Genome-scale engineering for systems and synthetic biology

Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targeted gene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering

Scattering of scalar perturbations with cosmological constant in low-energy and high-energy regimes

We study the absorption and scattering of massless scalar waves propagating in spherically symmetric spacetimes with dynamical cosmological constant both in low-energy and high-energy zones. In the former low-energy regime, we solve analytically the Regge-Wheeler wave equation and obtain an analytic absorption probability expression which varies with $M\sqrt{\Lambda}$, where $M$ is the central mass and $\Lambda$ is cosmological constant. The low-energy absorption probability, which is in the range of $[0, 0.986701]$, increases monotonically with increase in $\Lambda$. In the latter high-energy regime, the scalar particles adopt their geometric optics limit value. The trajectory equation with effective potential emerges and the analytic high-energy greybody factor, which is relevant with the area of classically accessible regime, also increases monotonically with increase in $\Lambda$, as long $\Lambda$ is less than or of the order of $10^4$. In this high-energy case, the null cosmological constant result reduces to the Schwarzschild value $27\pi r_g^2/4$.Comment: 12 pages, 6 figure

The Role of Genome Accessibility in Transcription Factor Binding in Bacteria

ChIP-seq enables genome-scale identification of regulatory regions that govern gene expression. However, the biological insights generated from ChIP-seq analysis have been limited to predictions of binding sites and cooperative interactions. Furthermore, ChIP-seq data often poorly correlate with in vitro measurements or predicted motifs, highlighting that binding affinity alone is insufficient to explain transcription factor (TF)-binding in vivo. One possibility is that binding sites are not equally accessible across the genome. A more comprehensive biophysical representation of TF-binding is required to improve our ability to understand, predict, and alter gene expression. Here, we show that genome accessibility is a key parameter that impacts TF-binding in bacteria. We developed a thermodynamic model that parameterizes ChIP-seq coverage in terms of genome accessibility and binding affinity. The role of genome accessibility is validated using a large-scale ChIP-seq dataset of the M. tuberculosis regulatory network. We find that accounting for genome accessibility led to a model that explains 63% of the ChIP-seq profile variance, while a model based in motif score alone explains only 35% of the variance. Moreover, our framework enables de novo ChIP-seq peak prediction and is useful for inferring TF-binding peaks in new experimental conditions by reducing the need for additional experiments. We observe that the genome is more accessible in intergenic regions, and that increased accessibility is positively correlated with gene expression and anti-correlated with distance to the origin of replication. Our biophysically motivated model provides a more comprehensive description of TF-binding in vivo from first principles towards a better representation of gene regulation in silico, with promising applications in systems biology

Self-consistent analysis of a quantum capacitor

We analyze the behavior of the magnetocapacitance for a three-probe capacitor. The self-consistent evaluation of the internal potential is found to play a large role in determining quantitative values of the capacitance. For capacitor plates of mesoscopic size, this potential reduces the charge accumulation by more than an order of magnitude compared to that obtained with noninteracting models. However, the qualitative behavior of the magnetocapacitance is not substantially altered by the self-consistency. A simple but physically motivated model gives an analytical formula which compares well with the numerical data.published_or_final_versio

Vacuum Rabi splitting and intracavity dark state in a cavity-atoms system

We report experimental measurements of the transmission spectrum of an optical cavity coupled with cold Rb atoms. We observe the multi-atom vacuum Rabi splitting of a composite cavity and atom system. When a coupling field is applied to the atoms and induces the resonant two-photon Raman transition with the cavity field in a Lamda-type three-level system, we observe a cavity transmission spectrum with two vacuum Rabi sidebands and a central peak representing the intracavity dark state. The central peak linewidth is significantly narrowed by the dark-state resonance and its position is insensitive to the frequency change of the empty cavity.Comment: 11 pages, 4 figure

