Open‐source molecular modeling software in chemical engineering focusing on the Molecular Simulation Design Framework

Cummings, Peter T.; McCabe, Clare; Iacovella, Christopher R.; Lédeczi, Ákos; Jankowski, Eric; Jayaraman, Arthi; Palmer, Jeremy C.; Maginn, Edward J.; Glotzer, Sharon C.; Anderson, Jon; Siepmann, J. Ilja; Potoff, Jeffrey J.; Matsumoto, Ray A.; Gilmer, Justin; DeFever, Ryan S.; Singh, Ramanish; Crawford, Brad

doi:10.1002/aic.17206

Cited by 25 publications

(20 citation statements)

References 47 publications

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“…Full details of the simulation parameters used and the accuracy of the individual CG RDFs as compared to their atomistic targets mapped to the CG level are provided in Sections S2 and S4. Simulations of the self-assembly of CG model membranes were initialized by randomizing the configuration and orientation of the lipids in the center of the simulation box and hydrating this lipid region with a randomized arrangement of water using the Molecular Simulation and Design Framework (MoSDeF) − mBuild software . The initial configuration of the lipid systems starts with the water and lipid phase separated; while this phase separation happens very rapidly for a fully mixed, isotropic system, the initialization of the system in phase separated configurations ensures that membranes form with their interface normal to one of the principle axes of the system for ease of analysis.…”

Section: Materials and Methodsmentioning

confidence: 99%

Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition

et al. 2022

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Molecular dynamics simulations of mixtures of the ceramide nonhydroxy-sphingosine (NS), cholesterol, and a free fatty acid are performed to gain molecular-level understanding of the structure of the lipids found in the stratum corneum layer of skin. A new coarse-grained force field for cholesterol was developed using the multistate iterative Boltzmann inversion (MS-IBI) method. The coarse-grained cholesterol force field is compatible with previously developed coarse-grained force fields for ceramide NS, free fatty acids, and water and validated against atomistic simulations of these lipids using the CHARMM force field. Self-assembly simulations of multilayer structures using these coarse-grained force fields are performed, revealing that a large fraction of the ceramides adopt extended conformations, which cannot occur in the single bilayer in water structures typically studied using molecular simulation. Cholesterol fluidizes the membrane by promoting packing defects, and an increase in cholesterol content is found to reduce the bilayer thickness due to an increase in interdigitation of the C 24 lipid tails, consistent with experimental observations. Using a reverse-mapping procedure, a self-assembled coarse-grained multilayer system is used to construct an equivalent structure with atomistic resolution. Simulations of this atomistic structure are found to closely agree with experimentally derived neutron scattering length density profiles. Significant interlayer hydrogen bonding is observed in the inner layers of the atomistic multilayer structure that are not found in the outer layers in contact with water or in equivalent bilayer structures. This work highlights the importance of simulating multilayer structures, as compared to the more commonly studied bilayer systems, to enable more appropriate comparisons with multilayer experimental membranes. These results also provide validation of the efficacy of the MS-IBI derived coarse-grained force fields and the framework for multiscale simulation.

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Section: Materials and Methodsmentioning

confidence: 99%

Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition

et al. 2022

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“…In MD simulations, Newton’s equation of motion is solved at each time step for each molecule, which thus provides insights into the interaction between different entities at the angstrom level . Despite the limited length and time scales, the information obtained is a valuable supplement to experiments, which fall short at such small resolutions.…”

Section: Introductionmentioning

confidence: 99%

“…In MD simulations, Newton's equation of motion is solved at each time step for each molecule, which thus provides insights into the interaction between different entities at the angstrom level. 19 Despite the limited length and time scales, 20 the information obtained is a valuable supplement to experiments, which fall short at such small resolutions. Membrane-based systems have been investigated via MD to understand the transportation of ions and water molecules, 21 cross-linking of polymer chains within the membrane, 22 as well as fouling induced by a variety of foulants including surfactantstabilized oil emulsion, 23 protein, 24 and humic substances.…”

Section: Introductionmentioning

confidence: 99%

Investigation of Surfactant–Membrane Interaction Using Molecular Dynamics Simulation with Umbrella Sampling

Velioğlu

Trinh

et al. 2021

ACS EST Eng.

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Membranes are effective for removing oil emulsions in oily wastewater treatments, which is important for environmental remediation as well as recovery of oil for economic benefits. Surfactants play a critical role in stabilizing the oil emulsions, but their effects on the inevitable membrane fouling phenomena remain poorly understood. The focus here is the interesting flux enhancement relative to water conferred by the cationic cetyltrimethylammonium bromide (CTAB) surfactant. Molecular dynamics simulations were performed to understand the interactions between three different surfactants and a hydrophilic polyvinylidene fluoride (PVDF) surface. Unbiased MD simulations quantify the surfactant–water, surfactant–membrane, and water–membrane interactions, but none appears well-correlated to the relative flux trends due to the interplay of all three interactions. To account for all interactions concurrently, umbrella sampling was performed to obtain the potential of mean force (PMF) curves. The adsorption of all three surfactants is driven by enthalpy (rather than entropy), and CTAB was found to have the most attractive binding free energy, smallest equilibrium distance, and looser water network near the PVDF surface, which are tied to the experimental observation of flux enhancement and highest retention. The Angstrom-scale results here reveal the need to consider all the interactions simultaneously rather than separately to fully account for mechanisms underlying membrane fouling by surfactants.

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“…Here, T c is the critical temperature, p c is the critical pressure, T r is the reduced temperature which is the absolute temperature per critical temperature, and α is the particular to the Redlich -Kwong equation of state. [1] Similarly, Redlich-kwong -soave equation of state is introduced which is the modified version of Redlich-kwong equation of state which is given by the following equation:…”

Section: Mathematical Statement Of Equations Of Statementioning

confidence: 99%

“…The main program sets the temperature, provides a vector of 6 pressures, equidistant from 1 to 27; pressure = [1,6,11,16,21,26]. The index goes from 0 to 5.…”

Section: Examples Of Solving Chemical Engineering Problems With the H...mentioning

confidence: 99%

Equations of State in Chemical Enginnering Using Python

Shukla¹,

Singh²

2022

IJEAST

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The python programming language is very useful for all kinds of scientific and engineering tasks by plotting data and analyzing various problems as well. We can use google Colab for python to numerically solve various chemical engineering problems which are difficult or even impossible to solve analytically. One of the best advantages of python programming language is that it is free of cost, and can be easily downloaded from the web. Solving equations of state allows us to find the specific volume of a gaseous mixture of various chemicals at a specified temperature and pressure. Without using the equation of state, it would bedifficult for us to design a chemical plant virtually. By knowing the specific volume, we can determine the size and cost of the chemical plant, including the diameter of pipes, distillation towers and chemical reactors, the horsepower of compressors and pumps. This paper illustrates how to solve the complicated equations of states easily by writing small codes using python programming language.

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Open‐source molecular modeling software in chemical engineering focusing on the Molecular Simulation Design Framework

Cited by 25 publications

References 47 publications

Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition

Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition

Investigation of Surfactant–Membrane Interaction Using Molecular Dynamics Simulation with Umbrella Sampling

Equations of State in Chemical Enginnering Using Python

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