Effects of Kinks on DNA Elasticity

We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of trans-gauche rotations in the backbone of the single-stranded DNA. The problem is solved both analytically and numerically by generalizing the well-known analogy to the Quantum Rotator. In the small stretching force regime, we find that the persistence length is renormalized due to the presence of the kinks. In the opposite regime, the response to the strong stretching is determined solely by the bare persistence length with exponential corrections due to the ``ideal gas of kinks''. This high-force behavior changes significantly in the limit of high bending rigidity of the chain. In that case, the leading corrections to the mechanical response are likely to be due to the formation of multi-kink structures, such as kink pairs.Comment: v1: 16 pages, 7 figures, LaTeX; submitted to Physical Review E; v2: a new subsection on soft kinks added to section Theory, sections Introduction and Conclusions expanded, references added, other minor changes; v3: a reference adde

Toeplitz Inverse Covariance-Based Clustering of Multivariate Time Series Data

Subsequence clustering of multivariate time series is a useful tool for discovering repeated patterns in temporal data. Once these patterns have been discovered, seemingly complicated datasets can be interpreted as a temporal sequence of only a small number of states, or clusters. For example, raw sensor data from a fitness-tracking application can be expressed as a timeline of a select few actions (i.e., walking, sitting, running). However, discovering these patterns is challenging because it requires simultaneous segmentation and clustering of the time series. Furthermore, interpreting the resulting clusters is difficult, especially when the data is high-dimensional. Here we propose a new method of model-based clustering, which we call Toeplitz Inverse Covariance-based Clustering (TICC). Each cluster in the TICC method is defined by a correlation network, or Markov random field (MRF), characterizing the interdependencies between different observations in a typical subsequence of that cluster. Based on this graphical representation, TICC simultaneously segments and clusters the time series data. We solve the TICC problem through alternating minimization, using a variation of the expectation maximization (EM) algorithm. We derive closed-form solutions to efficiently solve the two resulting subproblems in a scalable way, through dynamic programming and the alternating direction method of multipliers (ADMM), respectively. We validate our approach by comparing TICC to several state-of-the-art baselines in a series of synthetic experiments, and we then demonstrate on an automobile sensor dataset how TICC can be used to learn interpretable clusters in real-world scenarios.Comment: This revised version fixes two small typos in the published versio

Network Inference via the Time-Varying Graphical Lasso

Many important problems can be modeled as a system of interconnected entities, where each entity is recording time-dependent observations or measurements. In order to spot trends, detect anomalies, and interpret the temporal dynamics of such data, it is essential to understand the relationships between the different entities and how these relationships evolve over time. In this paper, we introduce the time-varying graphical lasso (TVGL), a method of inferring time-varying networks from raw time series data. We cast the problem in terms of estimating a sparse time-varying inverse covariance matrix, which reveals a dynamic network of interdependencies between the entities. Since dynamic network inference is a computationally expensive task, we derive a scalable message-passing algorithm based on the Alternating Direction Method of Multipliers (ADMM) to solve this problem in an efficient way. We also discuss several extensions, including a streaming algorithm to update the model and incorporate new observations in real time. Finally, we evaluate our TVGL algorithm on both real and synthetic datasets, obtaining interpretable results and outperforming state-of-the-art baselines in terms of both accuracy and scalability

A coherent phonon-induced hidden quadrupolar ordered state in Ca2_2RuO4_4

Ultrafast laser excitation provides a means to transiently realize long-range ordered electronic states of matter that are hidden in thermal equilibrium. Recently, this approach has unveiled a variety of thermally inaccessible ordered states in strongly correlated materials, including charge density wave, ferroelectric, magnetic, and intertwined charge-orbital ordered states. However, more exotic hidden states exhibiting higher multipolar ordering remain elusive owing to the challenge of directly manipulating and detecting them with light. Here we demonstrate a method to induce a dynamical transition from a thermally allowed to a thermally forbidden spin-orbit entangled quadrupolar ordered state in Ca$_2$RuO$_4$ by coherently exciting a phonon that is strongly coupled to the order parameter. Combining probe photon energy-resolved coherent phonon spectroscopy measurements with model Hamiltonian calculations, we show that the dynamical transition is manifested through anomalies in the temperature, pump excitation fluence, and probe photon energy dependence of the strongly coupled phonon. With this procedure, we introduce a general pathway to uncover hidden multipolar ordered states and to control their re-orientation on ultrashort timescales.Comment: 8 pages, 4 figure

Divergence and Shannon information in genomes

Shannon information (SI) and its special case, divergence, are defined for a DNA sequence in terms of probabilities of chemical words in the sequence and are computed for a set of complete genomes highly diverse in length and composition. We find the following: SI (but not divergence) is inversely proportional to sequence length for a random sequence but is length-independent for genomes; the genomic SI is always greater and, for shorter words and longer sequences, hundreds to thousands times greater than the SI in a random sequence whose length and composition match those of the genome; genomic SIs appear to have word-length dependent universal values. The universality is inferred to be an evolution footprint of a universal mode for genome growth.Comment: 4 pages, 3 tables, 2 figure

A Coherent Study of Emission Lines from Broad-Band Photometry: Specific Star-Formation Rates and [OIII]/H{\beta} Ratio at 3 < z < 6

We measure the H{\alpha} and [OIII] emission line properties as well as specific star-formation rates (sSFR) of spectroscopically confirmed 3<z<6 galaxies in COSMOS from their observed colors vs. redshift evolution. Our model describes consistently the ensemble of galaxies including intrinsic properties (age, metallicity, star-formation history), dust-attenuation, and optical emission lines. We forward-model the measured H{\alpha} equivalent-widths (EW) to obtain the sSFR out to z~6 without stellar mass fitting. We find a strongly increasing rest-frame H{\alpha} EW that is flattening off above z~2.5 with average EWs of 300-600A at z~6. The sSFR is increasing proportional to (1+z)^2.4 at z<2.2 and (1+z)^1.5 at higher redshifts, indicative of a fast mass build-up in high-z galaxies within e-folding times of 100-200Myr at z~6. The redshift evolution at z>3 cannot be fully explained in a picture of cold accretion driven growth. We find a progressively increasing [OIII]{\lambda}5007/H{\beta} ratio out to z~6, consistent with the ratios in local galaxies selected by increasing H{\alpha} EW (i.e., sSFR). This demonstrates the potential of using "local high-z analogs" to investigate the spectroscopic properties and relations of galaxies in the re-ionization epoch.Comment: 18 pages, 11 figures, 3 table

Modeling secondary level of HIV contact tracing: its impact on HIV intervention in Cuba

<p>Abstract</p> <p>Background</p> <p>Universal HIV testing/treatment program has currently been suggested and debated as a useful strategy for elimination of HIV epidemic in Africa, although not without practical issues regarding the costs and feasibility of a fully implemented program.</p> <p>Methods</p> <p>A mathematical model is proposed which considers two levels of detection of HIV-infectives through contact tracing of known infectives in addition to detections through other means such as random screening. Simulations based on Cuban contact tracing data were performed to ascertain the potential impact of the different levels of contact tracing.</p> <p>Results</p> <p>Simulation studies illustrate that: (1) contact tracing is an important intervention measure which, while less effective than random screening, is perhaps less costly and hence ideal for large-scale intervention programs in developing countries with less resources; (2) the secondary level of contact tracing could significantly change the basic disease transmission dynamics, depending on the parameter values; (3) the prevalence of the epidemic at the time of implementation of contact tracing program might be a crucial factor in determining whether the measure will be effective in preventing disease infections and its eventual eradication.</p> <p>Conclusions</p> <p>Our results indicate that contact tracing for detection of HIV infectives could be suitably used to remedy inadequacies in a universal HIV testing program when designing timely and effective intervention measures.</p

Signatures of Ultrafast Reversal of Excitonic Order in Ta₂NiSe₅

In the presence of electron-phonon coupling, an excitonic insulator harbors two degenerate ground states described by an Ising-type order parameter. Starting from a microscopic Hamiltonian, we derive the equations of motion for the Ising order parameter in the phonon coupled excitonic insulator Ta₂NiSe₅ and show that it can be controllably reversed on ultrashort timescales using appropriate laser pulse sequences. Using a combination of theory and time-resolved optical reflectivity measurements, we report evidence of such order parameter reversal in Ta₂NiSe₅ based on the anomalous behavior of its coherently excited order-parameter-coupled phonons. Our Letter expands the field of ultrafast order parameter control beyond spin and charge ordered materials