Molecular-Level Modeling of Interfacial Phenomena: Use of Molecular Dynamics Simulations in Tandem With Statistical Thermodynamics Models

2007 ◽  
Author(s):  
Van P. Carey
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Molecular Level ◽  
Md Simulations ◽  
Statistical Thermodynamics ◽  
Liquid Films ◽  
Thin Liquid Films ◽  
Interfacial Phenomena ◽  
Bulk Liquid ◽  
Interfacial Region

Nanoscale aspects of interfacial phenomena can be critically import in convective vaporization and condensation in nanochannels or microchannels. Molecular dynamics (MD) simulations have been extensively used to model and explore the physics of interfacial phenomena at the molecular level. Efforts to improve MD simulations have often focused on development of more physically realistic interaction potentials used to model intermolecular force interactions, or on development of more efficient computing strategies. An important, and often overlooked aspect of MD simulations is the role that theoretical models from statistical thermodynamics can play in MD simulations. This paper argues that use of alternate statistical thermodynamics models, and unconventional strategies for using them, can be effective ways of enhancing MD simulations. The advantages of these types of approaches are explored in the context of three recent MD simulation studies of interfacial region thermophysics that have made use of statistical thermodynamics theory in novel ways. Examples considered include studies of the interfacial region between bulk liquid and vapor phases, thin liquid films on solid surfaces, and stability free thin liquid films. These examples illustrate ways that MD simulations can be combined with other models to enhance computational efficiency or extract more information from the MD simulation results. Successful strategies for implementing these types of scheme are examined, and their general applicability is assessed.

Surface Tension Evaluation Via Thermodynamic Analysis of Statistical Data From Molecular Dynamics Simulations

Volume 4 ◽  
2004 ◽  
Author(s):  
Aaron P. Wemhoff ◽  
Van P. Carey
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Density Profile ◽  
Md Simulation ◽  
Md Simulations ◽  
Bulk Liquid ◽  
Interfacial Region ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones

Surface tension determination of liquid-vapor interfaces of polyatomic fluids using traditional methods has shown to be difficult due to the requirement of evaluating complex intermolecular potentials. However, analytical techniques have recently been developed that determine surface tension solely by means of the characteristics of the interfacial region between the bulk liquid and vapor regions. A post-simulation application of the excess free energy density integration (EFEDI) method was used for analysis of the resultant density profile of molecular dynamics (MD) simulations of argon using a simple Lennard-Jones potential and diatomic nitrogen using a two-center Lennard-Jones potential. MD simulations were also run for an approximation of nitrogen using the simple Lennard-Jones potential. In each MD simulation, a liquid film was initialized between vapor regions and NVE-type simulations were run to equilibrium. The simulation domain was divided into bins across the interfacial region for fluid density collection, and the resultant interfacial region density profile was used for surface tension evaluation. Application of the EFEDI method to these MD simulation results exhibited good approximations to surface tension as a function of temperature for both a simple and complex potential.

Exploration of Nanoscale Features of Thin Liquid Films on Solid Surfaces Using Molecular Dynamics Simulations

2004 ◽  
Author(s):  
Aaron P. Wemhoff ◽  
Van P. Carey
Keyword(s):  
Molecular Dynamics ◽  
Nucleate Boiling ◽  
Liquid Films ◽  
Thin Liquid Films ◽  
Solid Surfaces ◽  
Dynamics Simulation ◽  
Bulk Liquid ◽  
Metallic Surface ◽  
Interfacial Region ◽  
Far Field

Thin liquid films on solid surfaces are seen in a variety of systems including bubble growth during nucleate boiling and microgroove heat pipe evaporators and condensers. The small thickness of such films leads to difficult experimental observation of phenomena within various regions of the film: the wall-affected region, the bulk liquid, and the liquid-vapor interfacial region. A novel hybrid simulation methodology is used that combines a deterministic molecular dynamics simulation of the liquid regions with a stochastic treatment of the far-field vapor region boundary. In this simulation scheme, the imposed far-field pressure is iterated as the simulation is advanced in time until the mass in the system stabilizes at the specified temperature. This establishes the equilibrium saturation vapor pressure for the specified temperature as dictated by the intermolecular force interaction models for the fluid and molecules near the solid surface. Simulation results are presented for an argon liquid film on a metallic surface. The simulated surface tension values compare favorably with those from ASHRAE tables, although the simulated saturation density and pressure values behave as though the system is at a slightly higher temperature. The method presented here is a viable tool for simulating thin films on solid surfaces for systems operating far from the critical point.

