We investigate the statistical mechanics of long developable ribbons of finite width and very small thickness. The constraint of isometric deformations in these ribbonlike structures that follows from the geometric separation of scales introduces a coupling between bending and torsional degrees of freedom. Using analytical techniques and Monte Carlo simulations, we find that the tangent-tangent...

In pedicle screw instrumentation, it is common to use one or more transfixators that crosslink the longitudinal rods horizontally. Such a horizontal transfixation (HTF) of the longitudinal rods was shown to provide an additional stability in axial rotation and lateral bending but not in flexion extension. Most significant contribution of HTF was noted in axial rotational stability because the t...

We use open active contours to quantify cytoskeletal structures imaged by fluorescence microscopy in two and three dimensions. We developed an interactive software tool for segmentation, tracking, and visualization of individual fibers. Open active contours are parametric curves that deform to minimize the sum of an external energy derived from the image and an internal bending and stretching e...

Twisting is an important process to form a continuous yarn from short fibres and to determine the structure and properties of the resultant yarn. This paper proposes a new theoretical model of yarn dynamics in a generalized twisting system, which deals with two important phenomena simultaneously, that is, twist generation and twist propagation. Equations of yarn motion are established and the b...

Velocity fields for Poiseuille flow through tubes having general cross section are calculated using a path integral method involving the first-passage times of random walks in the interior of the cross sectional domain B of the pipe. This method is applied to a number of examples where exact results are available and to more complicated geometries of practical interest. These examples include a...

Protein–induced DNA looping is a key regulatory mechanism involved in important processes such as transcription, gene regulation and replication. The relationship between the induced loop topology and DNA–protein dynamics is essential for understanding these processes. Here, we use tethered–particle motion (TPM) to examine the impact of bending and twisting rigidity of protein–induced DNA loopi...

The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction characterizing the chain rigidity and the effective on-site potentials are calculated for three main types of protein secondary structure. The coupling inte...

We use the cyclization of small DNA molecules, approximately 200 bp in length, to study conformational properties of DNA fragments with single-stranded gaps. The approach is extremely sensitive to DNA conformational properties and, being complemented by computations, allows a very accurate determination of the fragment's conformational parameters. Sequence-specific nicking endonucleases are use...

Harmonic elastic constants of 3-11 bp duplex DNA fragments were evaluated using four 5 ns unrestrained molecular dynamics simulation trajectories of 17 bp duplexes with explicit inclusion of solvent and counterions. All simulations were carried out with the Cornell et al. force-field and particle mesh Ewald method for long-range electrostatic interactions. The elastic constants including anisot...

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariabl...