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Meristems continually supply new cells for post-embryonic plant development and coordinate the initiation of new organs, such as leaves and flowers. Meristem function is regulated by a large and interconnected dynamic system that includes transcription networks, intercellular protein signalling, polarized transport of hormones and a constantly changing cellular topology. Mathematical modelling, in
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar G (o) over bar -like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding behavior. It turns out that general, characteristic folding features of realistic proteins with a single free-energy barrier can also be observed in this
An atomic protein model with a minimalistic potential is developed and then tested on an α-helix and a β-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good approximation can be described by a simple two-state model, with parameters that are in reasonable quantitative agreement with experimental data. Despite the apparent two-stat
Motivation: The pairwise alignment of biological sequences obtained from an algorithm will in general contain both correct and incorrect parts. Hence, to allow for a valid interpretation of the alignment, the local trustworthiness of the alignment has to be quantified. Results: We present a novel approach that attributes a reliability index to every pair of residues, including gapped regions, in t
We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from a (conformation-dependent) Gaussian distribution that favors approximately local deformations of the chain. The degree of bias is controlled by a parameter b. The method is tested on a reduced model protein with 54 amino acids and
A novel artificial neural network heuristic (INN) for general constraint satisfaction problems is presented. extending a recently suggested method restricted to boolean variables. In contrast to conventional ANN methods, it employs a particular type of non-polynomial cost function, based on the information balance between variables and constraints in a mean-field setting. Implemented as an anneali
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is unstructured. We obtain significant differences in their binding behavior. The stable sequence has rigid docking as its preferred binding mode, while the unstru
We present a rate equation model for the TGF-beta pathway in endothelial cells together with novel measurements. This pathway plays a prominent role in inter- and intracellular communication and subversion can lead to cancer, fibrosis vascular disorders, and immune diseases. The model successfully describes the kinetics of experimental data and also correctly predicts the behavior in experiments w
The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a beta barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion, parametrized in terms of the end-to-end distance. In particular, the escape times can be evaluated as first passage times for a Brownian particle moving on the pro
Motivation: The above-ground tissues of higher plants are generated from a small region of cells situated at the plant apex called the shoot apical meristem. An important genetic control circuit modulating the size of the Arabidopsis thaliana meristem is a feed-back network between the CLAVATA3 and WUSCHEL genes. Although the expression patterns for these genes do not overlap, WUSCHEL activity is
Pharmacogenomics is the application of genomic technologies to drug discovery and development, as well as for the elucidation of the mechanisms of drug action on cells and organisms. DNA microarrays measure genome-wide gene expression patterns and are an important tool for pharmacogenomic applications, such as the identification of molecular targets for drugs, toxicological studies and molecular d
We discuss partially quenched chiral perturbation theory (PQ chi PT) and possible fitting strategies to lattice QCD data at next-to-next-to-leading order (NNLO) in the mesonic sector. We also present a complete calculation of the masses of the charged pseudoscalar mesons, in the supersymmetric formulation of PQ chi PT. Explicit analytical results are given for up to three nondegenerate sea-quark f
Obtaining DNA sequences is a time-consuming task, which typically requires one or several days for completion. One way of reducing analysis times is to be satisfied with long-range sequence patterns on the order of thousands of base pairs. DNA barcoding is a DNA-characterising technique that works according to this principle. It does so by using fluorescence microscopy to visualise long-range sequ
To optimize the weights in an artificial neural network most methods rely gradients, which are not always obtainable or desirable. Evolutionary algorithms are instead based on Darwinian evolution where no derivative is needed. These algorithms have a set of strategy parameters that can be dynamically updated during the search to increase performance. Two ways of updating the parameters are the so
In this thesis, theoretical models are applied to study some aspects of intrinsically disordered proteins, i.e. proteins that partly or entirely lack a stable native structure. In particular, focus is on peptide binding and aggregation. Knowledge about these mechanisms is important for understanding how proteins interact with each other and how mutations can affect the function and sometimes give
We investigate in some detail a recently suggested general class of ensembles of sparse undirected random graphs based on a hidden stub coloring, with or without the restriction to nondegenerate graphs. The calculability of local and global structural properties of graphs from the resulting ensembles is demonstrated. Cluster size statistics are derived with generating function techniques, yielding
Topological properties of "scale-free" networks are investigated by determining their spectral dimensions d(S), which reflect a diffusion process in the corresponding graphs. Data bases for citation networks and metabolic networks together with simulation results from the growing network model [A.-L. Barabasi and R. Albert, Science 286, 509 (1999)] are probed. For completeness and comparisons latt
Plant cells in tissues experience mechanical stress not only as a result of high turgor, but also through interaction with their neighbors. Cells can expand at different rates and in different directions from neighbors with which they share a cell wall. This in connection with specific tissue shapes and properties of the cell wall material can lead to intricate stress patterns throughout the tissu
A general method is discussed, the δ-test, which establishes functional dependencies given a table of measurements. The approach is based on calculating conditional probabilities from data densities. Imposing the requirement of continuity of the underlying function the obtained values of the conditional probabilities carry information on the variable dependencies. The power of the method is illust
