arXiv subjects

Robijn F. Bruinsma

Publications and source records attributed to Robijn F. Bruinsma.

11 recordsLinked to original sources

arXiv2023

Geometric Signatures of Switching Behavior in Mechanobiology

The proteins involved in cells' mechanobiological processes have evolved specialized and surprising responses to applied forces. Biochemical transformations that show catch-to-slip switching and force-induced pathway switching serve important functions in cell adhesion, mechano-sensing and signaling, and protein folding. We show that these switching behaviors are generated by singularities in the flow field that describes force-induced deformation of bound and transition states. These singularities allow for a complete characterization of switching mechanisms in 2-dimensional (2D) free energy landscapes, and provide a path toward elucidating novel forms of switching in higher dimensional models. Remarkably, the singularity that generates a catch-slip switch occurs in almost every 2D free energy landscape, implying that almost any bond admitting a 2D model will exhibit catch-slip behavior under appropriate force. We apply our analysis to models of P-selectin and antigen extraction to illustrate how these singularities provide an intuitive framework for explaining known behaviors and predicting new behaviors.

q-bio.BM↗

arXiv2020

Finite Temperature Phase Behavior of Viral Capsids as Oriented Particle Shells

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 transition and a collapse transition and is used to interpret the thermodynamics of microbiological shells.

physics.comp-ph↗

arXiv2016

Quasi-Equilibrium Self-Assembly of Small RNA Viruses

We propose a description for the quasi-equilibrium self-assembly of small, single-stranded (ss) RNA viruses whose capsid proteins (CPs) have flexible, positively charged, disordered tails that associate with the negatively charged RNA genome molecules. We describe the assembly of such viruses as the interplay between two coupled phase-transition like events: the formation of the protein shell (the capsid) by CPs and the condensation of a large ss viral RNA molecule. Electrostatic repulsion between the CPs competes with attractive hydrophobic interactions and attractive interaction between neutralized RNA segments mediated by the tail-groups. An assembly diagram is derived in terms of the strength of attractive interactions between CPs and between CPs and the RNA molecules. It is compared with the results of recent studies of viral assembly. We demonstrate that the conventional theory of self-assembly, which does describe the assembly of \textit{empty} capsids, is in general not applicable to the self-assembly of RNA-encapsidating virions.

cond-mat.soft↗

arXiv2008

Rhythmogenic neuronal networks, pacemakers, and k-cores

Neuronal networks are controlled by a combination of the dynamics of individual neurons and the connectivity of the network that links them together. We study a minimal model of the preBotzinger complex, a small neuronal network that controls the breathing rhythm of mammals through periodic firing bursts. We show that the properties of a such a randomly connected network of identical excitatory neurons are fundamentally different from those of uniformly connected neuronal networks as described by mean-field theory. We show that (i) the connectivity properties of the networks determines the location of emergent pacemakers that trigger the firing bursts and (ii) that the collective desensitization that terminates the firing bursts is determined again by the network connectivity, through k-core clusters of neurons.

q-bio.NC↗

arXiv2007

Nucleosome Switching

We present a statistical-mechanical analysis of the positioning of nucleosomes along one of the chromosomes of yeast DNA as a function of the strength of the binding potential and of the chemical potential of the nucleosomes. We find a significant density of two-level nucleosome switching regions where, as a function of the chemical potential, the nucleosome distribution undergoes a "micro" first-order transition. The location of these nucleosome switches shows a strong correlation with the location of transcription-factor binding sites.

cond-mat.soft↗

arXiv2007

Chirality and Equilibrium Biopolymer Bundles

We use continuum theory to show that chirality is a key thermodynamic control parameter for the aggregation of biopolymers: chirality produces a stable disperse phase of hexagonal bundles under moderately poor solvent conditions, as has been observed in {\it in-vitro} studies of F-actin [O. Pelletier {\it et al.}, Phys. Rev. Lett. {\bf 91}, 148102 (2003)]. The large characteristic radius of these chiral bundles is not determined by a mysterious long-range molecular interaction but by in-plane shear elastic stresses generated by the interplay between a chiral torque and an unusual, but universal, non-linear gauge term in the strain tensor of ordered chains that is imposed by rotational invariance.

cond-mat.soft↗

arXiv2007

Phase Diagram of Chiral Biopolymer Wigner Crystals

We study the statistical mechanics of counterion Wigner crystals associated with hexagonal bundles of chiral biopolymers. We show that, due to spontaneous chiral symmetry breaking induced by frustration, these Wigner crystals would be chiral even if the biopolymers themselves were not chiral. Using a duality transformation of the model onto a "spin-charge" Hamiltonian, we show that melting of the Wigner crystal is due to the unbinding of screw dislocations and that the melting temperature has a singular dependence on the intrinsic chirality of the biopolymers. Finally, we report that, if electrostatic interactions are strongly screened, the counterions can condense in the form of an intermediate achiral Wigner solid phase that melts by the unbinding of fractional topological charges.

cond-mat.soft↗

arXiv2006

Frustrated Polyelectrolyte Bundles and T=0 Josephson-Junction Arrays

We establish a one-to-one mapping between a model for hexagonal polyelectrolyte bundles and a model for two-dimensional, frustrated Josephson-junction arrays. We find that the T=0 insulator-to-superconductor transition of the {\it quantum} system corresponds to a continuous liquid-to-solid transition of the condensed charge in the finite temperature {\it classical} system. We find that the role of the vector potential in the quantum system is played by elastic strain in the classical system. Exploiting this correspondence we show that the transition is accompanied by a spontaneous breaking of chiral symmetry and that at the transition the polyelectrolyte bundle adopts a universal response to shear.

cond-mat.soft↗

arXiv2005

Structural Polymorphism of the Cytoskeleton: A Model of Linker-Assisted Filament Aggregation

The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of linkers in the solution modifies the effective inter-rod interaction and can lead to inter-filament attraction. Depending on the system's composition and physical properties such as linker binding energies, filaments will either orient perpendicular or parallel to each other, leading to network-like or bundled structures. We show that such a system can have one of three generic phase diagrams, one dominated by bundles, another by networks, and the third containing both bundle and network-like phases. The first two diagrams can be found over a wide range of interaction energies, while the third occurs only for a narrow range. These results provide theoretical understanding of the classification of linker proteins as bundling proteins or crosslinking proteins. In addition, they suggest possible mechanisms by which the cell may control cytoskeletal morphology.

cond-mat.soft↗

arXiv2003

Viral self-assembly as a thermodynamic process

The protein shells, or capsids, of all sphere-like viruses adopt icosahedral symmetry. In the present paper we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral capsids constructed from structurally identical protein subunits and that this symmetry requires (at least) two internal "switching" configurations of the protein. Our results indicate that icosahedral symmetry is not a generic consequence of free energy minimization but requires optimization of internal structural parameters of the capsid proteins.

cond-mat.soft↗

arXiv2002

Folding Langmuir Monolayers

The maximum pressure a two-dimensional surfactant monolayer is able to withstand is limited by the collapse instability towards formation of three-dimensional material. We propose a new description for reversible collapse based on a mathematical analogy between the formation of folds in surfactant monolayers and the formation of Griffith Cracks in solid plates under stress. The description, which is tested in a combined microscopy and rheology study of the collapse of a single-phase Langmuir monolayer of 2-hydroxy-tetracosanoic acid (2-OH TCA), provides a connection between the in-plane rheology of LM's and reversible folding.

cond-mat.soft↗