Imaginary-time matrix product state impurity solver for dynamical mean-field theory

We present a new impurity solver for dynamical mean-field theory based on imaginary-time evolution of matrix product states. This converges the self-consistency loop on the imaginary-frequency axis and obtains real-frequency information in a final real-time evolution. Relative to computations on the real-frequency axis, required bath sizes are much smaller and less entanglement is generated, so much larger systems can be studied. The power of the method is demonstrated by solutions of a three band model in the single and two-site dynamical mean-field approximation. Technical issues are discussed, including details of the method, efficiency as compared to other matrix product state based impurity solvers, bath construction and its relation to real-frequency computations and the analytic continuation problem of quantum Monte Carlo, the choice of basis in dynamical cluster approximation, and perspectives for off-diagonal hybridization functions.Comment: 8 pages + 4 pages appendix, 9 figure

An efficient perturbation theory of density matrix renormalization group

Density matrix renormalization group (DMRG) is one of the most powerful numerical methods available for many-body systems. In this work, we develop a perturbation theory of DMRG (PT-DMRG) to largely increase its accuracy in an extremely simple and efficient way. By using the canonical matrix product state (MPS) representation for the ground state of the considered system, a set of orthogonal basis functions $\left\lbrace | \psi_i \rangle \right\rbrace$ is introduced to describe the perturbations to the ground state obtained by the conventional DMRG. The Schmidt numbers of the MPS that are beyond the bond dimension cut-off are used to define such perturbation terms. The perturbed Hamiltonian is then defined as $\tilde{H}_{ij}= \langle \psi_i | \hat{H} | \psi_j \rangle$; its ground state permits to calculate physical observables with a considerably improved accuracy as compared to the original DMRG results. We benchmark the second-order perturbation theory with the help of one-dimensional Ising chain in a transverse field and the Heisenberg chain, where the precision of DMRG is shown to be improved $\rm O(10)$ times. Furthermore, for moderate length $L$ the errors of DMRG and PT-DMRG both scale linearly with $L^{-1}$. The linear relation between the dimension cut-off of DMRG and that of PT-DMRG with the same precision shows a considerable improvement of efficiency, especially for large dimension cut-off's. In thermodynamic limit we show that the errors of PT-DMRG scale with $\sqrt{L^{-1}}$. Our work suggests an effective way to define the tangent space of the ground state MPS, which may shed lights on the properties beyond the ground state. Such second-order PT-DMRG can be readily generalized to higher orders, as well as applied to the models in higher dimensions

Single-Shot Electron Diffraction using a Cold Atom Electron Source

Cold atom electron sources are a promising alternative to traditional photocathode sources for use in ultrafast electron diffraction due to greatly reduced electron temperature at creation, and the potential for a corresponding increase in brightness. Here we demonstrate single-shot, nanosecond electron diffraction from monocrystalline gold using cold electron bunches generated in a cold atom electron source. The diffraction patterns have sufficient signal to allow registration of multiple single-shot images, generating an averaged image with significantly higher signal-to-noise ratio than obtained with unregistered averaging. Reflection high-energy electron diffraction (RHEED) was also demonstrated, showing that cold atom electron sources may be useful in resolving nanosecond dynamics of nanometre scale near-surface structures.Comment: This is an author-created, un-copyedited version of an article published in Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at http://dx.doi.org/10.1088/0953-4075/48/21/21400

A Stochastic Multiscale Model of Cardiac Thin Filament Activation Using Brownian-Langevin Dynamics.

We use Brownian-Langevin dynamics principles to derive a coarse-graining multiscale myofilament model that can describe the thin-filament activation process during contraction. The model links atomistic molecular simulations of protein-protein interactions in the thin-filament regulatory unit to sarcomere-level activation dynamics. We first calculate the molecular interaction energy between tropomyosin and actin surface using Brownian dynamics simulations. This energy profile is then generalized to account for the observed tropomyosin transitions between its regulatory stable states. The generalized energy landscape then served as a basis for developing a filament-scale model using Langevin dynamics. This integrated analysis, spanning molecular to thin-filament scales, is capable of tracking the events of the tropomyosin conformational changes as it moves over the actin surface. The tropomyosin coil with flexible overlap regions between adjacent tropomyosins is represented in the model as a system of coupled stochastic ordinary differential equations. The proposed multiscale approach provides a more detailed molecular connection between tropomyosin dynamics, the trompomyosin-actin interaction-energy landscape, and the generated force by the sarcomere

Modeling effects of L-type ca(2+) current and na(+)-ca(2+) exchanger on ca(2+) trigger flux in rabbit myocytes with realistic T-tubule geometries.

