DNA Breathing Dynamics in the Presence of a Terahertz Field (2009)
Alexandrov, B. S., Gelev, V., Bishop, A. R., Usheva, A., Rasmussen, K. O.
We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain,...
Classical Propagation of Light in Spatio-Temporal Periodic Media (2006)
Alexandrov, B. S., Rasmussen, K. O., Findikoglu, A. T., Bishop, A. R., Kostadinov, I. Z.
We analyze the propagation of electromagnetic waves in media where the dielectric constants undergo rapid temporal periodic modulation. Both spatially homogeneous and periodic media are studied. Fast...
Bubble Statistics and Dynamics in Double-Stranded DNA (2006)
Alexandrov, B. S., Wille, L. T., Rasmussen, K. O., Bishop, A. R., Blagoev, K. B.
The dynamical properties of double-stranded DNA are studied in the framework of the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations are analyzed in terms of two probability...
Healing Length and Bubble Formation in DNA (2006)
Rapti, Z., Smerzi, A., Rasmussen, K. O., Bishop, A. R., Choi, C. H., Usheva, A.
We have recently suggested that the probability for the formation of thermally activated DNA bubbles is, to a very good approximation, proportional to the number of soft AT pairs over a length L(n)...
Probing the mechanical unzipping of DNA (2005)
Voulgarakis, N. K., Redondo, A., Bishop, A. R., Rasmussen, K. O.
A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the...
Comment on "Can one predict DNA Transcription Start Sites by Studying Bubbles?" (2005)
Choi, C. H., Usheva, A., Kalosakas, G., Rasmussen, K. O., Bishop, A. R.
Comment on T.S. van Erp, S. Cuesta-Lopez, J.-G. Hagmann, and M. Peyrard, Phys. Rev. Lett. 95, 218104 (2005) [arXiv: physics/0508094].
Theory of Bubble Nucleation and Cooperativity in DNA Melting (2004)
Ares, S., Voulgarakis, N. K., Rasmussen, K. O., Bishop, A. R.
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no...
Sequence-specific thermal fluctuations identify start sites for DNA transcription (2004)
Kalosakas,G., Rasmussen,K. O., Bishop,A. R., Choi,C. H., Usheva,A.
Exact Solutions of the Saturable Discrete Nonlinear Schrodinger Equation (2004)
Khare, Avinash, Rasmussen, K. O., Samuelsen, M. R., Saxena, A.
Exact solutions to a nonlinear Schr{\"o}dinger lattice with a saturable nonlinearity are reported. For finite lattices we find two different standing-wave-like solutions, and for an infinite lattice...
Detecting Breather Excitations with Inelastic Tunneling Spectroscopy (2004)
Zhu, Jian-Xin, Rasmussen, K. O., Bishop, A. R., Balatsky, A. V.
We propose inelastic electron tunneling spectroscopy scanning tunneling microscopy (IETS-STM) as a means of exciting and observing intrinsic localized modes (breathers) in a macromolecule. As a...
Origins of elastic properties in ordered nanocomposites (2004)
Thompson, R. B., Rasmussen, K. O., Lookman, T.
We predict a diblock copolymer melt in the lamellar phase with added spherical nanoparticles that have an affinity for one block to have a lower tensile modulus than a pure diblock copolymer system....
Sequence-specific thermal fluctuations identify start sites for DNA transcription (2004)
Kalosakas, G., Rasmussen, K. O., Bishop, A. R., Choi, C. H., Usheva, A.
Ferroelastic Dynamics and Strain Compatibility (2002)
Lookman, T., Shenoy, S. R., Rasmussen, K. O., Saxena, A., Bishop, A. R.
We derive underdamped evolution equations for the order-parameter (OP) strains of a ferroelastic material undergoing a structural transition, using Lagrangian variations with Rayleigh dissipation,...
Soliton motion in a parametrically ac-driven damped Toda lattice (1998)
Rasmussen, K. O., Malomed, Boris A., Bishop, A. R., Gronbech-Jensen, Niels
We demonstrate that a staggered parametric ac driving term can support stable progressive motion of a soliton in a Toda lattice with friction, while an unstaggered drivng force cannot. A physical...