scholarly journals Fully Atomistic Molecular Dynamics Computation of Physico-Mechanical Properties of PB, PS, and SBS

Nanomaterials ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 1088 ◽  
Author(s):  
Yang Kang ◽  
Dunhong Zhou ◽  
Qiang Wu ◽  
Fuyan Duan ◽  
Rufang Yao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Strain Rate ◽  
Strain Hardening ◽  
Md Simulation ◽  
Md Simulations ◽  
Strain Rates ◽  
Young’S Moduli ◽  
Plastic Modulus ◽  
Styrene Butadiene ◽  
Butadiene Styrene

The physical properties—including density, glass transition temperature (Tg), and tensile properties—of polybutadiene (PB), polystyrene (PS) and poly (styrene-butadiene-styrene: SBS) block copolymer were predicted by using atomistic molecular dynamics (MD) simulation. At 100 K, for PB and SBS under uniaxial tension with strain rate ε ˙ = 1010 s−1 and 109 s−1, their stress–strain curves had four features, i.e., elastic, yield, softening, and strain hardening. At 300 K, the tensile curves of the three polymers with strain rates between 108 s−1 and 1010 s−1 exhibited strain hardening following elastic regime. The values of Young’s moduli of the copolymers were independent of strain rate. The plastic modulus of PS was independent of strain rate, but the Young’s moduli of PB and SBS depended on strain rate under the same conditions. After extrapolating the Young’s moduli of PB and SBS at strain rates of 0.01–1 s−1 by the linearized Eyring-like model, the predicted results by MD simulations were in accordance well with experimental results, which demonstrate that MD results are feasible for design of new materials.

On the interface of organic aerosols: molecular level understanding of surface melting, mixing and water adsorption/desorption dynamics

2021 ◽  
Author(s):  
Josip Lovrić ◽  
Xiangrui Kong ◽  
Sofia M. Johansson ◽  
Erik S. Thomson ◽  
Jan B. C. Pettersson
Keyword(s):  
Physical Chemistry ◽  
Molecular Dynamics ◽  
Melting Point ◽  
Molecular Beam ◽  
Molecular Level ◽  
Organic Aerosols ◽  
Md Simulations ◽  
Valeric Acid ◽  
Good Representative ◽  
Hydrophilic Character

