitivity to lateral position. While it is known that many bilateral CI users are sensitive to interaural time differences (ITDs) in low-rate pulsatile stimulation, most contemporary CI processing strategies use high-rate, constant-rate pulse trains. In Study 3, we examined the effects of pulse rate and pulse timing on ITD discrimination, ITD lateralization, and speech recognition by bilateral CI listeners. Results showed that listeners were able to use low-rate pulse timing cues presented redundantly on multiple electrodes for ITD discrimination and lateralization of speech stimuli even when mixed with high rates on other electrodes. These results have contributed to a better understanding of those aspects of the auditory system that support speech understanding and binaural hearing, suggested vocoder parameters that may simulate aspects of electric hearing, and shown that redundant, low-rate pulse timing supports improved spatial hearing for bilateral CI listeners.

Modeling and Performance Improvement of the Constant Power Regulator Systems in Variable Displacement Axial Piston Pump

PubMed Central

Park, Sung Hwan; Lee, Ji Min; Kim, Jong Shik

2013-01-01

An irregular performance of a mechanical-type constant power regulator is considered. In order to find the cause of an irregular discharge flow at the cut-off pressure area, modeling and numerical simulations are performed to observe dynamic behavior of internal parts of the constant power regulator system for a swashplate-type axial piston pump. The commercial numerical simulation software AMESim is applied to model the mechanical-type regulator with hydraulic pump and simulate the performance of it. The validity of the simulation model of the constant power regulator system is verified by comparing simulation results with experiments. In order to find the cause of the irregular performance of the mechanical-type constant power regulator system, the behavior of main components such as the spool, sleeve, and counterbalance piston is investigated using computer simulation. The shape modification of the counterbalance piston is proposed to improve the undesirable performance of the mechanical-type constant power regulator. The performance improvement is verified by computer simulation using AMESim software. PMID:24282389

A cellular automaton for the signed particle formulation of quantum mechanics

NASA Astrophysics Data System (ADS)

Sellier, J. M.; Kapanova, K. G.; Dimov, I.

2017-02-01

Recently, a new formulation of quantum mechanics, based on the concept of signed particles, has been suggested. In this paper, we introduce a cellular automaton which mimics the dynamics of quantum objects in the phase-space in a time-dependent fashion. This is twofold: it provides a simplified and accessible language to non-physicists who wants to simulate quantum mechanical systems, at the same time it enables a different way to explore the laws of Physics. Moreover, it opens the way towards hybrid simulations of quantum systems by combining full quantum models with cellular automata when the former fail. In order to show the validity of the suggested cellular automaton and its combination with the signed particle formalism, several numerical experiments are performed, showing very promising results. Being this article a preliminary study on quantum simulations in phase-space by means of cellular automata, some conclusions are drawn about the encouraging results obtained so far and the possible future developments.

Mechanical Behavior and Fatigue Studies of Rubber Components Used in Tracked Vehicles

DTIC Science & Technology

2010-08-17

durability to this elastomers and polybutadiene is rubber , which gives rubber -like properties. SBR has good abrasion resistance and good aging ...SIMULATION, TESTING AND VALIDATION (MSTV) MINI-SYMPOSIUM AUGUST 17-19 DEARBORN, MICHIGAN MECHANICAL BEHAVIOR AND FATIGUE STUDIES OF RUBBER COMPONENTS USED...Analytics Group US Army TARDEC Warren, MI ABSTRACT In this study, a styrene butadiene rubber , which is similar to the rubber used in road wheel

Possible Mechanism of Action of the Electromagnetic Fields of Ultralow Frequency on G-protein

NASA Astrophysics Data System (ADS)

Nava, J. J. Godina; Segura, M. A. Rodríguez; García, M. N. Jiménez; Cadena, M. S. Reyes

2008-08-01

Based in several clinical achievements and mathematical simulation of the immune sytem, previously studied, permit us to establish that a possible Mechanism of Action of ultralow frequency Electromagnetic Fields (ELF) is on G-protein as it has been proposed in specialized literature.

Adaptive Mechanisms for Treating Missing Information: A Simulation Study

ERIC Educational Resources Information Center

Garcia-Retamero, Rocio; Rieskamp, Jorg

2008-01-01

People often make inferences with incomplete information. Previous research has led to a mixed picture of how people treat missing information. To explain these results, the authors follow the Brunswikian perspective on human inference and hypothesize that the mechanism's accuracy for treating missing information depends on how it is distributed…

Influence of Temperature on Transdermal Penetration Enhancing Mechanism of Borneol: A Multi-Scale Study

PubMed Central

Yin, Qianqian; Wang, Ran; Yang, Shufang; Wu, Zhimin; Guo, Shujuan; Dai, Xingxing; Qiao, Yanjiang; Shi, Xinyuan

2017-01-01

The influence of temperature on the transdermal permeation enhancing mechanism of borneol (BO) was investigated using a multi-scale method, containing a coarse-grained molecular dynamic (CG-MD) simulation, an in vitro permeation experiment, and a transmission electron microscope (TEM) study. The results showed that BO has the potential to be used as a transdermal penetration enhancer to help osthole (OST) penetrate into the bilayer. With the increasing temperature, the stratum corneum (SC) becomes more flexible, proving to be synergistic with the permeation enhancement of BO, and the lag time (TLag) of BO and OST are shortened. However, when the temperature increased too much, with the effect of BO, the structure of SC was destroyed; for example, a water pore was formed and the micelle reversed. Though there were a number of drugs coming into the SC, the normal bilayer structure was absent. In addition, through comparing the simulation, in vitro experiment, and TEM study, we concluded that the computer simulation provided some visually detailed information, and the method plays an important role in related studies of permeation. PMID:28106833

Effect of Knudsen thermal force on the performance of low-pressure micro gas sensor

NASA Astrophysics Data System (ADS)

Barzegar Gerdroodbary, M.; Ganji, D. D.; Taeibi-Rahni, M.; Vakilipour, Shidvash

2017-07-01

In this paper, Direct Simulation Monte Carlo (DSMC) simulations were applied to investigate the mechanism of the force generation inside a low-pressure gas sensor. The flow feature and force generation mechanism inside a rectangular enclosure with heat and cold arms as the non-isothermal walls are comprehensively explained. In addition, extensive parametric studies are done to study the effects of physical parameters on the performance and characteristics of this device in different operating conditions. In this research, the Knudsen number is varied from 0.1 to 4.5 (0.5 to 11torr) to reveal all the characteristics of the thermally driven force inside the MEMS sensor. In order to simulate a rarefied gas inside the micro gas detector, Boltzmann equations are applied to obtain high-precision results. The effects of ambient pressure and temperature difference of arms are comprehensively investigated. Our findings show that maximum force increases more than 7 times when the temperature difference of the cold and hot arms is increased from 10 to 100K. In addition, the results demonstrate that the thermal gradient at rarefied pressure induces complex structure, and the mechanism of force generation highly varies at different pressure conditions.

Evaluation of the phase properties of hydrating cement composite using simulated nanoindentation technique

NASA Astrophysics Data System (ADS)

Gautham, S.; Sindu, B. S.; Sasmal, Saptarshi

2017-10-01

Properties and distribution of the products formed during the hydration of cementitious composite at the microlevel are investigated using a nanoindentation technique. First, numerical nanoindentation using nonlinear contact mechanics is carried out on three different phase compositions of cement paste, viz. mono-phase Tri-calcium Silicate (C3S), Di-calcium Silicate (C2S) and Calcium-Silicate-Hydrate (CSH) individually), bi-phase (C3S-CSH, C2S-CSH) and multi-phase (more than 10 individual phases including water pores). To reflect the multi-phase characteristics of hydrating cement composite, a discretized multi-phase microstructural model of cement composite during the progression of hydration is developed. Further, a grid indentation technique for simulated nanoindentation is established, and employed to evaluate the mechanical characteristics of the hydrated multi-phase cement paste. The properties obtained from the numerical studies are compared with those obtained from experimental grid nanoindentation. The influence of composition and distribution of individual phase properties on the properties obtained from indentation are closely investigated. The study paves the way to establishing the procedure for simulated grid nanoindentation to evaluate the mechanical properties of heterogeneous composites, and facilitates the design of experimental nanoindentation.

Numerical simulation of X90 UOE pipe forming process

NASA Astrophysics Data System (ADS)

Zou, Tianxia; Ren, Qiang; Peng, Yinghong; Li, Dayong; Tang, Ding; Han, Jianzeng; Li, Xinwen; Wang, Xiaoxiu

2013-12-01

The UOE process is an important technique to manufacture large-diameter welding pipes which are increasingly applied in oil pipelines and offshore platforms. The forming process of UOE mainly consists of five successive operations: crimping, U-forming, O-forming, welding and mechanical expansion, through which a blank is formed into a pipe in a UOE pipe mill. The blank with an appropriate edge bevel is bent into a cylindrical shape by crimping (C-forming), U-forming and O-forming successively. After the O-forming, there is an open-seam between two ends of the plate. Then, the blank is welded by automatic four-electrode submerged arc welding technique. Subsequently, the welded pipe is expanded with a mechanical expander to get a high precision circular shape. The multiple operations in the UOE mill make it difficult to control the quality of the formed pipe. Therefore, process design mainly relies on experience in practical production. In this study, the UOE forming of an API X90 pipe is studied by using finite element simulation. The mechanical properties tests are performed on the API X90 pipeline steel blank. A two-dimensional finite element model under the hypothesis of plane strain condition is developed to simulate the UOE process according to data coming from the workshop. A kinematic hardening model is used in the simulation to take the Bauschinger effect into account. The deformation characteristics of the blank during the forming processes are analyzed. The simulation results show a significant coherence in the geometric configurations comparing with the practical manufacturing.

Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Trung D; Carrillo, Jan-Michael Y; Brown, W Michael

2014-01-01

The ability of liquid crystal (LC) molecules to respond to changes in their environment makes them an interesting candidate for thin film applications, particularly in bio-sensing, bio-mimicking devices, and optics. Yet the understanding of the (in)stability of this family of thin films has been limited by the inherent challenges encountered by experiment and continuum models. Using unprecedented largescale molecular dynamics (MD) simulations, we address the rupture origin of LC thin films wetting a solid substrate at length scales similar to those in experiment. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top ofmore » thermal nucleation, and importantly, for the first time, evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. We further demonstrate that the primary driving force for rupture is closely related to the tendency of the LC mesogens to recover their local environment in the bulk state. Our study not only provides new insights into the rupture mechanism of liquid crystal films, but also sets the stage for future investigations of thin film systems using peta-scale molecular dynamics simulations.« less

Simulated Space Environment Effects on a Candidate Solar Sail Material

NASA Technical Reports Server (NTRS)

Kang, Jin Ho; Bryant, Robert G.; Wilkie, W. Keats; Wadsworth, Heather M.; Craven, Paul D.; Nehls, Mary K.; Vaughn, Jason A.

2017-01-01

For long duration missions of solar sails, the sail material needs to survive harsh space environments and the degradation of the sail material controls operational lifetime. Therefore, understanding the effects of the space environment on the sail membrane is essential for mission success. In this study, we investigated the effect of simulated space environment effects of ionizing radiation, thermal aging and simulated potential damage on mechanical, thermal and optical properties of a commercial off the shelf (COTS) polyester solar sail membrane to assess the degradation mechanisms on a feasible solar sail. The solar sail membrane was exposed to high energy electrons (about 70 keV and 10 nA/cm2), and the physical properties were characterized. After about 8.3 Grad dose, the tensile modulus, tensile strength and failure strain of the sail membrane decreased by about 20 95%. The aluminum reflective layer was damaged and partially delaminated but it did not show any significant change in solar absorbance or thermal emittance. The effect on mechanical properties of a pre-cracked sample, simulating potential impact damage of the sail membrane, as well as thermal aging effects on metallized PEN (polyethylene naphthalate) film will be discussed.

A mapping variable ring polymer molecular dynamics study of condensed phase proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Pierre, Sadrach; Duke, Jessica R.; Hele, Timothy J. H.; Ananth, Nandini

2017-12-01

We investigate the mechanisms of condensed phase proton-coupled electron transfer (PCET) using Mapping-Variable Ring Polymer Molecular Dynamics (MV-RPMD), a recently developed method that employs an ensemble of classical trajectories to simulate nonadiabatic excited state dynamics. Here, we construct a series of system-bath model Hamiltonians for the PCET, where four localized electron-proton states are coupled to a thermal bath via a single solvent mode, and we employ MV-RPMD to simulate state population dynamics. Specifically, for each model, we identify the dominant PCET mechanism, and by comparing against rate theory calculations, we verify that our simulations correctly distinguish between concerted PCET, where the electron and proton transfer together, and sequential PCET, where either the electron or the proton transfers first. This work represents a first application of MV-RPMD to multi-level condensed phase systems; we introduce a modified MV-RPMD expression that is derived using a symmetric rather than asymmetric Trotter discretization scheme and an initialization protocol that uses a recently derived population estimator to constrain trajectories to a dividing surface. We also demonstrate that, as expected, the PCET mechanisms predicted by our simulations are robust to an arbitrary choice of the initial dividing surface.

Evaluation of mechanical deformation and distributive magnetic loads with different mechanical constraints in two parallel conducting bars

NASA Astrophysics Data System (ADS)

Lee, Ho-Young; Lee, Se-Hee

2017-08-01

Mechanical deformation, bending deformation, and distributive magnetic loads were evaluated numerically and experimentally for conducting materials excited with high current. Until now, many research works have extensively studied the area of magnetic force and mechanical deformation by using coupled approaches such as multiphysics solvers. In coupled analysis for magnetoelastic problems, some articles and commercial software have presented the resultant mechanical deformation and stress on the body. To evaluate the mechanical deformation, the Lorentz force density method (LZ) and the Maxwell stress tensor method (MX) have been widely used for conducting materials. However, it is difficult to find any experimental verification regarding mechanical deformation or bending deformation due to magnetic force density. Therefore, we compared our numerical results to those from experiments with two parallel conducting bars to verify our numerical setup for bending deformation. Before showing this, the basic and interesting coupled simulation was conducted to test the mechanical deformations by the LZ (body force density) and the MX (surface force density) methods. This resulted in MX gave the same total force as LZ, but the local force distribution in MX introduced an incorrect mechanical deformation in the simulation of a solid conductor.

Some aspects of cadmium flow in the U.S.

PubMed Central

Yost, K J

1979-01-01

A team of Purdue University engineers and scientists has been involved in studying sources, translocation mechanisms, and fate of cadmium in the environment. One of the principal results of this work has been the development of a cadmium flow model for the U. S. which involves simulating sources, use patterns, waste treatment and recovery techniques, waste disposal options, and environmental flow mechanisms. A series of model calculations performed specify cadmium environmental flow, fate, and human exposure for a variety of use pattern, waste treatment/recovery, and disposal scenarios over a ten-year-simulation period. PMID:488047

Rocket Launch Trajectory Simulations Mechanism

NASA Technical Reports Server (NTRS)

Margasahayam, Ravi; Caimi, Raoul E.; Hauss, Sharon; Voska, N. (Technical Monitor)

2002-01-01

The design and development of a Trajectory Simulation Mechanism (TSM) for the Launch Systems Testbed (LST) is outlined. In addition to being one-of-a-kind facility in the world, TSM serves as a platform to study the interaction of rocket launch-induced environments and subsequent dynamic effects on the equipment and structures in the close vicinity of the launch pad. For the first time, researchers and academicians alike will be able to perform tests in a laboratory environment and assess the impact of vibroacoustic behavior of structures in a moving rocket scenario on ground equipment, launch vehicle, and its valuable payload or spacecraft.

Study on Fluid-solid Coupling Mathematical Models and Numerical Simulation of Coal Containing Gas

NASA Astrophysics Data System (ADS)

Xu, Gang; Hao, Meng; Jin, Hongwei

2018-02-01

Based on coal seam gas migration theory under multi-physics field coupling effect, fluid-solid coupling model of coal seam gas was build using elastic mechanics, fluid mechanics in porous medium and effective stress principle. Gas seepage behavior under different original gas pressure was simulated. Results indicated that residual gas pressure, gas pressure gradient and gas low were bigger when original gas pressure was higher. Coal permeability distribution decreased exponentially when original gas pressure was lower than critical pressure. Coal permeability decreased rapidly first and then increased slowly when original pressure was higher than critical pressure.

The Living Heart Project: A robust and integrative simulator for human heart function.

PubMed

Baillargeon, Brian; Rebelo, Nuno; Fox, David D; Taylor, Robert L; Kuhl, Ellen

2014-11-01

The heart is not only our most vital, but also our most complex organ: Precisely controlled by the interplay of electrical and mechanical fields, it consists of four chambers and four valves, which act in concert to regulate its filling, ejection, and overall pump function. While numerous computational models exist to study either the electrical or the mechanical response of its individual chambers, the integrative electro-mechanical response of the whole heart remains poorly understood. Here we present a proof-of-concept simulator for a four-chamber human heart model created from computer topography and magnetic resonance images. We illustrate the governing equations of excitation-contraction coupling and discretize them using a single, unified finite element environment. To illustrate the basic features of our model, we visualize the electrical potential and the mechanical deformation across the human heart throughout its cardiac cycle. To compare our simulation against common metrics of cardiac function, we extract the pressure-volume relationship and show that it agrees well with clinical observations. Our prototype model allows us to explore and understand the key features, physics, and technologies to create an integrative, predictive model of the living human heart. Ultimately, our simulator will open opportunities to probe landscapes of clinical parameters, and guide device design and treatment planning in cardiac diseases such as stenosis, regurgitation, or prolapse of the aortic, pulmonary, tricuspid, or mitral valve.

Mechanical testing and finite element analysis of orthodontic teardrop loop.

PubMed

Coimbra, Maria Elisa Rodrigues; Penedo, Norman Duque; de Gouvêa, Jayme Pereira; Elias, Carlos Nelson; de Souza Araújo, Mônica Tirre; Coelho, Paulo Guilherme

2008-02-01

Understanding how teeth move in response to mechanical loads is an important aspect of orthodontic treatment. Treatment planning should include consideration of the appliances that will meet the desired loading of the teeth to result in optimized treatment outcomes. The purpose of this study was to evaluate the use of computer simulation to predict the force and the torsion obtained after the activation of tear drop loops of 3 heights. Seventy-five retraction loops were divided into 3 groups according to height (6, 7, and 8 mm). The loops were subjected to tensile load through displacements of 0.5, 1.0, 1.5, and 2.0 mm, and the resulting forces and torques were recorded. The loops were designed in AutoCAD software(2005; Autodesk Systems, Alpharetta, GA), and finite element analysis was performed with Ansys software(version 7.0; Swanson Analysis System, Canonsburg, PA). Statistical analysis of the mechanical experiment results was obtained by ANOVA and the Tukey post-hoc test (P < .01). The correlation test and the paired t test (P < .05) were used to compare the computer simulation with the mechanical experiment. The computer simulation accurately predicted the experimentally determined mechanical behavior of tear drop loops of different heights and should be considered an alternative for designing orthodontic appliances before treatment.