Systematics of mid-rapidity K-/pi ratio in heavy-ion collisions

It is observed that K-/pi in A+A and possibly p+p and pbar+p collisions follows an interesting systematic in omega, the pion transverse energy per unit of rapidity and transverse overlap area. The systematics show a linear increase of K-/pi with omega in the AGS and SPS energy regime and a saturation at RHIC energy. The systematics indicate that omega might be the relevant variable underlying K-/pi. At high energy, the omega variable is related to the gluon saturation scale in high density QCD, and perhaps to the initial energy density in the Bjorken picture.Comment: 4 pages, 3 figures. SQM-2001 proceeding

Quantum Memory Process with a Four-Level Atomic Ensemble

We examine in detail the quantum memory technique for photons in a double $\Lambda$ atomic ensemble in this work. The novel application of the present technique to create two different quantum probe fields as well as entangled states of them is proposed. A larger zero-degeneracy class besides dark-state subspace is investigated and the adiabatic condition is confirmed in the present model. We extend the single-mode quantum memory technique to the case with multi-mode probe fields, and reveal the exact pulse matching phenomenon between two quantized pulses in the present system.Comment: 7 pages, 1 figure, to appear in Euro. Phys. J.

Specific Interactions at Cosmic Ray Energies for Extensive Air Showers Experiments

The HIJING and VENUS models of relativistic hadron-nucleus and nucleus-nucleus collisions are used to study interactions of hadron-hadron, hadron-nitrogen and nucleus-nitrogen collisions, specific for the extensive air shower developments initiated by cosmic rays in the atmosphere. The transverse energy, transverse momenta and spectra of secondary particles as well as their energy and mass dependence have been investigated in detail. Results are presented with particular emphasis on the contributions of minijets in HIJING model and validity of superposition models in this energy range.Comment: latex, revtex, 44 pages, 20 figures, 7 tables , submitted to Astroparticle Physic

Volatility return intervals analysis of the Japanese market

We investigate scaling and memory effects in return intervals between price volatilities above a certain threshold $q$ for the Japanese stock market using daily and intraday data sets. We find that the distribution of return intervals can be approximated by a scaling function that depends only on the ratio between the return interval $\tau$ and its mean $$. We also find memory effects such that a large (or small) return interval follows a large (or small) interval by investigating the conditional distribution and mean return interval. The results are similar to previous studies of other markets and indicate that similar statistical features appear in different financial markets. We also compare our results between the period before and after the big crash at the end of 1989. We find that scaling and memory effects of the return intervals show similar features although the statistical properties of the returns are different.Comment: 11 page

The first-order phase transition between dimerized-antiferromagnetic and uniform-antiferromagnetic phases in Cu_(1-x)M_xGeO_3

We have performed detailed magnetic susceptibility measurements as well as synchrotron x-ray diffraction studies to determine the temperature vs concentration ($T$ - $x$) phase diagram of Cu${}_{1-x}$Mg${}_x$GeO${}_3$. We observe clear double peaks in the magnetic susceptibility implying two antiferromagnetic (AF) transition temperatures in samples with Mg concentrations in the range 0.0237 $\le x \le$ 0.0271. We also observe a drastic change in the inverse correlation length in this concentration range by x-ray diffraction. The drastic change of the AF transition temperature as well as the disappearance of the spin-Peierls (SP) phase have been clarified; these results are consistent with a first-order phase transition between dimerized AF (D-AF) and uniform AF (U-AF) phases as reported by T. Masuda {\it et al.} \lbrack Phys. Rev. Lett. {\bf 80}, 4566 (1998)\rbrack. The $T$ - $x$ phase diagram of Cu${}_{1-x}$Zn${}_x$GeO${}_3$ is similar to that of Cu${}_{1-x}$Mg${}_x$GeO${}_3$, which suggests that the present phase transition is universal for Cu${}_{1-x}M_{x}$GeO${}_3$.Comment: 7 pages, 5 figures. submitted to PR