<p>The detailed description of organic aerosols surfaces in the atmosphere remains an open issue, which limits our ability to understand and predict environmental change. Important research questions concern the hydrophobic/hydrophilic character of fresh and aged aerosols and the related influence on water uptake in solid, liquid as well in intermediate state.  Also, surface characterization remains big challenge but we find it reachable by conjunction of Molecular Dynamics (MD) simulations and the environmental molecular beam (EMB) experimental method.  A  picture of the detailed molecular-level behavior of water molecules on organic surfaces is beginning to rise based on detailed experimental and theoretical studies; one example is a recent study that investigates water interactions with solid and liquid n-butanol near the melting point [1], another example focus on interaction of water with solid nopinone [2]. From the other side, in order to characterize surface properties during and before melting we employ MD simulations of n-butanol, nopinone and valeric acid. Nopinone (C<sub>9</sub>H<sub>14</sub>O) is a reaction product formed during oxidation of β-pinene and has been found in both the gas and particle phases of atmospheric aerosol. n-butanol (C<sub>4</sub>H<sub>9</sub>OH) is primary alcohol, naturally occurs scarcely and here serves as good representative for alcohols. In the same way valeric acid (CH<sub>3</sub>(CH<sub>2</sub>)<sub>3</sub>COOH) serves as a good representative for a family of carboxylic acids. Valeric acid is, as n-butanol, straight-chain molecule. We show that a classical force field for organic material is able to model crystal and liquid structures. The surface properties near the melting point of the condensed phase are reported, and the hydrophobic and hydrophilic character of the surface layer is discussed.  Overall surface melting dynamic is presented and quantified in the terms of structural and geometrical properties. Mixing of a methanol with the solid nopinone surface is examined and hereby presented.</p><p><strong>References</strong></p><p>[1] Johansson, S. M., Lovrić, J., Kong, X., Thomson, E. S., Papagiannakopoulos, P., Briquez, S., Toubin, C, Pettersson, J. B. C. (2019). Understanding water interactions with organic surfaces: environmental molecular beam and molecular dynamics studies of the water–butanol system. Physical Chemistry Chemical Physics. https://doi.org/10.1039/C8CP04151B   </p><p>[2] Johansson, S. M., Lovrić, J., Kong, X., Thomson, E. S., Hallquist, M., & Pettersson, J. B. C. (2020). Experimental and Computational Study of Molecular Water Interactions with Condensed Nopinone Surfaces Under Atmospherically Relevant Conditions. The Journal of Physical Chemistry A, acs.jpca.9b10970. https://doi.org/10.1021/acs.jpca.9b10970</p><p>Keywords: Molecular Dynamics, organic crystal, organic aerosols, water uptake, surface procesess, molecular level</p>

A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase

2020 ◽  
Vol 36 (18) ◽  
pp. 4714-4720
Author(s):  
Farzin Sohraby ◽  
Mostafa Javaheri Moghadam ◽  
Masoud Aliyar ◽  
Hassan Aryapour
Keyword(s):  
Molecular Dynamics ◽  
Ligand Binding ◽  
Md Simulation ◽  
Src Kinase ◽  
Deep Understanding ◽  
Md Simulations ◽  
Binding Mode ◽  
Supplementary Information ◽  
Computational Resources ◽  
Binding Mechanisms

Abstract Summary Small molecules such as metabolites and drugs play essential roles in biological processes and pharmaceutical industry. Knowing their interactions with biomacromolecular targets demands a deep understanding of binding mechanisms. Dozens of papers have suggested that discovering of the binding event by means of conventional unbiased molecular dynamics (MD) simulation urges considerable amount of computational resources, therefore, only one who holds a cluster or a supercomputer can afford such extensive simulations. Thus, many researchers who do not own such resources are reluctant to take the benefits of running unbiased MD simulation, in full atomistic details, when studying a ligand binding pathway. Many researchers are impelled to be content with biased MD simulations which seek its validation due to its intrinsic preconceived framework. In this work, we have presented a workable stratagem to encourage everyone to perform unbiased (unguided) MD simulations, in this case a protein–ligand binding process, by typical desktop computers and so achieve valuable results in nanosecond time scale. Here, we have described a dynamical binding’s process of an anticancer drug, the dasatinib, to the c-Src kinase in full atomistic details for the first time, without applying any biasing force or potential which may lead the drug to artificial interactions with the protein. We have attained multiple independent binding events which occurred in the nanosecond time scales, surprisingly as little as ∼30 ns. Both the protonated and deprotonated forms of the dasatinib reached the crystallographic binding mode without having any major intermediate state during induction. Availability and implementation The links of the tutorial and technical documents are accessible in the article. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Nanoindentation simulations for large atomic systems : an analysis of molecular dynamics and bridged finite element - molecular dynamics methodologies

2021 ◽  
Author(s):  
Jonathan Vandersluis
Keyword(s):  
Molecular Dynamics ◽  
Finite Element ◽  
Md Simulation ◽  
Computational Simulation ◽  
Md Simulations ◽  
Single Step ◽  
Depth Interval ◽  
Simulation Tool ◽  
Custom Made ◽  
Computational Resources

