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Scholarly Works - Physics - Biological and Soft Systems


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Now showing 1 - 5 of 5
  • ItemOpen AccessAccepted version Peer-reviewed
    Suppressed Quenching and Strong-Coupling of Purcell-Enhanced Single-Molecule Emission in Plasmonic Nanocavities
    (American Chemical Society, 2018-01-17) Kongsuwan, N; Demetriadou, A; Chikkaraddy, R; Benz, F; Turek, VA; Keyser, UF; Baumberg, JJ; Hess, O; Chikkaraddy, Rohit [0000-0002-3840-4188]; Keyser, Ulrich [0000-0003-3188-5414]; Baumberg, Jeremy [0000-0002-9606-9488]
    An emitter in the vicinity of a metal nanostructure is quenched by its decay through nonradiative channels, leading to the belief in a zone of inactivity for emitters placed within <10 nm of a plasmonic nanostructure. Here we demonstrate and explain why in tightly coupled plasmonic resonators forming nanocavities “quenching is quenched” due to plasmon mixing. Unlike isolated nanoparticles, such plasmonic nanocavities show mode hybridization, which can massively enhance emitter excitation and decay via radiative channels, here experimentally confirmed by laterally dependent emitter placement through DNA-origami. We explain why this enhancement of excitation and radiative decay can be strong enough to facilitate single-molecule strong coupling, as evident in dynamic Rabi-oscillations.
  • ItemOpen AccessPublished version Peer-reviewed
    True Molecular Scale Visualization of Variable Clustering Properties of Ryanodine Receptors.
    (Elsevier BV, 2018-01-09) Jayasinghe, Izzy; Clowsley, Alexander H; Lin, Ruisheng; Lutz, Tobias; Harrison, Carl; Green, Ellen; Baddeley, David; Di Michele, Lorenzo; Soeller, Christian; Di Michele, Lorenzo [0000-0002-1458-9747]
    Signaling nanodomains rely on spatial organization of proteins to allow controlled intracellular signaling. Examples include calcium release sites of cardiomyocytes where ryanodine receptors (RyRs) are clustered with their molecular partners. Localization microscopy has been crucial to visualizing these nanodomains but has been limited by brightness of markers, restricting the resolution and quantification of individual proteins clustered within. Harnessing the remarkable localization precision of DNA-PAINT (<10 nm), we visualized punctate labeling within these nanodomains, confirmed as single RyRs. RyR positions within sub-plasmalemmal nanodomains revealed how they are organized randomly into irregular clustering patterns leaving significant gaps occupied by accessory or regulatory proteins. RyR-inhibiting protein junctophilin-2 appeared highly concentrated adjacent to RyR channels. Analyzing these molecular maps showed significant variations in the co-clustering stoichiometry between junctophilin-2 and RyR, even between nearby nanodomains. This constitutes an additional level of complexity in RyR arrangement and regulation of calcium signaling, intrinsically built into the nanodomains.
  • ItemOpen AccessAccepted version Peer-reviewed
    Physical descriptions of the bacterial nucleoid at large scales, and their biological implications.
    (IOP Publishing, 2012-07) Benza, Vincenzo G; Bassetti, Bruno; Dorfman, Kevin D; Scolari, Vittore F; Bromek, Krystyna; Cicuta, Pietro; Lagomarsino, Marco Cosentino; Cicuta, Pietro [0000-0002-9193-8496]
    Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation.
  • ItemOpen AccessAccepted version Peer-reviewed
    Emergence of biaxial nematic phases in solutions of semiflexible dimers.
    (American Physical Society (APS), 2017-10) Vaghela, Arvin; Teixeira, Paulo IC; Terentjev, Eugene M; Terentjev, Eugene [0000-0003-3517-6578]
    We investigate the isotropic, uniaxial nematic and biaxial nematic phases, and the transitions between them, for a model lyotropic mixture of flexible molecules consisting of two rigid rods connected by a spacer with variable bending stiffness. We apply density-functional theory within the Onsager approximation to describe strictly excluded-volume interactions in this athermal model and to self-consistently find the orientational order parameters dictated by its complex symmetry, as functions of the density. Earlier work on lyotropic ordering of rigid bent-rod molecules is reproduced and extended to show explicitly the continuous phase transition at the Landau point, at a critical bend angle of 36^{∘}. For flexible dimers with no intrinsic biaxiality, we find that a biaxial nematic phase can nevertheless form at a sufficiently high density and low bending stiffness. For bending stiffness κ>0.86k_{B}T, this biaxial phase manifests as dimer bending fluctuations occurring preferentially in one plane. When the dimers are more flexible, κ<0.86k_{B}T, the modal shape of the fluctuating dimer is a V with an acute opening angle, and one of the biaxial order parameters changes sign, indicating a rotation of the directors. These two regions are separated by a narrow strip of uniaxial nematic in the phase diagram, which we generate in terms of the spacer stiffness and particle density.
  • ItemOpen AccessPublished version Peer-reviewed
    Perspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systems
    (AIP Publishing, 2017-09-21) Cicuta, P; Cerbino, R; Cicuta, Pietro [0000-0002-9193-8496]
    Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of aqueous colloids, has lately been used to probe a variety of other complex fluids and biological systems with many different imaging methods, including dark-field, differential interference contrast, wide-field, light-sheet, and confocal microscopy. The number of adopting groups is rapidly increasing and so are the applications. Here, we briefly recall the working principles of DDM, we highlight its advantages and limitations, we outline recent experimental breakthroughs, and we provide a perspective on future challenges and directions. DDM can become a standard primary tool in every laboratory equipped with a microscope, at the very least as a first bias-free automated evaluation of the dynamics in a system.