SearcharxivSearch

arXiv subjects

Dieter W. Heermann

Publications and source records attributed to Dieter W. Heermann.

At least 19 recordsLinked to original sources

Causal Anomaly Detection for Lithium-Ion Battery Degradation

Reliable early detection of lithium-ion battery degradation requires health indicators that are physically interpretable and computable from routine cycler telemetry without access to the degradation region. We introduce \textsc{CausalHealth}, a framework that applies causal graph discovery and $k$-nearest-neighbour transfer entropy to per-cycle voltage, current, temperature, and resistance time series, and organises twelve resulting anomaly scores into three signal-class bundles (Magnitude-shift, Predictive-residual, Complexity-entropy) -- with Isolation Forest reported separately as it falls below the bundle reliability threshold -- to characterise detection sensitivity across ten commissioning fractions (5--30\,\%). The Magnitude-shift class achieves 100\,\% detection across all seven tested cells spanning LFP (MIT--Stanford MATR) and LCO (NASA PCoE, CALCE CS2) chemistries, with a lead time of up to 402 cycles before conventional capacity-threshold failure on gradual-fade cells. A Reliability-Weighted Master Health Index (RWMHI) -- a cross-bundle fusion of five high-reliability detectors weighted by inverse coefficient of variation -- improves lead time by 15--52 cycles over the class median on long-lived cells while maintaining 100\,\% detection. Validation against electrochemical impedance spectroscopy on an NMC prismatic cell provides independent physical grounding: transfer entropy $\mathrm{TE}(R \!\to\! V)$ correlates with charge-transfer resistance $R_{\mathrm{ct}}$ (pooled $r = +0.990$; temperature-controlled partial $r = +0.898$), and an Arrhenius analysis of both quantities yields an activation energy consistent with published NMC charge-transfer kinetics. These results are evaluated on seven cells across three benchmark datasets.

cond-mat.mtrl-sci

Intra-Chromosomal Potentials from Nucleosomal Positioning Data

No systematic method exists to derive intra-chromosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical properties of chromosomes. Thus, indirectly, they shed light on a possible mechanical genomic code along a chromosome. To develop a method yielding effective intra-chromosomal potentials between nucleosomes a generalized Lennard-Jones potential for the parameterization is developed based on nucleosomal positioning data. This approach eliminates some of the problems that the underlying nucleosomal positioning data has, rendering the extraction difficult on the individual nucleosomal level. Furthermore, patterns on which to base a classification along a chromosome appear on larger domains, such as hetero- and euchromatin. An intuitive selection strategy for the noisy-optimization problem is employed to derive effective exponents for the generalized potential. The method is tested on the Candida albicans genome. Applying k-means clustering based on potential parameters and thermodynamic compressibilities, a genome-wide clustering of nucleosome sequences is obtained for Candida albicans. This clustering shows that a chromosome beyond the classical dichotomic categories of hetero- and euchromatin, is more feature-rich.

physics.bio-ph

Prediction and Comparative Analysis of CTCF Binding Sites based on a First Principle Approach

We calculated the patterns for the CCCTC transcription factor (CTCF) binding sites across many genomes on a first principle approach. The validation of the first principle method was done on the human as well as on the mouse genome. The predicted human CTCF binding sites are consistent with the consensus sequence, ChIP-seq data for the K562 cell, nucleosome positions for IMR90 cell as well as the CTCF binding sites in the mouse HOXA gene. The analysis of Homo sapiens, Mus musculus, Sus scrofa, Capra hircus and Drosophila melanogaster whole genomes shows: binding sites are organized in cluster-like groups, where two consecutive sites obey a power-law with coefficient ranging from to $0.3292\pm0.0068$ to $0.5409\pm0.0064$; the distance between these groups varies from $18.08\pm0.52$kbp to $42.1\pm2.0$kbp. The genome of Aedes aegypti does not show a power law, but $19.9\%$ of binding sites are $144\pm4$ and $287\pm5$bp distant of each other. We run negative tests, confirming the under-representation of CTCF binding sites in Caenorhabditis elegans, Plasmodium falciparum and Arabidopsis thaliana complete genomes.

physics.bio-ph

Fractality and Topology of Self-Avoiding Walks

We have analyzed geometric and topological features of self-avoiding walks. We introduce a new kind of walk: the loop-deleted self-avoiding walk (LDSAW) motivated by the interaction of chromatin with the nuclear lamina. Its critical exponent is calculated and found to be different from that of the ordinary SAW. Taking the walks as point-clouds, the LDSAW is a subset of the SAW. We study the difference between the LDSAW and SAW by comparing their fractal dimensions and growth rates of the Betti number. In addition, the spatial distribution of the contacts inside a SAW, which is also a subset of SAW, is analyzed following the same routine. The results show that the contact-cloud has a multi-fractal property and different growth rates for the Betti number. Finally, for comparison, we have analyzed random subsets of the SAW, showing them to have the same fractal dimension as the SAW.

