scholarly journals Molecular dynamics study of multicomponent droplet dissolution in a sparingly miscible liquid

2017 ◽  
Vol 833 ◽  
pp. 54-69 ◽  
Author(s):  
Shantanu Maheshwari ◽  
Martin van der Hoef ◽  
Andrea Prosperetti ◽  
Detlef Lohse
Keyword(s):  
Molecular Dynamics ◽  
Theoretical Model ◽  
Numerical Experiments ◽  
Ternary Systems ◽  
Md Simulations ◽  
Bulk Liquid ◽  
Interface Concentration ◽  
Drop Interface ◽  
Binary And Ternary Systems ◽  
Drop Composition

The dissolution of a multicomponent nanodrop in a sparingly miscible liquid is studied by molecular dynamics (MD) simulations. We studied both binary and ternary systems, in which nanodroplets are formed from one and two components, respectively. Whereas for a single-component droplet the dissolution can easily be calculated, the situation is more complicated for a multicomponent drop, as the interface concentrations of the drop constituents depend on the drop composition, which changes with time. In this study, the variation of the interface concentration with the drop composition is determined from independent ‘numerical experiments’, which are then used in the theoretical model for the dissolution dynamics of a multicomponent drop. The MD simulations reveal that when the interaction strengths between the drop constituents and the surrounding bulk liquid are significantly different, the concentration of the more soluble component near the drop interface may become larger than in the drop bulk. This effect is the larger the smaller the drop radius. While the present study is limited to binary and ternary systems, the same method can be easily extended to a larger number of components.

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.

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.

Molecular dynamics simulations of homogeneous CO2 nucleation

2021 ◽  
Author(s):  
Valtteri Tikkanen ◽  
Kayane Dingilian ◽  
Roope Halonen ◽  
Bernhard Reischl ◽  
Barbara Wyslouzil ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Supersonic Nozzle ◽  
Heat Bath ◽  
Md Simulations ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Bulk Liquid ◽  
General Interest ◽  
Simulation Based

<p>The condensation of carbon dioxide (CO2) is a topic of general interest in view of global decarbonization targets, e.g. in low-temperature CO2 capture technologies promoting the phase transition of CO2 gas is the crucial step. Homogeneous nucleation of a mixture of CO2 and argon gas in a supersonic nozzle has been studied at temperatures from 78 to 92 K, and CO2 partial pressures between 70 and 800 Pa. The consistency between the current data and measurements at higher temperature suggests the critical clusters remain liquid-like even at these low temperatures.</p><p>Here we present large-scale atomistic molecular dynamics (MD) simulations of homogenous CO2 nucleation from the vapour phase at temperatures from 75 to 105 K. The MD approach is an unbiased method to study the nucleation process, including the phase and structure of even the smallest clusters. We used argon carrier gas as a heat bath for the CO2 molecules to avoid unphysical removal of latent heat.</p><p>Simulations confirm that despite strong undercooling, nucleation proceeds through liquid-like clusters. Also, by applying standard steady-state cluster growth kinetics, we are able to calculate the cluster formation free energies from the MD simulations. The results suggest a curvature correction to the classical liquid drop model used in the classical nucleation theory. The correction depends only on the bulk liquid properties, and hence the simulation-based correction can be applied to predict the nucleation rates of real CO2.</p><p>The simulation-based theory is able to capture the magnitude and the temperature-dependency of the nucleation rate rather well, whereas both standard CNT and its self-consistent version (SCNT) underestimate the rate by several orders of magnitude. Here we have corrected the theoretical values with the non-isothermal factor, which is about 0.01-0.1 for the studied system.</p>

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

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