Influence and evolution mechanism of different sharpness contact forms to mechanical property of cortical bone by nanoindentation

NASA Astrophysics Data System (ADS)

Sun, Xingdong; Guo, Yue; Li, Lijia; Liu, Zeyang; Wu, Di; Shi, Dong; Zhao, Hongwei; Zhang, Shizhong

2018-03-01

Based on different damage forms of various contact forms to bone, the mechanical response and mechanism were investigated by nanoindentation under different sharpness contact forms. For the purpose of simulating the different sharpness contact forms, two kinds of indenters were used in experiments and finite elements simulations. Through nanoindentation experiments, it was concluded that the residual depth of sharp indenter was bigger than that of blunt indenter with small penetration depth. However, the contrary law was obtained with bigger penetration depth. There was a turning point of transition from blunt tendency to sharp tendency. By calculation, it was concluded that the sharper the indenter was, the bigger the proportion of plastic energy in total energy was. Basically, results of finite elements simulation could correspond with the experimental conclusions. By the observation of FE-SEM, the surface of cortical bone compressed was more seriously directly below the blunt indenter than the lateral face. For the berkovich indenter, the surface of indentation compressed was less directly below the indenter, but seriously on three lateral faces. This research may provide some new references to the studies of bone fracture mechanism in different load patterns in the initial press-in stage and offer new explanation for bone trauma diagnosis in clinical treatment and criminal investigation.

Length-dependent mechanical properties of gold nanowires

NASA Astrophysics Data System (ADS)

Han, Jing; Fang, Liang; Sun, Jiapeng; Han, Ying; Sun, Kun

2012-12-01

The well-known "size effect" is not only related to the diameter but also to the length of the small volume materials. It is unfortunate that the length effect on the mechanical behavior of nanowires is rarely explored in contrast to the intensive studies of the diameter effect. The present paper pays attention to the length-dependent mechanical properties of <111>-oriented single crystal gold nanowires employing the large-scale molecular dynamics simulation. It is discovered that the ultrashort Au nanowires exhibit a new deformation and failure regime-high elongation and high strength. The constrained dislocation nucleation and transient dislocation slipping are observed as the dominant mechanism for such unique combination of high strength and high elongation. A mechanical model based on image force theory is developed to provide an insight to dislocation nucleation and capture the yield strength and nucleation site of first partial dislocation indicated by simulation results. Increasing the length of the nanowires, the ductile-to-brittle transition is confirmed. And the new explanation is suggested in the predict model of this transition. Inspired by the superior properties, a new approach to strengthen and toughen nanowires-hard/soft/hard sandwich structured nanowires is suggested. A preliminary evidence from the molecular dynamics simulation corroborates the present opinion.

Crack propagation of brittle rock under high geostress

NASA Astrophysics Data System (ADS)

Liu, Ning; Chu, Weijiang; Chen, Pingzhi

2018-03-01

Based on fracture mechanics and numerical methods, the characteristics and failure criterions of wall rock cracks including initiation, propagation, and coalescence are analyzed systematically under different conditions. In order to consider the interaction among cracks, adopt the sliding model of multi-cracks to simulate the splitting failure of rock in axial compress. The reinforcement of bolts and shotcrete supporting to rock mass can control the cracks propagation well. Adopt both theory analysis and simulation method to study the mechanism of controlling the propagation. The best fixed angle of bolts is calculated. Then use ansys to simulate the crack arrest function of bolt to crack. Analyze the influence of different factors on stress intensity factor. The method offer more scientific and rational criterion to evaluate the splitting failure of underground engineering under high geostress.

Linkage mechanisms in the vertebrate skull: Structure and function of three-dimensional, parallel transmission systems.

PubMed

Olsen, Aaron M; Westneat, Mark W

2016-12-01

Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing geometries and configurations, enabling novel interpretations of the mechanics of force transmission across a diversity of vertebrate feeding mechanisms and enhancing our understanding of musculoskeletal function and evolution. J. Morphol. 277:1570-1583, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Effect of Heliox on Respiratory Outcomes during Rigid Bronchoscopy in Term Lambs.

PubMed

Sowder, Justin C; Dahl, Mar Janna; Zuspan, Kaitlin R; Albertine, Kurt H; Null, Donald M; Barneck, Mitchell D; Grimmer, J Fredrik

2018-03-01

Objective To (1) compare physiologic changes during rigid bronchoscopy during spontaneous and mechanical ventilation and (2) evaluate the efficacy of a helium-oxygen (heliox) gas mixture as compared with room air during rigid bronchoscopy. Study Design Crossover animal study evaluating physiologic parameters during rigid bronchoscopy. Outcomes were compared with predicted computational fluid analysis. Setting Simulated ventilation via computational fluid dynamics analysis and term lambs undergoing rigid bronchoscopy. Methods Respiratory and physiologic outcomes were analyzed in a lamb model simulating bronchoscopy during foreign body aspiration to compare heliox with room air. The main outcome measures were blood oxygen saturation, heart rate, blood pressure, partial pressure of oxygen, and partial pressure of carbon dioxide. Computational fluid dynamics analysis was performed with SOLIDWORKS within a rigid pediatric bronchoscope during simulated ventilation comparing heliox with room air. Results For room air, lambs desaturated within 3 minutes during mechanical ventilation versus normal oxygen saturation during spontaneous ventilation ( P = .01). No improvement in respiratory outcomes was seen between heliox and room air during mechanical ventilation. Computational fluid dynamics analysis demonstrates increased turbulence within size 3.5 bronchoscopes when comparing heliox and room air. Meaningful comparisons could not be made due to the intolerance of the lambs to heliox in vivo. Conclusion During mechanical ventilation on room air, lambs desaturate more quickly during rigid bronchoscopy on settings that should be adequate. Heliox does not improve ventilation during rigid bronchoscopy.

A FSI-based structural approach for micromechanical characterization of adipose tissue

NASA Astrophysics Data System (ADS)

Seyfi, Behzad; Sabzalinejad, Masoumeh; Haddad, Seyed M. H.; Fatouraee, Nasser; Samani, Abbas

2017-03-01

This paper presents a novel computational method for micromechanical modeling of adipose tissue. The model can be regarded as the first step for developing an inversion based framework that uses adipose stiffness data obtained from elastography to determine its microstructural alterations. Such information can be used as biomarkers for diseases associated with adipose tissue microstructure alteration (e.g. adipose tissue fibrosis and inflammation in obesity). In contrast to previous studies, the presented model follows a multiphase structure which accounts for both solid and fluid components as well as their mechanical interaction. In the model, the lipid droplets and extracellular matrix were considered as the fluid and solid phase, respectively. As such, the fluid-structure interaction (FSI) problem was solved using finite element method. In order to gain insight into how microstructural characteristics influence the macro scale mechanical properties of the adipose tissue, a compression mechanical test was simulated using the FSI model and its results were fitted to corresponding experimental data. The simulation procedure was performed for adipocytes in healthy conditions while the stiffness of extracellular matrix in normal adipose tissue was found by varying it systematically within an optimization process until the simulation response agreed with experimental data. Results obtained in this study are encouraging and show the capability of the proposed model to capture adipose tissue macroscale mechanical behavior based on its microstructure under health and different pathological conditions.

Effects and possible mechanisms of simulated-microgravity on zebrafish embryonic cell

NASA Astrophysics Data System (ADS)

Hang, Xiaoming; Sun, Yeqing; Wu, Di; Li, Yixiao; Wang, Ruonan

2016-07-01

Cellular level studies are helpful for revealing the underlying mechanisms of microgravity effects on living organisms. Many cell types, ranging from bacteria to mammalian cells, are sensitive to the microgravity environment. In this study, zebrafish embryonic cells (ZF4) were exposed to simulated-microgravity (SMG) for different times to investigate the effects and possible mechanisms of microgravity on fibroblasts. A significant arrest in G2/M phase was detected in ZF4 cells after 24 or 48 hour of SMG exposure, respectively. The mRNA levels of G2/M phase regulators cyclinB1 and cdc2 were significantly decreased, while wee1 was significantly increased. Additionally, CEP135, a core centrosome protein throughout the cell cycle, seems to play a key role in modulating this effect. Quantitative analysis showed that cep135 expression was significantly increased, while CEP135 protein expression level was significantly decreased two times after SMG. Further investigation demonstrated the transfection of dre-miR-22a, a miRNA for targeting cep135, also induced G2/M arrest in ZF4 cells. These results suggest that SMG induced G2/M arrest in ZF4 cells may due to the regulation of dre-miR-22a and its target cep135. Key Words: Simulated-microgravity; zebrafish embryonic cell; G2/M arrest; molecular mechanism

Reactive Oxygen Species (ROS) generation by lunar simulants

NASA Astrophysics Data System (ADS)

Kaur, Jasmeet; Rickman, Douglas; Schoonen, Martin A.

2016-05-01

The current interest in human exploration of the Moon and past experiences of Apollo astronauts has rekindled interest into the possible harmful effects of lunar dust on human health. In comparison to the Apollo-era explorations, human explorers may be weeks on the Moon, which will raise the risk of inhalation exposure. The mineralogical composition of lunar dust is well documented, but its effects on human health are not fully understood. With the aim of understanding the reactivity of dusts that may be encountered on geologically different lunar terrains, we have studied Reactive Oxygen Species (ROS) generation by a suite of lunar simulants of different mineralogical-chemical composition dispersed in water and Simulated Lung Fluid (SLF). To further explore the reactivity of simulants under lunar environmental conditions, we compared the reactivity of simulants both in air and inert atmosphere. As the impact of micrometeorites with consequent shock-induced stresses is a major environmental factor on the Moon, we also studied the effect of mechanical stress on samples. Mechanical stress was induced by hand crushing the samples both in air and inert atmosphere. The reactivity of samples after crushing was analyzed for a period of up to nine days. Hydrogen peroxide (H2O2) in water and SLF was analyzed by an in situ electrochemical probe and hydroxyl radical (•OH) by Electron Spin Resonance (ESR) spectroscopy and Adenine probe. Out of all simulants, CSM-CL-S was found to be the most reactive simulant followed by OB-1 and then JSC-1A simulant. The overall reactivity of samples in the inert atmosphere was higher than in air. Fresh crushed samples showed a higher level of reactivity than uncrushed samples. Simulant samples treated to create agglutination, including the formation of zero-valent iron, showed less reactivity than untreated simulants. ROS generation in SLF is initially slower than in deionized water (DI), but the ROS formation is sustained for as long as 7.5 h. By contrast ROS is formed rapidly within 30 min when simulants are dispersed in DI, but then the concentration either stabilizes or decreases over time. The results indicate that mechanical stress and the absence of molecular oxygen and water, which are important environmental characteristics of the lunar environment, can lead to enhanced production of ROS in general. However, compositional difference among simulants is the most important factor in governing the production of ROS. Simulants with glass content in excess of 40 wt% appear to produce as much as of order of magnitude more ROS than simulants with lower glass content.

How to model supernovae in simulations of star and galaxy formation

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.; Wetzel, Andrew; Kereš, Dušan; Faucher-Giguère, Claude-André; Quataert, Eliot; Boylan-Kolchin, Michael; Murray, Norman; Hayward, Christopher C.; El-Badry, Kareem

2018-06-01

We study the implementation of mechanical feedback from supernovae (SNe) and stellar mass loss in galaxy simulations, within the Feedback In Realistic Environments (FIRE) project. We present the FIRE-2 algorithm for coupling mechanical feedback, which can be applied to any hydrodynamics method (e.g. fixed-grid, moving-mesh, and mesh-less methods), and black hole as well as stellar feedback. This algorithm ensures manifest conservation of mass, energy, and momentum, and avoids imprinting `preferred directions' on the ejecta. We show that it is critical to incorporate both momentum and thermal energy of mechanical ejecta in a self-consistent manner, accounting for SNe cooling radii when they are not resolved. Using idealized simulations of single SN explosions, we show that the FIRE-2 algorithm, independent of resolution, reproduces converged solutions in both energy and momentum. In contrast, common `fully thermal' (energy-dump) or `fully kinetic' (particle-kicking) schemes in the literature depend strongly on resolution: when applied at mass resolution ≳100 M⊙, they diverge by orders of magnitude from the converged solution. In galaxy-formation simulations, this divergence leads to orders-of-magnitude differences in galaxy properties, unless those models are adjusted in a resolution-dependent way. We show that all models that individually time-resolve SNe converge to the FIRE-2 solution at sufficiently high resolution (<100 M⊙). However, in both idealized single-SN simulations and cosmological galaxy-formation simulations, the FIRE-2 algorithm converges much faster than other sub-grid models without re-tuning parameters.

Simulating human photoreceptor optics using a liquid-filled photonic crystal fiber.

PubMed

Rativa, Diego; Vohnsen, Brian

2011-02-11

We introduce a liquid-filled photonic crystal fiber to simulate a retinal cone photoreceptor mosaic and the directionality selective mechanism broadly known as the Stiles-Crawford effect. Experimental measurements are realized across the visible spectrum to study waveguide coupling and directionality at different managed waveguide parameters. The crystal fiber method is a hybrid tool between theory and a real biological sample and a valuable addition as a retina model for real eye simulations.

Role of crystal arrangement on the mechanical performance of enamel.

PubMed

An, Bingbing; Wang, Raorao; Zhang, Dongsheng

2012-10-01

The superior mechanical properties of enamel, such as excellent penetration and crack resistance, are believed to be related to the unique microscopic structure. In this study, the effects of hydroxyapatite (HAP) crystallite orientation on the mechanical behavior of enamel have been investigated through a series of multiscale numerical simulations. A micromechanical model, which considers the HAP crystal arrangement in enamel prisms, the hierarchical structure of HAP crystals and the inelastic mechanical behavior of protein, has been developed. Numerical simulations revealed that, under compressive loading, plastic deformation progression took place in enamel prisms, which is responsible for the experimentally observed post-yield strain hardening. By comparing the mechanical responses for the uniform and non-uniform arrangement of HAP crystals within enamel prisms, it was found that the stiffness for the two cases was identical, while much greater energy dissipation was observed in the enamel with the non-uniform arrangement. Based on these results, we propose an important mechanism whereby the non-uniform arrangement of crystals in enamel rods enhances energy dissipation while maintaining sufficient stiffness to promote fracture toughness, mitigation of fracture and resistance to penetration deformation. Further simulations indicated that the non-uniform arrangement of the HAP crystals is a key factor responsible for the unique mechanical behavior of enamel, while the change in the nanostructure of nanocomposites could dictate the Young's modulus and yield strength of the biocomposite. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Finite Element Simulation of Articular Contact Mechanics with Quadratic Tetrahedral Elements

PubMed Central

Maas, Steve A.; Ellis, Benjamin J.; Rawlins, David S.; Weiss, Jeffrey A.

2016-01-01

Although it is easier to generate finite element discretizations with tetrahedral elements, trilinear hexahedral (HEX8) elements are more often used in simulations of articular contact mechanics. This is due to numerical shortcomings of linear tetrahedral (TET4) elements, limited availability of quadratic tetrahedron elements in combination with effective contact algorithms, and the perceived increased computational expense of quadratic finite elements. In this study we implemented both ten-node (TET10) and fifteen-node (TET15) quadratic tetrahedral elements in FEBio (www.febio.org) and compared their accuracy, robustness in terms of convergence behavior and computational cost for simulations relevant to articular contact mechanics. Suitable volume integration and surface integration rules were determined by comparing the results of several benchmark contact problems. The results demonstrated that the surface integration rule used to evaluate the contact integrals for quadratic elements affected both convergence behavior and accuracy of predicted stresses. The computational expense and robustness of both quadratic tetrahedral formulations compared favorably to the HEX8 models. Of note, the TET15 element demonstrated superior convergence behavior and lower computational cost than both the TET10 and HEX8 elements for meshes with similar numbers of degrees of freedom in the contact problems that we examined. Finally, the excellent accuracy and relative efficiency of these quadratic tetrahedral elements was illustrated by comparing their predictions with those for a HEX8 mesh for simulation of articular contact in a fully validated model of the hip. These results demonstrate that TET10 and TET15 elements provide viable alternatives to HEX8 elements for simulation of articular contact mechanics. PMID:26900037

Addressing spatial scales and new mechanisms in climate impact ecosystem modeling

NASA Astrophysics Data System (ADS)

Poulter, B.; Joetzjer, E.; Renwick, K.; Ogunkoya, G.; Emmett, K.

2015-12-01

Climate change impacts on vegetation distributions are typically addressed using either an empirical approach, such as a species distribution model (SDM), or with process-based methods, for example, dynamic global vegetation models (DGVMs). Each approach has its own benefits and disadvantages. For example, an SDM is constrained by data and few parameters, but does not include adaptation or acclimation processes or other ecosystem feedbacks that may act to mitigate or enhance climate effects. Alternatively, a DGVM model includes many mechanisms relating plant growth and disturbance to climate, but simulations are costly to perform at high-spatial resolution and there remains large uncertainty on a variety of fundamental physical processes. To address these issues, here, we present two DGVM-based case studies where i) high-resolution (1 km) simulations are being performed for vegetation in the Greater Yellowstone Ecosystem using a biogeochemical, forest gap model, LPJ-GUESS, and ii) where new mechanisms for simulating tropical tree-mortality are being introduced. High-resolution DGVM model simulations require not only computing and reorganizing code but also a consideration of scaling issues on vegetation dynamics and stochasticity and also on disturbance and migration. New mechanisms for simulating forest mortality must consider hydraulic limitations and carbon reserves and their interactions on source-sink dynamics and in controlling water potentials. Improving DGVM approaches by addressing spatial scale challenges and integrating new approaches for estimating forest mortality will provide new insights more relevant for land management and possibly reduce uncertainty by physical processes more directly comparable to experimental and observational evidence.

Chemical dynamics simulations of the monohydrated OH-(H2O) + CH3I reaction. Atomic-level mechanisms and comparison with experiment

NASA Astrophysics Data System (ADS)

Xie, Jing; Otto, Rico; Wester, Roland; Hase, William L.

2015-06-01

Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH-(H2O) + CH3I reaction. The SN2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH2I-, and to a lesser extent CH2I- (H2O), becomes important. The SN2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of SN2 and proton transfer pre-reaction complexes and intermediates, including [CH3--I--OH]-. In contrast, for the unsolvated OH- + CH3I SN2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH-(H2O) + CH3IߙSN2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the SN2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H2O molecule is unimportant. The SN2 reaction is dominated by events in which H2O leaves the reactive system as CH3OH is formed or before CH3OH formation. Formation of solvated products is unimportant and participation of the (H2O)CH3OH---I- post-reaction complex for the SN2 reaction is negligible.

Influence of Multidimensionality on Convergence of Sampling in Protein Simulation

NASA Astrophysics Data System (ADS)

Metsugi, Shoichi

2005-06-01

We study the problem of convergence of sampling in protein simulation originating in the multidimensionality of protein’s conformational space. Since several important physical quantities are given by second moments of dynamical variables, we attempt to obtain the time of simulation necessary for their sufficient convergence. We perform a molecular dynamics simulation of a protein and the subsequent principal component (PC) analysis as a function of simulation time T. As T increases, PC vectors with smaller amplitude of variations are identified and their amplitudes are equilibrated before identifying and equilibrating vectors with larger amplitude of variations. This sequential identification and equilibration mechanism makes protein simulation a useful method although it has an intrinsic multidimensional nature.

Development of a residuum/socket interface simulator for lower limb prosthetics.

