Tuning the Transdermal Transport by Application of External Continuous Electric Field: A Molecular Dynamics Coarse-Grained Study.

2021 ◽  
Author(s):  
Neila Machado ◽  
Clarissa Callegaro ◽  
Marcelo Augusto Christoffolete ◽  
Herculano da Silva Martinho
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Coarse Grained ◽  
Skin Permeability ◽  
Long Time ◽  
Transdermal Transport

The control of skin permeability to specific substances (e.g., drugs, vitamins, nutrients) have been prosecuted for a long time. Electroporation and iontophoresis are techniques that enable the transport of substances...

scholarly journals Quantification of in-plane flexoelectricity in lipid bilayers

2021 ◽  
Author(s):  
Nidhin Thomas ◽  
Ashutosh Agrawal
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Lipid Bilayers ◽  
Material Parameter ◽  
Membrane Surface ◽  
Dielectric Materials ◽  
Coarse Grained ◽  
Molecular Architecture ◽  
Dynamics Simulations ◽  
Continuum Theories

Lipid bilayers behave as 2D dielectric materials that undergo polarization and deformation in the presence of an electric field. This effect has been previously modeled by continuum theories which assume a polarization field oriented normal to the membrane surface. However, the molecular architecture of the lipids reveals that the heqadgroup dipoles are primarily oriented tangential to the membrane surface. Here, we perform atomistic and coarse-grained molecular dynamics simulations to quantify the in-plane polarization undergone by a flat bilayer and a spherical vesicle in the presence of an applied electric field. We use these predictions to compute an effective in-plane flexoelectric coefficient for four different lipid types. Our findings provide the first molecular proof of the in-plane polarization undergone by lipid bilayers and furnish the material parameter required to quantify membrane-electric field interactions.

scholarly journals The penetration of a charged peptide across a membrane under an external electric field: a coarse-grained molecular dynamics simulation

RSC Advances ◽  
2018 ◽  
Vol 8 (72) ◽  
pp. 41517-41525
Author(s):  
Bin Wang ◽  
Jianhua Zhang ◽  
Youyu Zhang ◽  
Zheng Mao ◽  
Nan Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Electric Field ◽  
External Electric Field ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Vesicle Membranes ◽  
Coarse Grained Molecular Dynamics

The processes of single polyarginine (R8) peptide penetration through planar and vesicle membranes under an external electric field are simulated via a coarse-grained molecular dynamics (CGMD) simulation.

Structure and dynamics of ions in dipolar solvent: A coarse-grained simulation study

Soft Matter ◽  
2021 ◽  
Author(s):  
Jicai Liang ◽  
Hao Wei ◽  
Kaifeng Yu ◽  
Chengjiang Lin ◽  
Hongfei Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Electric Field ◽  
Simulation Study ◽  
Dynamic Properties ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Ionic Solution ◽  
Structure And Dynamics ◽  
Coarse Grained Molecular Dynamics

We employ the coarse-grained molecular dynamics simulation to investigate the fundamental structural and dynamic properties of the ionic solution with and without the application of the electric field. Our simulations,...

scholarly journals Identification of electroporation sites in the complex lipid organization of the plasma membrane

2021 ◽  
Author(s):  
Lea Rems ◽  
Xinru Tang ◽  
Fangwei Zhao ◽  
Sergio Perez-Conesa ◽  
Ilaria Testa ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Plasma Membrane ◽  
Survival Analysis ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Machine Learning Methods ◽  
Lipid Organization ◽  
Dynamics Simulations

The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to a strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon, termed electroporation, is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. However, by analysing poration kinetics with Bayesian survival analysis we then show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.

Investigation of the Microscopic Viscoelastic Property for Cross-linked Polymer Network by Molecular Dynamics Simulation

2011 ◽  
Vol 39 (1) ◽  
pp. 44-58 ◽  
Author(s):  
Y. Masumoto ◽  
Y. Iida
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Analytical Method ◽  
Viscoelastic Properties ◽  
Polymer Network ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
The Cross ◽  
Microscopic Dynamic ◽  
Coarse Grained Molecular Dynamics

Abstract The purpose of this work is to develop a new analytical method for simulating the microscopic mechanical property of the cross-linked polymer system using the coarse-grained molecular dynamics simulation. This new analytical method will be utilized for the molecular designing of the tire rubber compound to improve the tire performances such as rolling resistance and wet traction. First, we evaluate the microscopic dynamic viscoelastic properties of the cross-linked polymer using coarse-grained molecular dynamics simulation. This simulation has been conducted by the coarse-grained molecular dynamics program in the OCTA) (http://octa.jp/). To simplify the problem, we employ the bead-spring model, in which a sequence of beads connected by springs denotes a polymer chain. The linear polymer chains that are cross-linked by the cross-linking agents express the three-dimensional cross-linked polymer network. In order to obtain the microscopic dynamic viscoelastic properties, oscillatory deformation is applied to the simulation cell. By applying the time-temperature reduction law to this simulation result, we can evaluate the dynamic viscoelastic properties in the wide deformational frequency range including the rubbery state. Then, the stress is separated into the nonbonding stress and the bonding stress. We confirm that the contribution of the nonbonding stress is larger at lower temperatures. On the other hand, the contribution of the bonding stress is larger at higher temperatures. Finally, analyzing a change of microscopic structure in dynamic oscillatory deformation, we determine that the temperature/frequency dependence of bond stress response to a dynamic oscillatory deformation depends on the temperature dependence of the average bond length in the equilibrium structure and the temperature/frequency dependence of bond orientation. We show that our simulation is a useful tool for studying the microscopic properties of a cross-linked polymer.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