cond-mat.stat-mech

Domain Boundary Detection in Hi-C Maps: A Probabilistic Graphical Model Approach

To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These experiments yield topological information, consistently showing a hierarchical subdivision of the genome into self-interacting domains across many organisms. Current methods for detecting these domains using the Hi-C contact matrix, i.e. a doubly-stochastic matrix, are mostly based on the assumption that the domains are distinct, thus non-overlapping. For overcoming this simplification and for being able to unravel a possible nested domain structure, we developed a probabilistic graphical model that makes no a priori assumptions on the domain structure. Within this approach, the Hi-C contact matrix is analyzed using an Ising like probabilistic graphical model whose coupling constant is proportional to each lattice point (entry in the contact matrix). The results show clear boundaries between identified domains and the background. These domain boundaries are dependent on the coupling constant, so that one matrix yields several clusters of different sizes, which show the self-interaction of the genome on different scales.

q-bio.QM

The Electronic Behavior of Zinc-Finger Protein Binding Sites in the Context of the DNA Extended Ladder Model

The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains, responsible for gene regulation and the spatial organization of DNA. To study and understand the zinc finger DNA-protein interaction, we use the extended ladder in the DNA model proposed by Zhu, Rasmussen, Balatsky \& Bishop (2007) \cite{Zhu-2007}. Considering one single spinless electron in each nucleotide $π$-orbital along a double DNA chain (dDNA), we find a typical pattern for the {\color{black} bottom of the occupied molecular orbital (BOMO)}, highest occupied molecular orbital (HOMO) and lowest unoccupied orbital (LUMO) along the binding sites. We specifically looked at two members of zinc finger protein family: specificity protein 1 (SP1) and early grown response 1 transcription factors (EGR1). When the valence band is filled, we find electrons in the purines along the nucleotide sequence, compatible with the electric charges of the binding amino acids in SP1 and EGR1 zinc finger.

q-bio.BM

Topological interactions between ring polymers: Implications for chromatin loops

Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The detailed topological and entropic forces between loops still remain elusive. Here, we quantitatively determine the potential of mean force between the centers of mass of two ring polymers, i.e. loops. We find that the transition from a linear to a ring polymer induces a strong increase in the entropic repulsion between these two polymers. On top, topological interactions such as the non-catenation constraint further reduce the number of accessible conformations of close-by ring polymers by about 50%, resulting in an additional effective repulsion. Furthermore, the transition from linear to ring polymers displays changes in the conformational and structural properties of the system. In fact, ring polymers adopt a markedly more ordered and aligned state than linear ones. The forces and accompanying changes in shape and alignment between ring polymers suggest an important regulatory function of such a topology in biopolymers. We conjecture that dynamic loop formation in chromatin might act as a versatile control mechanism regulating and maintaining different local states of compaction and order.

cond-mat.soft

Conformational properties of compact polymers

Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact conformations on a cubic LxLxL lattice with different occupancy fractions by modifying a recently proposed algorithm. The system sizes studied extend up to N=256000 monomers, going well beyond the limits of older publications on compact polymers. We analyze several conformational properties of these polymers, including segment correlations and screening of excluded volume. Most importantly we propose a scaling law for the end-to-end distance distribution and analyze the moments of this distribution. It shows universality with respect to different occupancy fractions, i.e. system densities. We further analyze the distance distribution between intrachain segments, which turns out to be of great importance for biological experiments. We apply these new findings to the problem of chromatin folding inside interphase nuclei and show that -- although chromatin is in a compacted state -- the classical theory of compact polymers does not explain recent experimental results.

cond-mat.soft

A modified Potts model for the interaction of surface-attached polymer complexes

We present a simple yet generic model for the behavior of a system of many surface-attached flexible polymers with rigid side chains. Beyond its potential application in describing the dynamics of the extracellular matrix of mammalian cells, the model itself shows an interesting phase transition behavior since the underlying models (a two-dimensional Potts model and a XY-model) undergo different phase transitions.

cond-mat.stat-mech

A 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.

cond-mat.soft

Superdiffusion in a Model for Diffusion in a Molecularly Crowded Environment

We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times, but anomalous diffusion at intermediate times. The effective exponents for square distance versus time usually are below one at these intermediate times, but can be also larger than one for high barrier concentrations. Thus we observe sub- as well as super-diffusion in a crowded environment.

