Osmosis in semi-permeable pores: an examination of the basic flow equations based on an experimental and molecular dynamics study

2007 ◽  
Vol 463 (2079) ◽  
pp. 881-896 ◽  
Author(s):  
I.S Davis ◽  
B Shachar-Hill ◽  
M.R Curry ◽  
K.S Kim ◽  
T.J Pedley ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Flow Rate ◽  
Order Effect ◽  
Hydraulic Conductance ◽  
Flow Coefficient ◽  
Dynamics Simulation ◽  
Flow Equations ◽  
Osmotic Flow ◽  
Rate Dependent ◽  
The Difference

Classically ‘semi-permeable’ pores are generally considered to mediate osmotic flow at a rate dependent upon the hydraulic conductance of the pore and the difference in water potential. The shape or size of the solute molecules is not considered to exert a first-order effect on the flow rate nor is the hydraulic conductance thought to be solute dependent. By the experimental measurement of osmosis in the biological pore AQP (aquaporin) and hard-sphere molecular dynamics simulation of a model pore, we show here that the solute radius can have a profound effect on the osmotic flow rate, causing it to decline steeply with decreasing solute radius. Using a simple non-equilibrium thermodynamic theory, we propose that an additional ‘osmotic flow coefficient’ is required to describe flows in semi-permeable structures such as AQPs, and that the fall in flow rate with radius represents a conversion from hydraulic to diffusive water flow due to increasing penetration of the pore by the solute. The interaction between the pore geometry and the solute size cannot, therefore, be overlooked, although for every solute the system obeys the criterion for semi-permeability required by basic thermodynamics. The osmotic pore theory therefore reveals a novel and potentially rich structure that remains to be explored in full.

Osmosis in small pores: a molecular dynamics study of the mechanism of solvent transport

2005 ◽  
Vol 461 (2053) ◽  
pp. 273-296 ◽  
Author(s):  
K. S. Kim ◽  
I. S. Davis ◽  
P. A. Macpherson ◽  
T. J. Pedley ◽  
A. E. Hill
Keyword(s):  
Molecular Dynamics ◽  
Flow Rate ◽  
Low Flow ◽  
Transport Parameters ◽  
Concentration Gradients ◽  
Cylindrical Pore ◽  
Osmotic Flow ◽  
Energy Gradient ◽  
Pressure Flows ◽  
Asymmetric Pores

Osmosis through semi–permeable pores is a complex process by which solvent is driven by its free energy gradient towards a solute–rich reservoir. We have studied osmotic flow across a semi–permeable cylindrical pore using hard–sphere molecular dynamics which simulates osmosis in the absence of attractive forces between solute and solvent. In addition, we recorded the rates of pressure–driven solvent flow and the diffusive flow of labelled solvent under concentration gradients. It is apparent that there are differences, which are radius dependent, between viscous and diffusive solvent permeabilities in small pores. The osmotic flow rate is decreased by allowing solute entry into part of the pore, an effect which is not due to solute obstruction. The flow rate is dependent on the structure of the pore, which for asymmetric pores leads, surprisingly, to flow asymmetry or osmotic rectification. In the absence of any possible viscous rectification at these very low flow rates the effect correlates with changes between diffusive and pressure flows created by the presence of solute, an effect which has been predicted from thermodynamic arguments. The geometry of a semi–permeable pore in relation to the solute size is therefore required to predict the osmotic flow rate, a departure from the classical picture. Finally, by extracting transport parameters from simulations with pure solvent, we examine the departure of observed flow rate from that predicted by continuum mechanics, obtaining drag coefficients which we compare with those derived from hydrodynamics alone.

scholarly journals Structure and properties of the low-energy deposited TiO2 thin films: results of the molecular dynamics simulation

2021 ◽  
Vol 2015 (1) ◽  
pp. 012051
Author(s):  
F.V. Grigoriev ◽  
V.B. Sulimov ◽  
A.V. Tikhonravov
Keyword(s):  
Molecular Dynamics ◽  
Titanium Dioxide ◽  
Molecular Dynamics Simulation ◽  
High Energy ◽  
Film Structure ◽  
Low Energy ◽  
Dynamics Simulation ◽  
Tio2 Thin Films ◽  
Titanium Dioxide Films ◽  
The Difference

Abstract The classical molecular dynamics simulation of the low-energy glancing angle deposition of titanium dioxide films is performed. The deposition angle varies from 60° to 80°. It is found that the film structure consists of parallel slanted columns which lead to the anisotropy of films properties. The difference between the main components of the refractive index tensor is about 0.14, which is close to the values obtained for high-energy titanium dioxide films and larger than 0.03 obtained earlier for silicon dioxide films.

The Simulation Research of Nano-Indentation Based on the Molecular Dynamics

2012 ◽  
Vol 500 ◽  
pp. 702-706
Author(s):  
Ying Zhu ◽  
Ling Ling Xie ◽  
Sen Song ◽  
Shun Hen Qi ◽  
Qian Qian Liu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Optimization Method ◽  
Dynamics Simulation ◽  
Simulation Research ◽  
Nano Indentation ◽  
Simulation Calculation ◽  
Simulation Results ◽  
The Difference

The work in the optimization of the simulation of nanoindentation based on the molecular dynamics was mainly introduced in this paper. One optimization method, freeze atoms method was proposed according to the characteristics of nanoindentation process itself, then did the simulation calculation through the use of freeze atoms method and the traditional calculation method, It was found that the difference between simulation results and experimental results of hardness decreased gradually with enlarge the scale of molecular dynamics simulation (with increase of the indentation depth), from 32.39% of 5nm decreased to 14.6% of 25nm. By comparison, it was found that the optimized algorithm could improve the efficiency of simulation in large-scale molecular dynamics simulation., confirmed the correctness and effectiveness of freeze atoms method.

