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The staphylococcal plasmid pC194 is replicated through the rolling-circle mechanism. Its replication protein RepA has been proposed to initiate replication by making a bond between Y214 and DNA phosphate via transesterification and to terminate it by hydrolyzing DNA with E210 and carrying out strand transfer. We tested this model by examining the catalytic functions of the protein with purified RepA proteins and single-stranded DNA oligomers. The wild-type RepA formed a covalent bond with the DNA phosphate at the predicted initiation site. It hydrolyzed the phosphodiester bond at the site, which activity was found to depend on the presence of a large pseudopalindrome contained in the replication origin. The protein carried out a strand-transfer reaction which mimicked the termination step of replication. A Y214F and an E210A mutant respectively lacked the transesterification and the hydrolytic activity. These results are consistent with the previously proposed model, which was based solely on molecular genetics results. In addition, an E142A mutant was found to lack both activities, suggesting that the residue may coordinate the divalent cation necessary for them. A possible role of the pseudopalindrome in controlling the two activities of RepA during a replication cycle is also discussed.

Out of equilibrium, the lack of reciprocity is the rule rather than the exception. Non-reciprocal interactions occur, for instance, in networks of neurons, directional growth of interfaces, and synthetic active materials. While wave propagation in non-reciprocal media has recently been under intense study, less is known about the consequences of non-reciprocity on the collective behavior of many-body systems. Here, we show that non-reciprocity leads to time-dependent phases where spontaneously broken symmetries are dynamically restored. The resulting phase transitions are controlled by spectral singularities called exceptional points. We describe the emergence of these phases using insights from bifurcation theory and non-Hermitian quantum mechanics. Our approach captures non-reciprocal generalizations of three archetypal classes of self-organization out of equilibrium: synchronization, flocking and pattern formation. Collective phenomena in these non-reciprocal systems range from active time-(quasi)crystals to exceptional-point enforced pattern-formation and hysteresis. Our work paves the way towards a general theory of critical phenomena in non-reciprocal matter., Comment: Supplementary movies at https://home.uchicago.edu/~vitelli/videos.html

Stochastic modeling of chemical reaction systems based on master equations has been an indispensable tool in physical sciences. In the long-time limit, the properties of these systems are characterized by stationary distributions of chemical master equations. In this paper, we describe a novel method for computing stationary distributions analytically, based on a parallel formalism between stochastic chemical reaction systems and second quantization. Anderson, Craciun, and Kurtz showed that, when the rate equation for a reaction network admits a complex-balanced steady-state solution, the corresponding stochastic reaction system has a stationary distribution of a product form of Poisson distributions. In a formulation of stochastic reaction systems using the language of second quantization initiated by Doi, product-form Poisson distributions correspond to coherent states. Pursuing this analogy further, we study the counterpart of squeezed states in stochastic reaction systems. Under the action of a squeeze operator, the time-evolution operator of the chemical master equation is transformed, and the resulting system describes a different reaction network, which does not admit a complex-balanced steady state. A squeezed coherent state gives the stationary distribution of the transformed network, for which analytic expression is obtained., Comment: 19 pages, 5 figures

We study a non-equilibrium unitary Fermi gas, being coupled with two baths with different values of chemical potential. Extending a T-matrix approximation developed in equilibrium Fermi gases to the non-equilibrium steady state by using the Keldysh Green’s function technique, we examine the superfluid phase transition out of equilibrium. We also clarify non-equilibrium effects on the pseudogap phenomenon by strong pairing fluctuations.

We develop a theory to describe the dynamics of a driven-dissipative many-body Fermi system, to pursue our proposal to realize exotic quantum states based on reservoir engineering. Our idea is to design the shape of a Fermi surface so as to have multiple Fermi edges, by properly attaching multiple reservoirs with different chemical potentials to a fermionic system. These emerged edges give rise to additional scattering channels that can destabilize the system into unconventional states, which is exemplified in this work by considering a driven-dissipative attractively interacting Fermi gas. By formulating a quantum kinetic equation using the Nambu-Keldysh Green's function technique, we explore nonequilibrium steady states in this system and assess their stability. We find that, in addition to the BCS-type isotropic pairing state, a Fulde-Ferrell-type anisotropic superfluid state being accompanied by Cooper pairs with non-zero center-of-mass momentum exists as a stable solution, even in the absence of a magnetic Zeeman field. Our result implies a great potential of realizing quantum matter beyond the equilibrium paradigm, by engineering the shape and topology of Fermi surfaces in both electronic and atomic systems., 23 pages, 11 figures

