A nonlinear dynamic model of DNA with a sequence-dependent stacking term (2009)
Alexandrov, Boian S., Gelev, Vladimir, Monisova, Yevgeniya, Alexandrov, Ludmil B., Bishop, Alan R., Rasmussen, Kim Ø., ...
No simple model exists that accurately describes the melting behavior and breathing dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially true for homogenous and...
Discrete Nonlinear Schrodinger Equations with arbitrarily high order nonlinearities (2006)
Khare, Avinash, Rasmussen, Kim Ø., Salerno, Mario, Samuelsen, Mogens R., Saxena, Avadh
A class of discrete nonlinear Schrodinger equations with arbitrarily high order nonlinearities is introduced. These equations are derived from the same Hamiltonian using different Poisson brackets...
DNA dynamically directs its own transcription initiation (2004)
Choi, Chu H., Kalosakas, George, Rasmussen, Kim Ø., Hiromura, Makoto, Bishop, Alan R., Usheva, Anny
It has long been known that double‐stranded DNA is subject to temporary, localized openings of its two strands. Particular regions along a DNA polymer are destabilized structurally by available...
DNA dynamically directs its own transcription initiation
Choi, Chu H., Kalosakas, George, Rasmussen, Kim Ø., Hiromura, Makoto, Bishop, Alan R., Usheva, Anny
It has long been known that double-stranded DNA is subject to temporary, localized openings of its two strands. Particular regions along a DNA polymer are destabilized structurally by available...
DNA dynamically directs its own transcription initiation
Choi, Chu H., Kalosakas, George, Rasmussen, Kim Ø., Hiromura, Makoto, Bishop, Alan R., Usheva, Anny
It has long been known that double-stranded DNA is subject to temporary, localized openings of its two strands. Particular regions along a DNA polymer are destabilized structurally by available...
Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter
Alexandrov, Boian S., Gelev, Vladimir, Yoo, Sang Wook, Bishop, Alan R., Rasmussen, Kim Ø., Usheva, Anny
Establishing the general and promoter-specific mechanistic features of gene transcription initiation requires improved understanding of the sequence-dependent structural/dynamic features of promoter...
Ordering and Reverse Ordering Mechanisms of Triblock Copolymers in the Presence of Solvent
Maniadis, Panagiotis, Rasmussen, Kim Ø., Thompson, Russell B., Kober, Edward M.
Self-consistent field theory is used to study the self-assembly of a triblock copolymer melt. Two different external factors (temperature and solvent) are shown to affect the self-assembly. Either...
A nonlinear dynamic model of DNA with a sequence-dependent stacking term
Alexandrov, Boian S., Gelev, Vladimir, Monisova, Yevgeniya, Alexandrov, Ludmil B., Bishop, Alan R., Rasmussen, Kim Ø., ...
No simple model exists that accurately describes the melting behavior and breathing dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially true for homogenous and...
Profiling the Thermodynamic Softness of Adenoviral Promoters
Choi, Chu H., Rapti, Zoi, Gelev, Vladimir, Hacker, Michele R., Alexandrov, Boian, Park, Evelyn J., ...
We showed previously that anharmonic DNA dynamical features correlate with transcriptional activity in selected viral promoters, and hypothesized that areas of DNA softness may represent loci of...
Nonlinearity in DNA and its Relation to Specific Functions
Alexandrov, Boian, Rasmussen, Kim Ø., Bishop, Alan R.
In memory of Alwyn Scott, we discuss the connection between the nonlinear dynamics of double-stranded DNA, experimental findings, and specific DNA functions. We begin by discussing how thermally...