A general phenomenological relation for the subdiffusive exponent of anomalous diffusion in disordered media

Alcázar‐Cano, Nerea; Delgado‐Buscalioni, Rafael

doi:10.1039/c8sm01961d

Cited by 21 publications

(23 citation statements)

References 42 publications

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“…11b) at all times reflecting larger displacements in the displacement maps. The reduced overlap and broadening (non-Gaussian behaviour) of the distribution at large r illustrates the presence of more than one sub-diffusive regime, a signature of anomalous diffusion 66 , as observed in the corresponding MSD data (Fig. 9a & b).…”

Section: Displacement Maps and Probability Distributionssupporting

confidence: 62%

“…Distinct non-Gaussian nature of P(r,t) for t > 200 ns suggest that lipid molecules are trapped in cages unable to fully sample phase lead-ing to dynamic heterogeneities and glass-like behaviour. 66,67 In this regime, relaxation is predominantly governed by co-operative motion of cages wherein lipid molecules are trapped by their neighbours. A similar observation of the sampling of phase space with time can be drawn for AHL bound DMPC bilayer as well ( Fig.…”

Section: Displacement Maps and Probability Distributionsmentioning

confidence: 99%

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Assessing the Extent of Structural and Dynamic Modulation of Membrane Lipids due to Pore Forming Toxins: Insights from Molecular Dynamics Simulations

Varadarajan¹,

Desikan²,

Ayappa

2020

Preprint

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Infections in many virulent bacterial strains are triggered by the release of pore forming toxins (PFTs), which form oligomeric transmembrane pore complexes on the target plasma membrane. The spatial extent of the perturbation to the surrounding lipids during pore formation is relatively unexplored. Using all-atom molecular dynamics simulations, we investigate the changes in the structure and dynamics of lipids in a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer in the presence of contrasting PFTs. Cytolysin A (ClyA) an α toxin with its inserted wedge shaped bundle of inserted α helices induces significant asymmetry across the membrane leaflets in comparison with α hemolysin (AHL) a β toxin. Despite the differences in hydrophobic mismatch and uniquely different topologies of the two oligomers, perturbation to lipid order as reflected in the tilt angle and order parameters, and membrane thinning is short ranged, lying within ∼ 2.5 nm from the periphery of the either pore complex, commensurate with distances typically associated with van der Waals forces. In contrast, the spatial extent of perturbations to the lipid dynamics extend outward to at least 4 nm for both proteins, and the continuous survival probabilities reveal the presence of a tightly bound shell of lipids in this region. Displacement probability distributions show long tails and the distinctly non-Gaussian features reflect the induced dynamic heterogeneity. A detailed profiling of the protein-lipid contacts with residues tyrosine, tryptophan, lysine and arginine show increased non-polar contacts in the cytoplasmic leaflet for both PFTs, with a higher number of atomic contacts in the case of AHL in the extracellular leaflet due to the mushroom-like topology of the pore complex. The short ranged nature of the perturbations observed in this simple one component membrane suggests an inherent plasticity of membrane lipids enabling recovery of structure and membrane fluidity even in the presence of these large oligomeric trans-membrane protein assemblies. This observation has implications in membrane repair processes such as budding or vesicle fusion events used to mitigate PFT virulence, where the underlying lipid dynamics and fluidity in the vicinity of the pore complex are expected to play an important role.

