arXiv subjects

Robijn Bruinsma

Publications and source records attributed to Robijn Bruinsma.

26 records · Page 2Linked to original sources

arXiv2003

Focal adhesion: Physics of a Biological Mechano-Sensor

Mechanical coupling between a cell and substrate relies on focal adhesions, clusters of adhesion proteins linking stress fibers (bundles of actin proteins) inside the cell with surrounding tissue. Focal adhesions have been demonstrated to both measure and regulate the mechanical traction along the stress fibers. We present a quantitative model for focal adhesion mechano-sensing and stress regulation based on stress amplification at the critical point of a condensation transition of the adhesion proteins.

cond-mat.soft↗

arXiv2003

Icosahedral packing of RNA viral genomes

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 symmetry. This paper proposes a model for the determination of quasi-icosahedral genome structures and discusses the connection between genomic structure and viral assembly kinetics.

cond-mat.soft↗

arXiv2001

Effects of mechanical strain on thermal denaturation of DNA

As sections of a strand duplexed DNA denature when exposed to high temperature, the excess linking number is taken up by the undenatured portions of the molecule. The mechanical energy that arises because of the overwinding of the undenatured sections can, in principle, alter the nature of the thermal denaturation process. Assuming that the strains associated with this overwinding are not relieved, we find that a simple model of strain-altered melting leads to a suppression of the melting transition when the unaltered transition is continuous. When the melting transition is first order in the absence of strain associated with overwinding, the modification is to a third order phase transition.

cond-mat.soft↗

arXiv1998

DNA-Protein Cooperative Binding through Long-Range Elastic Coupling

Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is proposed. These proteins are not in direct physical contact. DNA segments intercalating bound proteins are modeled as a Worm-Like Chain, which is free to deform in two dimensions. The tension-controlled protein-protein interaction is the consequence of two effects produced by the protein binding. The first is the introduction of a bend in the host DNA and the second is the modification of the bending modulus of the DNA in the immediate vicinity of the bound protein. The interaction between two bound proteins may be either attractive or repulsive, depending on their relative orientation on the DNA. Applied tension controls both the strength and the range of protein-protein interactions in this model. Properties of the cooperative interaction are discussed, along with experimental implications.

cond-mat.soft↗

arXiv1998

Screened and Unscreened Phases in Sedimenting Suspensions

A coarse-grained stochastic hydrodynamical description of velocity and concentration fluctuations in steadily sedimenting suspensions is constructed, and analyzed using self-consistent and renormalization group methods. We find that there exists a dynamical, non-equilibrium phase transition from an "unscreened" phase in which we recover the Caflisch-Luke (R.E. Caflisch and J.H.C. Luke, Phys. Fluids 28, 759 (1985)) divergence of the velocity variance to a "screened" phase where the velocity fluctuations have a finite correlation length growing as $ϕ^{-1/3}$ where $ϕ$ is the particle volume fraction, in agreement with Segrè et. al. (Phys. Rev. Lett. 79, 2574 (1997)) and the velocity variance is independent of system size. Detailed predictions are made for the correlation function in both phases and at the transition.

cond-mat.soft↗

arXiv1996

Nonequilibrium Fluctuations in Sedimenting Suspensions: A Dynamical Renormalization Group Theory

A nonlinear two-fluid stochastic hydrodynamical description of velocity and concentration fluctuations in sedimenting suspensions is constructed, and analyzed using self-consistent (SC) and renormalization group (RG) methods. The advection of particles by velocity fluctuations is shown to be ``relevant'' in all dimensions $d < 6$ . Both RG and SC analyses predict a strong reduction in the dependence of velocity fluctuations on system-size $L$ relative to the $L^{1/2}$ obtained in the linearized theory of Caflisch and Luke [Phys. Fluids {\bf 28}, 785 (1985)]. This is an important step towards resolving a ten-year old puzzle in the field.

cond-mat.soft↗

arXiv1995

Wulff Construction for Deformable Media

A domain in a Langmuir monolayer can be expected to have a shape that reflects the textural anisotropy of the material it contains. This paper explores the consequences of XY-like ordering. It is found that an extension of the Wulff construction allows for the calculation of two-dimensional domain shapes when each segment of the perimeter has an energy that depends both on its orientation and its location. This generalized Wulff construction, and newly-derived exact expressions for the order parameter texture in a circular domain, lead to results for the shape of a large domain. The most striking result is that under general conditions such domains will inevitably develop cusps. We show that the onset of a cusp is mathematically related to a phase transition. The present approach is equivalent to a Landau mean-field version of the theory.

cond-mat↗

arXiv1994

Shape of domains in two-dimensional systems: virtual singularities and a generalized Wulff construction

This is a report on the derivation and application of a generalized version of the Wulff construction in two dimensions. The construction is used to find the shape of a domain containing an XY-like order parameter. In such a domain the energy per unit length of a segment of the bounding curve depends not only on the orientation of the segment, but also on the segment's position, and this is why the Wulff construction must be generalized. When the domain is circular in shape we find that the problem of finding the texture that minimizes the bulk and boundary energies is exactly solvable in certain important cases. Using the generalized Wulff construction and the exact textures, describable in terms of virtual singularities, we find that, given reasonable assumptions concerning the from of the boundary energy, the domain will necessarily develop a cusp if it is sufficiently large. This result is in qualitative agreement with recent experimental observations.

cond-mat↗