ORCID Profile
0000-0002-8544-7658
Current Organisation
UNSW Sydney
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Microbiology not elsewhere classified | Systems biology | Biological mathematics | Applied mathematics | Biological physics
Publisher: American Physical Society (APS)
Date: 29-06-2011
Publisher: Cold Spring Harbor Laboratory
Date: 24-03-2023
DOI: 10.1101/2023.03.23.534032
Abstract: HIV can infect non- iding cells because the viral capsid can overcome the selective barrier of the nuclear pore complex and deliver the genome directly into the nucleus. Remarkably, the intact HIV capsid is over one thousand times greater than the size-limit prescribed by the nuclear pore’s diffusion barrier. This barrier is a phase-separated condensate in the central channel of the nuclear pore and is comprised of intrinsically-disordered nucleoporin domains enriched in phenylalanine-glycine (FG) dipeptides. Through multivalent FG-interactions, cellular karyopherins and their bound cargoes solubilise in this phase to drive nucleocytoplasmic transport. By performing an in vitro dissection of the nuclear pore complex, we show that a pocket on the surface of the HIV capsid similarly interacts with FG-motifs from multiple nucleoporins and that this interaction licenses capsids to penetrate nucleoporin condensates. This karyopherin mimicry model resolves a key conceptual challenge for the role of the HIV capsid in nuclear entry, and explains how an exogenous entity much larger than any known cellular cargo can non-destructively breach the nuclear envelope.
Publisher: Cambridge University Press (CUP)
Date: 10-02-2023
DOI: 10.1017/JFM.2023.18
Abstract: Morphodynamic equations governing the behaviour of active nematic fluids on deformable curved surfaces are constructed in the large deformation limit. Emphasis is placed on the formulation of objective rates that account for normal deformations whilst ensuring that tangential flows are Eulerian, and the use of the surface derivative (rather than the covariant derivative) in the nematic free energy, which elastically couples local order to out-of-plane bending of the surface. Focusing on surface geometry and its dynamical interplay with the hydrodynamics, several illustrative instabilities are then characterised. These include cases where the role of the Scriven–Love number and its nematic analogue are non-negligible, and where the active nematic forcing can be characterised by an analogue of the Föppl–von Kármán number. For the former, flows and changes to the nematic texture are coupled to surface geometry by viscous dissipation. This is shown to result in non-trivial relaxation dynamics for a nematic tube. For the latter, the nematic active forcing couples to the surface bending terms of the nematic free energy, resulting in extensile (active ruffling) and contractile (active pearling) instabilities in the tube shape, as well as active bend instabilities in the nematic texture. In comparison to the flat case, such bend instabilities now have a threshold set by the extrinsic curvature of the tube. Finally, we examine a topological defect located on an almost flat surface, and show that there exists a steady state where a combination of defect elasticity, activity and non-negligible spin connection drive a shape change in the surface.
Publisher: Oxford University Press (OUP)
Date: 26-07-2022
DOI: 10.1093/NAR/GKAC590
Abstract: The kinetics of DNA hybridization are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridize at different rates are not well understood. Secondary structure is one predictable factor that influences hybridization rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. In this context, we measured hybridization rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify our observations. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters. Our results indicate that greater repetition of Watson–Crick pairs increases the number of initial states able to proceed to full hybridization, with the stability of those pairings dictating the likelihood of such progression, thus providing new insight into the physical factors underpinning DNA hybridization rates.
Publisher: Elsevier
Date: 2019
Publisher: American Physical Society (APS)
Date: 03-01-2014
Publisher: American Physical Society (APS)
Date: 21-09-2010
Publisher: American Physical Society (APS)
Date: 18-09-2012
Publisher: American Physical Society (APS)
Date: 08-06-2016
Publisher: Elsevier BV
Date: 12-2021
DOI: 10.1016/J.SEMCDB.2021.07.001
Abstract: We review progress in active hydrodynamic descriptions of flowing media on curved and deformable manifolds: the state-of-the-art in continuum descriptions of single-layers of epithelial and/or other tissues during development. First, after a brief overview of activity, flows and hydrodynamic descriptions, we highlight the generic challenge of identifying the dependence on dynamical variables of so-called active kinetic coefficients- active counterparts to dissipative Onsager coefficients. We go on to describe some of the subtleties concerning how curvature and active flows interact, and the issues that arise when surfaces are deformable. We finish with a broad discussion around the utility of such theories in developmental biology. This includes limitations to analytical techniques, challenges associated with numerical integration, fitting-to-data and inference, and potential tools for the future, such as discrete differential geometry.
Publisher: Springer Science and Business Media LLC
Date: 08-10-2018
Publisher: Wiley
Date: 31-07-2020
Publisher: Springer Science and Business Media LLC
Date: 26-09-2013
DOI: 10.1038/SREP02764
Publisher: Elsevier BV
Date: 2017
Publisher: American Physical Society (APS)
Date: 21-08-2019
Publisher: Cold Spring Harbor Laboratory
Date: 31-07-2022
DOI: 10.1101/2022.07.28.501945
Abstract: By abruptly changing the size and composition of a population, bottlenecks can dramatically alter evolutionary trajectories. In the traditional picture, the faster a population recovers from a bottleneck, the more rapidly finite-size intrinsic fluctuations are suppressed and therefore the greater the likelihood of fixation to the attractor within whose basin the bottleneck constrained the population, initially. We now argue that this intuition is misleading demonstrating that precisely the opposite behaviour is also possible. Depending critically on the rate of mutation, increased population growth can drive fixation to attractors that are different to that from whose basin it started. These findings are explained in terms of statistically distinct regimes of demographic behaviour, drawing parallels with the notion of non-equilibrium phase transitions. Such dynamical demographic phases are delimited by sharp transitions in time, as a population grows, and ultimately result from a time-dependent antagonism between mutation and the stochastically-induced effects of frequency-dependent birth.
Publisher: American Physical Society (APS)
Date: 04-11-2015
Publisher: IOP Publishing
Date: 12-08-2014
Publisher: American Chemical Society (ACS)
Date: 22-03-2022
Abstract: Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multivalent interactions to form stable complexes that are also capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multisite competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo, an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to benefit future studies that use DNA origami structures to exploit multivalent interactions for the design and synthesis of a wide range of possible kinetic behaviors.
Publisher: American Physical Society (APS)
Date: 14-11-2022
Publisher: Elsevier BV
Date: 02-2023
Publisher: Springer Science and Business Media LLC
Date: 24-09-2018
Publisher: American Physical Society (APS)
Date: 09-02-2023
Publisher: Elsevier BV
Date: 06-2019
DOI: 10.1016/J.DEVCEL.2019.04.031
Abstract: RhoA stimulates cell contractility by recruiting downstream effectors to the cortical plasma membrane. We now show that direct binding by anillin is required for effective signaling: this antagonizes the otherwise labile membrane association of GTP-RhoA to promote effector recruitment. However, since its binding to RhoA blocks access by other effectors, we demonstrate that anillin must also concentrate membrane phosphoinositide-4,5-P
Publisher: American Physical Society (APS)
Date: 09-06-2014
Publisher: Springer Science and Business Media LLC
Date: 02-03-2020
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 2023
End Date: 12-2029
Amount: $35,000,000.00
Funder: Australian Research Council
View Funded Activity