scholarly journals Short Pyridine-Furan Springs Exhibit Bistable Dynamics of Duffing Oscillators

Nanomaterials ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3264
Author(s):  
Vladik A. Avetisov ◽  
Maria A. Frolkina ◽  
Anastasia A. Markina ◽  
Alexander D. Muratov ◽  
Vladislav S. Petrovskii
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Stochastic Resonance ◽  
Duffing Oscillator ◽  
Molecular Structures ◽  
Thermally Activated ◽  
Responsive Polymers ◽  
Bistable Dynamics ◽  
Dynamics Simulations ◽  
Intensive Development

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose dynamics are similar to those of bistable mechanical systems, such as Euler arches and Duffing oscillators. Of particular interest are the molecular structures capable of spontaneous vibrations and stochastic resonance. Recently, oligomeric molecules that were a few nanometers in size and exhibited the bistable dynamics of an Euler arch were identified through molecular dynamics simulations of short fragments of thermo-responsive polymers subject to force loading. In this article, we present molecular dynamics simulations of short pyridine-furan springs a few nanometers in size and demonstrated the bistable dynamics of a Duffing oscillator with thermally-activated spontaneous vibrations and stochastic resonance.

scholarly journals Explicit-pH Coarse-Grained Molecular Dynamics Simulations Enable Insights into Restructuring of Intestinal Colloidal Aggregates with Permeation Enhancers

Processes ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 29
Author(s):  
Shakhawath Hossain ◽  
Albin Parrow ◽  
Aleksei Kabedev ◽  
Rosita Carolina Kneiszl ◽  
Yuning Leng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ph Dependence ◽  
Molecular Structures ◽  
Aggregation Behavior ◽  
Coarse Grained ◽  
Permeation Enhancers ◽  
Fed State ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

Permeation enhancers (PEs) can increase the bioavailability of drugs. The mechanisms of action of these PEs are complex, but, typically, when used for oral administration, they can transiently induce the alteration of trans- and paracellular pathways, including increased solubilization and membrane fluidity, or the opening of the tight junctions. To elucidate these mechanistic details, it is important to understand the aggregation behavior of not only the PEs themselves but also other molecules already present in the intestine. Aggregation processes depend critically on, among other factors, the charge state of ionizable chemical groups, which is affected by the pH of the system. In this study, we used explicit-pH coarse-grained molecular dynamics simulations to investigate the aggregation behavior and pH dependence of two commonly used PEs—caprate and SNAC—together with other components of fasted- and fed-state simulated intestinal fluids. We also present and validate a coarse-grained molecular topology for the bile salt taurocholate suitable for the Martini3 force-field. Our results indicate an increase in the number of free molecules as a function of the system pH and for each combination of FaSSIF/FeSSIF and PEs. In addition, there are differences between caprate and SNAC, which are rationalized based on their different molecular structures and critical micelle concentrations.

Nanoscale Modeling and Simulation of Interfacial Bonding of Single-Walled Nanotube Reinforced Composites

2003 ◽  
Author(s):  
Jihua Gou ◽  
Shunliang Jiang ◽  
Bob Minaie ◽  
Zhiyong Liang ◽  
Chuck Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Epoxy Resin ◽  
Molecular Mechanics ◽  
Stress Transfer ◽  
Molecular Structures ◽  
Interfacial Bonding ◽  
Epoxy Composites ◽  
Reinforced Composites ◽  
Dynamics Simulations

Owning to the extraordinary mechanical, electrical and thermal properties of single-walled nanotubes (SWNTs), SWNT reinforced composites can be used for various applications. In the development of SWNT reinforced composites, one of the fundamental issues that scientists and engineers are confronting is the SWNT-polymer interfacial bonding, which will determine the load transfer capability from the polymer matrix to the nanotube. In single-walled nanotube (SWNT) reinforced epoxy composites, the epoxy resin molecules and the nanotubes are at the nano scale. the interaction at the SWNT/epoxy resin interface is highly dependent on their local molecular structures and bonding. At this small length scale, the lattice structures of the nanotube and the epoxy resin cannot be considered continuous, and their interfacial properties cannot be determined through continuum mechanics. In this paper, the interfacial bonding of SWNT reinforced epoxy composites is investigated using molecular mechanics and molecular dynamics simulations based on a cured epoxy resin model, which is constructed by incorporating three-dimensional crosslinks formed with Shell EPON 862 epoxy resin and EPI CURE W curing agent during polymerization. The interfacial bonding energy between the SWNT and the cured epoxy resin is analyzed using molecular mechanics. Furthermore, the pullout of a SWNT from the cured epoxy resin is investigated using molecular dynamics simulations. Based on the pullout simulation, the interfacial shear strength between the SWNT and the cured epoxy resin is calculated to be up to 75MPa. These analysis results indicate that there could be an effective stress transfer from the epoxy resin to the nanotube.

Validation of protein-unfolding transition states identified in molecular dynamics simulations

2001 ◽  
Vol 68 ◽  
pp. 83-93 ◽  
Author(s):  
Valerie Daggett
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Protein Unfolding ◽  
Molecular Structures ◽  
Simulation Studies ◽  
Molecular Models ◽  
Chymotrypsin Inhibitor 2 ◽  
Combined Use ◽  
Dynamics Simulations

Experimental and simulation studies can complement each other nicely in the area of protein folding. Experiment reports on the average properties of a large ensemble (approx. 10(17)-10(19) molecules), typically over time. Molecular dynamics simulations, on the other hand, provide detailed information for a single molecule, a component of the ensemble. By combining these approaches we can obtain not only a more complete picture of folding, but we can also take advantage of the strengths of different methods. For example, experiment cannot provide molecular structures. Molecular dynamics simulations can provide such information, but the simulations are meaningless without a linked experiment. Thus, the interrelated nature of simulation in assessing experimental assumptions and in providing structures to augment energetic descriptions, and experiment in judging whether the simulations are reasonable, provides more confidence in the resulting information about folding. This combination yields tested and testable molecular models of states that evade characterization by conventional methods. Therefore, we have explored the combined use of these methods to map folding/unfolding pathways at atomic resolution, in collaboration with Alan Fersht. Here we focus on chymotrypsin inhibitor 2, a small single-domain, two-state folding protein.

scholarly journals gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations

2018 ◽  
Author(s):  
M. Eric Irrgang ◽  
Jennifer M. Hays ◽  
Peter M. Kasson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Structures ◽  
Folding Kinetics ◽  
Conformational Ensembles ◽  
Simulation Engine ◽  
Dynamics Simulations ◽  
High Level ◽  
Abstract Interface ◽  
Simulation Package

AbstractSummaryMolecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are implementing custom interactions, for instance biases derived from experimental data, and running ensembles of simulations. We present a Python high-level interface for the popular simulation package GROMACS that 1) allows custom potential functions without modifying the simulation package code, 2) maintains the optimized performance of GROMACS, and 3) presents an abstract interface to building and executing computational graphs that allows transparent low-level optimization of data flow and task placement. Minimal dependencies make this integrated API for the GROMACS simulation engine simple, portable, and maintainable. We demonstrate this API for experimentally-driven refinement of protein conformational ensembles.AvailabilitySource and installation instructions are available at https://github.com/kassonlab/gmxapi.

Sign in / Sign up

Export Citation Format

Share Document