A Thorough Theoretical Exploration of Intriguing Characteristics of Cyclo[18]carbon: Geometry, Bonding Nature, Aromaticity, Weak Interaction, Reactivity, Excited States, Vibrations, Molecular Dynamics and Various Molecular Properties

2019 ◽  
Author(s):  
Tian Lu ◽  
Qinxue Chen ◽  
Zeyu Liu
Keyword(s):  
Molecular Dynamics ◽  
Excited States ◽  
Electronic Excitation ◽  
Ring Structure ◽  
Molecular Properties ◽  
Molecular Vibration ◽  
Full Characterization ◽  
Long Time ◽  
Almost All

Although cyclo[18]carbon has been theoretically and experimentally investigated since long time ago, only very recently it was prepared and directly observed by means of STM/AFM in condensed phase (Kaiser et al., <i>Science</i>, <b>365</b>, 1299 (2019)). The unique ring structure and dual 18-center π delocalization feature bring a variety of unusual characteristics and properties to the cyclo[18]carbon, which are quite worth to be explored. In this work, we present an extremely comprehensive and detailed investigation on almost all aspects of the cyclo[18]carbon, including (1) Geometric characteristics (2) Bonding nature (3) Electron delocalization and aromaticity (4) Intermolecular interaction (5) Reactivity (6) Electronic excitation and UV/Vis spectrum (7) Molecular vibration and IR/Raman spectrum (8) Molecular dynamics (9) Response to external field (10) Electron ionization, affinity and accompanied process (11) Various molecular properties. We believe that our full characterization of the cyclo[18]carbon will greatly deepen researchers' understanding of this system, and thereby help them to utilize it in practice and design its various valuable derivatives.

A Thorough Theoretical Exploration of Intriguing Characteristics of Cyclo[18]carbon: Geometry, Bonding Nature, Aromaticity, Weak Interaction, Reactivity, Excited States, Vibrations, Molecular Dynamics and Various Molecular Properties

2019 ◽  
Author(s):  
Tian Lu ◽  
Qinxue Chen ◽  
Zeyu Liu
Keyword(s):  
Molecular Dynamics ◽  
Excited States ◽  
Electronic Excitation ◽  
Ring Structure ◽  
Molecular Properties ◽  
Molecular Vibration ◽  
Full Characterization ◽  
Long Time ◽  
Almost All

Although cyclo[18]carbon has been theoretically and experimentally investigated since long time ago, only very recently it was prepared and directly observed by means of STM/AFM in condensed phase (Kaiser et al., <i>Science</i>, <b>365</b>, 1299 (2019)). The unique ring structure and dual 18-center π delocalization feature bring a variety of unusual characteristics and properties to the cyclo[18]carbon, which are quite worth to be explored. In this work, we present an extremely comprehensive and detailed investigation on almost all aspects of the cyclo[18]carbon, including (1) Geometric characteristics (2) Bonding nature (3) Electron delocalization and aromaticity (4) Intermolecular interaction (5) Reactivity (6) Electronic excitation and UV/Vis spectrum (7) Molecular vibration and IR/Raman spectrum (8) Molecular dynamics (9) Response to external field (10) Electron ionization, affinity and accompanied process (11) Various molecular properties. We believe that our full characterization of the cyclo[18]carbon will greatly deepen researchers' understanding of this system, and thereby help them to utilize it in practice and design its various valuable derivatives.

scholarly journals The Impact of the Electric Field on Surface Condensation of Water Vapor: Insight from Molecular Dynamics Simulation

Nanomaterials ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 64 ◽  
Author(s):  
Qin Wang ◽  
Hui Xie ◽  
Zhiming Hu ◽  
Chao Liu
Keyword(s):  
Molecular Dynamics ◽  
Water Vapor ◽  
Electric Field ◽  
Intermolecular Forces ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Attraction Force ◽  
Condensation Rate ◽  
Shape Transformation ◽  
The Impact

In this study, molecular dynamics simulations were carried out to study the coupling effect of electric field strength and surface wettability on the condensation process of water vapor. Our results show that an electric field can rotate water molecules upward and restrict condensation. Formed clusters are stretched to become columns above the threshold strength of the field, causing the condensation rate to drop quickly. The enhancement of surface attraction force boosts the rearrangement of water molecules adjacent to the surface and exaggerates the threshold value for shape transformation. In addition, the contact area between clusters and the surface increases with increasing amounts of surface attraction force, which raises the condensation efficiency. Thus, the condensation rate of water vapor on a surface under an electric field is determined by competition between intermolecular forces from the electric field and the surface.

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