PubMed

McGrath, Michael Paul; Gao, Jianliang; Tang, Jinghua; Laszczak, Piotr; Jiang, Liudi; Bader, Dan; Moser, David; Zahedi, Saeed

2017-03-01

Mechanical coupling at the interface between lower limb residua and prosthetic sockets plays an important role in assessing socket fitting and tissue health. However, most research lab-based lower limb prosthetic simulators to-date have implemented a rigid socket coupling. This study describes the fabrication and implementation of a lower limb residuum/socket interface simulator, designed to reproduce the forces and moments present during the key loading phases of amputee walking. An artificial residuum made with model bones encased in silicone was used, mimicking the compliant mechanical loading of a real residuum/socket interface. A 6-degree-of-freedom load cell measured the overall kinetics, having previously been incorporated into an amputee's prosthesis to collect reference data. The developed simulator was compared to a setup where a rigid pylon replaced the artificial residuum. A maximum uniaxial load of 850 N was applied, comparable to the peak vertical ground reaction force component during amputee walking. Load cell outputs from both pylon and residuum setups were compared. During weight acceptance, when including the artificial residuum, compression decreased by 10%, while during push off, sagittal bending and anterior-posterior shear showed a 25% increase and 34% decrease, respectively. Such notable difference by including a compliant residuum further highlighted the need for such an interface simulator. Subsequently, the simulator was adjusted to produce key load cell outputs briefly aligning with those from amputee walking. Force sensing resistors were deployed at load bearing anatomic locations on the residuum/socket interface to measure pressures and were compared to those cited in the literature for similar locations. The development of such a novel simulator provides an objective adjunct, using commonly available mechanical test machines. It could potentially be used to provide further insight into socket design, fit and the complex load transfer mechanics at the residuum/socket interface, as well as to evaluate the structural performance of prostheses.

Effect of extraoral aging conditions on mechanical properties of maxillofacial silicone elastomer.

PubMed

Hatamleh, Muhanad M; Polyzois, Gregory L; Silikas, Nick; Watts, David C

2011-08-01

The purpose of this study was to investigate the effect of extraoral human and environmental conditions on the mechanical properties (tensile strength and modulus, elongation, tear strength hardness) of maxillofacial silicone elastomer. Specimens were fabricated using TechSil-S25 silicone elastomer (Technovent Ltd, Leeds, UK). Eight groups were prepared (21 specimens in each group; eight tensile, eight tear, five hardness) and conditioned differently as follows (groups 1 through 8): Dry storage for 24 hours; dry storage in dark for 6 months; storage in simulated sebum solution for 6 months; storage in simulated acidic perspiration for 6 months; accelerated artificial daylight aging under controlled moisture for 360 hours; outdoor weathering for 6 months; storage in antimicrobial silicone-cleaning solution for 30 hours; and mixed conditioning of sebum storage and light aging for 360 hours. The conditioning period selected simulated a prosthesis being in service for up to 12 months. Tensile and tear test specimens were fabricated and tested according to the International Standards Organization (ISO) standards no. 37 and 34, respectively. Shore A hardness test specimens were fabricated and tested according to the American Standards for Testing and Materials (ASTM) D 2240. Data were analyzed with one-way ANOVA, Bonferroni, and Dunnett's T3 post hoc tests (p < 0.05). Weibull analysis was also used for tensile strength and tear strength. Statistically significant differences were evident among all properties tested. Mixed conditioning of simulated sebum storage under accelerated artificial daylight aging significantly degraded mechanical properties of the silicone (p < 0.05). Mechanical properties of maxillofacial elastomers are adversely affected by human and environmental factors. Mixed aging of storage in simulated sebum under accelerated daylight aging was the most degrading regime. Accelerated aging of silicone specimens in simulated sebum under artificial daylight for 12 months of simulated clinical service greatly affected functional properties of silicone elastomer; however, in real practice, the effect is modest, since sebum concentration is lower, and daylight is less concentrated. © 2011 by The American College of Prosthodontists.

Large-scale Thermo-Hydro-Mechanical Simulations in Complex Geological Environments

NASA Astrophysics Data System (ADS)

Therrien, R.; Lemieux, J.

2011-12-01

The study of a potential deep repository for radioative waste disposal in Canada context requires simulation capabilities for thermo-hydro-mechanical processes. It is expected that the host rock for the deep repository will be subjected to a variety of stresses during its lifetime such as in situ stresses in the rock, stressed caused by excavation of the repository and thermo-mechanical stresses. Another stress of concern for future Canadian climates will results from various episodes of glaciation. In that case, it can be expected that over 3 km of ice may be present over the land mass, which will create a glacial load that will be transmitted to the underlying geological materials and therefore impact their mechanical and hydraulic responses. Glacial loading will affect pore fluid pressures in the subsurface, which will in turn affect groundwater velocities and the potential migration of radionuclides from the repository. In addition, permafrost formation and thawing resulting from glacial advance and retreat will modify the bulk hydraulic of the geological materials and will have a potentially large impact on groundwater flow patterns, especially groundwater recharge. In the context of a deep geological repository for spent nuclear fuel, the performance of the repository to contain the spent nuclear fuel must be evaluated for periods that span several hundred thousand years. The time-frame for thermo-hydro-mechanical simulations is therefore extremely long and efficient numerical techniques must be developed. Other challenges are the representation of geological formations that have potentially complex geometries and physical properties and may contain fractures. The spatial extent of the simulation domain is also very large and can potentially reach the size of a sedimentary basin. Mass transport must also be considered because the fluid salinity in a sedimentary basin can be highly variable and the effect of fluid density on groundwater flow must be accounted for. Adding mass transport with density effect introduces further non-linearities in the governing equations, thus leading to increased simulation times. We will present challenges and current developments related to this topic in the Canadian context. Current efforts aim at improving simulation capabilities for large-scale 3D thermo-hydro-mechanical simulation in complex geologic materials. One topic of interest is to evaluate the appropriateness of simplifying the effect of glacial loading by using a one-dimensional hydro-mechanical representation that assumes purely vertical strain as opposed to the much more computationally intensive 3D representation.

Evaluation of reactive force fields for prediction of the thermo-mechanical properties of cellulose Iâ

Treesearch

Fernando L. Dri; Xiawa Wu; Robert J. Moon; Ashlie Martini; Pablo D. Zavattieri

2015-01-01

Molecular dynamics simulation is commonly used to study the properties of nanocellulose-based materials at the atomic scale. It is well known that the accuracy of these simulations strongly depends on the force field that describes energetic interactions. However, since there is no force field developed specifically for cellulose, researchers utilize models...

Augmented Reality-Based Simulators as Discovery Learning Tools: An Empirical Study

ERIC Educational Resources Information Center

Ibáñez, María-Blanca; Di-Serio, Ángela; Villarán-Molina, Diego; Delgado-Kloos, Carlos

2015-01-01

This paper reports empirical evidence on having students use AR-SaBEr, a simulation tool based on augmented reality (AR), to discover the basic principles of electricity through a series of experiments. AR-SaBEr was enhanced with knowledge-based support and inquiry-based scaffolding mechanisms, which proved useful for discovery learning in…

Understanding the Dynamics of MOOC Discussion Forums with Simulation Investigation for Empirical Network Analysis (SIENA)

ERIC Educational Resources Information Center

Zhang, Jingjing; Skryabin, Maxim; Song, Xiongwei

2016-01-01

This study attempts to make inferences about the mechanisms that drive network change over time. It adopts simulation investigation for empirical network analysis to examine the patterns and evolution of relationships formed in the context of a massive open online course (MOOC) discussion forum. Four network effects--"homophily,"…

Numerical simulation on the adaptation of forms in trabecular bone to mechanical disuse and basic multi-cellular unit activation threshold at menopause

NASA Astrophysics Data System (ADS)

Gong, He; Fan, Yubo; Zhang, Ming

2008-04-01

The objective of this paper is to identify the effects of mechanical disuse and basic multi-cellular unit (BMU) activation threshold on the form of trabecular bone during menopause. A bone adaptation model with mechanical- biological factors at BMU level was integrated with finite element analysis to simulate the changes of trabecular bone structure during menopause. Mechanical disuse and changes in the BMU activation threshold were applied to the model for the period from 4 years before to 4 years after menopause. The changes in bone volume fraction, trabecular thickness and fractal dimension of the trabecular structures were used to quantify the changes of trabecular bone in three different cases associated with mechanical disuse and BMU activation threshold. It was found that the changes in the simulated bone volume fraction were highly correlated and consistent with clinical data, and that the trabecular thickness reduced significantly during menopause and was highly linearly correlated with the bone volume fraction, and that the change trend of fractal dimension of the simulated trabecular structure was in correspondence with clinical observations. The numerical simulation in this paper may help to better understand the relationship between the bone morphology and the mechanical, as well as biological environment; and can provide a quantitative computational model and methodology for the numerical simulation of the bone structural morphological changes caused by the mechanical environment, and/or the biological environment.

Numerical Simulation of High-Speed Combustion Processes in Scramjet Configurations

NASA Astrophysics Data System (ADS)

Potturi, Amarnatha Sarma

Flows through scramjet configurations are simulated using hybrid large-eddy simulation / Reynolds-averaged Navier-Stokes techniques. Present study is performed in three parts: parametric studies to determine the sensitivities of the predictions to modeling and algorithmic variations; formulation, implementation, and testing of several subgrid closures aimed at modeling filtered species production rates, which account for turbulence-chemistry interactions in a finite rate chemistry large-eddy simulation framework; and as a final assessment of the complete methodology, cavity-stabilized ethylene combustion is simulated. Throughout the present study, emphasis is placed on characterizing facility-specific effects, since they can have a significant influence on the numerical solution. In Part One, non-reactive and reactive flows through a model scramjet combustor with a wedge shaped injector are simulated. Different grids, flux reconstruction methods, reaction mechanisms, and inflow boundary conditions are used. To enhance fuel-air mixing, a synthetic eddy method is used to generate turbulence in the injector boundary layers and the hydrogen jets. The results show that in all the cases a lifted flame is predicted with varying standoff distances, heat releases, and shapes. In Part Two, the subgrid closures for modeling the filtered species production rates are tested on two different scramjet configurations with fundamentally different flow patterns and flame structures, one with the wedge shaped injector placed at the center of the combustor section (first, used in Part One), another with a three-dimensional ramp injector located on the upper wall of the combustor section (second). While the impact of these closures on the flow through the first configuration is insignificant, they have a more pronounced effect on the flow through the second configuration. Error analysis and performance quantification of these closures reveal that, relative to a baseline model, two of the closures improve the accuracy of the predictions, but the degree of improvement is quite modest. Also, from a cost-benefit perspective none of the models are a significant improvement over the 'laminar-chemistry' closure (where turbulence-chemistry interactions are ignored), for the configurations tested and the mesh resolutions employed. In Part Three, reactive flow through an ethylene fueled cavity flameholder is simulated using 14- and 22-species ethylene oxidation mechanisms, and the synthetic eddy method (used in Part Two) is used to introduce turbulence at the inflow plane of the flameholder. For an equivalence ratio of 0.15, the 14-species mechanism resulted in a flame blow-out, and the 22-species mechanism predicted a cavity stabilized flame. Results predicted using the 22-species mechanism compare well with the experimental data, especially, water mole-fraction distribution and pressure along the upper wall of the combustor. In general, the predictions show excellent agreement with experimental data within the cavity region; further downstream, experimental results suggest that the heat release is over-predicted in the simulations.

Energy transfer and motion synchronization between mechanical oscillators through microhydrodynamic coupling

NASA Astrophysics Data System (ADS)

Wan, Yu; Jin, Kai; Ahmad, Talha J.; Black, Michael J.; Xu, Zhiping

2017-03-01

Fluidic environment is encountered for mechanical components in many circumstances, which not only damps the oscillation but also modulates their dynamical behaviors through hydrodynamic interactions. In this study, we examine energy transfer and motion synchronization between two mechanical micro-oscillators by performing thermal lattice-Boltzmann simulations. The coefficient of inter-oscillator energy transfer is measured to quantify the strength of microhydrodynamic coupling, which depends on their distance and fluid properties such as density and viscosity. Synchronized motion of the oscillators is observed in the simulations for typical parameter sets in relevant applications, with the formation and loss of stable anti-phase synchronization controlled by the oscillating frequency, amplitude, and hydrodynamic coupling strength. The critical ranges of key parameters to assure efficient energy transfer or highly synchronized motion are predicted. These findings could be used to advise mechanical design of passive and active devices that operate in fluid.

Influence of grain size on the mechanical properties of nano-crystalline copper; insights from molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Rida, A.; Makke, A.; Rouhaud, E.; Micoulaut, M.

2017-10-01

We use molecular dynamics simulations to study the mechanical properties of a columnar nanocrystalline copper with a mean grain size between 8.91 nm and 24 nm. The used samples were generated by using a melting cooling method. These samples were submitted to uniaxial tensile test. The results reveal the presence of a critical mean grain size between 16 and 20 nm, where there is an inversion in the conventional Hall-Petch tendency. This inversion is illustrated by the increase of flow stress with the increase of the mean grain size. This transition is caused by shifting of the deformation mechanism from dislocations to a combination of grain boundaries sliding and dislocations. Moreover, the effect of temperature on the mechanical properties of nanocrystalline copper has been investigated. The results show a decrease of the flow stress and Young's modulus when the temperature increases.

An elastic-plastic contact model for line contact structures

NASA Astrophysics Data System (ADS)

Zhu, Haibin; Zhao, Yingtao; He, Zhifeng; Zhang, Ruinan; Ma, Shaopeng

2018-06-01

Although numerical simulation tools are now very powerful, the development of analytical models is very important for the prediction of the mechanical behaviour of line contact structures for deeply understanding contact problems and engineering applications. For the line contact structures widely used in the engineering field, few analytical models are available for predicting the mechanical behaviour when the structures deform plastically, as the classic Hertz's theory would be invalid. Thus, the present study proposed an elastic-plastic model for line contact structures based on the understanding of the yield mechanism. A mathematical expression describing the global relationship between load history and contact width evolution of line contact structures was obtained. The proposed model was verified through an actual line contact test and a corresponding numerical simulation. The results confirmed that this model can be used to accurately predict the elastic-plastic mechanical behaviour of a line contact structure.

Mechanical Degradation of Graphite/PVDF Composite Electrodes: A Model-Experimental Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takahashi, Kenji; Higa, Kenneth; Mair, Sunil

2015-12-11

Mechanical failure modes of a graphite/polyvinylidene difluoride (PVDF) composite electrode for lithium-ion batteries were investigated by combining realistic stress-stain tests and mathematical model predictions. Samples of PVDF mixed with conductive additive were prepared in a similar way to graphite electrodes and tested while submerged in electrolyte solution. Young's modulus and tensile strength values of wet samples were found to be approximately one-fifth and one-half of those measured for dry samples. Simulations of graphite particles surrounded by binder layers given the measured material property values suggest that the particles are unlikely to experience mechanical damage during cycling, but that the fatemore » of the surrounding composite of PVDF and conductive additive depends completely upon the conditions under which its mechanical properties were obtained. Simulations using realistic property values produced results that were consistent with earlier experimental observations.« less

Biomedical Simulation Models of Human Auditory Processes

NASA Technical Reports Server (NTRS)

Bicak, Mehmet M. A.

2012-01-01

Detailed acoustic engineering models that explore noise propagation mechanisms associated with noise attenuation and transmission paths created when using hearing protectors such as earplugs and headsets in high noise environments. Biomedical finite element (FE) models are developed based on volume Computed Tomography scan data which provides explicit external ear, ear canal, middle ear ossicular bones and cochlea geometry. Results from these studies have enabled a greater understanding of hearing protector to flesh dynamics as well as prioritizing noise propagation mechanisms. Prioritization of noise mechanisms can form an essential framework for exploration of new design principles and methods in both earplug and earcup applications. These models are currently being used in development of a novel hearing protection evaluation system that can provide experimentally correlated psychoacoustic noise attenuation. Moreover, these FE models can be used to simulate the effects of blast related impulse noise on human auditory mechanisms and brain tissue.

Effect of Surface Impulsive Thermal Loads on Fatigue Behavior of Constant Volume Propulsion Engine Combustor Materials

NASA Technical Reports Server (NTRS)

Zhu, Dongming; Fox, Dennis S.; Miller, Robert A.; Ghosn, Louis J.; Kalluri, Sreeramesh

2004-01-01

The development of advanced high performance constant-volume-combustion-cycle engines (CVCCE) requires robust design of the engine components that are capable of enduring harsh combustion environments under high frequency thermal and mechanical fatigue conditions. In this study, a simulated engine test rig has been established to evaluate thermal fatigue behavior of a candidate engine combustor material, Haynes 188, under superimposed CO2 laser surface impulsive thermal loads (30 to 100 Hz) in conjunction with the mechanical fatigue loads (10 Hz). The mechanical high cycle fatigue (HCF) testing of some laser pre-exposed specimens has also been conducted under a frequency of 100 Hz to determine the laser surface damage effect. The test results have indicated that material surface oxidation and creep-enhanced fatigue is an important mechanism for the surface crack initiation and propagation under the simulated CVCCE engine conditions.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

PubMed

Šponer, Jiří; Banáš, Pavel; Jurečka, Petr; Zgarbová, Marie; Kührová, Petra; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal

2014-05-15

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

Neurite, a Finite Difference Large Scale Parallel Program for the Simulation of Electrical Signal Propagation in Neurites under Mechanical Loading

PubMed Central

García-Grajales, Julián A.; Rucabado, Gabriel; García-Dopico, Antonio; Peña, José-María; Jérusalem, Antoine

2015-01-01

With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, functions of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells, Neurite, has only very recently been proposed. In this paper, we present the implementation details of this model: a finite difference parallel program for simulating electrical signal propagation along neurites under mechanical loading. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to simulate the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The simulation of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the simulated cells grows. The solvers implemented in Neurite—explicit and implicit—were therefore parallelized using graphics processing units in order to reduce the burden of the simulation costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between electrophysiology and mechanics. This paper provides the details of the parallel implementation of Neurite, along with three different application examples: a long myelinated axon, a segmented dendritic tree, and a damaged axon. The capabilities of the program to deal with large scale scenarios, segmented neuronal structures, and functional deficits under mechanical loading are specifically highlighted. PMID:25680098

Evolution of egoism on semi-directed and undirected Barabási-Albert networks

NASA Astrophysics Data System (ADS)

Lima, F. W. S.

2015-05-01

Through Monte Carlo simulations, we study the evolution of the four strategies: Ethnocentric, altruistic, egoistic and cosmopolitan in one community of individuals. Interactions and reproduction among computational agents are simulated on undirected and semi-directed Barabási-Albert (BA) networks. We study the Hammond-Axelrod (HA) model on undirected and semi-directed BA networks for the asexual reproduction case. With a small modification in the traditional HA model, our simulations showed that egoism wins, differently from other results found in the literature where ethnocentric strategy is common. Here, mechanisms such as reciprocity are absent.

