Topics

Martini coarse-grained model for polyethylenimine.

07:00 EST 10th November 2018 | BioPortfolio

Summary of "Martini coarse-grained model for polyethylenimine."

As a polycation with diverse applications in biomedical and environmental engineering, polyethylenimine (PEI) can be synthesized with varying degrees of branching, polymerization, and can exist in different protonation states. There have been some interests in molecular modeling of PEI at all-atom or coarse-grained (CG) levels, but present CG models are limited to linear PEIs. Here we present the methodology to systematically categorize bond lengths, bond angles and dihedral angles, which allows us to model branched PEIs. The CG model was developed under the Martini scheme based on eight ~600 Da PEIs, with four different degree of branching at two different protonation states. Comparison of the CG model with all-atom simulations shows good agreement for both local (distributions for bonded interactions) and global (end-to-end distance, radius of gyration) properties, with and without salt. Compatibility of the PEI model with other CG bio-molecules developed under the Martini scheme will allow for large-scale simulations of many PEI-enabled processes. © 2018 Wiley Periodicals, Inc.

Affiliation

Journal Details

This article was published in the following journal.

Name: Journal of computational chemistry
ISSN: 1096-987X
Pages:

Links

DeepDyve research library

PubMed Articles [9257 Associated PubMed Articles listed on BioPortfolio]

Aggregation kinetics of short peptides: All-atom and coarse-grained molecular dynamics study.

Peptides can aggregate into ordered structures with different morphologies. The aggregation mechanism and evolving structures are the subject of intense research. In this paper we have used molecular ...

A Transferable, Multi-Resolution Coarse-Grained Model for Amorphous Silica Nanoparticles.

Despite the ubiquity of nanoparticles in modern materials research, computational scientists are often forced to choose between simulations featuring detailed models of only a few nanoparticles or sim...

Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure.

Lamellar and hexagonal lipid structures are of particular importance in the biological processes such as membrane fusion and budding. Atomistic simulations of formation of these phases and transitions...

Development of an ATP force field for coarse-grained simulation of ATPases and its application to the maltose transporter.

The biological functions of ATPases, such as myosin, kinesin, and ABC transporter, are due to large conformational motions driven by energy obtained from ATP. Elucidation of the mechanisms underlying ...

CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems.

Nanodiscs are discoidal protein-lipid complexes that have wide applications in membrane protein studies. Modeling and simulation of nanodiscs are challenging due to the absence of structures of many m...

Clinical Trials [2050 Associated Clinical Trials listed on BioPortfolio]

Antibacterial Properties of Silicon Incorporated With Quaternary Ammonium Polyethylenimine Nanoparticles

The aim of this study is to evaluate the antibacterial activity of crosslinked quaternary ammonium polyethylenimine (PEI) nanoparticles incorporated at 1-2% w/w in a commercial soft liner ...

Effect of Extra- Fine Versus Coarse-Particle Inhaled Corticosteroids (ICS) on Ventilation Heterogeneity in Children With Poorly Controlled Asthma

The primary objective of the study is to show that ventilation heterogeneity identified by hyperpolarized helium-3 lung MRI is prevalent children with poorly controlled asthma despite guid...

A Study in Healthy Men and Women to Test if Taking Different Formulations of BI 730357 Tablets Influences the Amount of BI 730357 in the Blood

The main objective of Trial Parts 1 and 2 is to investigate the relative bioavailability of two tablet strengths (low dose and high dose) of the intended Commercial Formulation of BI 73035...

Clinical Trial to Evaluate the Model SC9 IOL Compared to the Model LI61SE IOL (Bausch & Lomb)

To evaluate the Model SC9 Intraocular Lens for the improvement of near and intermediate vision when compared to a legally marketed monofocal IOL.

Brain Network Disruptions Related to Traumatic Coma

To provide a fine-grained description of the brain network dysfunctions induced by severe traumatic brain injury (TBI) or anoxic encephalopathy, that are responsible for the acute state of...

Medical and Biotech [MESH] Definitions

Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.

Theoretical models simulating behavior or activities in nursing, including nursing care, management and economics, theory, assessment, research, and education. Some examples of these models include Orem Self-Care Model, Roy Adaptation Model, and Rogers Life Process Model.

A principle of estimation in which the estimates of a set of parameters in a statistical model are those quantities minimizing the sum of squared differences between the observed values of a dependent variable and the values predicted by the model.

Production of a radiographic image of a small or very thin object on fine-grained photographic film under conditions which permit subsequent microscopic examination or enlargement of the radiograph at linear magnifications of up to several hundred and with a resolution approaching the resolving power of the photographic emulsion (about 1000 lines per millimeter).

Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.

Quick Search


DeepDyve research library

Relevant Topic

Collaborations in biotechnology
Commercial and academic collaborations are used throughout the biotechnology and pharmaceutical sector to enhance research and product development. Collaborations can take the form of research and evaluation agreements, licensing, partnerships etc. ...


Searches Linking to this Article