Root chemicals and the sequences of the internal transcribed spacers (ITSs) were analyzed for 9 Ligularia kanaitzensis and 3 L. subspicata samples collected in northwestern Yunnan and southwestern Sichuan, China. Subspicatins A and C were isolated from two L. kanaitzensis samples. Introgression of genes responsible for these compounds from L. subspicata was suggested by their strong connection with L. subspicata/L. lamarum and the geographical proximity of the samples to L. subspicata. DNA analysis of a set of 27 L. kanaitzensis samples including those analyzed previously showed that they belong to two clades, designated A and B. Together with the presence/absence of furanoeremophilane, the 27 samples were sorted into three groups: clade A/furan, clade B/furan, and clade B/non-furan. The ancestral plant presumably belonged to clade B/non-furan, because furanoeremophilanes are biosynthesized from eremophilan-8-ones. 1β-Angeloyloxyfukinone, a likely intermediate between fukinone and subspicatin C, was isolated for the first time. This finding allowed us to propose plausible biosynthetic pathways of subspicatins A and C.

Out of equilibrium, a lack of reciprocity is the rule rather than the exception. Non-reciprocity occurs, for instance, in active matter

The motion of the robot to realize assembly work includes the part where the reuse of the motion adjusted for the real objects is effective and the part where automatic generation in the simulator is suitable. In order to smoothly teach such assembly work, teaching software that enables to combine previously used motions and perform overall adjustment of the workflow and integrated environment representation in the simulator is expected. Some teaching tools focus on the function of making robot motion in detail, and it assumes that the adjustment of the whole workflow including system layout using the real work environment. For this reason, the environmental expression is not sufficient for the above purpose. Although offline teaching tools and motion planning tools are rich in the representation of the environment, there are not many studies on a systematic reuse mechanism of motions adjusted in a real environment, including environment representations. In this paper, we present software design to solve this problem and the implementation of it as a plugin for Choreonoid. By an experiment, we confirmed that we can describe a comparatively complicated assembly work with the proposed software.

The Higgs amplitude mode is a collective excitation studied and observed in a broad class of matter, including superconductors, charge density waves, antiferromagnets, 3He p-wave superfluid, and ultracold atomic condensates. In all the observations reported thus far, the amplitude mode was excited by perturbing the condensate out of equilibrium. Studying an exciton-polariton condensate, here we report the first observation of this mode purely driven by intrinsic quantum fluctuations without such perturbations. By using an ultrahigh quality microcavity and a Raman spectrometer to maximally reject photoluminescence from the condensate, we observe weak but distinct photoluminescence at energies below the condensate emission. We identify this as the so-called ghost branches of the amplitude mode arising from quantum depletion of the condensate into this mode. These energies, as well as the overall structure of the photoluminescence spectra, are in good agreement with our theoretical analysis.

Chemical constituents of Ligularia hookeri (Asteraceae) collected in Yunnan and Sichuan Provinces in China were examined for the first time. Seven furanoeremophilanes, five of which were new, as well as known bisabolane- and eudesmane-type sesquiterpenoids, were isolated. Spectroscopic evidence indicates that the previously reported 3β-(2'-methylpropenoyloxy)furanoeremophilan-15,6β-olide should be revised to 3β-(2'-methylpropenoyloxy)furanoeremophilan-15,6α-olide.

