3D soft tissue warping dynamics simulation based on force asynchronous diffusion model

2011 ◽  
Vol 22 (2-3) ◽  
pp. 251-259 ◽  
Author(s):  
Weixin Si ◽  
Zhiyong Yuan ◽  
Xiangyun Liao ◽  
Zhaoliang Duan ◽  
Yihua Ding ◽  
...  
Keyword(s):  
Soft Tissue ◽  
Diffusion Model ◽  
Dynamics Simulation ◽  
Simulation Based

Improved Sampling Strategies for Protein Model Refinement based on Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Lim Heo ◽  
Collin Arbour ◽  
Michael Feig
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structure Prediction ◽  
Protein Structures ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Model Refinement ◽  
Protein Model ◽  
Lower Accuracy ◽  
Simulation Based

Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict protein structures. Those methods utilize protein structure databases for structure prediction via template-based modeling or for training machine-learning models to generate predictions. Structure prediction for proteins distant from proteins with known structures often results in lower accuracy with respect to the true physiological structures. Physics-based protein model refinement methods can be applied to improve model accuracy in the predicted models. Refinement methods rely on conformational sampling around the predicted structures, and if structures closer to the native states are sampled, improvements in the model quality become possible. Molecular dynamics simulations have been especially successful for improving model qualities but although consistent refinement can be achieved, the improvements in model qualities are still moderate. To extend the refinement performance of a simulation-based protocol, we explored new schemes that focus on an optimized use of biasing functions and the application of increased simulation temperatures. In addition, we tested the use of alternative initial models so that the simulations can explore conformational space more broadly. Based on the insight of this analysis we are proposing a new refinement protocol that significantly outperformed previous state-of-the-art molecular dynamics simulation-based protocols in the benchmark tests described here. <br>

scholarly journals Comparison of Downdraught and Up Draft Passive Air Conduction Systems (PACS) in a Winery Building

Buildings ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 259
Author(s):  
Ádám László Katona ◽  
István Ervin Háber ◽  
István Kistelegdi
Keyword(s):  
Air Conditioning ◽  
Natural Ventilation ◽  
Dynamics Simulation ◽  
Computational Fluid Dynamics Simulation ◽  
General Applicability ◽  
Change Rate ◽  
Air Change Rate ◽  
Simulation Based ◽  
Ventilation Performance ◽  
Air Conduction

A huge portion of energy consumption in buildings comes from heating, ventilation, and air conditioning. Numerous previous works assessed the potential of natural ventilation compared to mechanical ventilation and proved their justification on the field. Nevertheless, it is a major difficulty to collect enough information from the literature to make decisions between different natural ventilation solutions with a given situation and boundary conditions. The current study tests the passive air conduction system (PACS) variations in the design phase of a medium-sized new winery’s cellar and production hall in Villány, Hungary. A computational fluid dynamics simulation based comparative analysis enabled to determine the differences in updraft (UD) and downdraught (DD) PACS, whereby the latter was found to be more efficient. While the DD PACS performed an air change range of 1.02 h−1 to 5.98 h−1, the UD PACS delivered −0.25 h−1 to 12.82 h−1 air change rate. The ventilation performance of the DD version possessed lower amplitudes, but the distribution was more balanced under different wind incident angles, thus this version was chosen for construction. It could be concluded that the DD PACS provides a more general applicability for natural ventilation in moderate climates and in small to medium scale industry hall domains with one in- and one outlet.

Study on Engine Kinematics and Dynamics Simulation Based on COSMOSMotion

2012 ◽  
Vol 503-504 ◽  
pp. 731-734
Author(s):  
Xiao Xu Liu ◽  
Min Chen ◽  
Ai Hua Tang
Keyword(s):  
Virtual Prototype ◽  
Dynamics Simulation ◽  
Kinematics And Dynamics ◽  
Engine Model ◽  
Kinematics Simulation ◽  
Simulation Based ◽  
Calculation Results ◽  
Simulation Results ◽  
Dynamics Simulations

The engine model with 4 cylinders is built by SolidWorks, the kinematics and dynamics simulations of the engine virtual prototype are done by COSMOSMotion, the results of kinematics simulation are checked, there are very small errors between the simulation results and the calculation results according to formulas. The mainly results of dynamics simulation are given. The simulation result consists with the parameters of the engine.

scholarly journals Investigation of the effect of Hydroxychloroquine, Remdesivir, Oseltamivir and some home remedies in the light of Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Keka Talukdar
Keyword(s):  
Molecular Dynamics ◽  
Clinical Trial ◽  
Computer Simulation ◽  
Molecular Dynamics Simulation ◽  
Human Cell ◽  
Physical Modeling ◽  
Chemical Species ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Simulation Based

Modeling and simulation is another way of finding the interaction between different drugs and chemical species with human cell. Preliminary studies before clinical trial involve computer simulation based on the physical modeling so that clinical trial can be made easier. In many aspects of drug developing, simulation is an essential tool. Here molecular dynamics simulation is performed for the interaction of the spike protein of Covid-19 virus and some of the recently used drugs. Also, the effect of caffeine, theanine, nicotine etc on the virus is found by simulation

Molecular Dynamics Simulation Based Cohesive Zone Representation of Intergranular Fracture Processes in Bicrystalline Graphene

2020 ◽  
Author(s):  
MD Imrul Reza Shishir ◽  
Alireza Tabarraei
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundaries ◽  
Cohesive Zone ◽  
Cohesive Zone Model ◽  
Dynamics Simulation ◽  
Zone Model ◽  
Zone Method ◽  
Simulation Based ◽  
Dynamics Simulations ◽  
Fracture Processes

Abstract The fracture properties of various grain boundaries in graphene are investigated using the cohesive zone method (CZM). Molecular dynamics simulations are conducted using REBO2+S potential in order to develop a cohesive zone model for graphene grain boundaries using a double cantilever bicrystalline graphene sheet. The cohesive zone model is used to investigate the traction–separation law to understand the separation-work and strength of grain boundaries.

A Simulation-Based Analysis of Electricity Access in Uganda

2015 ◽  
Vol 4 (1) ◽  
pp. 1-30 ◽  
Author(s):  
Donna Lillian Namujju ◽  
Gönenç Yücel ◽  
Erik Pruyt ◽  
Richard Okou
Keyword(s):  
Power Supply ◽  
Capacity Planning ◽  
Planning Process ◽  
Supply And Demand ◽  
Dynamics Simulation ◽  
Power Sector ◽  
Model Simulations ◽  
Root Cause ◽  
Simulation Based ◽  
Electricity Access

Access to power is tied to a country's development. It facilitates improved social welfare, education, health and income generating opportunities. Uganda's economy is stifled by its low electrification rates - 16% nationally. This study builds a working theory on the internal setup of Uganda's power sector utilizing this theory to surface influential behavior modes as they pertain to power generation and supply and how these ultimately affect electricity access. Based on this working theory a System Dynamics simulation model is built. The model simulations show how Uganda's power sector is expected to evolve over 80 years in terms of power supply and demand given existing market structure and prevailing conditions. The study finds major problems in the nature of power accessed specifically an insufficient and unreliable power supply. The root cause is found in the nature of the existing capacity planning process in terms of how future capacity requirements are determined and the agreements made with generators as to how and when they fulfill their investment obligations.

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