Tropospheric Distribution of Trace Species during the Oxidation Mechanism Observations (OMO-2015) campaign: Model Evaluation and sensitivity simulations

NASA Astrophysics Data System (ADS)

Ojha, Narendra; Pozzer, Andrea; Jöckel, Patrick; Fischer, Horst; Zahn, Andreas; Tomsche, Laura; Lelieveld, Jos

2017-04-01

The Asian monsoon convection redistributes trace species, affecting the tropospheric chemistry and radiation budget over Asia and downwind as far as the Mediterranean. It remains challenging to model these impacts due to uncertainties, e.g. associated with the convection parameterization and input emissions. Here, we perform a series of numerical experiments using the global ECHAM5/MESSy atmospheric chemistry model (EMAC) to investigate the tropospheric distribution of O3 and related tracers measured during the Oxidation Mechanism Observations (OMO) conducted during July-August 2015. The reference simulation can reproduce the spatio-temporal variations to some extent (e.g. r2 = 0.7 for O3, 0.6 for CO). However, this simulation underestimates mean CO in the lower troposphere by about 30 ppbv and overestimates mean O3 up to 35 ppbv, especially in the middle-upper troposphere. Interestingly, sensitivity simulations with 50% higher biofuel emissions of CO over South Asia had insignificant effect on CO underestimation, pointing to sources upwind of South Asia. Use of an alternative convection parameterization is found to significantly improve simulated O3. The study reveals the abilities as well as the limitations of the model to reproduce observations and study atmospheric chemistry and climate implications of the monsoon.

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

NASA Astrophysics Data System (ADS)

Gur, M.; Zomot, E.; Bahar, I.

2013-09-01

The Anton supercomputing technology recently developed for efficient molecular dynamics simulations permits us to examine micro- to milli-second events at full atomic resolution for proteins in explicit water and lipid bilayer. It also permits us to investigate to what extent the collective motions predicted by network models (that have found broad use in molecular biophysics) agree with those exhibited by full-atomic long simulations. The present study focuses on Anton trajectories generated for two systems: the bovine pancreatic trypsin inhibitor, and an archaeal aspartate transporter, GltPh. The former, a thoroughly studied system, helps benchmark the method of comparative analysis, and the latter provides new insights into the mechanism of function of glutamate transporters. The principal modes of motion derived from both simulations closely overlap with those predicted for each system by the anisotropic network model (ANM). Notably, the ANM modes define the collective mechanisms, or the pathways on conformational energy landscape, that underlie the passage between the crystal structure and substates visited in simulations. In particular, the lowest frequency ANM modes facilitate the conversion between the most probable substates, lending support to the view that easy access to functional substates is a robust determinant of evolutionarily selected native contact topology.

Penetration of Gold Nanoparticles through Human Skin: Unraveling Its Mechanisms at the Molecular Scale.

PubMed

Gupta, Rakesh; Rai, Beena

2016-07-28

Recent experimental studies suggest that nanosized gold nanoparticles (AuNPs) are able to penetrate into the deeper layer (epidermis and dermis) of rat and human skin. However, the mechanisms by which these AuNPs penetrate and disrupt the skin's lipid matrix are not well understood. In this study, we have used computer simulations to explore the translocation and the permeation of AuNPs through the model skin lipid membrane using both unconstrained and constrained coarse-grained molecular dynamics simulations. Each AuNP (1-6 nm) disrupted the bilayer packing and entered the interior of the bilayer rapidly (within 100 ns). It created a hydrophobic vacancy in the bilayer, which was mostly filled by skin constituents. Bigger AuNPs induced changes in the bilayer structure, and undulations were observed in the bilayer. The bilayer exhibited self-healing properties; it retained its original form once the simulation was run further after the removal of the AuNPs. Constrained simulation results showed that there was a trade-off between the kinetics and thermodynamics of AuNP permeation at a molecular scale. The combined effect of both resulted in a high permeation of small-sized AuNPs. The molecular-level information obtained through our simulations offers a very convenient method to design novel drug delivery systems and effective cosmetics.

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

PubMed

Vilseck, Jonah Z; Kostal, Jakub; Tirado-Rives, Julian; Jorgensen, William L

2015-10-15

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods. © 2015 Wiley Periodicals, Inc.

Tissue Acoustoelectric Effect Modeling From Solid Mechanics Theory.

PubMed

Song, Xizi; Qin, Yexian; Xu, Yanbin; Ingram, Pier; Witte, Russell S; Dong, Feng

2017-10-01

The acoustoelectric (AE) effect is a basic physical phenomenon, which underlies the changes made in the conductivity of a medium by the application of focused ultrasound. Recently, based on the AE effect, several biomedical imaging techniques have been widely studied, such as ultrasound-modulated electrical impedance tomography and ultrasound current source density imaging. To further investigate the mechanism of the AE effect in tissue and to provide guidance for such techniques, we have modeled the tissue AE effect using the theory of solid mechanics. Both bulk compression and thermal expansion of tissue are considered and discussed. Computation simulation shows that the muscle AE effect result, conductivity change rate, is 3.26×10 -3 with 4.3-MPa peak pressure, satisfying the theoretical value. Bulk compression plays the main role for muscle AE effect, while thermal expansion makes almost no contribution to it. In addition, the AE signals of porcine muscle are measured at different focal positions. With the same magnitude order and the same change trend, the experiment result confirms that the simulation result is effective. Both simulation and experimental results validate that tissue AE effect modeling using solid mechanics theory is feasible, which is of significance for the further development of related biomedical imaging techniques.

Mechanical properties and mechanism of single crystal Cu pillar by in situ TEM compression and molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Lin, Kai-Peng; Fang, Te-Hua; Lin, Ying-Jhin

2018-02-01

In this study, we investigate the mechanical properties of single-crystal copper (Cu) nanopillars. Critical deformation variations of Cu-nanopillared structures are estimated using in situ transmission electron microscopy compression tests and molecular dynamics simulations. The Young’s moduli of Cu nanopillars with diameters of 2-6 nm were 90.20-124.47 GPa. The contact stiffnesses of the Cu nanopillars with diameters of 400 and 500 nm were 1.33 and 3.86 N m-1, respectively; the Poisson’s ratios for these nanopillars were 0.32 and 0.33. The yield strength of the nanopillars varied from 0.25 GPa at 500 nm to 0.42 GPa at 400 nm; the yield strength of single-crystal Cu nanopillars decreased with increasing diameter. The values of the indented hardness of the Cu block were 0.27 and 1.06 GPa, respectively. Through experimental work and molecular dynamics simulations, we demonstrate that Cu nanopillars exhibit internal stress transmission during compression. When compression reaches the maximum strain, it can be observed that Cu slips. Our results are useful for understanding the mechanical properties, contact, and local deformation of Cu nanopillars.

Effect of simulated mechanical recycling processes on the structure and properties of poly(lactic acid).

PubMed

Beltrán, F R; Lorenzo, V; Acosta, J; de la Orden, M U; Martínez Urreaga, J

2018-06-15

The aim of this work is to study the effects of different simulated mechanical recycling processes on the structure and properties of PLA. A commercial grade of PLA was melt compounded and compression molded, then subjected to two different recycling processes. The first recycling process consisted of an accelerated ageing and a second melt processing step, while the other recycling process included an accelerated ageing, a demanding washing process and a second melt processing step. The intrinsic viscosity measurements indicate that both recycling processes produce a degradation in PLA, which is more pronounced in the sample subjected to the washing process. DSC results suggest an increase in the mobility of the polymer chains in the recycled materials; however the degree of crystallinity of PLA seems unchanged. The optical, mechanical and gas barrier properties of PLA do not seem to be largely affected by the degradation suffered during the different recycling processes. These results suggest that, despite the degradation of PLA, the impact of the different simulated mechanical recycling processes on the final properties is limited. Thus, the potential use of recycled PLA in packaging applications is not jeopardized. Copyright © 2017 Elsevier Ltd. All rights reserved.

Atomistic origin of size effects in fatigue behavior of metallic glasses

NASA Astrophysics Data System (ADS)

Sha, Zhendong; Wong, Wei Hin; Pei, Qingxiang; Branicio, Paulo Sergio; Liu, Zishun; Wang, Tiejun; Guo, Tianfu; Gao, Huajian

2017-07-01

While many experiments and simulations on metallic glasses (MGs) have focused on their tensile ductility under monotonic loading, the fatigue mechanisms of MGs under cyclic loading still remain largely elusive. Here we perform molecular dynamics (MD) and finite element simulations of tension-compression fatigue tests in MGs to elucidate their fatigue mechanisms with focus on the sample size effect. Shear band (SB) thickening is found to be the inherent fatigue mechanism for nanoscale MGs. The difference in fatigue mechanisms between macroscopic and nanoscale MGs originates from whether the SB forms partially or fully through the cross-section of the specimen. Furthermore, a qualitative investigation of the sample size effect suggests that small sample size increases the fatigue life while large sample size promotes cyclic softening and necking. Our observations on the size-dependent fatigue behavior can be rationalized by the Gurson model and the concept of surface tension of the nanovoids. The present study sheds light on the fatigue mechanisms of MGs and can be useful in interpreting previous experimental results.

Evaluation of mechanical properties of Aluminum-Copper cold sprayed and alloy 625 wire arc sprayed coatings

NASA Astrophysics Data System (ADS)

Bashirzadeh, Milad

This study examines microstructural-based mechanical properties of Al-Cu composite deposited by cold spraying and wire arc sprayed nickel-based alloy 625 coating using numerical modeling and experimental techniques. The microhardness and elastic modulus of samples were determined using the Knoop hardness technique. Hardness in both transverse and longitudinal directions on the sample cross-sections has been measured. An image-based finite element simulation algorithm was employed to determine the mechanical properties through an inverse analysis. In addition mechanical tests including, tensile, bending, and nano-indentation tests were performed on alloy 625 wire arc sprayed samples. Overall, results from the experimental tests are in relatively good agreement for deposited Al-Cu composites and alloy 625 coating. However, results obtained from numerical simulation are significantly higher in value than experimentally obtained results. Examination and comparison of the results are strong indications of the influence of microstructure characteristics on the mechanical properties of thermally spray deposited coatings.

Theoretical study on mechanisms of structural rearrangement and ionic dissociation in the HCl(H 2O) 4 cluster with path-integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sugawara, Shuichi; Yoshikawa, Takehiro; Takayanagi, Toshiyuki; Tachikawa, Masanori

2011-01-01

The structural rearrangement process for the HCl(H2O)4 cluster has been studied by path-integral molecular dynamics simulations, where 'on-the-fly' calculation of the potential energy surface is done with the PM3-MAIS semiempirical level. The mechanisms of the rearrangement were analyzed using appropriate collective coordinates as well as detailed potential energy diagrams derived from low-lying stationary points. It was found that the vibrational entropy mainly determines the stability of the cluster structure especially at high temperatures. We have also found that the acidity of HCl in the cluster correlates with the coordination number of chlorine with respect water molecules.

Computer Simulation Studies of Ion Channel Gating: Characteristics of the M2 Channel of Influenza-A Virus in a Phospholipid Bilayer

NASA Technical Reports Server (NTRS)

Schweighofer, Karl J.; Pohorille, Andrew; DeVincenzi, D. (Technical Monitor)

1999-01-01

The 25 amino acids long, transmembrane fragment of the Influenza virus M2 protein forms a homotetrameric channel that transports protons across lipid bilayers. It has been postulated that high efficiency and selectivity of this process is due to gating by four histidine residues that occlude the channel lumen in the closed state. Two mechanisms of gating have been postulated. In one mechanism, the proton is "shuttled" through the gate by attaching to the delta nitrogen atom on the extracellular side of the imidazole ring, followed by the release of the proton attached to the epsilon nitrogen atom on the opposite side. In the second mechanism, the four histidines move away from each other due to electrostatic repulsion upon protonation, thus opening the gate sufficiently that a wire of water molecules can penetrate the gate. Then, protons are transported by "hopping" along the wire. In this paper, both mechanisms are evaluated in a series of molecular dynamics simulations by investigating stability of different protonation states of the channel that are involved in these mechanisms. For the shuttle mechanism, these are states with all epsilon protonated histidines, one biprotonated residue or one histidine protonated in the delta position. For the gate opening mechanism, this is the state in which all four histidines are biprotonated. In addition, a state with two biprotonated histidines is considered. For each system, composed of the protein channel embedded in phospholipid bilayer located between two water lamellae, a molecular dynamics trajectory of approximately 1.3 ns (after equilibration) was obtained. It is found that the states involved in the shuttle mechanism are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfers involved in the shuttle. In contract, the fully biprotonated state, implicated in the gate opening mechanism, is not stable and the channel looses its structural integrity. If only two histidines are biprotonated the channel deforms but remains intact with the gate mostly closed. In summary, the results of this study lend support to the shuttle mechanism but not to the gate opening mechanism of proton gating in M2.

Mechanical and electrochemical response of a LiCoO 2 cathode using reconstructed microstructures

DOE PAGES

Mendoza, Hector; Roberts, Scott Alan; Brunini, Victor; ...

2016-01-01

As LiCoO 2 cathodes are charged, delithiation of the LiCoO 2 active material leads to an increase in the lattice spacing, causing swelling of the particles. When these particles are packed into a bicontinuous, percolated network, as is the case in a battery electrode, this swelling leads to the generation of significant mechanical stress. In this study we performed coupled electrochemical-mechanical simulations of the charging of a LiCoO 2 cathode in order to elucidate the mechanisms of stress generation and the effect of charge rate and microstructure on these stresses. Energy dispersive spectroscopy combined with scanning electron microscopy imaging wasmore » used to create 3D reconstructions of a LiCoO 2 cathode, and the Conformal Decomposition Finite Element Method is used to automatically generate computational meshes on this reconstructed microstructure. Replacement of the ideal solution Fickian diffusion model, typically used in battery simulations, with a more general non-ideal solution model shows substantially smaller gradients of lithium within particles than is typically observed in the literature. Using this more general model, lithium gradients only appear at states of charge where the open-circuit voltage is relatively constant. While lithium gradients do affect the mechanical stress state in the particles, the maximum stresses are always found in the fully-charged state and are strongly affected by the local details of the microstructure and particle-to-particle contacts. These coupled electrochemical-mechanical simulations begin to yield insight into the partitioning of volume change between reducing pore space and macroscopically swelling the electrode. Lastly, preliminary studies that include the presence of the polymeric binder suggest that it can greatly impact stress generation and that it is an important area for future research.« less

Fluid-driven fracture propagation in heterogeneous media: Probability distributions of fracture trajectories

NASA Astrophysics Data System (ADS)

Santillán, David; Mosquera, Juan-Carlos; Cueto-Felgueroso, Luis

2017-11-01

Hydraulic fracture trajectories in rocks and other materials are highly affected by spatial heterogeneity in their mechanical properties. Understanding the complexity and structure of fluid-driven fractures and their deviation from the predictions of homogenized theories is a practical problem in engineering and geoscience. We conduct a Monte Carlo simulation study to characterize the influence of heterogeneous mechanical properties on the trajectories of hydraulic fractures propagating in elastic media. We generate a large number of random fields of mechanical properties and simulate pressure-driven fracture propagation using a phase-field model. We model the mechanical response of the material as that of an elastic isotropic material with heterogeneous Young modulus and Griffith energy release rate, assuming that fractures propagate in the toughness-dominated regime. Our study shows that the variance and the spatial covariance of the mechanical properties are controlling factors in the tortuousness of the fracture paths. We characterize the deviation of fracture paths from the homogenous case statistically, and conclude that the maximum deviation grows linearly with the distance from the injection point. Additionally, fracture path deviations seem to be normally distributed, suggesting that fracture propagation in the toughness-dominated regime may be described as a random walk.

Organization of the cytokeratin network in an epithelial cell.

PubMed

Portet, Stéphanie; Arino, Ovide; Vassy, Jany; Schoëvaërt, Damien

2003-08-07

The cytoskeleton is a dynamic three-dimensional structure mainly located in the cytoplasm. It is involved in many cell functions such as mechanical signal transduction and maintenance of cell integrity. Among the three cytoskeletal components, intermediate filaments (the cytokeratin in epithelial cells) are the best candidates for this mechanical role. A model of the establishment of the cytokeratin network of an epithelial cell is proposed to study the dependence of its structural organization on extracellular mechanical environment. To implicitly describe the latter and its effects on the intracellular domain, we use mechanically regulated protein synthesis. Our model is a hybrid of a partial differential equation of parabolic type, governing the evolution of the concentration of cytokeratin, and a set of stochastic differential equations describing the dynamics of filaments. Each filament is described by a stochastic differential equation that reflects both the local interactions with the environment and the non-local interactions via the past history of the filament. A three-dimensional simulation model is derived from this mathematical model. This simulation model is then used to obtain examples of cytokeratin network architectures under given mechanical conditions, and to study the influence of several parameters.

Fluid-driven fracture propagation in heterogeneous media: Probability distributions of fracture trajectories.

PubMed

Santillán, David; Mosquera, Juan-Carlos; Cueto-Felgueroso, Luis

2017-11-01

Hydraulic fracture trajectories in rocks and other materials are highly affected by spatial heterogeneity in their mechanical properties. Understanding the complexity and structure of fluid-driven fractures and their deviation from the predictions of homogenized theories is a practical problem in engineering and geoscience. We conduct a Monte Carlo simulation study to characterize the influence of heterogeneous mechanical properties on the trajectories of hydraulic fractures propagating in elastic media. We generate a large number of random fields of mechanical properties and simulate pressure-driven fracture propagation using a phase-field model. We model the mechanical response of the material as that of an elastic isotropic material with heterogeneous Young modulus and Griffith energy release rate, assuming that fractures propagate in the toughness-dominated regime. Our study shows that the variance and the spatial covariance of the mechanical properties are controlling factors in the tortuousness of the fracture paths. We characterize the deviation of fracture paths from the homogenous case statistically, and conclude that the maximum deviation grows linearly with the distance from the injection point. Additionally, fracture path deviations seem to be normally distributed, suggesting that fracture propagation in the toughness-dominated regime may be described as a random walk.

Detection of plasticity mechanisms in an energetic molecular crystal through shock-like 3D unidirectional compressions: A Molecular Dynamics study

NASA Astrophysics Data System (ADS)

Lafourcade, Paul; Denoual, Christophe; Maillet, Jean-Bernard

2017-06-01

TATB crystal structure consists in graphitic-like sheets arranged in the a-b plane where a, b and c define the edge vectors of the unit cell. This type of stacking provides the TATB monocrystal very anisotropic physical, chemical and mechanical properties. In order to explore which mechanisms are involved in TATB plasticity, we use a Molecular Dynamics code in which the overall deformation is prescribed as a function of time, for any deformation path. Furthermore, a computation of the Green-Lagrange strain tensor is proposed, which helps reveal various defects and plasticity mechanisms. Through prescribed large strain of shock-like deformations, a three-dimensional characterization of TATB monocrystal yield stress has been obtained, confirming the very anisotropic behavior of this energetic material. Various plasticity mechanisms are triggered during these simulations, including counter intuitive defects onset such as gliding along transveral planes containing perfect dislocations and twinning. Gliding in the a-b plane occurs systematically and does not lead to significant plastic behavior, in accordance with a previous study on dislocation core structures for this plane, based on a coupling between the Peierls-Nabarro-Galerkin method and Molecular Dynamics simulations.