This thesis develops a molecular dynamics (MD) custom made computational tool to perform nanoindentation simulations on copper nanomaterials, a Face Centred Cubic (FCC) metal. The Embedding Atom Method (EAM) is used to model the interatomic forces with the substrate. Further, a bridged finite element - molecular dynamics (FE-MD) simulation tool is also adapted to perform nanoindentation experimentation. Using this bridged FE-MD simulation tool, nanoindentations are performed much more effectively than the MD simulations while saving substantial computational simulation time. While the MD simulation experienced difficulties capturing the behaviour of the system during indentation especially at faster indentation speeds, the bridged FE-MD method is capable of reaching a state of equilibrium within a single step for each indentation depth interval analyzed throughout the nanoindentation. Although the hardness values for these simulations cannot be obtained without larger scale simulations using more powerful computational resources, the simulations provide insight into the behaviour of the copper nanomaterial during nanoindentation. As a result, it is clear that the bridged FE-MD nanoindentation tool is much more effective for executing nanoindentation simulations than the traditional MD methodologies.

scholarly journals Neural relational inference to learn allosteric long-range interactions in proteins from molecular dynamics simulations

2021 ◽  
Author(s):  
Jingxuan Zhu ◽  
Juexin Wang ◽  
Weiwei Han ◽  
Dong Xu
Keyword(s):  
Molecular Dynamics ◽  
Long Range ◽  
Md Simulation ◽  
Biological Process ◽  
Dynamic Networks ◽  
Md Simulations ◽  
Amino Acid Mutation ◽  
Long Range Interactions ◽  
Decoder Architecture ◽  
Dynamics Simulations

Abstract Protein allostery is a biological process facilitated by spatially long-range intra-protein communication, whereby ligand binding or amino acid mutation at a distant site affects the active site remotely. Molecular dynamics (MD) simulation provides a powerful computational approach to probe the allosteric effect. However, current MD simulations cannot reach the time scales of whole allosteric processes. The advent of deep learning made it possible to evaluate both spatially short and long-range communications for understanding allostery. For this purpose, we applied a neural relational inference (NRI) model based on a graph neural network (GNN), which adopts an encoder-decoder architecture to simultaneously infer latent interactions to probe protein allosteric processes as dynamic networks of interacting residues. From the MD trajectories, this model successfully learned the long-range interactions and pathways that can mediate the allosteric communications between the two distant sites in the Pin1, SOD1, and MEK1 systems.

STUDY OF AFFINITIES BETWEEN SINGLE-WALLED NANOTUBE AND EPOXY RESIN USING MOLECULAR DYNAMICS SIMULATION

2006 ◽  
Vol 05 (01) ◽  
pp. 131-144 ◽  
Author(s):  
JIHUA GOU ◽  
BIN FAN ◽  
GANGBING SONG ◽  
AURANGZEB KHAN
Keyword(s):  
Molecular Dynamics ◽  
Epoxy Resin ◽  
Md Simulation ◽  
Average Distance ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Repulsive Interaction ◽  
Curing Agent ◽  
Single Walled Nanotubes ◽  
Simulation Results

In the processing of carbon nanotube/polymer composites, the interactions between the nanotube and polymer matrix will occur at the molecular level. Understanding their interactions before curing is crucial for nanocomposites processing. In this study, molecular dynamics (MD) simulations were employed to reveal molecular interactions between (10, 10) single-walled nanotube and two kinds of epoxy resin systems. The two kinds of resin systems were EPON 862/EPI-CURE W curing agent (DETDA) and DGEBA (diglycidylether of bisphenol A)diethylenetriamine (DETA) curing agent. The MD simulation results show that the EPON 862, DETDA and DGEBA molecules had strong attractive interactions with single-walled nanotubes and their molecules changed their conformation to align their aromatic rings parallel to the nanotube surface due to π-stacking effect, whereas the DETA molecule had a repulsive interaction with the single-walled nanotubes. The interaction energies of the molecular systems were also calculated. Furthermore, an affinity index (AI) of the average distance between the atoms of the resin molecule and nanotube surface was defined to quantify the affinities between the nanotubes and resin molecules. The MD simulation results show that the EPON 862/EPI-CURE W curing agent system has good affinities with single-walled nanotubes.

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