Performance of molecular dynamics simulation for predicting of solvation free energy of neutral solutes in methanol

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Mohammad Emamian ◽  
Hedayat Azizpour ◽  
Hojatollah Moradi ◽  
Kamran Keynejad ◽  
Hossein Bahmanyar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Solvation Free Energy ◽  
Summation Method ◽  
Dynamics Simulation ◽  
Experimental Result ◽  
Coefficient Of Determination ◽  
Solvation Model ◽  
The Difference

Abstract In this study, molecular dynamics simulation was applied for calculating solvation free energy of 16 solute molecules in methanol solvent. The thermodynamic integration method was used because it was possible to calculate the difference in free energy in any thermodynamic path. After comparing results for solvation free energy in different force fields, COMPASS force field was selected since it had the lowest error compared to experimental result. Group-based summation method was used to compute electrostatic and van der Waals forces at 298.15 K and 1 atm. The results of solvation free energy were obtained from molecular dynamics simulation and were compared to the results from Solvation Model Density (SMD) and Universal Continuum Solvation Model (denoted as SM8), which were obtained from other research works. Average square-root-error for molecular dynamics simulation, SMD and SM8 models were 0.096091, 0.595798, and 0.70649. Furthermore, the coefficient of determination (R 2) for molecular dynamics simulation was 0.9618, which shows higher accuracy of MD simulation for calculating solvation free energy comparing to two other models.

DEVELOPMENT OF A FORCE FIELD FOR ARTEMISININ AND MOLECULAR DYNAMICS SIMULATION OF THE DISSOLUTION OF ARTEMISININ IN DIFFERENT SOLVENTS

2013 ◽  
Vol 12 (05) ◽  
pp. 1350038 ◽  
Author(s):  
QUAN YANG ◽  
LUKE E. ACHENIE
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Force Field ◽  
Ethyl Acetate ◽  
Dynamics Simulation ◽  
Chemical Calculation ◽  
Dissolution Property ◽  
Simulation Results ◽  
The Difference ◽  
Acetate Aqueous Solution

Artemisinin is widely employed to treat malaria. A variety of experiments have been done to research the dissolution property of artemisinin in different solvents. To have an in-depth understanding of the property, it is essential to explore the dissolution property from molecular level with molecular dynamics (MD) simulation, which needs a satisfactory force field of artemisinin. Therefore in the research a quantum chemistry based force field was developed. The quantum chemical calculation at different levels was done and Hartree–Fock (HF) level calculation gives satisfactory results. The charge distribution was then determined successfully. The van der Waals (VDW) parameters of the C unit with sp3-C were tuned according to the difference between the dissolution enthalpy of artemisinin in ethanol and ethyl acetate. With the developed force field, MD method was employed to successfully simulate the dissolution property of artemisinin in different solvents. The simulation results show that artemisinin molecules tends to aggregate in water, while in the aqueous solution of ethanol, the same number of artemisinin molecules tends to disperse. Furthermore, simulation results show that 8 M ethyl acetate aqueous solution has better dissolution ability than 8 M ethanol aqueous. The simulation gave agreements with the experimental results.

scholarly journals A simple method for high-precision evaluation of valve flow coefficient by computational fluid dynamics simulation

2017 ◽  
Vol 9 (7) ◽  
pp. 168781401771370 ◽  
Author(s):  
Xiao-Ming Zhou ◽  
Zhi-Kun Wang ◽  
Yi-Fang Zhang
Keyword(s):  
Fluid Dynamics ◽  
Computational Fluid Dynamics ◽  
Pressure Drop ◽  
Adaptation Strategy ◽  
Flow Coefficient ◽  
Dynamics Simulation ◽  
Accurate Estimation ◽  
Simple Method ◽  
Pressure Losses ◽  
The Difference

Flow coefficient is an important performance index associated with the energy efficiency of a valve, and an effective method to evaluate valve flow coefficient is necessary for valve industry. However, theoretical estimation often results in poor accuracy, while experimental measurements involve significant costs in time and equipment. In this article, a computational fluid dynamics method is proposed to achieve simple and accurate evaluation of valve flow coefficient. For each valve, a computational fluid dynamics model is established containing a valve section, an upstream section, and a downstream section. A grid-adaptation strategy is then applied to improve the accuracy of simulation. To calculate flow coefficient, the most important issue is to determine the net pressure loss induced by valve (Δ Pv). Herein, the overall pressure drop (Δ Po) is obtained first, and the pipe-induced pressure drop (Δ Pp) is estimated by linear fitting. Then, Δ Pv is calculated as the difference between Δ Po and Δ Pp. To ensure accurate estimation of the pressure losses, a length of 26 times of pipe diameter is preferred for the upstream section. The experiments demonstrated that the presented method can accurately predict flow coefficient for various types of valves and thus has great potential to be widely used in the valve industry.

Sign in / Sign up

Export Citation Format

Share Document