q-bio.SC

Chromatin Folding in Relation to Human Genome Function

Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D physical distance between pairwise labeled genomic positions in gene-dense, highly transcribed domains and gene-poor less active areas on chromosomes 1 and 11 in G1 nuclei of human primary fibroblasts, using fluorescence in situ hybridization. Interpretation of our results and those published by others, based on polymer physics, shows that the folding of the chromatin fiber can be described as a polymer in a globular state (GS), maintained by intra-polymer attractive interactions that counteract self-avoidance forces. The GS polymer model is able to describe chromatin folding in as well the highly expressed domains as the lowly expressed ones, indicating that they differ in Kuhn length and chromatin compaction. Each type of genomic domain constitutes an ensemble of relatively compact globular folding states, resulting in a considerable cellto- cell variation between otherwise identical cells. We present evidence for different polymer folding regimes of the chromatin fiber on the length scale of a few mega base pairs and on that of complete chromosome arms (several tens of Mb). Our results present a novel view on the folding of the chromatin fiber in interphase and open the possibility to explore the nature of the intra-chromatin fiber interactions.

q-bio.GN

Percolation in a Class of Band Structured Random Matrices

We define a class of random matrix ensembles that pertain to random looped polymers. Such random looped polymers are a possible model for bio-polymers such as chromatin in the cell nucleus. It is shown that the distribution of the largest eigenvalue $λ_{max}$ depends on a percolation transition in the entries of the random matrices. Below the percolation threshold the distribution is multi-peaked and changes above the threshold to the Tracy-Widom distribution. We also show that the distribution of the eigenvalues is neither of the Wigner form nor gaussian.

cond-mat.stat-mech

Monte Carlo simulations reveal the straightening up of an end-grafted flexible chain with a rigid side chain

We have studied the conformational properties of a flexible end-grafted chain (length $N$) with a rigid side chain (length $S$) by means of Monte Carlo simulations. Depending on the lengths $N$ and $S$ and the branching site, $b$, we observe a considerable straightening of the flexible backbone as quantified via the gyration tensor. For $b=N$, i.e. when attaching the side chain to the free end of the flexible backbone, the effect was strongest.

cond-mat.soft

Structure of Polymer Brushes in Cylindrical Tubes: A Molecular Dynamics Simulation

Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $σ$ are varied over a wide range and the crossover from ``mushroom'' to ``brush'' behavior is studied for three pore diameters. The monomer density profile and the distribution of the free chain ends are computed and compared to the corresponding model of polymer brushes at flat substrates. It is found that there exists a regime of $N$ and $σ$ for large enough pore diameter where the brush height in the pore exceeds the brush height on the flat substrate, while for large enough $N$ and $σ$ (and small enough pore diameters) the opposite behavior occurs, i.e. the brush is compressed by confinement. These findings are used to discuss the corresponding theories on polymer brushes at concave substrates.

cond-mat.soft

Knots in Macromolecules in Constraint Space

We find a power law for the number of knot-monomers with an exponent $0.39 \pm0.13$ in agreement with previous simulations. For the average size of a knot we also obtain a power law $N_m=2.56\cdot N^{0.20\pm0.04}$. We further present data on the average number of knots given a certain chain length and confirm a power law behaviour for the number of knot-monomers. Furthermore we study the average crossing number for random and self-avoiding walks as well as for a model polymer with and without geometric constraints. The data confirms the $aN\log N + bN$ law in the case of without excluded volume and determines the constants $a$ and $b$ for various cases. For chains with excluded volume the data for chains up to N=1500 is consistent with $aN\log N + bN$ rather than the proposed $N^{4/3}$ law. Nevertheless our fits show that the $N^{4/3}$ law is a suitable approximation.

cond-mat.soft

The two-angle model and the phase diagram for Chromatin

We have studied the phase diagram for chromatin within the framework of the two-angle model. Rather than improving existing models with finer details our main focus of the work is getting mathematically rigorous results on the structure, especially on the excluded volume effects and the effects on the energy due to the long-range forces and their screening. Thus we present a phase diagram for the allowed conformations and the Coulomb energies.

cond-mat.soft

Reconstruction of the Free Energy in the Metastable Region using the Path Ensemble

By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent distributions from which we reconstruct the free energy as a function of the magnetic field, temperature and system size. From the reconstructed free energy, we obtain the free energy barrier that is associated with the transition from a metastable state to the stable equilibrium state. Although mean-field theory predicts a sharp transition between the metastable and the unstable region where the free energy barrier is zero, the results for the nearest-neighbour Ising model show that the free energy barrier does not go zero.

cond-mat.stat-mech