Ultracold Chemistry and its Reaction Kinetics

We study the reaction kinetics of chemical processes occurring in the ultracold regime and systematically investigate their dynamics. Quantum entanglement is found to play a key role in driving an ultracold reaction towards a dynamical equilibrium. In case of multiple concurrent reactions Hamiltonian chaos dominates the phase space dynamics in the mean field approximation.Comment: 15 pages, 5 figure

Unfrustrated Qudit Chains and their Ground States

We investigate chains of 'd' dimensional quantum spins (qudits) on a line with generic nearest neighbor interactions without translational invariance. We find the conditions under which these systems are not frustrated, i.e. when the ground states are also the common ground states of all the local terms in the Hamiltonians. The states of a quantum spin chain are naturally represented in the Matrix Product States (MPS) framework. Using imaginary time evolution in the MPS ansatz, we numerically investigate the range of parameters in which we expect the ground states to be highly entangled and find them hard to approximate using our MPS method.Comment: 5 pages, 5 figures. Typos correcte

The power of quantum systems on a line

We study the computational strength of quantum particles (each of finite dimensionality) arranged on a line. First, we prove that it is possible to perform universal adiabatic quantum computation using a one-dimensional quantum system (with 9 states per particle). This might have practical implications for experimentalists interested in constructing an adiabatic quantum computer. Building on the same construction, but with some additional technical effort and 12 states per particle, we show that the problem of approximating the ground state energy of a system composed of a line of quantum particles is QMA-complete; QMA is a quantum analogue of NP. This is in striking contrast to the fact that the analogous classical problem, namely, one-dimensional MAX-2-SAT with nearest neighbor constraints, is in P. The proof of the QMA-completeness result requires an additional idea beyond the usual techniques in the area: Not all illegal configurations can be ruled out by local checks, so instead we rule out such illegal configurations because they would, in the future, evolve into a state which can be seen locally to be illegal. Our construction implies (assuming the quantum Church-Turing thesis and that quantum computers cannot efficiently solve QMA-complete problems) that there are one-dimensional systems which take an exponential time to relax to their ground states at any temperature, making them candidates for being one-dimensional spin glasses.Comment: 21 pages. v2 has numerous corrections and clarifications, and most importantly a new author, merged from arXiv:0705.4067. v3 is the published version, with additional clarifications, publisher's version available at http://www.springerlink.co

BB rat Gimap gene expression in sorted lymphoid T and B cells

Aims: The Gimap gene family has been shown to be integral to T cell survival and development. A frameshift mutation in Gimap5, one of seven members of the Gimap family, results in lymphopenia and is a prerequisite for spontaneous type 1 diabetes (T1D) in the BioBreeding (BB) rat. While not contributing to lymphopenia, the Gimap family members proximal to Gimap5, encompassed within the Iddm39 quantitative trait locus (QTL), have been implicated in T1D. We hypothesized that expression of the Gimap family members within the Iddm39 QTL, during thymocyte development as well as in peripheral T and B cells contribute to T1D. Main methods: Cell sorted subpopulations were analyzed by quantitative real time (qRT) PCR. Key findings: Gimap4 expression was reduced in DR.(lyp/lyp) rat double negative, double positive and CD8 single positive (SP) thymocytes while expression of Gimap8, Gimap6, and Gimap7 was reduced only in CD8 SP thymocytes. Interestingly, expression of the entire Gimap gene family was reduced in DR.(lyp/lyp) rat peripheral T cells compared to non-lymphopenic, non-diabetic DR.(+/+) rats. With the exception of Gimap6. the Gimap family genes were not expressed in B cells from spleen and mesenteric lymph node (MLN). Expression of Gimap9 was only detected in hematopoietic cells of non B cell lineage such as macrophage, dendritic or NK cells. Significance: These results suggest that lack of the Gimap5 protein in the DR.(lyp/lyp) congenic rat was associated with impaired expression of the entire family of Gimap genes and may regulate T cell homeostasis in the peripheral lymphoid organs. (C) 2011 Elsevier Inc. All rights reserved

Identification of the first surrogate agonists for the G protein-coupled receptor GPR132

This is the accepted manuscript. The final version is available at http://pubs.rsc.org/en/Content/ArticleLanding/2015/RA/c5ra04804d#!divAbstract.GPR132 is an orphan Class A G protein-coupled receptor. It has been proposed to be activated by protons\ud and to regulate apoptosis, atherosclerosis and inflammation, but these results are still preliminary. In the\ud current work, we now designed and screened a focused compound library using a ?-arrestin recruitment\ud assay, and thereby identified the first disclosed surrogate GPR132 agonist 1 with a potency of 3.4 ?M.\ud This constitutes the first available pharmacological tool for the in vitro characterization of the orphan\ud receptor GPR132. The testing of 32 analogs furthermore identified a number of compounds with lower\ud activity - of which six were agonists and two were antagonists - that were used to construct preliminary\ud structure-activity relationships. Docking followed by molecular dynamics simulation of compound 1 in a\ud structural model of GPR132 displayed the putative interactions for the key ligand functionalities.M.A.S. was supported by a research scholarship from the\ud Drug Research Academy and Novo Nordisk A/S. D.E.G.\ud and H.B.-O. gratefully acknowledge financial support by\ud the Carlsberg Foundation. D.E.G. and D.S.P. gratefully\ud acknowledges financial support by the Lundbeck\ud Foundation. Nils Nyberg is acknowledged for help with\ud NMR spectroscopy. NMR equipment used in this work\ud was purchased via a grant from The Lundbeck\ud Foundation (R77-A6742)

Polynomial-time algorithm for simulation of weakly interacting quantum spin systems

