The instability of Alexander-McTague crystals and its implication for nucleation

We show that the argument of Alexander and McTague, that the bcc crystalline structure is favored in those crystallization processes where the first order character is not too pronounced, is not correct. We find that any solution that satisfies the Alexander-McTague condition is not stable. We investigate the implication of this result for nucleation near the pseudo- spinodal in near-meanfield systems.Comment: 20 pages, 0 figures, submitted to Physical Review

Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis

Mathematical modeling is required for understanding the complex behavior of large signal transduction networks. Previous attempts to model signal transduction pathways were often limited to small systems or based on qualitative data only. Here, we developed a mathematical modeling framework for understanding the complex signaling behavior of CD95(APO-1/Fas)-mediated apoptosis. Defects in the regulation of apoptosis result in serious diseases such as cancer, autoimmunity, and neurodegeneration. During the last decade many of the molecular mechanisms of apoptosis signaling have been examined and elucidated. A systemic understanding of apoptosis is, however, still missing. To address the complexity of apoptotic signaling we subdivided this system into subsystems of different information qualities. A new approach for sensitivity analysis within the mathematical model was key for the identification of critical system parameters and two essential system properties: modularity and robustness. Our model describes the regulation of apoptosis on a systems level and resolves the important question of a threshold mechanism for the regulation of apoptosis

Zeros of the Partition Function and Pseudospinodals in Long-Range Ising Models

The relation between the zeros of the partition function and spinodal critical points in Ising models with long-range interactions is investigated. We find the spinodal is associated with the zeros of the partition function in four-dimensional complex temperature/magnetic field space. The zeros approach the real temperature/magnetic field plane as the range of interaction increases.Comment: 20 pages, 9 figures, accepted to PR

Avalanches in the Weakly Driven Frenkel-Kontorova Model

A damped chain of particles with harmonic nearest-neighbor interactions in a spatially periodic, piecewise harmonic potential (Frenkel-Kontorova model) is studied numerically. One end of the chain is pulled slowly which acts as a weak driving mechanism. The numerical study was performed in the limit of infinitely weak driving. The model exhibits avalanches starting at the pulled end of the chain. The dynamics of the avalanches and their size and strength distributions are studied in detail. The behavior depends on the value of the damping constant. For moderate values a erratic sequence of avalanches of all sizes occurs. The avalanche distributions are power-laws which is a key feature of self-organized criticality (SOC). It will be shown that the system selects a state where perturbations are just able to propagate through the whole system. For strong damping a regular behavior occurs where a sequence of states reappears periodically but shifted by an integer multiple of the period of the external potential. There is a broad transition regime between regular and irregular behavior, which is characterized by multistability between regular and irregular behavior. The avalanches are build up by sound waves and shock waves. Shock waves can turn their direction of propagation, or they can split into two pulses propagating in opposite directions leading to transient spatio-temporal chaos. PACS numbers: 05.70.Ln,05.50.+q,46.10.+zComment: 33 pages (RevTex), 15 Figures (available on request), appears in Phys. Rev.

Simulation of thermal conductivity and heat transport in solids

Using molecular dynamics (MD) with classical interaction potentials we present calculations of thermal conductivity and heat transport in crystals and glasses. Inducing shock waves and heat pulses into the systems we study the spreading of energy and temperature over the configurations. Phonon decay is investigated by exciting single modes in the structures and monitoring the time evolution of the amplitude using MD in a microcanonical ensemble. As examples, crystalline and amorphous modifications of Selenium and $\rm{SiO_2}$ are considered.Comment: Revtex, 8 pages, 11 postscript figures, accepted for publication in PR

Random loop model for long polymers.

While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding may depend locally on gene density and transcriptional activity and show a leveling-off at long distances where approximately $\sim O(1)$. We propose a new model that can explain this leveling-off by the formation of random loops. We derive an analytical expression for the mean square displacement between two beads where the average is taken over the thermal ensemble with a fixed but random loop configuration, while quenched averaging over the ensemble of different loop configurations -- which turns out to be equivalent to averaging over an ensemble of random matrices -- is performed numerically. A detailed investigation of this model shows that loops on all scales are necessary to fit experimental data.Comment: 8 pages, 7 figures; major changes: added paragraph with calculation of the annealed ensembl