Related papers: Group theory of icosahedral virus capsids: a dynam…
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to…
Living systems exhibit complex yet organized behavior on multiple spatiotemporal scales. To investigate the nature of multiscale coordination in living systems, one needs a meaningful and systematic way to quantify the complex dynamics, a…
Many viruses rely on the self-assembly of their capsids to protect and transport their genomic material. For many viral systems, in particular for human viruses like hepatitis B, adeno or human immunodeficiency virus, that lead to…
We develop a clear theoretical description of radial swelling in virus-like particles which delineates the importance of electrostatic contributions to swelling in absence of any conformational changes. The model couples the elastic…
We discuss the dynamic behavior of a tagged particle close to a classical localization transition in the framework of the mode-coupling theory of the glass transition. Asymptotic results are derived for the order parameter as well as the…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the…
Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins…
We employ the Stern-Gerlach experiment to highlight the basics of a minimalist, non-interpretational top-down approach to quantum foundations. Certain benefits of the here highlighted "quantum structural studies" are detected and discussed.…
Recent studies reveal that certain viruses package a portion of their genome in a manner that mirrors the icosahedral symmetry of the protein container, or capsid. Graph theoretical constraints forbid exact realization of icosahedral…
A model of growth of icosahedral viral capsids is proposed. It takes into account the diversity of hexamers' compositions, leading to definite capsid size. We show that the observed yield of capsid production implies a very high level of…
Single-stranded RNA viruses co-assemble their capsid with the genome and variations in capsid structures can have significant functional relevance. In particular, viruses need to respond to a dehydrating environment to prevent genomic…
We present a rigorously formulated, novel operator-based framework that merges ideas from condensed matter physics, continuum mechanics, and quantum-inspired theory to analyze collective virion behavior in complex environments. By modeling…
We use a simple mode-coupling approach to investigate glassy dynamics of partially pinned fluid systems. Our approach is different from the mode-coupling theory developed by Krakoviack [Phys. Rev. Lett. 94, 065703 (2005), Phys. Rev. E 84,…
Topological phase of matter is now a mainstream of research in condensed matter physics, of which the classification, synthesis, and detection of topological states have brought excitements over the recent decade while remain incomplete…
This study aims to capture aerodynamic causality from snapshot data with a time-varying mode decomposition technique referred to as information-theoretic machine learning. The current approach extracts time-dependent informative vortical…
We study viral transmission in crowds via the short-ranged airborne pathway using a purely model-based approach. Our goal is two-pronged. Firstly, we illustrate with a concrete and pedagogical case study how to estimate the risks of new…
We show that the icosahedral packings of protein capsomeres proposed by Caspar and Klug for spherical viruses become unstable to faceting for sufficiently large virus size, in analogy with the buckling instability of disclinations in…
We analyse biased ensembles of trajectories for a two-dimensional system of particles, evolving by Langevin dynamics in a channel geometry. This bias controls the degree of particle clustering. On biasing to large clustering, we observe a…
We develop a class of models with which we simulate the assembly of particles into T1 capsid-like objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive…