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Deciphering interactions of ionic liquids with biomembrane

Biophysical Reviews 2018年第3期10卷 721-734页

作者： Sharma, V.K. Mukhopadhyay, R. Solid State Physics Division Bhabha Atomic Research Centre Mumbai 400085 India

Ionic liquids (ILs) are a special class of low-temperature (typically < 100 °C) molten salts, which have huge upsurge interest in the field of chemical synthesis, catalysis, electrochemistry, pharmacology, and biotechnology, mainly due to their highly tunable nature and exceptional properties. However, practical uses of ILs are restricted mainly due to their adverse actions on organisms. Understanding interactions of ILs with biomembrane is prerequisite to assimilate the actions of these ionic compounds on the organism. Here, we review different biophysical methods to characterize interactions between ILs and phospholipid membrane, a model biomembrane. All these studies indicate that ILs interact profoundly with the lipid bilayer and modulate the structure, microscopic dynamics, and phase behavior of the membrane, which could be the fundamental cause of the observed toxicity of ILs. Effects of ILs on the membrane are found to be strongly dependent on the lipophilicity of the IL and are found to increase with the alkyl chain length of IL. This can be correlated with the observed higher toxicity of IL with the longer alkyl chain length. These informations would be useful to tune the toxicity of IL which is required in designing environment-friendly nontoxic solvents of the so-called green chemistry for various practical applications. © 2018, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： Ionic liquids Neutron scattering Phase behavior Phospholipid membrane structure and dynamics Toxicity

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Dynamical, structural and chemical heterogeneities in a binary metallic glass-forming liquid

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JOURNAL OF PHYSICS-CONDENSED MATTER 2018年第14期30卷 145701-145701页

作者： Puosi, F. Jakse, N. Pasturel, A. Univ Grenoble Alpes CNRS Grenoble INP SIMaP F-38000 Grenoble France

As it approaches the glass transition, particle motion in liquids becomes highly heterogeneous and regions with virtually no mobility coexist with liquid-like domains. This complex dynamic is believed to be responsible for different phenomena including non-exponential relaxation and the breakdown of the Stokes-Einstein relation. Understanding the relationships between dynamical heterogeneities and local structure in metallic liquids and glasses is a major scientific challenge. Here we use classical molecular dynamics simulations to study the atomic dynamics and microscopic structure of Cu50Zr50 alloy in the supercooling regime. Dynamical heterogeneities are identified via an isoconfigurational analysis. We demonstrate the transition from isolated to clustering low mobility with decreasing temperature. These slow clusters, whose sizes grow upon cooling, are also associated with concentration fluctuations, characterized by a Zr-enriched phase, with a composition CuZr2. In addition, a structural analysis of slow clusters based on Voronoi tessellation evidences an increase with respect of the bulk system of the fraction of Cu atoms having a local icosahedral order. These results are in agreement with the consolidated scenario of the relevant role played by icosahedral order in the dynamic slowing-down in supercooled metal alloys.

关键词： metallic liquids and glasses heterogeneities structure and dynamics molecular dynamics simulations

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Using Force to Punch Holes: Mechanics of Contractile Nanomachines

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TRENDS IN CELL BIOLOGY 2017年第9期27卷 623-632页

作者： Brackmann, Maximilian Nazarov, Sergey Wang, Jing Basler, Marek Univ Basel Biozentrum Focal Area Infect Biol Basel Switzerland

Using physical force to translocate macromolecules across a membrane has the advantage of being a universal solution independent of the properties of the target membrane. However, physically punching a stiff membrane is not a trivial task and three things are necessary for success: a sharp tip, a source of energy, and the ability to strongly bind to the target. In this review we describe the basic mechanism of membrane puncturing by contractile nanomachines with a focus on the T4 phage, R-type pyocin, and the bacterial Type VI secretion system (T6SS) based on recent studies of the structures and dynamics of their assembly.

关键词： Type VI secretion system contractile bacteriophages protein translocation membrane bacterial toxins structure and dynamics

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The Problem with the 'Information' in Integrated Information Theory

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JOURNAL OF CONSCIOUSNESS STUDIES 2017年第7-8期24卷 130-154页

作者： Mindt, Garrett Cent European Univ Budapest Hungary

The integrated information theory (IIT) of consciousness is becoming an increasingly popular neuroscientific account of phenomenal experience. IIT claims that consciousness is integrated information in a system. I set this theory against the hard problem of consciousness (Chalmers, 1996;1995) as the goal for a theory of consciousness to meet. In this paper I look to examine and ultimately critique IIT's use of the notion of information to base a theory of consciousness. I argue that the notion of information in IIT is a purely structural-dynamical notion, and so falls afoul of the structure and dynamics argument (Chalmers, 2003). I bolster these claims by appeal to the explanatory gap argument and show how HT succumbs to this argument as well. For these reasons, I call into doubt IIT's ability to answer the hard problem of consciousness. Although this paper argues against the notion of information in HT, in a broader context the criticisms which I raise here can be brought against any theory that attempts to explain consciousness as an information theoretic phenomenon.