Three natural hybrids and an introgressed individual of Ligularia were evaluated based on a combination of morphology, root chemicals, and nucleotide sequences of evolutionally neutral regions to understand the chemical outcomes of hybridization and introgression. Six previously undescribed eremophilane sesquiterpenes were isolated from hybrids between L. cyathiceps and L. lamarum/L. subspicata, and benzofurans were isolated from L. subspicata for the first time. Their structures were elucidated based on spectroscopic analyses. Some compounds produced by hybrids have not been detected in either parental species, indicating that the metabolic profile was altered by hybridization and introgression., Phytochemistry, 140, pp.69-76; 2017

Chemical compositions and internal transcribed spacer (ITS) sequences of five samples of Ligularia lamarum collected in Sichuan Province, China, were analyzed. Fourteen compounds, including four new eremophilanes and one new seco-eremophilane, were isolated and their structures were elucidated by spectroscopic methods. Intra-specific diversity in the chemical composition was found to be higher than previously known. The result of DNA analysis suggested that one of the samples was introgressed, although its chemical composition was typical of L. lamarum., Phytochemistry Letters, 20, pp.139-145; 2017

We theoretically investigate the normal state properties of a Bose–Fermi mixture with a strong attractive interaction between Fermi and Bose atoms. We extend the ordinary T-matrix approximation (TMA) with respect to Bose–Fermi pairing fluctuations, to include the Hugenholtz–Pines’ relation for all Bose Green’s functions appearing in TMA self-energy diagrams. This extension is shown to be essentially important to correctly describe the physical properties of the Bose–Fermi mixture, especially near the Bose–Einstein condensation instability. Using this improved TMA, we clarify how the formation of composite fermions affects Bose and Fermi single-particle excitation spectra, over the entire interaction strength.

Critical phenomena arise ubiquitously in various context of physics, from condensed matter, high energy physics, cosmology, to biological systems, and consist of slow and long-distance fluctuations near a phase transition or critical point. Usually, these phenomena are associated with the softening of a massive mode. Here we show that a novel, non-Hermitian-induced mechanism of critical phenomena that do not fall into this class can arise in the steady state of generic driven-dissipative many-body systems with coupled binary order parameters such as exciton-polariton condensates and driven-dissipative Bose-Einstein condensates in a double-well potential. The criticality of this ``critical exceptional point'' is attributed to the coalescence of the collective eigenmodes that convert all the thermal-and-dissipative-noise activated fluctuations to the Goldstone mode, leading to anomalously giant phase fluctuations that diverge at spatial dimensions $d\le 4$. Our dynamic renormalization group analysis shows that this gives rise to a strong-coupling fixed point at dimensions as high as $d, 16 pages, 3 figures including appendices

We propose a novel mechanism for a nonequilibrium phase transition in a $U(1)$-broken phase of an electron-hole-photon system, from a Bose-Einstein condensate of polaritons to a photon laser, induced by the non-Hermitian nature of the condensate. We show that a (uniform) steady state of the condensate can always be classified into two types, namely, arising either from lower or upper-branch polaritons. We prove (for a general model) and demonstrate (for a particular model of polaritons) that an exceptional point where the two types coalesce marks the endpoint of a first-order-like phase boundary between the two types, similar to a critical point in a liquid-gas phase transition. Since the phase transition found in this paper is not in general triggered by population inversion, our result implies that the second threshold observed in experiments is not necessarily a strong-to-weak-coupling transition, contrary to the widely-believed understanding. Although our calculation mainly aims to clarify polariton physics, our discussion is applicable to general driven-dissipative condensates composed of two complex fields., Revised version. 6 pages and 4 figures + 13 pages and 6 figures of Supplemental Material

The composition of root chemicals was examined for samples of L. cyathiceps × L. duciformis, L. duciformis × L. yunnanensis, and L. yunnanensis. Various furanoeremophilanes were isolated from a sample of L. cyathiceps × L. duciformis and found to be very similar to those isolated from L. cyathiceps. Lupeol and docosyl ferulate were isolated from L. yunnanensis, L. duciformis, and L. duciformis × L. yunnanensis.

We theoretically investigate strong-coupling properties of an ultracold Fermi gas in the BCS-BEC crossover regime in the non-equilibrium steady state, being coupled with two fermion baths. By developing a non-equilibrium strong-coupling theory based on the combined $T$-matrix approximation with the Keldysh Green's function technique, we show that the chemical potential bias applied by the two baths gives rise to the anomalous enhancement of Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) type pairing fluctuations (although the system has no spin imbalance), resulting in the re-entrant behavior of the non-equilibrium superfluid phase transition in the BCS-unitary regime. These pairing fluctuations are also found to anomalously enhance the pseudogap phenomenon. Since various non-equilibrium phenomena have recently been measured in ultracold Fermi gases, our non-equilibrium strong-coupling theory would be useful to catch up this experimental development in this research field., Comment: 21pages,15figures

