scholarly journals Transient effects of drying creep in nanoporous solids: understanding the effects of nanoscale energy barriers

2016 ◽  
Vol 472 (2191) ◽  
pp. 20160490 ◽  
Author(s):  
Robert Sinko ◽  
Matthieu Vandamme ◽  
Zdeněk P. Bažant ◽  
Sinan Keten
Keyword(s):  
Water Flow ◽  
Coarse Grained ◽  
Confined Water ◽  
Transient Effects ◽  
Energy Barriers ◽  
Creep Stress ◽  
Model And Simulation ◽  
Nanoporous Solids ◽  
Dynamics Simulations ◽  
Drying Creep

The Pickett effect is the phenomenon of creep enhancement during transient drying. It has been observed for many nanoporous solids, including concrete, wood and Kevlar. While the existing micromechanical models can partially explain this effect, they have yet to consider nanoscale dynamic effects of water in nanopores, which are believed to be of paramount importance. Here, we examine how creep deformations in a slit pore are accelerated by the motion of water due to drying forces using coarse-grained molecular dynamics simulations. We find that the drying that drives water flow in the nanopores lowers both the activation energy of pore walls sliding past one another and the apparent viscosity of confined water molecules. This lowering can be captured with an analytical Arrhenius relationship accounting for the role of water flow in overcoming the energy barriers. Notably, we use this model and simulation results to demonstrate that the drying creep strain is not linearly dependent on the applied creep stress at the nanopore level. Our findings establish the scaling relationships that explain how the creep driving force, drying force and fluid properties are related. Thus, we establish the nanoscale origins of the Pickett effect and provide strategies for minimizing the additional displacements arising from this effect.

scholarly journals Wettability effect on nanoconfined water flow

2017 ◽  
Vol 114 (13) ◽  
pp. 3358-3363 ◽  
Author(s):  
Keliu Wu ◽  
Zhangxin Chen ◽  
Jing Li ◽  
Xiangfang Li ◽  
Jinze Xu ◽  
...  
Keyword(s):  
Water Flow ◽  
Industrial Applications ◽  
Contact Angles ◽  
Confined Water ◽  
Nanoconfined Water ◽  
Flow Capacity ◽  
Apparent Slip ◽  
Effective Slip ◽  
Water Viscosity ◽  
Dynamics Simulations

Understanding and controlling the flow of water confined in nanopores has tremendous implications in theoretical studies and industrial applications. Here, we propose a simple model for the confined water flow based on the concept of effective slip, which is a linear sum of true slip, depending on a contact angle, and apparent slip, caused by a spatial variation of the confined water viscosity as a function of wettability as well as the nanopore dimension. Results from this model show that the flow capacity of confined water is 10−1∼107 times that calculated by the no-slip Hagen–Poiseuille equation for nanopores with various contact angles and dimensions, in agreement with the majority of 53 different study cases from the literature. This work further sheds light on a controversy over an increase or decrease in flow capacity from molecular dynamics simulations and experiments.

scholarly journals An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guy G. Butcher ◽  
William S. Harwin ◽  
Chris I. Jones
Keyword(s):  
Molecular Dynamics ◽  
Alpha Helix ◽  
Interaction Force ◽  
Coiled Coils ◽  
Coarse Grained ◽  
Simulation Framework ◽  
Force Estimation ◽  
Model And Simulation ◽  
Target Force ◽  
Dynamics Simulations

AbstractThe alpha-helix coiled-coils within talin’s rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome the current limitations of force measuring in molecular dynamics simulations, a new simulation framework was developed which operated directly within the force domain. Along with a corresponding alpha-helix modelling method, the simulation framework was developed drawing on robotic kinematics to specifically target force interactions. Coordinate frames were used efficiently to compartmentalise the simulation structures and static analysis was applied to determine the propagation of forces and torques through the protein structure. The results of the electrostatic approximation using Coulomb’s law shows a simulated force interaction within the physiological relevant range of 5–40 pN for the rod sub-domains of talin. This covers the range of forces talin operates in and is 2–3 orders of magnitude closer to experimentally measured values than the compared all-atom and coarse-grained molecular dynamics. This targeted, force-based simulation is, therefore, able to produce more realistic forces values than previous simulation methods.

scholarly journals A nanoscale perspective on the effects of transverse microprestress on drying creep of nanoporous solids

2018 ◽  
Vol 474 (2209) ◽  
pp. 20170570 ◽  
Author(s):  
Robert Sinko ◽  
Zdeněk P. Bažant ◽  
Sinan Keten
Keyword(s):  
Activation Energy ◽  
Energy Barrier ◽  
Creep Behaviour ◽  
Quantitative Relationship ◽  
Solid Material ◽  
Relative Displacement ◽  
Progressive Relaxation ◽  
Coarse Grained ◽  
Energy Barriers ◽  
Drying Creep

The Pickett effect describes the excess non-additive strain developed during drying of a nanoporous solid material under creep. One explanation for its origins, developed using micromechanical models, is the progressive relaxation of internally developed microprestress. However, these models have not explicitly considered the effects of this microprestress on nanoscale energy barriers that govern the relative motion and displacement between nanopore walls during deformation. Here, we evaluate the nanoscale effects of transverse microprestresses on the drying creep behaviour of a nanoscale slit pore using coarse-grained molecular dynamics. We find that the underlying energy barrier depends exponentially on the transverse microprestress, which is attributed to changes in the effective viscosity and degree of nanoconfinement of molecules in the water interlayer. Specifically, as the transverse microprestress is relaxed (i.e. its magnitude decreases), the activation energy barrier is reduced, thereby leading to an acceleration of the creep behaviour and a stronger Pickett effect. Based on our simulation results, we introduce a new microprestress-dependent energy term into our existing Arrhenius model, which describes the relative displacement of pore walls as a function of the underlying activation energy barriers. Our findings further verify the existing micromechanical theories for the origin of the Pickett effect and establish a quantitative relationship between the transverse microprestress and the intensity of the Pickett effect.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

Sign in / Sign up

Export Citation Format

Share Document