Formation of nanopores in DiynePC–DPPC complex lipid bilayers triggered by on-demand photo-polymerization

Chun, Min Jung; Choi, Yeol Kyo; Ahn, Dong June

doi:10.1039/c8ra04908d

Cited by 6 publications

(7 citation statements)

References 42 publications

(38 reference statements)

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“…Polymers have been used for a wide range of applications, such as smart surfaces, sensors, actuators, bioimaging, drug delivery, , and energy devices, − as they are versatile and can be easily mass-produced and processed. To date, owing to technological advances in various fields, more effective and eco-friendly polymer materials are being designed and produced in each application. , However, it is challenging to design new polymer-based materials because of the significant time and cost to synthesize prototypes and analyze their physicochemical properties.…”

Section: Introductionmentioning

confidence: 99%

“…Polymers have been used for a wide range of applications, such as smart surfaces, 1 sensors, 2 actuators, 3 bioimaging, 4 drug delivery, 5,6 and energy devices, 7−10 as they are versatile and can be easily mass-produced and processed. To date, owing to technological advances in various fields, more effective and eco-friendly polymer materials are being designed and produced in each application.…”

Section: Introductionmentioning

confidence: 99%

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CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers

Choi

Park

et al. 2021

J. Chem. Theory Comput.

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Molecular modeling and simulations are invaluable tools for polymer science and engineering, which predict physicochemical properties of polymers and provide molecular-level insight into the underlying mechanisms. However, building realistic polymer systems is challenging and requires considerable experience because of great variations in structures as well as length and time scales. This work describes Polymer Builder in CHARMM-GUI (), a web-based infrastructure that provides a generalized and automated process to build a relaxed polymer system. Polymer Builder not only provides versatile modeling methods to build complex polymer structures, but also generates realistic polymer melt and solution systems through the built-in coarse-grained model and all-atom replacement. The coarse-grained model parametrization is generalized and extensively validated with various experimental data and all-atom simulations. In addition, the capability of Polymer Builder for generating relaxed polymer systems is demonstrated by density calculations of 34 homopolymer melt systems, characteristic ratio calculations of 170 homopolymer melt systems, a morphology diagram of poly(styrene-b-methyl methacrylate) block copolymers, and self-assembly behavior of amphiphilic poly(ethylene oxide-b-ethylethane) block copolymers in water. We hope that Polymer Builder is useful to carry out innovative and novel polymer modeling and simulation research to acquire insight into structures, dynamics, and underlying mechanisms of complex polymer-containing systems.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers

Choi

Park

et al. 2021

J. Chem. Theory Comput.

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“…Upon light irradiation (λ = 254 nm) DC 8,9 PC photopolymerizes (Fig. 1B), entailing the production of defects at the domain boundaries that cause the formation of pores (36)(37)(38) through which the encapsulated content is released.…”

Section: Resultsmentioning

confidence: 99%

Stimuli-responsive vesicles as distributed artificial organelles for bacterial activation

Gispert

Hindley

Pilkington

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Intercellular communication is a hallmark of living systems. As such, engineering artificial cells that possess this behavior has been at the heart of activities in bottom-up synthetic biology. Communication between artificial and living cells has potential to confer novel capabilities to living organisms that could be exploited in biomedicine and biotechnology. However, most current approaches rely on the exchange of chemical signals that cannot be externally controlled. Here, we report two types of remote-controlled vesicle-based artificial organelles that translate physical inputs into chemical messages that lead to bacterial activation. Upon light or temperature stimulation, artificial cell membranes are activated, releasing signaling molecules that induce protein expression in Escherichia coli . This distributed approach differs from established methods for engineering stimuli-responsive bacteria. Here, artificial cells (as opposed to bacterial cells themselves) are the design unit. Having stimuli-responsive elements compartmentalized in artificial cells has potential applications in therapeutics, tissue engineering, and bioremediation. It will underpin the design of hybrid living/nonliving systems where temporal control over population interactions can be exerted.

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“…The third example consists of a supported lipid bilayer (SLB), which is a popular model of cell membranes with potential biotechnological applications . Many experimental techniques such as atomic force microscopy (AFM), quartz crystal microbalance with dissipation monitoring (QCM-D), and ellipsometry have been employed to investigate the structure and physical properties of lipid bilayers reconstituted with membrane proteins; , however, most of these methods provide only superficial information or lack molecular-level insight into underlying mechanisms. Figure D shows an SLB system built using a combination of Nanomaterial Modeler, Membrane Builder, − and Multicomponent Assembler modules.…”

Section: Results and Discussionmentioning

confidence: 99%

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

Choi

Kern

Kim

et al. 2021

J. Chem. Theory Comput.

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Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide molecular-level insight into underlying mechanisms. However, building nanomaterial-containing systems remains challenging due to the lack of reliable and integrated cyberinfrastructures. Here we present Nanomaterial Modeler in CHARMM-GUI, a web-based cyberinfrastructure that provides an automated process to generate various nanomaterial models, associated topologies, and configuration files to perform state-of-the-art molecular dynamics simulations using most simulation packages. The nanomaterial models are based on the interface force field, one of the most reliable force fields (FFs). The transferability of nanomaterial models among the simulation programs was assessed by single-point energy calculations, which yielded 0.01% relative absolute energy differences for various surface models and equilibrium nanoparticle shapes. Three widely used Lennard-Jones (LJ) cutoff methods are employed to evaluate the compatibility of nanomaterial models with respect to conventional biomolecular FFs: simple truncation at r = 12 Å (12 cutoff), force-based switching over 10 to 12 Å (10−12 fsw), and LJ particle mesh Ewald with no cutoff (LJPME). The FF parameters with these LJ cutoff methods are extensively validated by reproducing structural, interfacial, and mechanical properties. We find that the computed density and surface energies are in good agreement with reported experimental results, although the simulation results increase in the following order: 10−12 fsw <12 cutoff < LJPME. Nanomaterials in which LJ interactions are a major component show relatively higher deviations (up to 4% in density and 8% in surface energy differences) compared with the experiment. Nanomaterial Modeler's capability is also demonstrated by generating complex systems of nanomaterial−biomolecule and nanomaterial−polymer interfaces with a combination of existing CHARMM-GUI modules. We hope that Nanomaterial Modeler can be used to carry out innovative nanomaterial modeling and simulations to acquire insight into the structure, dynamics, and underlying mechanisms of complex nanomaterial-containing systems.

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Formation of nanopores in DiynePC–DPPC complex lipid bilayers triggered by on-demand photo-polymerization

Abstract: Nanopores generated upon photo-polymerization of the lipid membrane containing DiynePC were identified and their size was controllable.

Cited by 6 publications

References 42 publications

CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers

CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers

Stimuli-responsive vesicles as distributed artificial organelles for bacterial activation

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

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