We investigate strong-coupling properties of a two-dimensional ultracold Fermi gas in the normal phase. In the three-dimensional case, it has been shown that the so-called pseudogap phenomena can be well described by a (non-self-consistent) $T$-matrix approximation (TMA). In the two-dimensional case, while this strong coupling theory can explain the pseudogap phenomenon in the strong-coupling regime, it unphysically gives large pseudogap size in the crossover region, as well as in the weak-coupling regime. We show that this difficulty can be overcome when one improve TMA to include higher order pairing fluctuations within the framework of a self-consistent $T$-matrix approximation (SCTMA). The essence of this improvement is also explained. Since the observation of the BKT transition has recently been reported in a two-dimensional $^6$Li Fermi gas, our results would be useful for the study of strong-coupling physics associated with this quasi-long-range order., Comment: 7pages, 4 figures, Proceedings of QFS2016

We investigate thermodynamic properties and effects of quantum fluctuations in the Bardeen–Cooper–Schrieffer (BCS)–Bose–Einstein condensation (BEC) crossover region of a superfluid Fermi gas in the low-temperature limit. Including strong-coupling corrections within the framework of an extended T-matrix approximation, we numerically compute the isothermal compressibility $$\chi _n$$ . While quantum fluctuation effects on $$\chi _n$$ in the strong-coupling BEC regime are explained by the quantum depletion due to a repulsive interaction between tightly bound molecules, effects of self-energy shift on the Fermi chemical potential are found to enhance $$\chi _n$$ in the weak-coupling BCS region. We also show that the calculated $$\chi _n$$ agrees well with the recent experiment on a $$^6$$ Li Fermi gas done from the weak-coupling region to the unitarity limit. Our result would be useful for the study of many-body quantum corrections in the BCS–BEC crossover region of a strongly interacting Fermi superfluid.

Two samples with morphologies intermediate between Ligularia tongolensis and L. cymbulifera were collected in Desha, Sichuan Province, and one, in Pachahai, Yunnan Province, P. R. China. The DNA sequencing confirmed that the samples were hybrids of the two species. Tetradymol (1), the major compound of L. cymbulifera not found in L. tongolensis, was isolated from the hybrid samples collected at both locations, while furanoeremophilan-15-oic acid derivative 4, a compound characteristic to L. tongolensis, was found in the Pachahai hybrid but not in the Desha hybrids. Thus, the chemical consequence of hybridization can be variable. In addition, analysis of L. tongolensis samples at Pachahai indicated that introgression has been a mechanism of generating chemical diversity in the plant. Eleven compounds including three new ones were isolated.

The importance of system integration is widely recognized in robotics. This motivates the application of Model-Based Systems Engineering (MBSE) approaches to improve the development process of robo...

Chemical constituents of Ligularia hookeri (Asteraceae) collected in Yunnan and Sichuan Provinces in China were examined for the first time. Seven furanoeremophilanes, five of which were new, as well as known bisabolane- and eudesmane-type sesquiterpenoids, were isolated. Spectroscopic evidence indicates that the previously reported 3β-(2'-methylpropenoyloxy)furanoeremophilan-15,6β-olide should be revised to 3β-(2'-methylpropenoyloxy)furanoeremophilan-15,6α-olide.

We investigate theoretically nonequilibrium effects on photoluminescence and gain/absorption spectra of a driven-dissipative exciton-polariton condensate, by employing the combined Hartree-Fock-Bogoliubov theory with the generalized random phase approximation extended to the Keldysh formalism. Our calculated photoluminescence spectra is in semiquantitative agreement with experiments, where features such as a blue shift of the emission from the condensate, the appearance of the dispersionless feature of a diffusive Goldstone mode, and the suppression of the dispersive profile of the mode are obtained. We show that the nonequilibrium nature of the exciton-polariton condensate strongly suppresses the visibility of the Bogoliubov dispersion in the negative energy branch (ghost branch) in photoluminescence spectra. We also show that the trace of this branch can be captured as a hole burning effect in gain/absorption spectra. Our results indicate that the nonequilibrium nature of the exciton-polariton condensate strongly reduces quantum depletion, while a scattering channel to the ghost branch is still present., 25 pages, 21 figures