The Influence of Altering Push Force Effectiveness on Upper Extremity Demand during Wheelchair Propulsion

PubMed Central

Rankin, Jeffery W.; Kwarciak, Andrew M.; Richter, W. Mark; Neptune, Richard R.

2010-01-01

Manual wheelchair propulsion has been linked to a high incidence of overuse injury and pain in the upper extremity, which may be caused by the high load requirements and low mechanical efficiency of the task. Previous studies have suggested that poor mechanical efficiency may be due to a low effective handrim force (i.e. applied force that is not directed tangential to the handrim). As a result, studies attempting to reduce upper extremity demand have used various measures of force effectiveness (e.g. fraction effective force, FEF) as a guide for modifying propulsion technique, developing rehabilitation programs and configuring wheelchairs. However, the relationship between FEF and upper extremity demand is not well understood. The purpose of this study was to use forward dynamics simulations of wheelchair propulsion to determine the influence of FEF on upper extremity demand by quantifying individual muscle stress, work and handrim force contributions at different values of FEF. Simulations maximizing and minimizing FEF resulted in higher average muscle stresses (23% and 112%) and total muscle work (28% and 71%) compared to a nominal FEF simulation. The maximal FEF simulation also shifted muscle use from muscles crossing the elbow to those at the shoulder (e.g. rotator cuff muscles), placing greater demand on shoulder muscles during propulsion. The optimal FEF value appears to represent a balance between increasing push force effectiveness to increase mechanical efficiency and minimizing upper extremity demand. Thus, care should be taken in using force effectiveness as a metric to reduce upper extremity demand. PMID:20674921

Optimized deformation behavior of a dielectric elastomer generator

NASA Astrophysics Data System (ADS)

Foerster, Florentine; Schlaak, Helmut F.

2014-03-01

Dielectric elastomer generators (DEGs) produce electrical energy by converting mechanical into electrical energy. Efficient operation requires an optimal deformation of the DEG during the energy harvesting cycle. However, the deformation resulting from an external load has to be applied to the DEG. The deformation behavior of the DEG is dependent on the type of the mechanical interconnection between the elastic DEG and a stiff support area. The maximization of the capacitance of the DEG in the deformed state leads to the maximum absolute energy gain. Therefore several configurations of mechanical interconnections between a single DEG module as well as multiple stacked DEG modules and stiff supports are investigated in order to find the optimal mechanical interconnection. The investigation is done with numerical simulations using the FEM software ANSYS. A DEG module consists of 50 active dielectric layers with a single layer thickness of 50 μm. The elastomer material is silicone (PDMS) while the compliant electrodes are made of graphite powder. In the simulation the real material parameters of the PDMS and the graphite electrodes are included to compare simulation results to experimental investigations in the future. The numerical simulations of the several configurations are carried out as coupled electro-mechanical simulation for the first step in an energy harvesting cycle with constant external load strain. The simulation results are discussed and an optimal mechanical interconnection between DEG modules and stiff supports is derived.

Development of interatomic potential of Ge(1- x - y )Si x Sn y ternary alloy semiconductors for classical lattice dynamics simulation

NASA Astrophysics Data System (ADS)

Tomita, Motohiro; Ogasawara, Masataka; Terada, Takuya; Watanabe, Takanobu

2018-04-01

We provide the parameters of Stillinger-Weber potentials for GeSiSn ternary mixed systems. These parameters can be used in molecular dynamics (MD) simulations to reproduce phonon properties and thermal conductivities. The phonon dispersion relation is derived from the dynamical structure factor, which is calculated by the space-time Fourier transform of atomic trajectories in an MD simulation. The phonon properties and thermal conductivities of GeSiSn ternary crystals calculated using these parameters mostly reproduced both the findings of previous experiments and earlier calculations made using MD simulations. The atomic composition dependence of these properties in GeSiSn ternary crystals obtained by previous studies (both experimental and theoretical) and the calculated data were almost exactly reproduced by our proposed parameters. Moreover, the results of the MD simulation agree with the previous calculations made using a time-independent phonon Boltzmann transport equation with complicated scattering mechanisms. These scattering mechanisms are very important in complicated nanostructures, as they allow the heat-transfer properties to be more accurately calculated by MD simulations. This work enables us to predict the phonon- and heat-related properties of bulk group IV alloys, especially ternary alloys.

Effects of dimensionality on kinetic simulations of laser-ion acceleration in the transparency regime

NASA Astrophysics Data System (ADS)

Stark, D. J.; Yin, L.; Albright, B. J.; Guo, F.

2017-05-01

A particle-in-cell study of laser-ion acceleration mechanisms in the transparency regime illustrates how two-dimensional (2D) S and P simulations (laser polarization in and out of the simulation plane, respectively) capture different physics characterizing these systems, visible in their entirety often in cost-prohibitive three-dimensional (3D) simulations. The electron momentum anisotropy induced in the target by a laser pulse is dramatically different in the two 2D cases, manifested in differences in target expansion timescales, electric field strengths, and density thresholds for the onset of relativistically induced transparency. In particular, 2D-P simulations exhibit dramatically greater electron heating in the simulation plane, whereas 2D-S ones show a much more isotropic energy distribution, similar to 3D. An ion trajectory analysis allows one to isolate the fields responsible for ion acceleration and to characterize the acceleration regimes in time and space. The artificial longitudinal electron heating in 2D-P exaggerates the effectiveness of target-normal sheath acceleration into its dominant acceleration mechanism throughout the laser-plasma interaction, whereas 2D-S and 3D both have sizable populations accelerated preferentially during transparency.

Modeling of optical mirror and electromechanical behavior

NASA Astrophysics Data System (ADS)

Wang, Fang; Lu, Chao; Liu, Zishun; Liu, Ai Q.; Zhang, Xu M.

2001-10-01

This paper presents finite element (FE) simulation and theoretical analysis of novel MEMS fiber-optical switches actuated by electrostatic attraction. FE simulation for the switches under static and dynamic loading are first carried out to reveal the mechanical characteristics of the minimum or critical switching voltages, the natural frequencies, mode shapes and response under different levels of electrostatic attraction load. To validate the FE simulation results, a theoretical (or analytical) model is then developed for one specific switch, i.e., Plate_40_104. Good agreement is found between the FE simulation and the analytical results. From both FE simulation and theoretical analysis, the critical switching voltage for Plate_40_104 is derived to be 238 V for the switching angel of 12 degree(s). The critical switching on and off times are 431 microsecond(s) and 67 microsecond(s) , respectively. The present study not only develops good FE and analytical models, but also demonstrates step by step a method to simplify a real optical switch structure with reference to the FE simulation results for analytical purpose. With the FE and analytical models, it is easy to obtain any information about the mechanical behaviors of the optical switches, which are helpful in yielding optimized design.

Effects of dimensionality on kinetic simulations of laser-ion acceleration in the transparency regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stark, David James; Yin, Lin; Albright, Brian James

2017-05-03

A particle-in-cell study of laser-ion acceleration mechanisms in the transparency regime illustrates how two-dimensional (2D) S and P simulations (laser polarization in and out of the simulation plane, respectively) capture different physics characterizing these systems, visible in their entirety in often cost-prohibitive three-dimensional (3D) simulations. The electron momentum anisotropy induced in the target by the laser pulse is dramatically different in the two 2D cases, manifested in differences in target expansion timescales, electric field strengths, and density thresholds for the onset of relativistically induced transparency. In particular, 2D-P simulations exhibit dramatically greater electron heating in the simulation plane, whereas 2D-Smore » ones show a much more isotropic energy distribution, similar to 3D. An ion trajectory analysis allows one to isolate the fields responsible for ion acceleration and to characterize the acceleration regimes in time and space. The artificial longitudinal electron heating in 2D-P exaggerates the effectiveness of target-normal sheath acceleration into its dominant acceleration mechanism throughout the laser-plasma interaction, whereas 2D-S and 3D both have sizable populations accelerated preferentially during transparency.« less

Development of the dynamic motion simulator of 3D micro-gravity with a combined passive/active suspension system

NASA Technical Reports Server (NTRS)

Yoshida, Kazuya; Hirose, Shigeo; Ogawa, Tadashi

1994-01-01

The establishment of those in-orbit operations like 'Rendez-Vous/Docking' and 'Manipulator Berthing' with the assistance of robotics or autonomous control technology, is essential for the near future space programs. In order to study the control methods, develop the flight models, and verify how the system works, we need a tool or a testbed which enables us to simulate mechanically the micro-gravity environment. There have been many attempts to develop the micro-gravity testbeds, but once the simulation goes into the docking and berthing operation that involves mechanical contacts among multi bodies, the requirement becomes critical. A group at the Tokyo Institute of Technology has proposed a method that can simulate the 3D micro-gravity producing a smooth response to the impact phenomena with relatively simple apparatus. Recently the group carried out basic experiments successfully using a prototype hardware model of the testbed. This paper will present our idea of the 3D micro-gravity simulator and report the results of our initial experiments.

Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Nagaya, Kiyonobu; Shimojo, Fuyuki; Yao, Makoto

2015-08-01

The dynamic properties of liquid B2O3 under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B2O3 shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8).

A parameters optimization method for planar joint clearance model and its application for dynamics simulation of reciprocating compressor

NASA Astrophysics Data System (ADS)

Hai-yang, Zhao; Min-qiang, Xu; Jin-dong, Wang; Yong-bo, Li

2015-05-01

In order to improve the accuracy of dynamics response simulation for mechanism with joint clearance, a parameter optimization method for planar joint clearance contact force model was presented in this paper, and the optimized parameters were applied to the dynamics response simulation for mechanism with oversized joint clearance fault. By studying the effect of increased clearance on the parameters of joint clearance contact force model, the relation of model parameters between different clearances was concluded. Then the dynamic equation of a two-stage reciprocating compressor with four joint clearances was developed using Lagrange method, and a multi-body dynamic model built in ADAMS software was used to solve this equation. To obtain a simulated dynamic response much closer to that of experimental tests, the parameters of joint clearance model, instead of using the designed values, were optimized by genetic algorithms approach. Finally, the optimized parameters were applied to simulate the dynamics response of model with oversized joint clearance fault according to the concluded parameter relation. The dynamics response of experimental test verified the effectiveness of this application.

Three-dimentional simulation of flow-induced platelet activation in artificial heart valves

NASA Astrophysics Data System (ADS)

Hedayat, Mohammadali; Asgharzadeh, Hafez; Borazjani, Iman

2015-11-01

Since the advent of heart valve, several valve types such as mechanical and bio-prosthetic valves have been designed. Mechanical Heart Valves (MHV) are durable but suffer from thromboembolic complications that caused by shear-induced platelet activation near the valve region. Bio-prosthetic Heart Valves (BHV) are known for better hemodynamics. However, they usually have a short average life time. Realistic simulations of heart valves in combination with platelet activation models can lead to a better understanding of the potential risk of thrombus formation in such devices. In this study, an Eulerian approach is developed to calculate the platelet activation in three-dimensional simulations of flow through MHV and BHV using a parallel overset-curvilinear immersed boundary technique. A curvilinear body-fitted grid is used for the flow simulation through the anatomic aorta, while the sharp-interface immersed boundary method is used for simulation of the Left Ventricle (LV) with prescribed motion. In addition, dynamics of valves were calculated numerically using under-relaxed strong-coupling algorithm. Finally, the platelet activation results for BMV and MHV are compared with each other.

Melittin Aggregation in Aqueous Solutions: Insight from Molecular Dynamics Simulations.

PubMed

Liao, Chenyi; Esai Selvan, Myvizhi; Zhao, Jun; Slimovitch, Jonathan L; Schneebeli, Severin T; Shelley, Mee; Shelley, John C; Li, Jianing

2015-08-20

Melittin is a natural peptide that aggregates in aqueous solutions with paradigmatic monomer-to-tetramer and coil-to-helix transitions. Since little is known about the molecular mechanisms of melittin aggregation in solution, we simulated its self-aggregation process under various conditions. After confirming the stability of a melittin tetramer in solution, we observed—for the first time in atomistic detail—that four separated melittin monomers aggregate into a tetramer. Our simulated dependence of melittin aggregation on peptide concentration, temperature, and ionic strength is in good agreement with prior experiments. We propose that melittin mainly self-aggregates via a mechanism involving the sequential addition of monomers, which is supported by both qualitative and quantitative evidence obtained from unbiased and metadynamics simulations. Moreover, by combining computer simulations and a theory of the electrical double layer, we provide evidence to suggest why melittin aggregation in solution likely stops at the tetramer, rather than forming higher-order oligomers. Overall, our study not only explains prior experimental results at the molecular level but also provides quantitative mechanistic information that may guide the engineering of melittin for higher efficacy and safety.

Multiscale mechanics of graphene oxide and graphene based composite films

NASA Astrophysics Data System (ADS)

Cao, Changhong

The mechanical behavior of graphene oxide is length scale dependent: orders of magnitude different between the bulk forms and monolayer counterparts. Understanding the underlying mechanisms plays a significant role in their versatile application. A systematic multiscale mechanical study from monolayer to multilayer, including the interactions between layers of GO, can provide fundamental support for material engineering. In this thesis, an experimental coupled with simulation approach was used to study the multiscale mechanics of graphene oxide (GO) and the methods developed for GO study are proved to be applicable also to mechanical study of graphene based composites. GO is a layered nanomaterial comprised of hierarchical units whose characteristic dimension lies between monolayer GO (0.7 nm - 1.2 nm) and bulk GO papers (≥ 1 mum). Mechanical behaviors of monolayer GO and GO nanosheets (10 nm- 100 nm) were comprehensively studied this work. Monolayer GO was measured to have an average strength of 24.7 GPa,, orders of magnitude higher than previously reported values for GO paper and approximately 50% of the 2D intrinsic strength of pristine graphene. The huge discrepancy between the strength of monolayer GO and that of bulk GO paper motivated the study of GO at the intermediate length scale (GO nanosheets). Experimental results showed that GO nanosheets possess high strength in the gigapascal range. Molecular Dynamic simulations showed that the transition in the failure behavior from interplanar fracture to intraplanar fracture was responsible for the huge strength discrepancy between nanometer scale GO and bulk GO papers. Additionally, the interfacial shear strength between GO layers was found to be a key contributing factor to the distinct mechanical behavior among hierarchical units of GO. The understanding of the multiscale mechanics of GO is transferrable in heterogeneous layered nanomaterials, such as graphene-metal oxide based anode materials in Li-ion batteries. The novel methods developed in this work to study GO multilayered structures were also applied to study the mechanics of graphene-TiO 2 composites. It was found that a critical thickness range of TiO2 deposition on graphene is required for the observed stiffness enhancement effect of graphene to influence the mechanical behavior of the composite.

Mechanical characterization of diesel soot nanoparticles: in situ compression in a transmission electron microscope and simulations

NASA Astrophysics Data System (ADS)

Jenei, Istvan Zoltan; Dassenoy, Fabrice; Epicier, Thierry; Khajeh, Arash; Martini, Ashlie; Uy, Dairene; Ghaednia, Hamed; Gangopadhyay, Arup

2018-02-01

Incomplete fuel burning inside an internal combustion engine results in the creation of soot in the form of nanoparticles. Some of these soot nanoparticles (SNP) become adsorbed into the lubricating oil film present on the cylinder walls, which adversely affects the tribological performance of the lubricant. In order to better understand the mechanisms underlying the wear caused by SNPs, it is important to understand the behavior of SNPs and to characterize potential changes in their mechanical properties (e.g. hardness) caused by (or during) mechanical stress. In this study, the behavior of individual SNPs originating from diesel engines was studied under compression. The experiments were performed in a transmission electron microscope using a nanoindentation device. The nanoparticles exhibited elasto-plastic behavior in response to consecutive compression cycles. From the experimental data, the Young’s modulus and hardness of the SNPs were calculated. The Young’s modulus and hardness of the nanoparticles increased with the number of compression cycles. Using an electron energy loss spectroscopy technique, it was shown that the sp2/sp3 ratio within the compressed nanoparticle decreases, which is suggested to be the cause of the increase in elasticity and hardness. In order to corroborate the experimental findings, molecular dynamics simulations of a model SNP were performed. The SNP model was constructed using carbon and hydrogen atoms with morphology and composition comparable to those observed in the experiment. The model SNP was subjected to repeated compressions between two virtual rigid walls. During the simulation, the nanoparticle exhibited elasto-plastic behavior like that in the experiments. The results of the simulations confirm that the increase in the elastic modulus and hardness is associated with a decrease in the sp2/sp3 ratio.

Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β42 monomer: insights from molecular dynamics simulations.

PubMed

Shuaib, Suniba; Goyal, Bhupesh

2018-02-01

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β 42 (Aβ 42 ) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ 42 aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ 42 . MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ 42 by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aβ 42 monomer. Overall, MD simulations reveal that C1 inhibits Aβ 42 aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ 42 .

Mechanical characterization of diesel soot nanoparticles: in situ compression in a transmission electron microscope and simulations.

PubMed

Jenei, Istvan Zoltan; Dassenoy, Fabrice; Epicier, Thierry; Khajeh, Arash; Martini, Ashlie; Uy, Dairene; Ghaednia, Hamed; Gangopadhyay, Arup

2018-02-23

Incomplete fuel burning inside an internal combustion engine results in the creation of soot in the form of nanoparticles. Some of these soot nanoparticles (SNP) become adsorbed into the lubricating oil film present on the cylinder walls, which adversely affects the tribological performance of the lubricant. In order to better understand the mechanisms underlying the wear caused by SNPs, it is important to understand the behavior of SNPs and to characterize potential changes in their mechanical properties (e.g. hardness) caused by (or during) mechanical stress. In this study, the behavior of individual SNPs originating from diesel engines was studied under compression. The experiments were performed in a transmission electron microscope using a nanoindentation device. The nanoparticles exhibited elasto-plastic behavior in response to consecutive compression cycles. From the experimental data, the Young's modulus and hardness of the SNPs were calculated. The Young's modulus and hardness of the nanoparticles increased with the number of compression cycles. Using an electron energy loss spectroscopy technique, it was shown that the sp 2 /sp 3 ratio within the compressed nanoparticle decreases, which is suggested to be the cause of the increase in elasticity and hardness. In order to corroborate the experimental findings, molecular dynamics simulations of a model SNP were performed. The SNP model was constructed using carbon and hydrogen atoms with morphology and composition comparable to those observed in the experiment. The model SNP was subjected to repeated compressions between two virtual rigid walls. During the simulation, the nanoparticle exhibited elasto-plastic behavior like that in the experiments. The results of the simulations confirm that the increase in the elastic modulus and hardness is associated with a decrease in the sp 2 /sp 3 ratio.

Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer†

PubMed Central

Song, Yuhua; Guallar, Victor; Baker, Nathan A.