We describe an algorithm that computes the ground state energy and correlation functions for 2-local Hamiltonians in which interactions between qubits are weak compared to single-qubit terms. The running time of the algorithm is polynomial in the number of qubits and the required precision. Specifically, we consider Hamiltonians of the form $H=H_0+\epsilon V$, where H_0 describes non-interacting qubits, V is a perturbation that involves arbitrary two-qubit interactions on a graph of bounded degree, and $\epsilon$ is a small parameter. The algorithm works if $|\epsilon|$ is below a certain threshold value that depends only upon the spectral gap of H_0, the maximal degree of the graph, and the maximal norm of the two-qubit interactions. The main technical ingredient of the algorithm is a generalized Kirkwood-Thomas ansatz for the ground state. The parameters of the ansatz are computed using perturbative expansions in powers of $\epsilon$. Our algorithm is closely related to the coupled cluster method used in quantum chemistry.Comment: 27 page

GRB 060313: A New Paradigm for Short-Hard Bursts?

We report the simultaneous observations of the prompt emission in the gamma-ray and hard X-ray bands by the Swift-BAT and the KONUS-Wind instruments of the short-hard burst, GRB 060313. The observations reveal multiple peaks in both the gamma-ray and hard X-ray bands suggesting a highly variable outflow from the central explosion. We also describe the early-time observations of the X-ray and UV/Optical afterglows by the Swift XRT and UVOT instruments. The combination of the X-ray and UV/Optical observations provide the most comprehensive lightcurves to date of a short-hard burst at such an early epoch. The afterglows exhibit complex structure with different decay indices and flaring. This behavior can be explained by the combination of a structured jet, radiative loss of energy, and decreasing microphysics parameters occurring in a circum-burst medium with densities varying by a factor of approximately two on a length scale of 10^17 cm. These density variations are normally associated with the environment of a massive star and inhomogeneities in its windy medium. However, the mean density of the observed medium (n approximately 10^−4 cm^3) is much less than that expected for a massive star. Although the collapse of a massive star as the origin of GRB 060313 is unlikely, the merger of a compact binary also poses problems for explaining the behavior of this burst. Two possible suggestions for explaining this scenario are: some short bursts may arise from a mechanism that does not invoke the conventional compact binary model, or soft late-time central engine activity is producing UV/optical but no X-ray flaring.Comment: 28 pages, 6 figures. Accepted for publication in ApJ. Clarifications made and typos correcte

Redshift Filtering by Swift Apparent X-ray Column Density

We remark on the utility of an observational relation between the absorption column density in excess of the Galactic absorption column density, $\Delta N_{\rm H} = N_{\rm H, fit} - N_{\rm H, gal}$, and redshift, z, determined from all 55 Swift-observed long bursts with spectroscopic redshifts as of 2006 December. The absorption column densities, $N_{\rm H, fit}$, are determined from powerlaw fits to the X-ray spectra with the absorption column density left as a free parameter. We find that higher excess absorption column densities with $\Delta N_{\rm H} > 2\times 10^{21}$ cm$^{-2}$ are only present in bursts with redshifts z$<$2. Low absorption column densities with $\Delta N_{\rm H} < 1\times 10^{21}$ cm$^{-2}$ appear preferentially in high-redshift bursts. Our interpretation is that this relation between redshift and excess column density is an observational effect resulting from the shift of the source rest-frame energy range below 1 keV out of the XRT observable energy range for high redshift bursts. We found a clear anti-correlation between $\Delta N_{\rm H}$ and z that can be used to estimate the range of the maximum redshift of an afterglow. A critical application of our finding is that rapid X-ray observations can be used to optimize the instrumentation used for ground-based optical/NIR follow-up observations. Ground-based spectroscopic redshift measurements of as many bursts as possible are crucial for GRB science.Comment: revised version including updates and the referee's comments, accepted for publication in the Astronomical Journal, 12 pages, 2 figures, 2 tables - v3 contains an update on the reference lis

The orphan G protein-coupled receptor GPR139 is activated by the peptides:Adrenocorticotropic hormone (ACTH), α-, and β-melanocyte stimulating hormone (α-MSH, and β-MSH), and the conserved core motif HFRW

GPR139 is an orphan G protein-coupled receptor that is expressed primarily in the brain. Not much is known regarding the function of GPR139. Recently we have shown that GPR139 is activated by the amino acids l-tryptophan and l-phenylalanine (EC(50) values of 220 μM and 320 μM, respectively), as well as di-peptides comprised of aromatic amino acids. This led us to hypothesize that GPR139 may be activated by peptides. Sequence alignment of the binding cavities of all class A GPCRs, revealed that the binding pocket of the melanocortin 4 receptor is similar to that of GPR139. Based on the chemogenomics principle “similar targets bind similar ligands”, we tested three known endogenous melanocortin 4 receptor agonists; adrenocorticotropic hormone (ACTH) and α- and β-melanocyte stimulating hormone (α-MSH and β-MSH) on CHO-k1 cells stably expressing the human GPR139 in a Fluo-4 Ca(2+)-assay. All three peptides, as well as their conserved core motif HFRW, were found to activate GPR139 in the low micromolar range. Moreover, we found that peptides consisting of nine or ten N-terminal residues of α-MSH activate GPR139 in the submicromolar range. α-MSH(1-9) was found to correspond to the product of a predicted cleavage site in the pre-pro-protein pro-opiomelanocortin (POMC). Our results demonstrate that GPR139 is a peptide receptor, activated by ACTH, α-MSH, β-MSH, the conserved core motif HFRW as well as a potential endogenous peptide α-MSH(1-9). Further studies are needed to determine the functional relevance of GPR139 mediated signaling by these peptides

Chaste: an open source C++ library for computational physiology and biology

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials