Langevin Thermostat for Rigid Body Dynamics

We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of freedom to correctly sample the NVT distribution in a simulation of rigid molecules. We propose simple, quasi-symplectic second-order numerical integrators and test their performance on the TIP4P model of water. We also investigate the optimal choice of thermostat parameters.Comment: 15 pages, 13 figures, 1 tabl

Spatiotemporal complexity of the universe at subhorizon scales

This is a short note on the spatiotemporal complexity of the dynamical state(s) of the universe at subhorizon scales (up to 300 Mpc). There are reasons, based mainly on infrared radiative divergences, to believe that one can encounter a flicker noise in the time domain, while in the space domain, the scaling laws are reflected in the (multi)fractal distribution of galaxies and their clusters. There exist recent suggestions on a unifying treatment of these two aspects within the concept of spatiotemporal complexity of dynamical systems driven out of equilibrium. Spatiotemporal complexity of the subhorizon dynamical state(s) of the universe is a conceptually nice idea and may lead to progress in our understanding of the material structures at large scalesComment: references update

Deterministic Dicke state preparation with continuous measurement and control

We characterize the long-time projective behavior of the stochastic master equation describing a continuous, collective spin measurement of an atomic ensemble both analytically and numerically. By adding state based feedback, we show that it is possible to prepare highly entangled Dicke states deterministically.Comment: Additional information is available at http://minty.caltech.edu/Ensemble

The Impact of Entropy on the Spatial Organization of Synaptonemal Complexes within the Cell Nucleus

We employ 4Pi-microscopy to study SC organization in mouse spermatocyte nuclei allowing for the three-dimensional reconstruction of the SC's backbone arrangement. Additionally, we model the SCs in the cell nucleus by confined, self-avoiding polymers, whose chain ends are attached to the envelope of the confining cavity and diffuse along it. This work helps to elucidate the role of entropy in shaping pachytene SC organization. The framework provided by the complex interplay between SC polymer rigidity, tethering and confinement is able to qualitatively explain features of SC organization, such as mean squared end-to-end distances, mean squared center-of-mass distances, or SC density distributions. However, it fails in correctly assessing SC entanglement within the nucleus. In fact, our analysis of the 4Pi-microscopy images reveals a higher ordering of SCs within the nuclear volume than what is expected by our numerical model. This suggests that while effects of entropy impact SC organization, the dedicated action of proteins or actin cables is required to fine-tune the spatial ordering of SCs within the cell nucleus

Haemogenic endocardium contributes to transient definitive haematopoiesis.

Haematopoietic cells arise from spatiotemporally restricted domains in the developing embryo. Although studies of non-mammalian animal and in vitro embryonic stem cell models suggest a close relationship among cardiac, endocardial and haematopoietic lineages, it remains unknown whether the mammalian heart tube serves as a haemogenic organ akin to the dorsal aorta. Here we examine the haemogenic activity of the developing endocardium. Mouse heart explants generate myeloid and erythroid colonies in the absence of circulation. Haemogenic activity arises from a subset of endocardial cells in the outflow cushion and atria earlier than in the aorta-gonad-mesonephros region, and is transient and definitive in nature. Interestingly, key cardiac transcription factors, Nkx2-5 and Isl1, are expressed in and required for the haemogenic population of the endocardium. Together, these data suggest that a subset of endocardial/endothelial cells serve as a de novo source for transient definitive haematopoietic progenitors

Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes

BACKGROUND: The continuous and non-synchronous nature of postnatal male germ-cell development has impeded stage-specific resolution of molecular events of mammalian meiotic prophase in the testis. Here the juvenile onset of spermatogenesis in mice is analyzed by combining cytological and transcriptomic data in a novel computational analysis that allows decomposition of the transcriptional programs of spermatogonia and meiotic prophase substages. RESULTS: Germ cells from testes of individual mice were obtained at two-day intervals from 8 to 18 days post-partum (dpp), prepared as surface-spread chromatin and immunolabeled for meiotic stage-specific protein markers (STRA8, SYCP3, phosphorylated H2AFX, and HISTH1T). Eight stages were discriminated cytologically by combinatorial antibody labeling, and RNA-seq was performed on the same samples. Independent principal component analyses of cytological and transcriptomic data yielded similar patterns for both data types, providing strong evidence for substage-specific gene expression signatures. A novel permutation-based maximum covariance analysis (PMCA) was developed to map co-expressed transcripts to one or more of the eight meiotic prophase substages, thereby linking distinct molecular programs to cytologically defined cell states. Expression of meiosis-specific genes is not substage-limited, suggesting regulation of substage transitions at other levels. CONCLUSIONS: This integrated analysis provides a general method for resolving complex cell populations. Here it revealed not only features of meiotic substage-specific gene expression, but also a network of substage-specific transcription factors and relationships to potential target genes. BMC Genomics 2016 Aug 12; 17(1):628

The universal Glivenko-Cantelli property

Let F be a separable uniformly bounded family of measurable functions on a standard measurable space, and let N_{[]}(F,\epsilon,\mu) be the smallest number of \epsilon-brackets in L^1(\mu) needed to cover F. The following are equivalent: 1. F is a universal Glivenko-Cantelli class. 2. N_{[]}(F,\epsilon,\mu)0 and every probability measure \mu. 3. F is totally bounded in L^1(\mu) for every probability measure \mu. 4. F does not contain a Boolean \sigma-independent sequence. It follows that universal Glivenko-Cantelli classes are uniformity classes for general sequences of almost surely convergent random measures.Comment: 26 page

A Quantum Langevin Formulation of Risk-Sensitive Optimal Control

In this paper we formulate a risk-sensitive optimal control problem for continuously monitored open quantum systems modelled by quantum Langevin equations. The optimal controller is expressed in terms of a modified conditional state, which we call a risk-sensitive state, that represents measurement knowledge tempered by the control purpose. One of the two components of the optimal controller is dynamic, a filter that computes the risk-sensitive state. The second component is an optimal control feedback function that is found by solving the dynamic programming equation. The optimal controller can be implemented using classical electronics. The ideas are illustrated using an example of feedback control of a two-level atom