2008-01-01

Salicylate, an amphiphilic molecule and a popular member of non-steroidal antiinflammatory drug family, is known to affect hearing through reduction of the electromechanical coupling in the outer hair cells of the ear. This reduction of electromotility by salicylate has been widely studied but the molecular mechanism of the phenomenon is still unknown. In this study, we investigated one aspect of salicylate’s action; namely, the perturbation of electrical and mechanical membrane properties by salicylate in the absence of cytoskeletal or membrane-bound motor proteins such as prestin. In particular, we simulated the interaction of salicylate with a dipalmitoylphosphatidylcholine (DPPC) bilayer via atomically-detailed molecular dynamics simulations to observe the effect of salicylate on the microscopic and mesoscopic properties of the bilayer. The results demonstrate that salicylate interacts with the bilayer by associating at the water-DPPC interface in a nearly perpendicular orientation and penetrating more deeply into the bilayer than either sodium or chloride. This association has several affects on the membrane properties. First, binding of salicylate to the membrane displaces chloride from the bilayer-water interface. Second, salicylate influences the electrostatic potential and dielectric properties of the bilayer, with significant changes at the water-lipid bilayer interface. Third, salicylate association results in structural changes including decreased head group area per lipid and increased lipid tail order. However, salicylate does not significantly alter the mechanical properties of the DPPC bilayer; bulk compressibility, area compressibility, and bending modulus were only perturbed by small, statistically-insignificant amounts, by the presence of salicylate. The observations from these simulations are in qualitative agreement with experimental data and support the conclusion that salicylate influences the electrical but not the mechanical properties of DPPC membranes. PMID:16216066

Inverse modeling of ground surface uplift and pressure with iTOUGH-PEST and TOUGH-FLAC: The case of CO2 injection at In Salah, Algeria

NASA Astrophysics Data System (ADS)

Rinaldi, Antonio P.; Rutqvist, Jonny; Finsterle, Stefan; Liu, Hui-Hai

2017-11-01

Ground deformation, commonly observed in storage projects, carries useful information about processes occurring in the injection formation. The Krechba gas field at In Salah (Algeria) is one of the best-known sites for studying ground surface deformation during geological carbon storage. At this first industrial-scale on-shore CO2 demonstration project, satellite-based ground-deformation monitoring data of high quality are available and used to study the large-scale hydrological and geomechanical response of the system to injection. In this work, we carry out coupled fluid flow and geomechanical simulations to understand the uplift at three different CO2 injection wells (KB-501, KB-502, KB-503). Previous numerical studies focused on the KB-502 injection well, where a double-lobe uplift pattern has been observed in the ground-deformation data. The observed uplift patterns at KB-501 and KB-503 have single-lobe patterns, but they can also indicate a deep fracture zone mechanical response to the injection. The current study improves the previous modeling approach by introducing an injection reservoir and a fracture zone, both responding to a Mohr-Coulomb failure criterion. In addition, we model a stress-dependent permeability and bulk modulus, according to a dual continuum model. Mechanical and hydraulic properties are determined through inverse modeling by matching the simulated spatial and temporal evolution of uplift to InSAR observations as well as by matching simulated and measured pressures. The numerical simulations are in agreement with both spatial and temporal observations. The estimated values for the parameterized mechanical and hydraulic properties are in good agreement with previous numerical results. In addition, the formal joint inversion of hydrogeological and geomechanical data provides measures of the estimation uncertainty.

Inverse modeling of ground surface uplift and pressure with iTOUGH-PEST and TOUGH-FLAC: The case of CO2 injection at In Salah, Algeria

DOE PAGES

Rinaldi, Antonio P.; Rutqvist, Jonny; Finsterle, Stefan; ...

2016-10-24

Ground deformation, commonly seen in storage projects, carries useful information about processes occurring in the injection formation. The Krechba gas field at In Salah (Algeria) is one of the best-known sites for studying ground surface deformation during geological carbon storage. At this first industrial-scale on-shore CO 2 demonstration project, satellite-based ground-deformation monitoring data of high quality are available and used to study the large-scale hydrological and geomechanical response of the system to injection. In this work, we carry out coupled fluid flow and geomechanical simulations to understand the uplift at three different CO 2 injection wells (KB-501, KB-502, KB-503). Previousmore » numerical studies focused on the KB-502 injection well, where a double-lobe uplift pattern has been observed in the ground-deformation data. The observed uplift patterns at KB-501 and KB-503 have single-lobe patterns, but they can also indicate a deep fracture zone mechanical response to the injection.The current study improves the previous modeling approach by introducing an injection reservoir and a fracture zone, both responding to a Mohr-Coulomb failure criterion. In addition, we model a stress-dependent permeability and bulk modulus, according to a dual continuum model. Mechanical and hydraulic properties are determined through inverse modeling by matching the simulated spatial and temporal evolution of uplift to InSAR observations as well as by matching simulated and measured pressures. The numerical simulations are in agreement with both spatial and temporal observations. The estimated values for the parameterized mechanical and hydraulic properties are in good agreement with previous numerical results. In addition, the formal joint inversion of hydrogeological and geomechanical data provides measures of the estimation uncertainty.« less

Understanding the mechanism of LCST phase separation of mixed ionic liquids in water by MD simulations.

PubMed

Zhao, Yuling; Wang, Huiyong; Pei, Yuanchao; Liu, Zhiping; Wang, Jianji

2016-08-17

Recently, it has been found experimentally that two different amino acid ionic liquids (ILs) can be mixed to show unique lowest critical solution temperature (LCST) phase separation in water. However, little is known about the mechanism of phase separation in these IL/water mixtures at the molecular level. In this work, five kinds of amino acid ILs were chosen to study the mechanism of LCST-type phase separation by molecular dynamics (MD) simulations. Toward this end, a series of all-atom MD simulations were carried out on the ternary mixtures consisting of two different ILs and water at different temperatures. The various interaction energies and radial distribution functions (RDFs) were calculated and analyzed for these mixed systems. It was found that for amino acid ILs, the -NH2 or -COOH group of one anion could have a hydrogen bonding interaction with the -COO(-) group of another anion. With the increase of temperature, this kind of hydrogen bonding interaction between anions was strengthened and then the anion-H2O electrostatic interaction was weakened, which led to the LCST-type phase separation of the mixed ILs in water. In addition, a series of MD simulations for [P6668]1[Lys]n[Asp]1-n/H2O systems were also performed to study the effect of the mixing ratio of ILs on phase separation. It was also noted that the experimental critical composition corresponding to the lowest critical solution temperature was well predicted from the total electrostatic interaction energies as a function of mole fraction of [P6668][Lys] in these systems. The conclusions drawn from this study may provide new insight into the LCST-type phase behavior of ILs in water, and motivate further studies on practical applications.

Control of cardiac alternans by mechanical and electrical feedback.

PubMed

Yapari, Felicia; Deshpande, Dipen; Belhamadia, Youssef; Dubljevic, Stevan

2014-07-01

A persistent alternation in the cardiac action potential duration has been linked to the onset of ventricular arrhythmia, which may lead to sudden cardiac death. A coupling between these cardiac alternans and the intracellular calcium dynamics has also been identified in previous studies. In this paper, the system of PDEs describing the small amplitude of alternans and the alternation of peak intracellular Ca(2+) are stabilized by optimal boundary and spatially distributed actuation. A simulation study demonstrating the successful annihilation of both alternans on a one-dimensional cable of cardiac cells by utilizing the full-state feedback controller is presented. Complimentary to these studies, a three variable Nash-Panfilov model is used to investigate alternans annihilation via mechanical (or stretch) perturbations. The coupled model includes the active stress which defines the mechanical properties of the tissue and is utilized in the feedback algorithm as an independent input from the pacing based controller realization in alternans annihilation. Simulation studies of both control methods demonstrate that the proposed methods can successfully annihilate alternans in cables that are significantly longer than 1 cm, thus overcoming the limitations of earlier control efforts.

A perturbation analysis of a mechanical model for stable spatial patterning in embryology

NASA Astrophysics Data System (ADS)

Bentil, D. E.; Murray, J. D.

1992-12-01

We investigate a mechanical cell-traction mechanism that generates stationary spatial patterns. A linear analysis highlights the model's potential for these heterogeneous solutions. We use multiple-scale perturbation techniques to study the evolution of these solutions and compare our solutions with numerical simulations of the model system. We discuss some potential biological applications among which are the formation of ridge patterns, dermatoglyphs, and wound healing.

Seeing the World through Another Person's Eyes: Simulating Selective Attention via Action Observation

ERIC Educational Resources Information Center

Frischen, Alexandra; Loach, Daniel; Tipper, Steven P.

2009-01-01

Selective attention is usually considered an egocentric mechanism, biasing sensory information based on its behavioural relevance to oneself. This study provides evidence for an equivalent allocentric mechanism that allows passive observers to selectively attend to information from the perspective of another person. In a negative priming task,…

Large Eddy Simulation of Turbulent Combustion

DTIC Science & Technology

2006-03-15

described accurately by the skeletal mechanism , usually the major reactants and products, NO and NO2 if we are interested in NOx formation, and any...LARGE EDDY SIMULATION OF TURBULENT COMBUSTION Principle Investigator: Heinz Pitsch Flow Physics and Computation Department of Mechanical Engineering ...are identified. These de- tailed mechanisms are reduced independently for various conditions and accuracy requirements. The skeletal mechanisms form

Dislocation mechanisms in stressed crystals with surface effects

NASA Astrophysics Data System (ADS)

Wu, Chi-Chin; Crone, Joshua; Munday, Lynn; Discrete Dislocation Dynamics Team

2014-03-01

Understanding dislocation properties in stressed crystals is the key for important processes in materials science, including the strengthening of metals and the stress relaxation during the growth of hetero-epitaxial structures. Despite existing experimental approaches and theories, many dislocation mechanisms with surface effects still remain elusive in experiments. Even though discrete dislocation dynamics (DDD) simulations are commonly employed to study dislocations, few demonstrate sufficient computational capabilities for massive dislocations with the combined effects of surfaces and stresses. Utilizing the Army's newly developed FED3 code, a DDD computation code coupled with finite elements, this work presents several dislocation mechanisms near different types of surfaces in finite domains. Our simulation models include dislocations in a bended metallic cantilever beam, near voids in stressed metals, as well as threading and misfit dislocations in as-grown semiconductor epitaxial layers and their quantitative inter-correlations to stress relaxation and surface instability. Our studies provide not only detailed physics of individual dislocation mechanisms, but also important collective dislocation properties such as dislocation densities and strain-stress profiles and their interactions with surfaces.

Bone fracture healing in mechanobiological modeling: A review of principles and methods.

PubMed

Ghiasi, Mohammad S; Chen, Jason; Vaziri, Ashkan; Rodriguez, Edward K; Nazarian, Ara

2017-06-01

Bone fracture is a very common body injury. The healing process is physiologically complex, involving both biological and mechanical aspects. Following a fracture, cell migration, cell/tissue differentiation, tissue synthesis, and cytokine and growth factor release occur, regulated by the mechanical environment. Over the past decade, bone healing simulation and modeling has been employed to understand its details and mechanisms, to investigate specific clinical questions, and to design healing strategies. The goal of this effort is to review the history and the most recent work in bone healing simulations with an emphasis on both biological and mechanical properties. Therefore, we provide a brief review of the biology of bone fracture repair, followed by an outline of the key growth factors and mechanical factors influencing it. We then compare different methodologies of bone healing simulation, including conceptual modeling (qualitative modeling of bone healing to understand the general mechanisms), biological modeling (considering only the biological factors and processes), and mechanobiological modeling (considering both biological aspects and mechanical environment). Finally we evaluate different components and clinical applications of bone healing simulation such as mechanical stimuli, phases of bone healing, and angiogenesis.

Research of mechanics of the compact bone microvolume and porous ceramics under uniaxial compression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolmakova, T. V., E-mail: kolmakova@ftf.tsu.ru; Buyakova, S. P., E-mail: sbuyakova@ispms.tsc.ru; Kul’kov, S. N., E-mail: kulkov@ms.tsc.ru

2015-11-17

The research results of the mechanics are presented and the effective mechanical characteristics under uniaxial compression of the simulative microvolume of the compact bone are defined subject to the direction of the collagen-mineral fibers, porosity and mineral content. The experimental studies of the mechanics are performed and the effective mechanical characteristics of the produced porous zirconium oxide ceramics are defined. The recommendations are developed on the selection of the ceramic samples designed to replace the fragment of the compact bone of a definite structure and mineral content.

Simulating direct shear tests with the Bullet physics library: A validation study.

PubMed

Izadi, Ehsan; Bezuijen, Adam

2018-01-01

This study focuses on the possible uses of physics engines, and more specifically the Bullet physics library, to simulate granular systems. Physics engines are employed extensively in the video gaming, animation and movie industries to create physically plausible scenes. They are designed to deliver a fast, stable, and optimal simulation of certain systems such as rigid bodies, soft bodies and fluids. This study focuses exclusively on simulating granular media in the context of rigid body dynamics with the Bullet physics library. The first step was to validate the results of the simulations of direct shear testing on uniform-sized metal beads on the basis of laboratory experiments. The difference in the average angle of mobilized frictions was found to be only 1.0°. In addition, a very close match was found between dilatancy in the laboratory samples and in the simulations. A comprehensive study was then conducted to determine the failure and post-failure mechanism. We conclude with the presentation of a simulation of a direct shear test on real soil which demonstrated that Bullet has all the capabilities needed to be used as software for simulating granular systems.

Temperature dependence of creep compliance of highly cross-linked epoxy: A molecular simulation study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khabaz, Fardin, E-mail: rajesh.khare@ttu.edu; Khare, Ketan S., E-mail: rajesh.khare@ttu.edu; Khare, Rajesh, E-mail: rajesh.khare@ttu.edu

2014-05-15

We have used molecular dynamics (MD) simulations to study the effect of temperature on the creep compliance of neat cross-linked epoxy. Experimental studies of mechanical behavior of cross-linked epoxy in literature commonly report creep compliance values, whereas molecular simulations of these systems have primarily focused on the Young’s modulus. In this work, in order to obtain a more direct comparison between experiments and simulations, atomistically detailed models of the cross-linked epoxy are used to study their creep compliance as a function of temperature using MD simulations. The creep tests are performed by applying a constant tensile stress and monitoring themore » resulting strain in the system. Our results show that simulated values of creep compliance increase with an increase in both time and temperature. We believe that such calculations of the creep compliance, along with the use of time temperature superposition, hold great promise in connecting the molecular insight obtained from molecular simulation at small length- and time-scales with the experimental behavior of such materials. To the best of our knowledge, this work is the first reported effort that investigates the creep compliance behavior of cross-linked epoxy using MD simulations.« less

Model and Simulation of an SMA Enhanced Lip Seal

NASA Astrophysics Data System (ADS)

Qiao, Rui; Gao, Xiujie; Brinson, L. Catherine

2011-07-01

The feasibility of using SMA wires to improve the seal effectiveness has been studied experimentally and numerically. In this article, we present only the numerical study of simulating the thermo-mechanical behavior for an SMA enhanced lip seal, leaving the test setup and results in the experimental counterpart. A pseudo 3D SMA model, considering 1D SMA behavior in the major loading direction and elastic response in other directions, was used to capture the thermo-mechanical behavior of SMA wires. The model was then implemented into ABAQUS using the user-defined material subroutine to inherit most features of the commercial finite element package. Two-way shape memory effect was also considered since the SMA material exhibits strong two-way effects. An axisymmetric finite element model was constructed to simulate a seal mounting on a shaft and the sealing pressure was calculated for both the regular seal and the SMA enhanced seal. Finally, the result was qualitatively compared with the experimental observation.

Simulating Extraterrestrial Ices in the Laboratory

NASA Astrophysics Data System (ADS)

Berisford, D. F.; Carey, E. M.; Hand, K. P.; Choukroun, M.

2017-12-01

Several ongoing experiments at JPL attempt to simulate the ice environment for various regimes associated with icy moons. The Europa Penitent Ice Experiment (EPIX) simulates the surface environment of an icy moon, to investigate the physics of ice surface morphology growth. This experiment features half-meter-scale cryogenic ice samples, cryogenic radiative sink environment, vacuum conditions, and diurnal cycling solar simulation. The experiment also includes several smaller fixed-geometry vacuum chambers for ice simulation at Earth-like and intermediate temperature and vacuum conditions for development of surface morphology growth scaling relations. Additionally, an ice cutting facility built on a similar platform provides qualitative data on the mechanical behavior of cryogenic ice with impurities under vacuum, and allows testing of ice cutting/sampling tools relevant for landing spacecraft. A larger cutting facility is under construction at JPL, which will provide more quantitative data and allow full-scale sampling tool tests. Another facility, the JPL Ice Physics Laboratory, features icy analog simulant preparation abilities that range icy solar system objects such as Mars, Ceres and the icy satellites of Saturn and Jupiter. In addition, the Ice Physics Lab has unique facilities for Icy Analog Tidal Simulation and Rheological Studies of Cryogenic Icy Slurries, as well as equipment to perform thermal and mechanical properties testing on icy analog materials and their response to sinusoidal tidal stresses.

Earthquake source parameters along the Hellenic subduction zone and numerical simulations of historical tsunamis in the Eastern Mediterranean

NASA Astrophysics Data System (ADS)

Yolsal-Çevikbilen, Seda; Taymaz, Tuncay

2012-04-01

We studied source mechanism parameters and slip distributions of earthquakes with Mw ≥ 5.0 occurred during 2000-2008 along the Hellenic subduction zone by using teleseismic P- and SH-waveform inversion methods. In addition, the major and well-known earthquake-induced Eastern Mediterranean tsunamis (e.g., 365, 1222, 1303, 1481, 1494, 1822 and 1948) were numerically simulated and several hypothetical tsunami scenarios were proposed to demonstrate the characteristics of tsunami waves, propagations and effects of coastal topography. The analogy of current plate boundaries, earthquake source mechanisms, various earthquake moment tensor catalogues and several empirical self-similarity equations, valid for global or local scales, were used to assume conceivable source parameters which constitute the initial and boundary conditions in simulations. Teleseismic inversion results showed that earthquakes along the Hellenic subduction zone can be classified into three major categories: [1] focal mechanisms of the earthquakes exhibiting E-W extension within the overriding Aegean plate; [2] earthquakes related to the African-Aegean convergence; and [3] focal mechanisms of earthquakes lying within the subducting African plate. Normal faulting mechanisms with left-lateral strike slip components were observed at the eastern part of the Hellenic subduction zone, and we suggest that they were probably concerned with the overriding Aegean plate. However, earthquakes involved in the convergence between the Aegean and the Eastern Mediterranean lithospheres indicated thrust faulting mechanisms with strike slip components, and they had shallow focal depths (h < 45 km). Deeper earthquakes mainly occurred in the subducting African plate, and they presented dominantly strike slip faulting mechanisms. Slip distributions on fault planes showed both complex and simple rupture propagations with respect to the variation of source mechanism and faulting geometry. We calculated low stress drop values (Δσ < 30 bars) for all earthquakes implying typically interplate seismic activity in the region. Further, results of numerical simulations verified that damaging historical tsunamis along the Hellenic subduction zone are able to threaten especially the coastal plains of Crete and Rhodes islands, SW Turkey, Cyprus, Levantine, and Nile Delta-Egypt regions. Thus, we tentatively recommend that special care should be considered in the evaluation of the tsunami risk assessment of the Eastern Mediterranean region for future studies.

