Biomedical subjects

D Hennig

Publications and source records attributed to D Hennig.

At least 19 recordsLinked to original sources

PubMed2006

Regular patterns in dichotomically driven activator-inhibitor dynamics.

We investigate Turing pattern formation in the presence of additive dichotomous fluctuations in the context of an extended system with diffusive coupling and FitzHugh-Nagumo kinetics. The fluctuations vary in space and/or time. Depending on the realization of the dichotomous switching the system is, at a given time (for spatial disorder at a given position) in one of two possible excitable dynamical regimes. Each of the two excitable dynamics for itself does not support pattern formation. With proper dichotomous fluctuations, however, the homogeneous steady state is destabilized via a Turing instability. We investigate the influence of different switching rates (different correlation length of the spatial disorder) on pattern formation. We find three distinct mechanisms: For slow switching existing boundaries become unstable, for high rates the system exhibits "effective bistability" which allows for a Turing instability. For medium rates the fluctuations create spatial structures via a new mechanism where the influence of the fluctuations is twofold. First they produce local inhomogeneities, which then grow (again caused by fluctuations) until the whole space is covered. Utilizing a nonlinear map approach we show bistability of a period-one and a period-two orbit being associated with the steady homogeneous and the Turing pattern state, respectively. Finally, for purely static dichotomous disorder we find destabilization of homogeneous steady states for finite nonzero correlation length of the disorder resulting again in Turing patterns.

Journal Article↗

PubMed2005

Localization properties of electronic states in a polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers.

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling is completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.

Biophysical Phenomena↗

PubMed2005

Modelling the thermal evolution of enzyme-created bubbles in DNA.

The formation of bubbles in nucleic acids (NAs) is fundamental in many biological processes such as DNA replication, recombination, telomere formation and nucleotide excision repair, as well as RNA transcription and splicing. These processes are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the frame of a nonlinear dynamics approach, we model the structure of the DNA duplex by a nonlinear network of coupled oscillators. We show that, in fact, from certain local structural distortions, there originate oscillating localized patterns, that is, radial and torsional breathers, which are associated with localized H-bond deformations, reminiscent of the replication bubble. We further study the temperature dependence of these oscillating bubbles. To this aim, the underlying nonlinear oscillator network of the DNA duplex is brought into contact with a heat bath using the Nosé-Hoover method. Special attention is paid to the stability of the oscillating bubbles under the imposed thermal perturbations. It is demonstrated that the radial and torsional breathers sustain the impact of thermal perturbations even at temperatures as high as room temperature. Generally, for non-zero temperature, the H-bond breathers move coherently along the double chain, whereas at T=0 standing radial and torsional breathers result.

DNA↗

PubMed2001

Mobile polaron solutions and nonlinear electron transfer in helical protein models.

We consider the electron transfer along helical forms of proteins. The spatial structure of the protein helices is modeled by three-dimensional oscillator networks whose constituents represent peptide groups. Covalent and hydrogen bonds between the peptide units are modeled by point-point interaction potentials. The electronic degree of freedom is described by a tight-binding system including besides the nearest-neighbor exchange interactions between covalently connected units also third- or fourth-nearest neighbor interactions between hydrogen-bonded sites. In addition each peptide unit possesses an internal vibrational degree of freedom. The various dynamical degrees of freedom are coupled to each other making the exchange of electronic, intramolecular, and bond-vibrational energy possible. In the first part of the paper we investigate the static polaron formation resulting from strong interactions between the electron and the intramolecular vibrations. The 3-10 helix and the alpha helix are investigated. Polaron states are constructed analytically on the basis of a variational approach. Compared to the alpha helix the 3-10 helix supports stronger localized polarons. In the second part of the paper we take the coupling of the polaron with the vibrations of the three-dimensional protein matrix into account focusing interest on the bond-assisted initiation of polaron motion. In detail it is demonstrated that the interplay of the protein matrix and the polaron dynamics conspire to activate not only the polaron motion but also to maintain a long-lived coherently traveling localized pattern along the lattice of peptide units. Starting from a nonequilibrium state it is shown that coexisting electron and bond-vibration breathers assist the relaxation dynamics towards energy equilibration and the attainment of a stationary regime.

Electrons↗

PubMed2000

Solitonic energy transfer in a coupled exciton-vibron system

We consider the exciton transfer along a one-dimensional molecular chain. The exciton motion is influenced by longitudinal vibrations evolving in a Toda lattice potential. It is shown how the soliton solutions of the vibron system coupled to the exciton system induce solitonic exciton transfer. To this aim the existence of a regime of suppressed energy exchange between the coupled excitonic and vibrational degrees of freedom is established in the case of which a nonlinear Schrodinger equation for the exciton variable is derived. The nonlinear Schrodinger equation possesses soliton solutions corresponding to coherent transfer of the localized exciton.

Journal Article↗

PubMed2000

Electron-vibron-breather interaction

We study the interaction of breathers in the context of a coupled electron-vibron lattice system. Starting with single-site excitations, it is demonstrated that constellations exist for which the coexistence of electronic and vibronic breathers is assured. The energy exchange between the vibrational and electronic subsystems and its impact on the breather formation are discussed in detail. The coupled electron-vibron dynamics shows a tendency toward energy redistribution into the vibronic degrees of freedom at the expense of the electronic energy content. Attention is paid to the relaxation dynamics in the energy exchange and we discuss the attainment of a steady regime for the coupled electron-vibron dynamics starting from a nonequilibrium state. It is demonstrated that the presence of breathers has a strong impact on the relaxation dynamics. Breathers can assist the relaxation process. With the help of a linear stability analysis, we show why the electronic subsystem acts as an energy donor while the vibron system serves as the energy acceptor. To this end we investigate the existence and stability of localized breathing eigenmodes capable of energy trapping. A frequency analysis reveals that strong exchange also occurs due to a temporal transition from single-frequency breathers to those oscillating with two frequencies and their temporal resonance interaction. Finally, the self-stabilized electron-vibron system relaxes to a combined electron-vibron breather. On increasing the electron-vibron coupling strength, only a vibronic phonobreather of large amplitude survives, whereas the electronic subsystem tends to energy equipartition.

Journal Article↗

PubMed1998

A formiminotransferase cyclodeaminase isoform is localized to the Golgi complex and can mediate interaction of trans-Golgi network-derived vesicles with microtubules.

A protein of 60 kDa (p60) has been identified using a quantitative in vitro vesicle-microtubule binding assay. Purified p60 induces co-sedimentation with microtubules of trans-Golgi network-derived vesicles isolated from polarized, perforated Madin-Darby canine kidney cells. Sequencing of the cDNA coding for this protein revealed that it is the chicken homologue of formiminotransferase cyclodeaminase (FTCD), a liver-specific enzyme involved in the histidine degradation pathway. Purified p60 from chicken liver has formiminotransferase activity, confirming that it is FTCD or an isoform of this enzyme. Isoforms of FTCD were identified in chicken hepatoma and HeLa cells, and immunolocalize to the region of the Golgi complex and vesicular structures in its vicinity. Furthermore, 58K, a previously identified microtubule-binding Golgi protein from rat liver (Bloom, G. S., and Brashear, T. A. (1989) J. Biol. Chem. 264, 16083-16092), is identical to FTCD. Both proteins co-purify with microtubules and co-localize with membranes of the Golgi complex. The capacity of FTCD to bind both to microtubules and Golgi-derived membranes may suggest that this protein, or one of its isoforms, might have in addition to its enzymatic activity, a second physiological function in mediating interaction of Golgi-derived membranes with microtubules.

Amino Acid Sequence↗

PubMed1996