Subspace Variational Quantum Simulator

Quantum simulation is one of the key applications of quantum computing, which can accelerate research and development in chemistry, material science, etc. Here, we propose an efficient method to simulate the time evolution driven by a static Hamiltonian, named subspace variational quantum simulator (SVQS). SVQS employs the subspace-search variational eigensolver (SSVQE) to find a low-energy subspace and further extends it to simulate dynamics within the low-energy subspace. More precisely, using a parameterized quantum circuit, the low-energy subspace of interest is encoded into a computational subspace spanned by a set of computational basis, where information processing can be easily done. After the information processing, the computational subspace is decoded to the original low-energy subspace. This allows us to simulate the dynamics of low-energy subspace with lower overhead compared to existing schemes. While the dimension is restricted for feasibility on near-term quantum devices, the idea is similar to quantum phase estimation and its applications such as quantum linear system solver and quantum metropolis sampling. Because of this simplicity, we can successfully demonstrate the proposed method on the actual quantum device using Regetti Quantum Cloud Service. Furthermore, we propose a variational initial state preparation for SVQS, where the initial states are searched from the simulatable eigensubspace. Finally, we demonstrate SVQS on Rigetti Quantum Cloud Service

Emergence of diversity in a model ecosystem

The biological requirements for an ecosystem to develop and maintain species diversity are in general unknown. Here we consider a model ecosystem of sessile and mutually excluding organisms competing for space [Mathiesen et al. Phys. Rev. Lett. 107, 188101 (2011)]. The competition is controlled by an interaction network with fixed links chosen by a Bernoulli process. New species are introduced in the system at a predefined rate. In the limit of small introduction rates, the system becomes bistable and can undergo a phase transition from a state of low diversity to high diversity. We suggest that patches of isolated meta-populations formed by the collapse of cyclic relations are essential for the transition to the state of high diversity.Comment: 7 pages, 6 figures. Accepted for publication in PRE. Typos corrected, Fig.3A and Fig.6 update

Continuous monitoring of near-bottom mesoplankton communities in the East China Sea during a series of typhoons

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Journal of Oceanography 71 (2015): 115-124, doi:10.1007/s10872-014-0268-y.Typhoons are a common feature of summer and autumn months in the East China Sea. These events often promote phytoplankton growth in surface waters as a result of upwelling and transport of nutrients, but their effects on sub-surface waters and ecosystems are little known. Furthermore, biological studies tend to focus on phytoplankton (using chlorophyll a assays), rather than on heterotrophic zooplankton. Indeed, measurements of biological and physicochemical changes induced by the storms are difficult to perform and risky, using standard shipboard sampling techniques. Using a camera mounted on an underwater, cabled observatory system in shallow coastal waters of Okinawa, Japan, we collected the first continuous, in-situ observations of the near-bottom, mesoplankton community during a series of typhoons. An increase in diatoms and radiolarians was found during all typhoons, whereas the response of larger zooplankton groups was variable between typhoons. A bloom of Trichodesmium cyanobacteria and diatoms was seen after a series of typhoons, while the total chlorophyll a concentration remained nearly unchanged at the sampling location. These findings shed new light on short-term responses of sub-surface ecosystems during typhoons.This work was funded by the Special Framework budget, Okinawa Promotion for Education and Research Project awarded to OIST for the 2012 fiscal year.2015-12-3

Non-ideal behavior of intramolecular structure factor of dilute polymers in a theta solvent

We study the configurational properties of single polymers in a theta solvent by Monte Carlo simulation of the bond fluctuation model. The intramolecular structure factor at the theta point is found to be distinctively different from that of the ideal chain. The structure factor shows a hump around $q\sim 5/R_g$ and a dip around $q\sim 10/R_g$ in the Kratky plot with $R_g$ being the radius of gyration. This feature is apparently similar to that in a melt. The theoretical expression by the simple perturbation expansion to the first order in terms of the Mayer function can be fitted to the obtained structure factor quite well, but the second virial coefficient cannot be set to zero.Comment: 8 pages, 7figure

Circuit architecture explains functional similarity of bacterial heat shock responses

Heat shock response is a stress response to temperature changes and a consecutive increase in amounts of unfolded proteins. To restore homeostasis, cells upregulate chaperones facilitating protein folding by means of transcription factors (TF). We here investigate two heat shock systems: one characteristic to gram negative bacteria, mediated by transcriptional activator sigma32 in E. coli, and another characteristic to gram positive bacteria, mediated by transcriptional repressor HrcA in L. lactis. We construct simple mathematical model of the two systems focusing on the negative feedbacks, where free chaperons suppress sigma32 activation in the former, while they activate HrcA repression in the latter. We demonstrate that both systems, in spite of the difference at the TF regulation level, are capable of showing very similar heat shock dynamics. We find that differences in regulation impose distinct constrains on chaperone-TF binding affinities: the binding constant of free sigma32 to chaperon DnaK, known to be in 100 nM range, set the lower limit of amount of free chaperon that the system can sense the change at the heat shock, while the binding affinity of HrcA to chaperon GroE set the upper limit and have to be rather large extending into the micromolar range.Comment: 17 pages, 5 figure

Ecosystems with mutually exclusive interactions self-organize to a state of high diversity

Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large species diversity on long time scales are in general unknown. Using lichen communities as an example, we propose a model for the evolution of mutually excluding organisms that compete for space. We suggest that chain-like or cyclic invasions involving three or more species open for creation of spatially separated sub-populations that subsequently can lead to increased diversity. In contrast to its non-spatial counterpart, our model predicts robust co-existence of a large number of species, in accordance with observations on lichen growth. It is demonstrated that large species diversity can be obtained on evolutionary timescales, provided that interactions between species have spatial constraints. In particular, a phase transition to a sustainable state of high diversity is identified.Comment: 4 pages, 4 figure