A theoretical study on tunneling based biosensor having a redox-active monolayer using physics based simulation

NASA Astrophysics Data System (ADS)

Kim, Kyoung Yeon; Lee, Won Cheol; Yun, Jun Yeon; Lee, Youngeun; Choi, Seoungwook; Jin, Seonghoon; Park, Young June

2018-01-01

We developed a numerical simulator to model the operation of a tunneling based biosensor which has a redox-active monolayer. The simulator takes a realistic device structure as a simulation domain, and it employs the drift-diffusion equation for ion transport, the non-equilibrium Green's function formalism for electron tunneling, and the Ramo-Shockley theorem for accurate calculation of non-faradaic current. We also accounted for the buffer reaction and the immobilized peptide layer. For efficient transient simulation, the implicit time integration scheme is employed where the solution at each time step is obtained from the coupled Newton-Raphson method. As an application, we studied the operation of a recently fabricated reference-electrode free biosensor in various bias conditions and confirmed the effect of buffer reaction and the current flowing mechanism. Using the simulator, we also found a strategy to maximize the sensitivity of the tunneling based sensor.

A model of mechanical interactions between heart and lungs.

PubMed

Fontecave Jallon, Julie; Abdulhay, Enas; Calabrese, Pascale; Baconnier, Pierre; Gumery, Pierre-Yves

2009-12-13

To study the mechanical interactions between heart, lungs and thorax, we propose a mathematical model combining a ventilatory neuromuscular model and a model of the cardiovascular system, as described by Smith et al. (Smith, Chase, Nokes, Shaw & Wake 2004 Med. Eng. Phys.26, 131-139. (doi:10.1016/j.medengphy.2003.10.001)). The respiratory model has been adapted from Thibault et al. (Thibault, Heyer, Benchetrit & Baconnier 2002 Acta Biotheor. 50, 269-279. (doi:10.1023/A:1022616701863)); using a Liénard oscillator, it allows the activity of the respiratory centres, the respiratory muscles and rib cage internal mechanics to be simulated. The minimal haemodynamic system model of Smith includes the heart, as well as the pulmonary and systemic circulation systems. These two modules interact mechanically by means of the pleural pressure, calculated in the mechanical respiratory system, and the intrathoracic blood volume, calculated in the cardiovascular model. The simulation by the proposed model provides results, first, close to experimental data, second, in agreement with the literature results and, finally, highlighting the presence of mechanical cardiorespiratory interactions.

Simulation of κ-Carbide Precipitation Kinetics in Aged Low-Density Fe-Mn-Al-C Steels and Its Effects on Strengthening

NASA Astrophysics Data System (ADS)

Lee, Jaeeun; Park, Siwook; Kim, Hwangsun; Park, Seong-Jun; Lee, Keunho; Kim, Mi-Young; Madakashira, Phaniraj P.; Han, Heung Nam

2018-03-01

Fe-Al-Mn-C alloy systems are low-density austenite-based steels that show excellent mechanical properties. After aging such steels at adequate temperatures for adequate time, nano-scale precipitates such as κ-carbide form, which have profound effects on the mechanical properties. Therefore, it is important to predict the amount and size of the generated κ-carbide precipitates in order to control the mechanical properties of low-density steels. In this study, the microstructure and mechanical properties of aged low-density austenitic steel were characterized. Thermo-kinetic simulations of the aging process were used to predict the size and phase fraction of κ-carbide after different aging periods, and these results were validated by comparison with experimental data derived from dark-field transmission electron microscopy images. Based on these results, models for precipitation strengthening based on different mechanisms were assessed. The measured increase in the strength of aged specimens was compared with that calculated from the models to determine the exact precipitation strengthening mechanism.

Fracture Mechanics Analyses of Subsurface Defects in Reinforced Carbon-Carbon Joggles Subjected to Thermo-Mechanical Loads

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Raju, Ivatury S.; Song, Kyongchan

2011-01-01

Coating spallation events have been observed along the slip-side joggle region of the Space Shuttle Orbiter wing-leading-edge panels. One potential contributor to the spallation event is a pressure build up within subsurface voids or defects due to volatiles or water vapor entrapped during fabrication, refurbishment, or normal operational use. The influence of entrapped pressure on the thermo-mechanical fracture-mechanics response of reinforced carbon-carbon with subsurface defects is studied. Plane-strain simulations with embedded subsurface defects are performed to characterize the fracture mechanics response for a given defect length when subjected to combined elevated-temperature and subsurface-defect pressure loadings to simulate the unvented defect condition. Various subsurface defect locations of a fixed-length substrate defect are examined for elevated temperature conditions. Fracture mechanics results suggest that entrapped pressure combined with local elevated temperatures have the potential to cause subsurface defect growth and possibly contribute to further material separation or even spallation. For this anomaly to occur, several unusual circumstances would be required making such an outcome unlikely but plausible.

Mechanical properties of drug loaded diblock copolymer bilayers: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Grillo, Damián A.; Albano, Juan M. R.; Mocskos, Esteban E.; Facelli, Julio C.; Pickholz, Mónica; Ferraro, Marta B.

2018-06-01

In this work, we present results of coarse-grained simulations to study the encapsulation of prilocaine (PLC), both neutral and protonated, on copolymer bilayers through molecular dynamics simulations. Using a previously validated membrane model, we have simulated loaded bilayers at different drug concentrations and at low (protonated PLC) and high (neutral PLC) pH levels. We have characterized key structural parameters of the loaded bilayers in order to understand the effects of encapsulation of PLC on the bilayer structure and mechanical properties. Neutral PLC was encapsulated in the hydrophobic region leading to a thickness increase, while the protonated species partitioned between the water phase and the poly(ethylene oxide)-poly(butadiene) (PBD) interface, relaxing the PBD region and leading to a decrease in the thickness. The tangential pressures of the studied systems were calculated, and their components were decomposed in order to gain insights on their compensation. In all cases, it is observed that the loading of the membrane does not significantly decrease the stability of the bilayer, indicating that the system could be used for drug delivery.

Mechanical properties of drug loaded diblock copolymer bilayers: A molecular dynamics study.

PubMed

Grillo, Damián A; Albano, Juan M R; Mocskos, Esteban E; Facelli, Julio C; Pickholz, Mónica; Ferraro, Marta B

2018-06-07

In this work, we present results of coarse-grained simulations to study the encapsulation of prilocaine (PLC), both neutral and protonated, on copolymer bilayers through molecular dynamics simulations. Using a previously validated membrane model, we have simulated loaded bilayers at different drug concentrations and at low (protonated PLC) and high (neutral PLC) pH levels. We have characterized key structural parameters of the loaded bilayers in order to understand the effects of encapsulation of PLC on the bilayer structure and mechanical properties. Neutral PLC was encapsulated in the hydrophobic region leading to a thickness increase, while the protonated species partitioned between the water phase and the poly(ethylene oxide)-poly(butadiene) (PBD) interface, relaxing the PBD region and leading to a decrease in the thickness. The tangential pressures of the studied systems were calculated, and their components were decomposed in order to gain insights on their compensation. In all cases, it is observed that the loading of the membrane does not significantly decrease the stability of the bilayer, indicating that the system could be used for drug delivery.

Mechanical design of NASA Ames Research Center vertical motion simulator

NASA Technical Reports Server (NTRS)

Engelbert, D. F.; Bakke, A. P.; Chargin, M. K.; Vallotton, W. C.

1976-01-01

NASA has designed and is constructing a new flight simulator with large vertical travel. Several aspects of the mechanical design of this Vertical Motion Simulator (VMS) are discussed, including the multiple rack and pinion vertical drive, a pneumatic equilibration system, and the friction-damped rigid link catenaries used as cable supports.

Formulation and validation of a reduced order model of 2D materials exhibiting a two-phase microstructure as applied to graphene oxide

NASA Astrophysics Data System (ADS)

Benedetti, Ivano; Nguyen, Hoang; Soler-Crespo, Rafael A.; Gao, Wei; Mao, Lily; Ghasemi, Arman; Wen, Jianguo; Nguyen, SonBinh; Espinosa, Horacio D.

2018-03-01

Novel 2D materials, e.g., graphene oxide (GO), are attractive building blocks in the design of advanced materials due to their reactive chemistry, which can enhance interfacial interactions while providing good in-plane mechanical properties. Recent studies have hypothesized that the randomly distributed two-phase microstructure of GO, which arises due to its oxidized chemistry, leads to differences in nano- vs meso-scale mechanical responses. However, this effect has not been carefully studied using molecular dynamics due to computational limitations. Herein, a continuum mechanics model, formulated based on density functional based tight binding (DFTB) constitutive results for GO nano-flakes, is establish for capturing the effect of oxidation patterns on the material mechanical properties. GO is idealized as a continuum heterogeneous two-phase material, where the mechanical response of each phase, graphitic and oxidized, is informed from DFTB simulations. A finite element implementation of the model is validated via MD simulations and then used to investigate the existence of GO representative volume elements (RVE). We find that for the studied GO, an RVE behavior arises for monolayer sizes in excess to 40 nm. Moreover, we reveal that the response of monolayers with two main different functional chemistries, epoxide-rich and hydroxyl-rich, present distinct differences in mechanical behavior. In addition, we explored the role of defect density in GO, and validate the applicability of the model to larger length scales by predicting membrane deflection behavior, in close agreement with previous experimental and theoretical observations. As such the work presents a reduced order modeling framework applicable in the study of mechanical properties and deformation mechanisms in 2D multiphase materials.

Molecular dynamics simulations and novel drug discovery.

PubMed

Liu, Xuewei; Shi, Danfeng; Zhou, Shuangyan; Liu, Hongli; Liu, Huanxiang; Yao, Xiaojun

2018-01-01

Molecular dynamics (MD) simulations can provide not only plentiful dynamical structural information on biomacromolecules but also a wealth of energetic information about protein and ligand interactions. Such information is very important to understanding the structure-function relationship of the target and the essence of protein-ligand interactions and to guiding the drug discovery and design process. Thus, MD simulations have been applied widely and successfully in each step of modern drug discovery. Areas covered: In this review, the authors review the applications of MD simulations in novel drug discovery, including the pathogenic mechanisms of amyloidosis diseases, virtual screening and the interaction mechanisms between drugs and targets. Expert opinion: MD simulations have been used widely in investigating the pathogenic mechanisms of diseases caused by protein misfolding, in virtual screening, and in investigating drug resistance mechanisms caused by mutations of the target. These issues are very difficult to solve by experimental methods alone. Thus, in the future, MD simulations will have wider application with the further improvement of computational capacity and the development of better sampling methods and more accurate force fields together with more efficient analysis methods.

Start-to-end simulation of the shot-noise driven microbunching instability experiment at the Linac Coherent Light Source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiang, J.; Ding, Y.; Emma, P.

The shot-noise driven microbunching instability can significantly degrade electron beam quality in x-ray free electron laser light sources. Experiments were carried out at the Linac Coherent Light Source (LCLS) to study this instability. Here in this paper, we present start-to-end simulations of the shot-noise driven microbunching instability experiment at the LCLS using the real number of electrons. The simulation results reproduce the measurements quite well. A microbunching self-heating mechanism is also illustrated in the simulation, which helps explain the experimental observation.

Start-to-end simulation of the shot-noise driven microbunching instability experiment at the Linac Coherent Light Source

DOE PAGES

Qiang, J.; Ding, Y.; Emma, P.; ...

2017-05-23

The shot-noise driven microbunching instability can significantly degrade electron beam quality in x-ray free electron laser light sources. Experiments were carried out at the Linac Coherent Light Source (LCLS) to study this instability. Here in this paper, we present start-to-end simulations of the shot-noise driven microbunching instability experiment at the LCLS using the real number of electrons. The simulation results reproduce the measurements quite well. A microbunching self-heating mechanism is also illustrated in the simulation, which helps explain the experimental observation.

Molecular Simulations in Astrobiology

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.

2000-01-01

One of the main goals of astrobiology is to understand the origin of cellular life. The most direct approach to this problem is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing energy and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following questions about these proteins: (1) How do small proteins self-organize into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides form membrane-spanning structures (e.g. channels)? (3) By what mechanisms do such structures perform their functions? The simulations are performed using the molecular dynamics method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated in real space while long-range forces are evaluated in reciprocal space, using a particle-mesh algorithm which is of order O(NInN). With a time step of 2 femtoseconds, problems occurring on multi-nanosecond time scales (10(exp 6)-10(exp 8) time steps) are accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude, which requires algorithmic improvements and codes scalable to a large number of processors. Work in this direction is in progress. Two series of simulations are discussed. In one series, it is shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and fold into helical structures (see Figure). Once in the membrane, the peptides exhibit orientational flexibility with changing conditions, which may have provided a mechanism of transmitting signals between the protocell and its environment. In another series of simulations, the mechanism by which a simple protein channel efficiently mediates proton transport across membranes was investigated. This process is a key step in cellular bioenergetics. In the channel under study, proton transport is gated by four histidines that occlude the channel pore. The simulations identify the mechanisms by which protons move through the gate.

[Mathematical simulation of biomechanical background of osteophyte formation in cervical vertebra].

PubMed

Barsa, P; Novák, J; Souček, T; Maršík, F; Suchomel, P

2011-01-01

The aim of this study was to simulate different types of cervical vertebra loading and to find out whether mechanical stress would concentrate in regions known in clinical practice as predilection sites for osteophyte formation. The objective was to develop a theoretical model that would elucidate clinical observations concerning the predilection site of bone remodelling in view of the physiological changes inside the cervical vertebral body. A real 3D-geometry of the fourth cervical vertebra had been made by the commercially available system ATOS II. This is a high-resolution measuring system using principles of optical triangulation. This flexible optical measuring machine projects fringe patterns on the surface of a selected object and the pattern is observed with two cameras. 3D coordinates for each camera pixel were calculated with high precision and a polygon mesh of the object's surface was further generated. In the next step an ANSYS programme was used to calculate strains and stresses in each finite element of the virtual vertebra. The applied forces used in the experiment corresponded in both magnitude and direction to physiological stress. Mechanical loading in neutral position was characterized by a distribution of 80% mechanical stress to the vertebral body and 10% to each of the zygoapophyseal joints. Hyperlordotic loading was simulated by 60% force transfer to the vertebral body end-plate and 20% to each of the small joint while kyphotic loading involved a 90% load on the vertebral body endplate and 5% on each facet. Mechanical stress distribution calculated in a neutral position of the model correlated well with bone mineral distribution of a healthy vertebra, and verified the model itself. The virtual mechanical loading of a vertebra in kyphotic position concentrated deformation stress into the uncinate processes and the dorsal apophyseal rim of the vertebral body. The simulation of mechanical loading in hyperlordosis, on the other hand, shifted the region of maximum deformation into the articulation process of the Z-joint. All locations are known as areas of osteophyte formation in degenerated cervical vertebrae. The theoretical model developed during this study corresponded well with human spine behaviour in terms of predilection sites for osteodegenerative changes, as observed in clinical practice. A mathematical simulation of mechanical stress distribution in pre-operative planning may lead to the optimisation of post-operative anatomical relationship between adjacent vertebrae. Such improvement in our surgical practice may further reduce the incidence of degenerative changes in adjacent motion segments of the cervical spine and possibly also lead to better subjective and clinical results after cervical spine reconstruction.

Determination of mechanical behavior of nanoscale materials using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Heo, Seongjun

It is important to understand the mechanical properties of nanometer-scale materials for use in such applications as microelectromechanical systems (MEMS) and nanoelectromechanical systems (NEMS). These properties are difficult to measure directly using experimental methods due to their small sizes. Computational simulations provide important insights that complement experimental data and lead to improved understanding of the mechanical properties of nanometer-scale systems. Molecular dynamics (MD) simulations, which are used to investigate the properties of materials at the atomic scale, is used in my research to determine (1) best thermostat managing way for acceptable mechanical behavior of nanoscale systems; (2) filling effect on the bending and compressive properties of carbon nanotubes (CNTs); (3) vibrational behavior of bridged and cantilevered CNT bombarded by external fluid atoms; (4) frictional behavior of filled CNT bundles and the effect of external molecules on friction; (5) effect of sliding orientations on the tribological properties of polyethylene (PE). In all the simulations the reactive empirical bond-order (REBO) potential combined with the Lennard Jones potential is applied to control inter-atomic interactions. During the MD simulations, thermostats are used to maintain the system temperature at a constant value. Tests indicate that the simulations describe the mechanical behavior of CNTs differently depending on the type of thermostat used, and the relative fraction of the system to which the thermostat is applied. The results indicate that Langevin and velocity rescaling thermostats are more reliable for temperature control than the Nose-Hoover thermostat. In examining CNT bending and compression, the simulations predict filled CNTs are more resistant to external bending and compressive forces than hollow CNTs. The mechanical properties deteriorate with increases in temperature and number of CNT wall defects. MD simulations of the vibrational behavior of bridged and cantilevered CNTs are found to match the results of continuum mechanics calculations. The principal vibration frequency of the CNT is predicted to decrease with increasing nanotube length, gas pressure, and the atomic mass of the external fluid. In studies of CNT tribology, simulations show that two layers of filled CNTs are more resistant to compressive forces and exhibit lower friction coefficients during sliding than unfilled CNTs. The friction coefficient increases with the thickness of the CNT layer due to the increase in effective friction interface. The addition of an external, molecular fluid of benzene molecules is predicted to reduce the friction coefficient of CNTs because of the lubricity of the molecules. Lastly, simulation results illustrate the effect of relative orientation on the tribological properties of polyethylene (PE) sliding surfaces. The friction coefficient of perpendicular sliding is much higher than that of parallel sliding based on the polymer chain orientation. The PE exhibits stick-slip motion during sliding regardless of the sliding orientation. In addition, the PE shows no surface morphology change due to the higher strength of the PE bonds, which is in contrast to the behavior of other polymers, such as polytetrafluoroethylene (PTFE), which exhibits bond breaking and realignment of surface chains along the sliding direction in the less favorable orientation.

Recent advances in computational methodology for simulation of mechanical circulatory assist devices

PubMed Central

Marsden, Alison L.; Bazilevs, Yuri; Long, Christopher C.; Behr, Marek

2014-01-01

Ventricular assist devices (VADs) provide mechanical circulatory support to offload the work of one or both ventricles during heart failure. They are used in the clinical setting as destination therapy, as bridge to transplant, or more recently as bridge to recovery to allow for myocardial remodeling. Recent developments in computational simulation allow for detailed assessment of VAD hemodynamics for device design and optimization for both children and adults. Here, we provide a focused review of the recent literature on finite element methods and optimization for VAD simulations. As VAD designs typically fall into two categories, pulsatile and continuous flow devices, we separately address computational challenges of both types of designs, and the interaction with the circulatory system with three representative case studies. In particular, we focus on recent advancements in finite element methodology that has increased the fidelity of VAD simulations. We outline key challenges, which extend to the incorporation of biological response such as thrombosis and hemolysis, as well as shape optimization methods and challenges in computational methodology. PMID:24449607

A hierarchical dislocation-grain boundary interaction model based on 3D discrete dislocation dynamics and molecular dynamics

NASA Astrophysics Data System (ADS)

Gao, Yuan; Zhuang, Zhuo; You, XiaoChuan

2011-04-01

We develop a new hierarchical dislocation-grain boundary (GB) interaction model to predict the mechanical behavior of polycrystalline metals at micro and submicro scales by coupling 3D Discrete Dislocation Dynamics (DDD) simulation with the Molecular Dynamics (MD) simulation. At the microscales, the DDD simulations are responsible for capturing the evolution of dislocation structures; at the nanoscales, the MD simulations are responsible for obtaining the GB energy and ISF energy which are then transferred hierarchically to the DDD level. In the present model, four kinds of dislocation-GB interactions, i.e. transmission, absorption, re-emission and reflection, are all considered. By this methodology, the compression of a Cu micro-sized bi-crystal pillar is studied. We investigate the characteristic mechanical behavior of the bi-crystal compared with that of the single-crystal. Moreover, the comparison between the present penetrable model of GB and the conventional impenetrable model also shows the accuracy and efficiency of the present model.

