scholarly journals Conformation and Dynamics of Long-Chain End-Tethered Polymers in Microchannels

Polymers ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 488 ◽  
Author(s):  
Tamal Roy ◽  
Kai Szuttor ◽  
Jens Smiatek ◽  
Christian Holm ◽  
Steffen Hardt
Keyword(s):  
Single Molecule ◽  
Oil Recovery ◽  
Deoxyribonucleic Acid ◽  
Dynamics Simulation ◽  
Relaxation Dynamics ◽  
Simulation Techniques ◽  
Simulation Based ◽  
Tethered Polymers ◽  
Materials Used ◽  
External Forces

Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest in polyelectrolytes inside microchannels stems from genetic analysis, considering that deoxyribonucleic acid (DNA) molecules are polyelectrolytes. This review summarizes the single-molecule experimental and molecular dynamics simulation-based studies of end-tethered polyelectrolytes, especially addressing their relaxation dynamics and deformation characteristics under various external forces in micro-confined environments. In most of these studies, DNA is considered as a model polyelectrolyte. Apart from summarizing the results obtained in that area, the most important experimental and simulation techniques are explained.

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 Pore-Scale Simulation of Particle Flooding for Enhancing Oil Recovery

Energies ◽  
2021 ◽  
Vol 14 (8) ◽  
pp. 2305
Author(s):  
Xiangbin Liu ◽  
Le Wang ◽  
Jun Wang ◽  
Junwei Su
Keyword(s):  
Oil Recovery ◽  
Flow Behavior ◽  
Ct Scanning ◽  
Water Flooding ◽  
Pore Scale ◽  
Simulation Techniques ◽  
Three Phase ◽  
Remaining Oil ◽  
Three Phase Flow ◽  
Displacement Force

The particles, water and oil three-phase flow behaviors at the pore scale is significant to clarify the dynamic mechanism in the particle flooding process. In this work, a newly developed direct numerical simulation techniques, i.e., VOF-FDM-DEM method is employed to perform the simulation of several different particle flooding processes after water flooding, which are carried out with a porous structure obtained by CT scanning of a real rock. The study on the distribution of remaining oil and the displacement process of viscoelastic particles shows that the capillary barrier near the location with the abrupt change of pore radius is the main reason for the formation of remaining oil. There is a dynamic threshold in the process of producing remaining oil. Only when the displacement force exceeds this threshold, the remaining oil can be produced. The flow behavior of particle–oil–water under three different flooding modes, i.e., continuous injection, alternate injection and slug injection, is studied. It is found that the particle size and the injection mode have an important influence on the fluid flow. On this basis, the flow behavior, pressure characteristics and recovery efficiency of the three injection modes are compared. It is found that by injecting two kinds of fluids with different resistance increasing ability into the pores, they can enter into different pore channels, resulting in the imbalance of the force on the remaining oil interface and formation of different resistance between the channels, which can realize the rapid recovery of the remaining oil.

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 Detecting Single Molecule Deoxyribonucleic Acid in a Cell Using a Three‐Dimensionally Integrated Nanopore (Small Methods 9/2021)

Small Methods ◽  
2021 ◽  
Vol 5 (9) ◽  
pp. 2170043
Author(s):  
Makusu Tsutsui ◽  
Kazumichi Yokota ◽  
Akihide Arima ◽  
Takashi Washio ◽  
Yoshinobu Baba ◽  
...  
Keyword(s):  
Single Molecule ◽  
Deoxyribonucleic Acid ◽  
A Cell

scholarly journals Recent Developments in Using Molecular Dynamics Simulation Techniques to Study Biomolecules

2017 ◽  
Vol 33 (7) ◽  
pp. 1354-1365 ◽  
Author(s):  
Liao-Ran CAO ◽  
◽  
Chun-Yu ZHANG ◽  
Ding-Lin ZHANG ◽  
Hui-Ying CHU ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Simulation Techniques ◽  
Recent Developments

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

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