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Section: Displacement Maps and Probability Distributionssupporting

confidence: 62%

Section: Displacement Maps and Probability Distributionsmentioning

confidence: 99%

Assessing the Extent of Structural and Dynamic Modulation of Membrane Lipids due to Pore Forming Toxins: Insights from Molecular Dynamics Simulations

Varadarajan¹,

Desikan²,

Ayappa

2020

Preprint

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“…Details of this procedure are explained in Ref. [48]. This step is rejected if a bead crosses the wall (if y i < 0) or if different beads in the chain overlap.…”

Section: Monte Carlo Sampling Of Initial Configurations and Height Prmentioning

confidence: 99%

Hydrodynamics of Quartz-Crystal-Microbalance DNA Sensors Based on Liposome Amplifiers

et al. 2020

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The quartz-crystal microbalance (QCM) has become an important technique for the detection of biomolecules and their interactions. Acoustic sensing of DNA requires hybridizing the oligonucleotide chain with a nanoparticle that acts as an acoustic amplifier. In this device, the amplifier remains suspended in the liquid, nanometers away from the surface. The hydrodynamics of nonadsorbed nanoparticles in QCM sensing devices has, however, been overlooked in the literature. Here, we show that the acoustic response (shifts in frequency, f , and dissipation, D) of the amplifier-target complex is determined by the hydrodynamic wall stress. Our study focuses on an alternative type of DNA sensor based on liposome-DNA complexes and provides a theoretical analysis backed up by experiments with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine liposomes. The target DNA strands are attached on one side to surface-adsorbed neutravidin through a biotin linker, while the other side is anchored to a liposome acting as an amplifier. A range of liposome radii and double-stranded-DNA contour lengths are studied, covering sizes up to the wave penetration depth (δ ∼ 100 nm). Simulations, based on the immersed boundary method and an elastic-network model, are in excellent agreement with the experiments. We derive an analytical expression for the acoustic impedance, which reflects strong signal amplification as the liposome gets closer to the wall. This enhancement is due to hydrodynamic reflection: the ambient flow induces a stress on the liposome surface, which propagates back to the resonator. For this reason, acoustic signals are extremely sensitive to the distribution of the liposome-wall distance (which we determine from the mechanical properties of double-stranded-DNA chains). Our approach helps in deciphering the role of hydrodynamics in acoustic sensing and reveals the role of parameters hitherto largely unexplored. A practical consequence may be improvements in the design of biosensors and detection schemes.

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“…Similarly, during the desorption process (substance is released to the bulk), diffusion compensates for the increase in concentration near the substrate. Therefore, understanding how these two phenomena work together is crucial not only in separation process but in several other systems where diffusion and adsorption occur together, such as biochemical reactions in living systems [9,10], in the electrical response of weak electrolytes [11], in cancer [12] and population dynamics [13,14], and many others [15][16][17][18][19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Diffusion in Heterogenous Media and Sorption—Desorption Processes

Koltun

Lenzi

2021

Fractal Fract

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We investigate particle diffusion in a heterogeneous medium limited by a surface where sorption–desorption processes are governed by a kinetic equation. We consider that the dynamics of the particles present in the medium are governed by a diffusion equation with a spatial dependence on the diffusion coefficient, i.e., K(x) = D|x|−η, with −1 < η and D = const, respectively. This system is analyzed in a semi-infinity region, i.e., the system is defined in the interval [0,∞) for an arbitrary initial condition. The solutions are obtained and display anomalous spreading, that is, the dynamics may be viewed as anomalous diffusion, which in turn is related, and hence, the model can be directly applied to several complex systems ranging from biological fluids to electrolytic cells.

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A general phenomenological relation for the subdiffusive exponent of anomalous diffusion in disordered media

Abstract: Distinction between mobile and trapped tracers in disordered media reveals a simple phenomenological law for the subdiffusive exponent which reproduces the behaviour observed in a wide range of obstacles structures.

Cited by 21 publications

References 42 publications

Assessing the Extent of Structural and Dynamic Modulation of Membrane Lipids due to Pore Forming Toxins: Insights from Molecular Dynamics Simulations

Assessing the Extent of Structural and Dynamic Modulation of Membrane Lipids due to Pore Forming Toxins: Insights from Molecular Dynamics Simulations

Hydrodynamics of Quartz-Crystal-Microbalance DNA Sensors Based on Liposome Amplifiers

Diffusion in Heterogenous Media and Sorption—Desorption Processes

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