Investigation of a Macromechanical Approach to Analyzing Triaxially-Braided Polymer Composites

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Blinzler, Brina J.; Binienda, Wieslaw K.

2010-01-01

A macro level finite element-based model has been developed to simulate the mechanical and impact response of triaxially-braided polymer matrix composites. In the analytical model, the triaxial braid architecture is simulated by using four parallel shell elements, each of which is modeled as a laminated composite. The commercial transient dynamic finite element code LS-DYNA is used to conduct the simulations, and a continuum damage mechanics model internal to LS-DYNA is used as the material constitutive model. The material stiffness and strength values required for the constitutive model are determined based on coupon level tests on the braided composite. Simulations of quasi-static coupon tests of a representative braided composite are conducted. Varying the strength values that are input to the material model is found to have a significant influence on the effective material response predicted by the finite element analysis, sometimes in ways that at first glance appear non-intuitive. A parametric study involving the input strength parameters provides guidance on how the analysis model can be improved.

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

PubMed

Formoso, Elena; Matxain, Jon M; Lopez, Xabier; York, Darrin M

2010-06-03

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.

Molecular Dynamics Simulation of Bovine Pancreatic Ribonuclease A - CpA and Transition State-like Complexes

PubMed Central

Formoso, Elena; Matxain, Jon M.; Lopez, Xabier; York, Darrin M.

2010-01-01

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, in order to study the conformational dynamics, structural relaxation, and differential solvation that occurs at discreet stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics, and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogs. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3′,5′-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen bond patterns are presented and compared. The integrity of the overall backbone structure is preserved in the simulations, and support a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen bond donation to the non-bridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate, and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step. PMID:20455590

Provably unbounded memory advantage in stochastic simulation using quantum mechanics

NASA Astrophysics Data System (ADS)

Garner, Andrew J. P.; Liu, Qing; Thompson, Jayne; Vedral, Vlatko; Gu, mile

2017-10-01

Simulating the stochastic evolution of real quantities on a digital computer requires a trade-off between the precision to which these quantities are approximated, and the memory required to store them. The statistical accuracy of the simulation is thus generally limited by the internal memory available to the simulator. Here, using tools from computational mechanics, we show that quantum processors with a fixed finite memory can simulate stochastic processes of real variables to arbitrarily high precision. This demonstrates a provable, unbounded memory advantage that a quantum simulator can exhibit over its best possible classical counterpart.

Proposal for a new mass distribution control system and its simulation for vibration reduction on rotating machinery

NASA Astrophysics Data System (ADS)

Enginoglu, Ozan; Ozturk, Hasan

2016-12-01

This study presents a new mass distribution control system (MDCS) along with its analysis and simulation. It is aimed to balance a system containing rotating parts in order to minimize the dynamic vibration on it. For this purpose, a test mechanism rotating with an angular velocity of ω is simulated. The mechanism consists of a pair of MDCS, each containing three flaps connected to the shaft. The flaps rotate in relation to the shaft's plane of rotation. The center of gravity (COG) of the MDCS is concentric with the shaft axis when all three flaps are stretched out but the COG changes as the flaps rotate. By adjusting the orientations of the flaps in both systems, it is possible to create a counterforce which suppresses the imbalance force, reducing the vibration to a minimum.

Membrane Fusion Involved in Neurotransmission: Glimpse from Electron Microscope and Molecular Simulation

PubMed Central

Yang, Zhiwei; Gou, Lu; Chen, Shuyu; Li, Na; Zhang, Shengli; Zhang, Lei

2017-01-01

Membrane fusion is one of the most fundamental physiological processes in eukaryotes for triggering the fusion of lipid and content, as well as the neurotransmission. However, the architecture features of neurotransmitter release machinery and interdependent mechanism of synaptic membrane fusion have not been extensively studied. This review article expounds the neuronal membrane fusion processes, discusses the fundamental steps in all fusion reactions (membrane aggregation, membrane association, lipid rearrangement and lipid and content mixing) and the probable mechanism coupling to the delivery of neurotransmitters. Subsequently, this work summarizes the research on the fusion process in synaptic transmission, using electron microscopy (EM) and molecular simulation approaches. Finally, we propose the future outlook for more exciting applications of membrane fusion involved in synaptic transmission, with the aid of stochastic optical reconstruction microscopy (STORM), cryo-EM (cryo-EM), and molecular simulations. PMID:28638320

Influence of microscale heterogeneity and microstructure on the tensile behavior of crystalline rocks

NASA Astrophysics Data System (ADS)

Mahabadi, O. K.; Tatone, B. S. A.; Grasselli, G.

2014-07-01

This study investigates the influence of microscale heterogeneity and microcracks on the failure behavior and mechanical response of a crystalline rock. The thin section analysis for obtaining the microcrack density is presented. Using micro X-ray computed tomography (μCT) scanning of failed laboratory specimens, the influence of heterogeneity and, in particular, biotite grains on the brittle fracture of the specimens is discussed and various failure patterns are characterized. Three groups of numerical simulations are presented, which demonstrate the role of microcracks and the influence of μCT-based and stochastically generated phase distributions. The mechanical response, stress distribution, and fracturing process obtained by the numerical simulations are also discussed. The simulation results illustrate that heterogeneity and microcracks should be considered to accurately predict the tensile strength and failure behavior of the sample.

Pipe Flow Simulation Software: A Team Approach to Solve an Engineering Education Problem.

ERIC Educational Resources Information Center

Engel, Renata S.; And Others

1996-01-01

A computer simulation program for use in the study of fluid mechanics is described. The package is an interactive tool to explore the fluid flow characteristics of a pipe system by manipulating the physical construction of the system. The motivation, software design requirements, and specific details on how its objectives were met are presented.…

Development and Use of a Cyclic Voltammetry Simulator to Introduce Undergraduate Students to Electrochemical Simulations

ERIC Educational Resources Information Center

Brown, Jay H.

2015-01-01

Cyclic voltammetry (CV) is a popular technique for the study of electrochemical mechanisms because the method can provide useful information on the redox couple. The technique involves the application of a potential ramp on an unstirred solution while the current is monitored, and then the ramp is reversed for a return sweep. CV is sometimes…

Kyle Benne | NREL

Science.gov Websites

developer. He is a member of the OpenStudio development team, where he focuses on creating new simulation expertise in fluid mechanics and numerical simulation. Education M.S. Mechanical Engineering, Missouri

The Brain in its Body: Motor Control and Sensing in a Biomechanical Context

PubMed Central

Chiel, Hillel J.; Ting, Lena H.; Ekeberg, Orjan; Hartmann, Mitra J. Z.

2009-01-01

Although it is widely recognized that adaptive behavior emerges from the ongoing interactions among the nervous system, the body, and the environment, it has only become possible in recent years to experimentally study and to simulate these interacting systems. We briefly review work on molluscan feeding, maintenance of postural control in cats and humans, simulations of locomotion in lamprey, insect, cat and salamander, and active vibrissal sensing in rats to illustrate the insights that can be derived from studies of neural control and sensing within a biomechanical context. These studies illustrate that control may be shared between the nervous system and the periphery, that neural activity organizes degrees of freedom into biomechanically meaningful subsets, that mechanics alone may play crucial roles in enforcing gait patterns, and that mechanics of sensors is crucial for their function. PMID:19828793

Dynamic finite element analysis and moving particle simulation of human enamel on a microscale.

PubMed

Yamaguchi, Satoshi; Coelho, Paulo G; Thompson, Van P; Tovar, Nick; Yamauchi, Junpei; Imazato, Satoshi

2014-12-01

The study of biomechanics of deformation and fracture of hard biological tissues involving organic matrix remains a challenge as variations in mechanical properties and fracture mode may have time-dependency. Finite element analysis (FEA) has been widely used but the shortcomings of FEA such as the long computation time owing to re-meshing in simulating fracture mechanics have warranted the development of alternative computational methods with higher throughput. The aim of this study was to compare dynamic two-dimensional FEA and moving particle simulation (MPS) when assuming a plane strain condition in the modeling of human enamel on a reduced scale. Two-dimensional models with the same geometry were developed for MPS and FEA and tested in tension generated with a single step of displacement. The displacement, velocity, pressure, and stress levels were compared and Spearman׳s rank-correlation coefficients R were calculated (p<0.001). The MPS and FEA were significantly correlated for displacement, velocity, pressure, and Y-stress. The MPS may be further developed as an alternative approach without mesh generation to simulate deformation and fracture phenomena of dental and potentially other hard tissues with complex microstructure. Copyright © 2014 Elsevier Ltd. All rights reserved.

Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution.

PubMed

Abolfath, Ramin M; Biswas, P K; Rajnarayanam, R; Brabec, Thomas; Kodym, Reinhard; Papiez, Lech

2012-04-19

Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to understanding the indirect effect of ionizing radiation. Previous studies address the problem with truncated DNA bases as ab initio quantum simulations required to study such electronic-spin-dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid quantum mechanical-molecular mechanical simulation to study the interaction of OH radicals with a guanine-deoxyribose-phosphate DNA molecular unit in the presence of water, where all of the water molecules and the deoxyribose-phosphate fragment are treated with the simplistic classical molecular mechanical scheme. Our result illustrates that the presence of water strongly alters the hydrogen-abstraction reaction as the hydrogen bonding of OH radicals with water restricts the relative orientation of the OH radicals with respect to the DNA base (here, guanine). This results in an angular anisotropy in the chemical pathway and a lower efficiency in the hydrogen-abstraction mechanisms than previously anticipated for identical systems in vacuum. The method can easily be extended to single- and double-stranded DNA without any appreciable computational cost as these molecular units can be treated in the classical subsystem, as has been demonstrated here. © 2012 American Chemical Society

In situ nanoindentation study on plasticity and work hardening in aluminium with incoherent twin boundaries.

PubMed

Bufford, D; Liu, Y; Wang, J; Wang, H; Zhang, X

2014-09-10

Nanotwinned metals have been the focus of intense research recently, as twin boundaries may greatly enhance mechanical strength, while maintaining good ductility, electrical conductivity and thermal stability. Most prior studies have focused on low stacking-fault energy nanotwinned metals with coherent twin boundaries. In contrast, the plasticity of twinned high stacking-fault energy metals, such as aluminium with incoherent twin boundaries, has not been investigated. Here we report high work hardening capacity and plasticity in highly twinned aluminium containing abundant Σ3{112} incoherent twin boundaries based on in situ nanoindentation studies in a transmission electron microscope and corresponding molecular dynamics simulations. The simulations also reveal drastic differences in deformation mechanisms between nanotwinned copper and twinned aluminium ascribed to stacking-fault energy controlled dislocation-incoherent twin boundary interactions. This study provides new insight into incoherent twin boundary-dominated plasticity in high stacking-fault energy twinned metals.

Design of a rapid magnetic microfluidic mixer

NASA Astrophysics Data System (ADS)

Ballard, Matthew; Owen, Drew; Mills, Zachary Grant; Hanasoge, Srinivas; Hesketh, Peter; Alexeev, Alexander

2015-11-01

Using three-dimensional simulations and experiments, we demonstrate rapid mixing of fluid streams in a microchannel using orbiting magnetic microbeads. We use a lattice Boltzmann model coupled to a Brownian dynamics model to perform numerical simulations that study in depth the effect of system parameters such as channel configuration and fluid and bead velocities. We use our findings to aid the design of an experimental micromixer. Using this experimental device, we demonstrate rapid microfluidic mixing over a compact channel length, and validate our numerical simulation results. Finally, we use numerical simulations to study the physical mechanisms leading to microfluidic mixing in our system. Our findings demonstrate a promising method of rapid microfluidic mixing over a short distance, with applications in lab-on-a-chip sample testing.

Influence of Dissipative Particle Dynamics parameters and wall models on planar micro-channel flows

NASA Astrophysics Data System (ADS)

Wang, Yuyi; She, Jiangwei; Zhou, Zhe-Wei; microflow Group Team

2017-11-01

Dissipative Particle Dynamics (DPD) is a very effective approach in simulating mesoscale hydrodynamics. The influence of solid boundaries and DPD parameters are typically very strong in DPD simulations. The present work studies a micro-channel Poisseuille flow. Taking the neutron scattering experiment and molecular dynamics simulation result as bench mark, the DPD results of density distribution and velocity profile are systematically studied. The influence of different levels of coarse-graining, the number densities of wall and fluid, conservative force coefficients, random and dissipative force coefficients, different wall model and reflective boundary conditions are discussed. Some mechanisms behind such influences are discussed and the artifacts in the simulation are identified with the bench mark. Chinese natural science foundation (A020405).

Excess protons in water-acetone mixtures. II. A conductivity study.

PubMed

Semino, Rocío; Longinotti, M Paula

2013-10-28

In the present work we complement a previous simulation study [R. Semino and D. Laria, J. Chem. Phys. 136, 194503 (2012)] on the disruption of the proton transfer mechanism in water by the addition of an aprotic solvent, such as acetone. We provide experimental measurements of the mobility of protons in aqueous-acetone mixtures in a wide composition range, for water molar fractions, xw, between 0.05 and 1.00. Furthermore, new molecular dynamics simulation results are presented for rich acetone mixtures, which provide further insight into the proton transport mechanism in water-non-protic solvent mixtures. The proton mobility was analyzed between xw 0.05 and 1.00 and compared to molecular dynamics simulation data. Results show two qualitative changes in the proton transport composition dependence at xw ∼ 0.25 and 0.8. At xw < 0.25 the ratio of the infinite dilution molar conductivities of HCl and LiCl, Λ(0)(HCl).Λ(0)(LiCl)(-1), is approximately constant and equal to one, since the proton diffusion is vehicular and equal to that of Li(+). At xw ∼ 0.25, proton mobility starts to differ from that of Li(+) indicating that above this concentration the Grotthuss transport mechanism starts to be possible. Molecular dynamics simulation results showed that at this threshold concentration the probability of interconversion between two Eigen structures starts to be non-negligible. At xw ∼ 0.8, the infinite molar conductivity of HCl concentration dependence qualitatively changes. This result is in excellent agreement with the analysis presented in the previous simulation work and it has been ascribed to the interchange of water and acetone molecules in the second solvation shell of the hydronium ion.

Application of two hydrologic models with different runoff mechanisms to a hillslope dominated watershed in the northeastern US: A comparison of HSPF and SMR

USGS Publications Warehouse

Johnson, M.S.; Coon, W.F.; Mehta, V.K.; Steenhuis, T.S.; Brooks, E.S.; Boll, J.

2003-01-01

Differences in the simulation of hydrologic processes by watershed models directly affect the accuracy of results. Surface runoff generation can be simulated as either: (1) infiltration-excess (or Hortonian) overland flow, or (2) saturation-excess overland flow. This study compared the Hydrological Simulation Program - FORTRAN (HSPF) and the Soil Moisture Routing (SMR) models, each representing one of these mechanisms. These two models were applied to a 102 km2 watershed in the upper part of the Irondequoit Creek basin in central New York State over a seven-year simulation period. The models differed in both the complexity of simulating snowmelt and baseflow processes as well as the detail in which the geographic information was preserved by each model. Despite their differences in structure and representation of hydrologic processes, the two models simulated streamflow with almost equal accuracy. Since streamflow is an integral response and depends mainly on the watershed water balance, this was not unexpected. Model efficiency values for the seven-year simulation period were 0.67 and 0.65 for SMR and HSPF, respectively. HSPF simulated winter streamflow slightly better than SMR as a result of its complex snowmelt routine, whereas SMR simulated summer flows better than HSPF as a result of its runoff and baseflow processes. An important difference between model results was the ability to predict the spatial distribution of soil moisture content. HSPF aggregates soil moisture content, which is generally related to a specific pervious land unit across the entire watershed, whereas SMR predictions of moisture content distribution are geographically specific and matched field observations reasonably well. Important is that the saturated area was predicted well by SMR and confirmed the validity of using saturation-excess mechanisms for this hillslope dominated watershed. ?? 2003 Elsevier B.V. All rights reserved.

Radiatively driven stratosphere-troposphere interactions near the tops of tropical cloud clusters

NASA Technical Reports Server (NTRS)

Churchill, Dean D.; Houze, Robert A., Jr.

1990-01-01

Results are presented of two numerical simulations of the mechanism involved in the dehydration of air, using the model of Churchill (1988) and Churchill and Houze (1990) which combines the water and ice physics parameterizations and IR and solar-radiation parameterization with a convective adjustment scheme in a kinematic nondynamic framework. One simulation, a cirrus cloud simulation, was to test the Danielsen (1982) hypothesis of a dehydration mechanism for the stratosphere; the other was to simulate the mesoscale updraft in order to test an alternative mechanism for 'freeze-drying' the air. The results show that the physical processes simulated in the mesoscale updraft differ from those in the thin-cirrus simulation. While in the thin-cirrus case, eddy fluxes occur in response to IR radiative destabilization, and, hence, no net transfer occurs between troposphere and stratosphere, the mesosphere updraft case has net upward mass transport into the lower stratosphere.

Human swallowing simulation based on videofluorography images using Hamiltonian MPS method

NASA Astrophysics Data System (ADS)

Kikuchi, Takahiro; Michiwaki, Yukihiro; Kamiya, Tetsu; Toyama, Yoshio; Tamai, Tasuku; Koshizuka, Seiichi

2015-09-01

In developed nations, swallowing disorders and aspiration pneumonia have become serious problems. We developed a method to simulate the behavior of the organs involved in swallowing to clarify the mechanisms of swallowing and aspiration. The shape model is based on anatomically realistic geometry, and the motion model utilizes forced displacements based on realistic dynamic images to reflect the mechanisms of human swallowing. The soft tissue organs are modeled as nonlinear elastic material using the Hamiltonian MPS method. This method allows for stable simulation of the complex swallowing movement. A penalty method using metaballs is employed to simulate contact between organ walls and smooth sliding along the walls. We performed four numerical simulations under different analysis conditions to represent four cases of swallowing, including a healthy volunteer and a patient with a swallowing disorder. The simulation results were compared to examine the epiglottic downfolding mechanism, which strongly influences the risk of aspiration.

i3Drive, a 3D interactive driving simulator.

PubMed

Ambroz, Miha; Prebil, Ivan

2010-01-01

i3Drive, a wheeled-vehicle simulator, can accurately simulate vehicles of various configurations with up to eight wheels in real time on a desktop PC. It presents the vehicle dynamics as an interactive animation in a virtual 3D environment. The application is fully GUI-controlled, giving users an easy overview of the simulation parameters and letting them adjust those parameters interactively. It models all relevant vehicle systems, including the mechanical models of the suspension, power train, and braking and steering systems. The simulation results generally correspond well with actual measurements, making the system useful for studying vehicle performance in various driving scenarios. i3Drive is thus a worthy complement to other, more complex tools for vehicle-dynamics simulation and analysis.