An evaluation of the capacitive behavior of supercapacitors as a function of the radius of cations using simulations with a constant potential method.

2022 ◽  
Author(s):  
Antenor José Paulista Neto ◽  
Débora Ariana Corrêa da Silva ◽  
Vanessa A. Gonçalves ◽  
Hudson Zanin ◽  
Renato Garcia Freitas ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Potential Method ◽  
Electrochemical Supercapacitors ◽  
Capacitive Behavior ◽  
Electrolyte Interface ◽  
Constant Potential

We report on the molecular dynamics atomistic applying the constant potential method to determine the structural and electrostatic interactions at the electrode-electrolyte interface of electrochemical supercapacitors as a function of...

scholarly journals Investigation of the Ionic Liquid Graphene Electric Double Layer in Supercapacitors Using Constant Potential Simulations

Nanomaterials ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2181
Author(s):  
Baris Demir ◽  
Debra Searles
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Double Layer ◽  
Electric Double Layer ◽  
Potential Method ◽  
Bulk Region ◽  
Structure And Dynamics ◽  
Constant Potential ◽  
Dynamics Simulations ◽  
O 10

In this work, we investigate the effect of the cation structure on the structure and dynamics of the electrode–electrolyte interface using molecular dynamics simulations. A constant potential method is used to capture the behaviour of 1-ethyl-3-methylimidazolium bis (trifluoromethane)sulfonimide ([C2mim][NTf2]) and butyltrimethylammonium bis(trifluoromethane) sulfonimide ([N4,1,1,1][NTf2]) ionic liquids at varying potential differences applied across the supercapacitor. We find that the details of the structure in the electric double layer and the dynamics differ significantly, yet the charge profile and capacitance do not vary greatly. For the systems considered, charging results in the rearrangement and reorientation of ions within ∼1 nm of the electrode rather than the diffusion of ions to/from the bulk region. This occurs on timescales of O(10 ns) for the ionic liquids considered, and depends on the viscosity of the fluid.

scholarly journals Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 3018 ◽  
Author(s):  
Gao Tu ◽  
Tingting Fu ◽  
Fengyuan Yang ◽  
Lixia Yao ◽  
Weiwei Xue ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Electrostatic Interactions ◽  
Binding Free Energy ◽  
Computational Simulation ◽  
Critical Role ◽  
Dynamics Simulation ◽  
Peptide Docking ◽  
C Terminus ◽  
Free Energy Decomposition

The interaction of death-associated protein kinase 1 (DAPK1) with the 2B subunit (GluN2B) C-terminus of N-methyl-D-aspartate receptor (NMDAR) plays a critical role in the pathophysiology of depression and is considered a potential target for the structure-based discovery of new antidepressants. However, the 3D structures of C-terminus residues 1290–1310 of GluN2B (GluN2B-CT1290-1310) remain elusive and the interaction between GluN2B-CT1290-1310 and DAPK1 is unknown. In this study, the mechanism of interaction between DAPK1 and GluN2B-CT1290-1310 was predicted by computational simulation methods including protein–peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed by the mechanics generalized born surface area (MM/GBSA) approach. The simulation results showed that hydrophobic, van der Waals, and electrostatic interactions are responsible for the binding of GluN2B-CT1290–1310/DAPK1. Moreover, through per-residue free energy decomposition and in silico alanine scanning analysis, hotspot residues between GluN2B-CT1290-1310 and DAPK1 interface were identified. In conclusion, this work predicted the binding mode and quantitatively characterized the protein–peptide interface, which will aid in the discovery of novel drugs targeting the GluN2B-CT1290-1310 and DAPK1 interface.

scholarly journals SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

2019 ◽  
Vol 24 (9) ◽  
pp. 928-938 ◽  
Author(s):  
Luca Palazzolo ◽  
Chiara Paravicini ◽  
Tommaso Laurenzi ◽  
Sara Adobati ◽  
Simona Saporiti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Amino Acid Residues ◽  
Dibasic Amino Acid ◽  
Novel Target ◽  
Function Relationship ◽  
Dynamics Simulations

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

scholarly journals Effect of Lysyllysine on non-covalent hybridization of single walled carbon nanotube by single-stranded DNA homodimer: in silico approach

2019 ◽  
Vol 9 (4) ◽  
pp. 315-321
Author(s):  
Fateme Bagherolhashemi ◽  
Mohammad Reza Bozorgmehr ◽  
Mohammad Momen-Heravi
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Electrostatic Interactions ◽  
Membered Ring ◽  
Binding Energies ◽  
Van Der Waals Interactions ◽  
Dynamics Simulation ◽  
Quantum Calculations ◽  
Single Walled Carbon Nanotube ◽  
Sensor Properties

Abstract In this work, the interactions between adenine–adenine di-nucleotide (DA2N) and carbon nanotube (CNT) in the presence of Lysyllysine (LL) was studied by the molecular dynamics simulation. Different carbon nanotubes including (5.5), (6.6) and (7.7) were used to investigate the effect of CNT type. The binding energies were calculated using the molecular mechanics-Poisson Bolzmann surface area method. The results showed that the contribution of the van der Waals interactions between DA2N and CNT was greater than that of the electrostatic interactions. The LL significantly enhanced the electrostatic interactions between the DA2N and CNT (6.6). The quantum calculations revealed that the sensor properties of the DA2N were not significantly affected by the CNT and LL. However, the five-membered ring of adenine played a more important role in the sensing properties of the DA2N. The obtained results are consistent with the previous experimental observations that can help to understand the molecular mechanism of the interaction of DA2N with CNT. Graphic abstract

scholarly journals Ab-initio binding of barnase–barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach

2020 ◽  
Vol 19 (04) ◽  
pp. 2050016
Author(s):  
Mahesh Koirala ◽  
Emil Alexov
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
3D Structure ◽  
Binding Mode ◽  
Steered Molecular Dynamics ◽  
Biological Processes ◽  
Close Proximity ◽  
Ligand Interactions ◽  
Pulling Force

Receptor–ligand interactions are involved in various biological processes, therefore understanding the binding mechanism and ability to predict the binding mode are essential for many biological investigations. While many computational methods exist to predict the 3D structure of the corresponding complex provided the knowledge of the monomers, here we use the newly developed DelPhiForce steered Molecular Dynamics (DFMD) approach to model the binding of barstar to barnase to demonstrate that first-principles methods are also capable of modeling the binding. Essential component of DFMD approach is enhancing the role of long-range electrostatic interactions to provide guiding force of the monomers toward their correct binding orientation and position. Thus, it is demonstrated that the DFMD can successfully dock barstar to barnase even if the initial positions and orientations of both are completely different from the correct ones. Thus, the electrostatics provides orientational guidance along with pulling force to deliver the ligand in close proximity to the receptor.

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