A Simple Molecular Dynamics Lab To Calculate Viscosity as a Function of Temperature

Nascimento

Biochem Molecular Bio Educ

2021

A computational biochemistry laboratory, fitted for bioinformatics students, is presented. The molecular dynamics package GROMACS is used to prepare and simulate a solvated protein. Students analyze the trajectory with different available tools (GROMACS and VMD) to probe the structural stability of the protein during the simulation. Students are also required to make use of Python libraries and write their own code to probe non-covalent interactions between the amino acid side chains. Based on these results, students characterize the system in a qualitatively approach but also assess the importance of each specific interaction through time. This work mobilizes biochemical concepts and programming skills, fostering critical thinking and group work and developing presenting skills.

Section: Discussionmentioning

confidence: 99%

“…MD‐based computational approaches are also available for the study of thermodynamic properties such as viscosity, 43 gas properties, 44 and bulk water properties 45 …”

Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulations and analysis for bioinformatics undergraduate students

Nascimento

Biochem Molecular Bio Educ

2021

“…The GAFF and FF99SB force fields without modifications were utilized to generate the corresponding topologies (Wang et al, 2004;Wickstrom et al, 2009). The minimization, heating (NVT ensemble), and production protocols were implemented to calculate the self-diffusion coefficients and density parameters using the previously published MD protocol (Eckler and Nee, 2016). Production runs of 250 ps in the NPT ensemble with a step size of 1 fs provided ample data to determine the viscosity values from the mean-squared displacement by means of by the Einstein-Smoluchowski and Stokes-Einstein equations (Eckler;Nee, 2016).…”

Section: Methodsmentioning

confidence: 99%

Probing inclusion complexes of 2-hydroxypropyl-β-cyclodextrin with mono-amino mono-carboxylic acids: physicochemical specification, characterization and molecular modeling

Esmaeilpour

Hussein

Almalki

et al. 2020

Heliyon

Density (ρ), viscosity (η) and surface tension (γ) of three amino acids (valine, alanine, and glycine) have been measured at a different mass fraction (0.002 -0.009) of aqueous hydroxypropyl-β-cyclodextrin (HPβCD) mixtures and different temperatures (278.15 -295.15 K). The formation of inclusion complexes has been analyzed via evaluating the amounts of apparent and limiting apparent molar volumes, limiting apparent molar expansibilities, activation energy, kinematic, relative, intrinsic, spatial, and dynamic viscosities. The surface tension studies indicated that the inclusion complexes have been formed with 1:1 stoichiometry and mediated by hydrophobic effects and electrostatic forces. Additionally, the ρ and η parameters were evaluated by molecular modeling experiments to provide more details on the mechanisms of the complexation.

“…aspects of calculating MSD with the use of a variety of experimental data (16,17). A number of laboratory exercises on characterizing diffusive systems have been described (18)(19)(20)(21)(22)(23), but our goal here is to provide a laboratory exercise to introduce upper-level undergraduates to MSD that is flexible, modular, and applicable to a variety of institutions, departments, and teaching modalities. In our version of the exercise we focus our analysis on one practical consideration of MSD, ergodicity, in which averaging can either be taken over a single trajectory (time averaging) or as an average over many independent trajectories (ensemble averaging) (24,25).…”

Section: Introductionmentioning

confidence: 99%

A Flexible Laboratory Exercise Introducing Practical Aspects of Mean Squared Displacement

Mantilla

Kuwada

2021

The Biophysicist

Mean squared displacement is a standard biophysical tool for characterizing the motion of particles in a thermally dominated environment, yet it is rarely formally introduced or discussed in undergraduate curriculum. Here, we provide a flexible and adaptable experimental or computational lab activity that provides a practical introduction to mean squared displacement and anomalous diffusion that includes optional experimental protocols and computational simulation techniques for data collection and discusses a variety of analysis techniques. This lab activity has been implemented both face-to-face and completely online and provides crucial experience in important research techniques, helping to bridge traditional undergraduate curriculum and modern biophysics research.