Related papers: A mechanical model of bacteriophage DNA ejection
The motion of a classical test particle moving on a 4-dimensional brane embedded in an $n$-dimensional bulk is studied in which the brane is allowed to fluctuate along the extra dimensions. It is shown that these fluctuations produce three…
Many bacteria rely on active cell appendages, such as type IV pili, to move over substrates and interact with neighboring cells. Here, we study the motion of individual cells and bacterial colonies, mediated by the collective interactions…
Single flagellated bacteria are ubiquitous in nature. They exhibit various swimming modes using their flagella to explore complex surroundings such as soil and porous polymer networks. Some single-flagellated bacteria swim with two distinct…
The variability in cell size of an isogenic population of Escherichia coli has been widely reported in experiment. The probability density function (PDF) of cell lengths has been variously described by exponential and lognormal functions.…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
The internal motions of DNA immersed in bio-fluid are investigated. The interactions between the fragments of DNA and the surrounding bio-fluid are modeled using the gauge fluid lagrangian. In the model, the bio-fluid is coupled to the…
Experiments on particles' motion in living cells show that it is often subdiffusive. This subdiffusion may be due to trapping, percolation-like structures, or viscoelatic behavior of the medium. While the models based on trapping (leading…
We carried out three-dimensional simulations, with about 1.4 million particles, of phase segregation in a low density binary fluid mixture, described mesoscopically by energy and momentum conserving Boltzmann-Vlasov equations. Using a…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
A droplet placed on a hydrophilic conical fiber tends to move toward the end of larger radii due to capillary action. Experimental investigations are performed to explore the dynamics of droplets with varying viscosities and volumes on…
Bacteriophage viruses, one of the most abundant entities in our planet, lack the ability to move independently. Instead, they crowd fluid environments in anticipation of a random encounter with a bacterium. Once they land on the cell body…
Inspired by its central role in many biological processes, the transport of biopolymers across nanoscale pores is at the heart of a single-molecule sensing technology aimed at nucleic acid and protein sequencing, as well as biomarker…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA…
Based on symmetry consideration of migration and shape deformations, we formulate phenomenologically the dynamics of cell crawling in two dimensions. Forces are introduced to change the cell shape. The shape deformations induce migration of…
Recent experiments of imbibition in columnar geometries show interfacial fluctuations whose dynamic scaling is not compatible with the usual non local model governed by surface tension that results from a macroscopic description. To explore…
In a recent experiment, a single DNA double helix is stretched and relaxed in the presence of spermidine, a short positive polyelectrolyte, and the pulling force is measured as a function of DNA extension. In a certain range of spermidine…
Periodic arrays of micro- or nano-pillars constitute solid state matrices with excellent properties for DNA size separation. Nanofabrication technologies offer many solutions to tailor the geometry of obstacle arrays, yet most studies have…
Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of…