关键词： consciousness integrated information theory hard problem of consciousness hard problem of information structure and dynamics explanatory gap

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The Episodic Nature of Experience: A Dynamical Systems Analysis

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COGNITIVE SCIENCE 2017年第5期41卷 1377-1393页

作者： Sreekumar, Vishnu Dennis, Simon Doxas, Isidoros Ohio State Univ Dept Psychol Columbus OH 43210 USA Univ Newcastle Sch Psychol Callaghan NSW Australia Univ Colorado Ctr Integrated Plasma Studies Boulder CO 80309 USA BAE Syst Columbia MD USA

Context is an important construct in many domains of cognition, including learning, memory, and emotion. We used dynamical systems methods to demonstrate the episodic nature of experience by showing a natural separation between the scales over which within-context and between-context relationships operate. To do this, we represented an individual's emails extending over about 5years in a high-dimensional semantic space and computed the dimensionalities of the subspaces occupied by these emails. Personal discourse has a two-scaled geometry with smaller within-context dimensionalities than between-context dimensionalities. Prior studies have shown that reading experience (Doxas, Dennis, & Oliver, 2010) and visual experience (Sreekumar, Dennis, Doxas, Zhuang, & Belkin, 2014) have a similar two-scaled structure. Furthermore, the recurrence plot of the emails revealed that experience is predictable and hierarchical, supporting the constructs of some influential theories of memory. The results demonstrate that experience is not scale-free and provide an important target for accounts of how experience shapes cognition.

关键词： Dynamical systems Human experience Context Memory Rational analysis structure and dynamics

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The Role of the Membrane in the structure and Biophysical Robustness of the Dengue Virion Envelope

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structure 2016年第3期24卷 375-382页

作者： Reddy, Tyler Sansom, Mark S. P. Univ Oxford Dept Biochem S Parks Rd Oxford OX1 3QU England

The dengue virion is surrounded by an envelope of membrane proteins surrounding a lipid bilayer. We have combined the cryoelectron microscopy structures of the membrane proteins (PDB: 3J27) with a lipid bilayer whose composition is based on lipidomics data for insect cell membranes, to obtain a near-atomic resolution computational model of the envelope of the dengue virion. A coarse-grained molecular dynamics simulation on the microsecond timescale enables analysis of key biophysical properties of the dengue outer envelope. Properties analyzed include area per lipid values (for a spherical virion with a mixed lipid composition), bilayer thickness, and lipid diffusion coefficients. Despite the absence of cholesterol from the lipid bilayer, the virion exhibits biophysical robustness (slow lipid diffusion alongside stable bilayer thickness, virion diameter, and shape) that matches the cholesterolrich membrane of influenza A, with similarly anomalous diffusion of lipids. Biophysical robustness of the envelope may confer resilience to environmental perturbations.

关键词： viral envelope lipid bilayer structure and dynamics diffusion dengue virus

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MOLECULAR dynamics SIMULATION ON THE structure and dynamics OF WATER IN THE 1-BUTYL-3-METHYLIMIDAZOLIUM TETRAFLUOROBORATE/WATER MIXTURE

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JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2010年第3期9卷 573-584页

作者： Tian, Guocai Li, Jian Kunming Univ Sci & Technol Fac Met & Energy Engn Kunming 650093 Yunnan Province Peoples R China

The micro-structure, and IR spectrum of water molecules in 1-butyl-3-methylimidazolium tetrafluoroborate([ Bmim] BF4)/water mixture with different concentrations (x(1) = 25.0%, 50.0%, 75.0%, and 90.0%) were studied with molecular dynamics simulation at room temperature. It was shown that water molecules tend to be isolated from each other in mixtures with more ions than water molecules in pure water. With the increase of the molar fraction of water in the mixture, the rotation bands and the bending bands of water display red shift from 566.2 to 651.4 cm(-1) and from 1638.4 to 1683.2 cm(-1) respectively, whereas the O-H stretch bands show blue shift from 3519.8 to 3452 cm(-1), which agree well with the experimental results. This suggests that the molecules are hindered and their motions are difficult and slow, due to the hydrogen-bond interactions and the inharmonic interactions between the inter-or intra-molecular modes of water molecules.

