Related papers: The dynamics of viruslike capsid assembly and disa…
Molecular simulations of the self-assembly of cone-shaped particles with specific, attractive interactions are performed. Upon cooling from random initial conditions, we find that the cones self assemble into clusters and that clusters…
Eukaryotic cells intrinsically change their shape, by changing the composition of their membrane and by restructuring their underlying cytoskeleton. We present here further studies and extensions of a minimal physical model, describing a…
A dynamical formulation of coupled cluster theory is derived using a variational principle. By allowing time-dependent single-particle functions, a high degree of adaptivity is introduced, allowing complex systems to be simulated with high…
Crystallization of biological molecules has high potential to solve some challenges in drug manufacturing. Thus, understanding the process is critical to efficiently adapting crystallization to biopharmaceutical manufacturing. This article…
We present a top-down approach to the study of the dynamics of icosahedral virus capsids, in which each protein is approximated by a point mass. Although this represents a rather crude coarse-graining, we argue that it highlights several…
The assembly of virus capsids from free coat proteins proceeds by a complicated cascade of association and dissociation steps, the great majority of which cannot be directly experimentally observed. This has made capsid assembly a rich…
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 study the microrheology of nanoparticle shells [Dinsmore et al. Science 298, 1006 (2002)] and viral capsids [Ivanovska et al. PNAS 101, 7600 (2004)] by computing the mechanical response function and thermal fluctuation spectrum of a…
The ability of virus shells to encapsulate a wide range of functional cargoes, especially multiple cargoes - siRNAs, enzymes, and chromophores - has made them an essential tool in biotechnology for advancing drug delivery applications and…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
Efficient replication and assembly of virus particles are integral to the establishment of infection. In addition to the primary role of the capsid protein (CP) in encapsidating the RNA progeny, experimental evidence on positive sense…
This paper analyzes a simplified model of viral infection and evolution using the 'grand canonical ensemble' and formalisms from statistical mechanics and thermodynamics to enumerate all possible viruses and to derive thermodynamic…
Motivated by recent experimental findings in chemical synthesis of colloidal particles, we draw an analogy between self-assembly processes occurring in biological systems (e.g. protein folding) and a new exciting possibility in the field of…
A general phase-plot is proposed for discrete particle shells that allows for thermal fluctuations of the shell geometry and of the inter-particle connectivities. The phase plot contains a first-order melting transition, a buckling…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
It is shown that diffusion-limited classical nucleation theory (CNT) can be recovered as a simple limit of the recently proposed dynamical theory of nucleation based on fluctuating hydrodynamics (Lutsko, JCP 136, 034509 (2012)). The same…
In a seminal paper Caspar and Klug established a theory that provides a family of polyhedra as blueprints for the structural organisation of viral capsids. In particular, they encode the locations of the proteins in the shells that…
A biophysical issue how the nuclear size dynamically scales with the cellular size remains mysterious. We develop a theoretical framework in which the interactions between polydisperse biomolecules and the mechanical elasticity of the cell…
Previous kinetic models had assumed that the reaction medium was reacting at random and without a turnover associated to thermodynamics exchanges, with a rigid active site on the enzyme. The experimental studies show that coupling factor 1…
We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and…