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Themed collection Theoretical Modelling at Nano-bio Interfaces

28 items
Editorial

Theoretical modeling of interactions at the bio-nano interface

Ruhong Zhou, Thomas Weikl and Yu-qiang Ma introduce the Nanoscale themed issue on Theoretical Modelling at Biointerfaces.

Graphical abstract: Theoretical modeling of interactions at the bio-nano interface
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Computational investigation of geometrical effects in 2D boron nitride nanopores for DNA detection

Boron nitride nanopores with circular, hexagonal, quadrangular and triangular shape were studied for their potential in DNA detection.

Graphical abstract: Computational investigation of geometrical effects in 2D boron nitride nanopores for DNA detection
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Open Access Paper

Size-dependent aggregation of hydrophobic nanoparticles in lipid membranes

Aggregation of hydrophobic spherical nanoparticles in lipid membranes depends on nanoparticle size. Nanoparticles of ∼3 nm sense and induce membrane curvature.

Graphical abstract: Size-dependent aggregation of hydrophobic nanoparticles in lipid membranes
From the themed collection: Recent Open Access Articles
Paper

Binding patterns and dynamics of double-stranded DNA on the phosphorene surface

Molecular dynamics simulations and electrophoresis experiments show that dsDNA can form a stable binding on the phosphorene surface through the terminal base pairs and adopt an upright orientation regardless of its initial configurations.

Graphical abstract: Binding patterns and dynamics of double-stranded DNA on the phosphorene surface
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Pore formation induced by nanoparticles binding to a lipid membrane

A nanoparticle needs to be both sharp and large enough in order to spontaneously pierce a membrane.

Graphical abstract: Pore formation induced by nanoparticles binding to a lipid membrane
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Enhancing the targeting ability of nanoparticles via protected copolymers

In this work, we reported a comprehensive study showing that protected copolymers can be harnessed to maximize the uptake difference between the cancer cells and the normal cells by using molecular simulations and in vitro experiments.

Graphical abstract: Enhancing the targeting ability of nanoparticles via protected copolymers
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Nanoscale in silico classification of ligand functionalised surfaces for protein adsorption resistance

Non-specific protein adsorption represents a challenge for the design of efficient and safe nanoparticles for biomedical applications. An in silico method is presented to design ligands imparting protein resistance to functional surfaces.

Graphical abstract: Nanoscale in silico classification of ligand functionalised surfaces for protein adsorption resistance
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Length feature of ssDNA adsorption onto graphene oxide with both large unoxidized and oxidized regions

DNA/GO functional structures have been widely used in biosensors, biomedicine and materials science.

Graphical abstract: Length feature of ssDNA adsorption onto graphene oxide with both large unoxidized and oxidized regions
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

A biointerface effect on the self-assembly of ribonucleic acids: a possible mechanism of RNA polymerisation in the self-replication cycle

The self-assembly was found to be more favoured in a vesicle-cell membrane, rather than in the bulk system. The result will contribute to a better understanding of the origin of life on the primitive Earth.

Graphical abstract: A biointerface effect on the self-assembly of ribonucleic acids: a possible mechanism of RNA polymerisation in the self-replication cycle
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Permeation of nanoparticles across the intestinal lipid membrane: dependence on shape and surface chemistry studied through molecular simulations

In-silico design & testing of nanoparticles for oral drug delivery applications.

Graphical abstract: Permeation of nanoparticles across the intestinal lipid membrane: dependence on shape and surface chemistry studied through molecular simulations
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Thermo- and pH-responsive fibrillization of squid suckerin A1H1 peptide

The aggregation and disaggregation of A1H1 peptides is pH and temperature-dependent. The thermo- and pH-responsive properties of A1H1 aggregates may enable novel applications, such as drug delivery, diagnostics, tissue engineering, and biosensors.

Graphical abstract: Thermo- and pH-responsive fibrillization of squid suckerin A1H1 peptide
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly

Molecular dynamics simulations reveal how anionic surfactant SDS and heat unfold full-length proteins.

Graphical abstract: Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Anisotropic protein diffusion on nanosurface

The migration of protein is regulated by the puckered surface of α-PC, resulting in quick and highly directional diffusion. In combination with the bio-compatibility, α-PC is expected to be a novel functional drug delivery agent in biomedical research.

Graphical abstract: Anisotropic protein diffusion on nanosurface
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Orientational DNA binding and directed transport on nanomaterial heterojunctions

Directional DNA transporting is realized by formation of in-plane nanomaterial heterojunction where the DNA maintains a stable helix structure. This phenomenon could guide the future studies of design of functional nano-heterojunctions for biomedical applications.

Graphical abstract: Orientational DNA binding and directed transport on nanomaterial heterojunctions
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Potential interference with microtubule assembly by graphene: a tug-of-war

With the ever-increasing demand for graphene-based materials and their promising applications in numerous nanotechnologies, the biological effects of graphene on living systems have become crucial and ought to be well understood.

Graphical abstract: Potential interference with microtubule assembly by graphene: a tug-of-war
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Simulated revelation of the adsorption behaviours of acetylcholinesterase on charged self-assembled monolayers

Electrostatically driven enzyme orientation leads to different enzyme activities and electron transfer rates on different charged surfaces.

Graphical abstract: Simulated revelation of the adsorption behaviours of acetylcholinesterase on charged self-assembled monolayers
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Nanoparticle translocation across the lung surfactant film regulated by grafting polymers

Conditioning of grafting polymers, including their length, terminal charge, and grafting density, can result in different translocation processes of nanoparticles across the lung surfactant film.

Graphical abstract: Nanoparticle translocation across the lung surfactant film regulated by grafting polymers
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Optimization of hydrophobic nanoparticles to better target lipid rafts with molecular dynamics simulations

Due to different interactions between lipids and proteins, a plasma membrane can segregate into different membrane domains.

Graphical abstract: Optimization of hydrophobic nanoparticles to better target lipid rafts with molecular dynamics simulations
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Expanding the structural diversity of peptide assemblies by coassembling dipeptides with diphenylalanine

Coassembly of dipeptides and FF leads to diverse nanostructures.

Graphical abstract: Expanding the structural diversity of peptide assemblies by coassembling dipeptides with diphenylalanine
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

The effect of phenylalanine ligands on the chiral-selective oxidation of glucose on Au(111)

It is shown that L-Phe-capped Au(111) prefers to adsorb D-glucose and, similarly, D-Phe-capped Au(111) prefers to adsorb L-glucose.

Graphical abstract: The effect of phenylalanine ligands on the chiral-selective oxidation of glucose on Au(111)
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Radial aggregation of proteins prevails over axial aggregation on membrane tubes

Our simulations show that radial aggregation of proteins prevails over axial aggregation on membrane tubes.

Graphical abstract: Radial aggregation of proteins prevails over axial aggregation on membrane tubes
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Mechanistic modeling of spontaneous penetration of carbon nanocones into membrane vesicles

Truncated carbon nanocones with a length comparable to the thickness of a vesicle membrane can self-insert into the membrane and cause cell-related toxicity.

Graphical abstract: Mechanistic modeling of spontaneous penetration of carbon nanocones into membrane vesicles
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

The role of electrostatic potential polarization in the translocation of graphene quantum dots across membranes

With GQDs changed from non-polarized to highly polarized, the favorable location of GQDs in the simulation system translocated from the inner membrane region to the membrane–water interface.

Graphical abstract: The role of electrostatic potential polarization in the translocation of graphene quantum dots across membranes
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Membrane lipids destabilize short interfering ribonucleic acid (siRNA)/polyethylenimine nanoparticles

Negatively charged lipids destabilize siRNA/PEI nanoparticles, which could adversely affect their gene delivery performance.

Graphical abstract: Membrane lipids destabilize short interfering ribonucleic acid (siRNA)/polyethylenimine nanoparticles
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Optimal ligand–receptor binding for highly efficient capture of vesicles in nanofluidic transportation

Tailoring the intrinsic properties can be a versatile strategy in optimizing the ligand–receptor binding towards advantageous biomedical applications.

Graphical abstract: Optimal ligand–receptor binding for highly efficient capture of vesicles in nanofluidic transportation
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

The molecular mechanism of robust macrophage immune responses induced by PEGylated molybdenum disulfide

Molecular dynamics simulation and experiments reveal that PEGylated MoS2 triggers more sustained stimulation to macrophage than pristine MoS2via slower/prolonged membrane penetration and stronger membrane adsorption.

Graphical abstract: The molecular mechanism of robust macrophage immune responses induced by PEGylated molybdenum disulfide
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Polymer stiffness governs template mediated self-assembly of liposome-like nanoparticles: simulation, theory and experiment

This study suggests that the self-assembly of a template-mediated liposome (TML) can be utilized as a general method to produce liposomes with controlled sizes.

Graphical abstract: Polymer stiffness governs template mediated self-assembly of liposome-like nanoparticles: simulation, theory and experiment
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
Paper

Curvature-mediated cooperative wrapping of multiple nanoparticles at the same and opposite membrane sides

Combining molecular dynamics simulations and theoretical analysis, we reveal the importance of the magnitude and direction of the membrane bend in regulating curvature-mediated interactions and cooperative wrapping of multiple nanoparticles.

Graphical abstract: Curvature-mediated cooperative wrapping of multiple nanoparticles at the same and opposite membrane sides
From the themed collection: Theoretical Modelling at Nano-bio Interfaces
28 items

About this collection

About the collection:

Guest Edited by Yuqiang Ma, Ruhong Zhou, and Thomas Weikl

This collection aims to highlight the most recent and high-quality theoretical/computational works on this topic, which we believe can deepen the understanding of the interaction of nano-bio interface at the molecular level, and may also provide useful guidelines on experimental design of nanomaterials in biomedical applications.

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