Biomedical subjects

Dirk Lebiedz

Publications and source records attributed to Dirk Lebiedz.

8 recordsLinked to original sources

PubMed2005

Influence of coadsorbates on the NO dissociation on a rhodium(311) surface.

Density functional theory (DFT) studies were performed to investigate the influence of coadsorbates on the nitrogen oxide dissociation on the vicinal rhodium(311) surface. This study amplifies prior studies on the dissociation of oxygen and nitrogen oxide on the (111) facet of rhodium. The influence of coadsorbates on the kinetic parameters and thermochemistry of the NO dissociation on Rh311 was studied. In addition, the activation energy and thermochemistry of this reaction were determined as a function of oxygen preoccupation/initial coverage. Steric and electronic effects and their influence on the dissociation reaction were examined. The results are discussed in the face of an NOx dissociation catalyst system proposed by Nakatsuji.

Journal Article↗

PubMed2005

Automatic network coupling analysis for dynamical systems based on detailed kinetic models.

We introduce a numerical complexity reduction method for the automatic identification and analysis of dynamic network decompositions in (bio)chemical kinetics based on error-controlled computation of a minimal model dimension represented by the number of (locally) active dynamical modes. Our algorithm exploits a generalized sensitivity analysis along state trajectories and subsequent singular value decomposition of sensitivity matrices for the identification of these dominant dynamical modes. It allows for a dynamic coupling analysis of (bio)chemical species in kinetic models that can be exploited for the piecewise computation of a minimal model on small time intervals and offers valuable functional insight into highly nonlinear reaction mechanisms and network dynamics. We present results for the identification of network decompositions in a simple oscillatory chemical reaction, time scale separation based model reduction in a Michaelis-Menten enzyme system and network decomposition of a detailed model for the oscillatory peroxidase-oxidase enzyme system.

Algorithms↗

PubMed2005

Linear relationship between activation energies and reaction energies for coverage-dependent dissociation reactions on rhodium surfaces.

Evidence of a relationship between activation energies and enthalpy changes of various dissociation reactions on transition metals has been reported recently. A reconsideration of density functional theory results for dissociation energies of oxygen and NO on different rhodium surfaces (low-index and stepped) and their dependencies on oxygen precoverage reveal that also here a linear Brønsted-Evans-Polanyi (BEP) relationship exists. The establishment of such a general concept would be of tremendous importance for the development of detailed, elementary-step reaction mechanisms, because the activation energies of reaction steps as well as their coverage dependencies could be estimated based on the adsorption energies calculated by means of DFT.

Linear Models↗

PubMed2005

Influence of initial oxygen coverage and magnetic moment on the NO decomposition on rhodium (111).

In this study, density functional theory calculations were performed to investigate the influence of oxygen preoccupation on the nitrogen oxide decomposition on rhodium. Besides gauging the coverage dependence of the adsorption energy of NO on the (111) rhodium facet, the influence of the initial oxygen coverage on the kinetics and thermodynamics of the nitrogen oxide decomposition reaction was also studied. The results are discussed with respect to a novel NOx decomposition catalyst. Furthermore, the influence of spin effects on the adsorption geometry as well as the adsorption energy is examined. It will be addressed why spin effects only have a minor influence on the behavior of NO on a rhodium surface.

Journal Article↗

PubMed2005

Coverage dependence of oxygen decomposition and surface diffusion on rhodium 111: a DFT study.

A systematic study of oxygen adsorption, decomposition and diffusion on Rh111 and its dependence on coadsorbed oxygen molecules has been performed using density functional theory calculations. First, the bonding strength between metal surface and adsorbed oxygen molecules has been studied as a function of initial oxygen coverage. The bonding strength decreases with increasing oxygen coverage, which points towards a self-inhibition of the adsorption process. The potential energy hypersurface (PES) for the dissociation of oxygen molecules adsorbed on a threefold fcc position perpendicular to the surface was calculated using a combined linear/quadratic synchronous transit method with conjugate gradient refinements. The results indicate that a minor amount of oxygen on the surface enhances the decomposition of further oxygen molecules, while this process is inhibited at higher coverage. Moreover, PES calculations of a single site jump of atomic oxygen on rhodium 111 indicate that the activation energy increases as well with increasing oxygen coverage. All results are discussed with respect to a rhodium based catalytic NOx reduction/decomposition system proposed by Nakatsuji, which decomposes nitrogen oxides in oxygen excess.

Journal Article↗

PubMed2005

Specific external forcing of spatiotemporal dynamics in reaction-diffusion systems.

Self-organization behavior and in particular pattern forming spatiotemporal dynamics play an important role in far from equilibrium chemical and biochemical systems. Specific external forcing and control of self-organizing processes might be of great benefit in various applications ranging from technical systems to modern biomedical research. We demonstrate that in a cellular chemotaxis system modeled by one-dimensional reaction-diffusion equations particular forms of spatiotemporal dynamics can be induced and stabilized by controlling spatially distributed influx patterns of a chemical species as a function of time. In our model study we show that a propagating wave with certain shape and velocity and static symmetrical and asymmetrical patterns can be forced and manipulated by numerically computing open-loop optimal influx controls.

Biophysics↗

PubMed2004

Dynamic control and information processing in chemical reaction systems by tuning self-organization behavior.

Specific external control of chemical reaction systems and both dynamic control and signal processing as central functions in biochemical reaction systems are important issues of modern nonlinear science. For example nonlinear input-output behavior and its regulation are crucial for the maintainance of the life process that requires extensive communication between cells and their environment. An important question is how the dynamical behavior of biochemical systems is controlled and how they process information transmitted by incoming signals. But also from a general point of view external forcing of complex chemical reaction processes is important in many application areas ranging from chemical engineering to biomedicine. In order to study such control issues numerically, here, we choose a well characterized chemical system, the CO oxidation on Pt(110), which is interesting per se as an externally forced chemical oscillator model. We show numerically that tuning of temporal self-organization by input signals in this simple nonlinear chemical reaction exhibiting oscillatory behavior can in principle be exploited for both specific external control of dynamical system behavior and processing of complex information.

Biochemistry↗

PubMed2003

Manipulation of self-aggregation patterns and waves in a reaction-diffusion system by optimal boundary control strategies.

Reaction-diffusion systems are of considerable importance in many areas of physical sciences. For many reasons, an external manipulation of the dynamics of these processes is desirable. Here we show numerically how spatiotemporal behavior like pattern formation and wave propagation in a two component nonlinear reaction-diffusion model of bacterial chemotaxis can be externally controlled. We formulate the control goal as an objective functional and apply numerical optimization for the solution of the resulting control problem.

Journal Article↗