关键词： Molecular dynamics simulation hydrogen bond structure and dynamics IR spectrum time correlation function 1-butyl-3-methylimidazolium tetrafluoroborate/water mixture

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Spatiotemporal Control of Energy Transfer in Optically Trapped Systems

Spatiotemporal Control of Energy Transfer in Optically Trapp...

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INTERNATIONAL YOUNG SCIENTISTS FORUM ON APPLIED PHYSICS (YSF)

作者： Mondal, Dipankar Roy, Debjit Goswami, Debabrata Indian Inst Technol Kanpur Dept Chem Kanpur 208016 Uttar Pradesh India

ISBN: (纸本)9781467369763

We demonstrate control over two photon fluorescence (TPF) resonance energy transfer under femtosecond optically tweezed condition. We also extract information about the structure and dynamics of the trapped particles and their clusters as observed from the TPF decay times of the trapped multiple microspheres (0.50 mu m size) by varying the polarization of the trapping laser. This micron to nano regime of the energy transfer process has provided us the necessary control over the molecular level energy transfer rate due to the different overlap integral of excitation and emission spectra of the dye that is coated on the surface of 1.0 mu m polystyrene particles. Our background free detection method thus provides additional structural information about multiple trapping events.

关键词： optical trapping two photon fluorescence resonance energy transfer structure and dynamics

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Probing Lipid Coating dynamics of Quantum Dot Core Micelles via Forster Resonance Energy Transfer

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SMALL 2014年第6期10卷 1163-1170页

作者： Zhao, Yiming Schapotschnikow, Philipp Skajaa, Torjus Vlugt, Thijs J. H. Mulder, Willem J. M. Donega, Celso de Mello Meijerink, Andries Univ Utrecht Debye Inst NL-3584 CC Utrecht Netherlands Delft Univ Technol Proc & Energy Lab NL-2628 CA Delft Netherlands Ichan Sch Med Mt Sinai Translat & Mol Imaging Inst New York NY 10029 USA Univ Amsterdam Acad Med Ctr Dept Vasc Med NL-1105 AZ Amsterdam Netherlands

Lipid coated nanocrystal assemblies are among the most extensively investigated nanoparticle platforms for biomedical imaging and therapeutic purposes. However, very few efforts have been addressed to the lipid coating exchange dynamics in such systems, which is key to our understanding of the nanoparticles' coating stability and their interactions with the environment. Here, we apply the Forster resonance energy transfer (FRET) from quantum dot (QD) core to Cy5.5 dye labeled lipids at the surface to monitor the lipid exchange dynamics in situ and to study its dependence on concentration, temperature and solvent. A kinetic model is developed to describe the experimental data, allowing the rate constants and the activation energy for lipid exchange to be determined. The activation energy for lipid exchange on QD micelles is 155 kJ/mol in saline environment and 130 kJ/mol in pure water. The findings presented here provide basic knowledge on these self-assembled structures and contribute to understanding their performance and to further design of nanomedicine.

关键词： forster resonance energy transfer lipid exchange nanocrystal micelle quantum dots structure and dynamics

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AFM based dielectric spectroscopy: Extended frequency range through excitation of cantilever higher eigenmodes

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ULTRAMICROSCOPY 2014年 146卷 55-61页

作者： Miccio, Luis A. Kummali, Mohammed M. Schwartz, Gustavo A. Alegria, Angel Colmenero, Juan CSIC UPV EHU Ctr Fis Mat San Sebastian 20018 Spain Donostia Int Phys Ctr San Sebastian 20018 Spain Univ Basque Country Dept Fis Mat San Sebastian 20018 Spain

In the last years, a new AFM based dielectric spectroscopy approach has been developed for measuring the dielectric relaxation of materials at the nanoscale, the so called ricmoDielectric Spectroscopy (nDS). In spite of the effort done so far, some experimental aspects of this technique remain still unclear. In particular, one of these aspects is the possibility of extending the experimental frequency range, to date limited at high frequencies by the resonance frequency of the AFM cantilever as a main factor. In order to overcome this limitation, the electrical excitation of cantilever higher eigenmodes for measuring the dielectric relaxation is here explored. Thus, in this work we present a derailed experimental analysis of the electrical excitation of the cantilever second eigenmode. Based on this analysis we show that the experimental frequency range of the AFM based dielectric spectroscopy can be extended by nearly two decades with a good signal-to-noise ratio. By using the combination of first and second cantilever eigenmodes we study dissipation processes on well known PVAc based polymeric samples. Both, relaxation spectra and images with molecular dynamics contrast were thus obtained over this broader frequency range. (C) 2014 Elsevier B.V. All rights reserved.

关键词： AFM Dielectric spectroscopy structure and dynamics Polymer blends

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