The transverse tubular system of rabbit ventricular myocytes consists of cell membrane invaginations (t-tubules) that are essential for efficient cardiac excitation-contraction coupling. In this study, we investigate how t-tubule micro-anatomy, L-type Ca(2+) channel (LCC) clustering, and allosteric activation of Na(+)/Ca(2+) exchanger by L-type Ca(2+) current affects intracellular Ca(2+) dynamics. Our model includes a realistic 3D geometry of a single t-tubule and its surrounding half-sarcomeres for rabbit ventricular myocytes. The effects of spatially distributed membrane ion-transporters (LCC, Na(+)/Ca(2+) exchanger, sarcolemmal Ca(2+) pump, and sarcolemmal Ca(2+) leak), and stationary and mobile Ca(2+) buffers (troponin C, ATP, calmodulin, and Fluo-3) are also considered. We used a coupled reaction-diffusion system to describe the spatio-temporal concentration profiles of free and buffered intracellular Ca(2+). We obtained parameters from voltage-clamp protocols of L-type Ca(2+) current and line-scan recordings of Ca(2+) concentration profiles in rabbit cells, in which the sarcoplasmic reticulum is disabled. Our model results agree with experimental measurements of global Ca(2+) transient in myocytes loaded with 50 μM Fluo-3. We found that local Ca(2+) concentrations within the cytosol and sub-sarcolemma, as well as the local trigger fluxes of Ca(2+) crossing the cell membrane, are sensitive to details of t-tubule micro-structure and membrane Ca(2+) flux distribution. The model additionally predicts that local Ca(2+) trigger fluxes are at least threefold to eightfold higher than the whole-cell Ca(2+) trigger flux. We found also that the activation of allosteric Ca(2+)-binding sites on the Na(+)/Ca(2+) exchanger could provide a mechanism for regulating global and local Ca(2+) trigger fluxes in vivo. Our studies indicate that improved structural and functional models could improve our understanding of the contributions of L-type and Na(+)/Ca(2+) exchanger fluxes to intracellular Ca(2+) dynamics

Influence of Patagonian glaciers on Antarctic dust deposition during the last glacial period

Dust in the atmosphere plays a role in the transparency of the atmosphere1, the mineral nourishment of the oceans and can be used to constrain global circulation models today and in the past. Antarctic ice cores provide an 800,000 year record of changes in dust flux thought to reflect changes in the vigour of global atmospheric circulation and environmental conditions in source areas. Here for the first time we link the source of Last Glacial dust peaks in Antarctica to the gravel outwash plains of Patagonian glaciers in the Magellan area of southernmost South America. We find that there is an on-off switch in that the peaks coincide with episodes when glaciers discharge sediment directly onto outwash plains but not when they terminate in lakes. This finding helps solve several long-standing puzzles, namely: why both dust and fresh water diatom concentrations during glacial maxima are so much higher (x ~20) than at the present day; why dust peaks occur only below a certain temperature threshold; and why the decline in dust concentrations at the end of glacial cycles precedes the main phase of warming, the rise in sea level, and the reduction in southern hemisphere sea ice extent

Warren McCulloch and the British cyberneticians

Warren McCulloch was a significant influence on a number of British cyberneticians, as some British pioneers in this area were on him. He interacted regularly with most of the main figures on the British cybernetics scene, forming close friendships and collaborations with several, as well as mentoring others. Many of these interactions stemmed from a 1949 visit to London during which he gave the opening talk at the inaugural meeting of the Ratio Club, a gathering of brilliant, mainly young, British scientists working in areas related to cybernetics. This paper traces some of these relationships and interaction

Molecular and Subcellular-Scale Modeling of Nucleotide Diffusion in the Cardiac Myofilament Lattice

AbstractContractile function of cardiac cells is driven by the sliding displacement of myofilaments powered by the cycling myosin crossbridges. Critical to this process is the availability of ATP, which myosin hydrolyzes during the cross-bridge cycle. The diffusion of adenine nucleotides through the myofilament lattice has been shown to be anisotropic, with slower radial diffusion perpendicular to the filament axis relative to parallel, and is attributed to the periodic hexagonal arrangement of the thin (actin) and thick (myosin) filaments. We investigated whether atomistic-resolution details of myofilament proteins can refine coarse-grain estimates of diffusional anisotropy for adenine nucleotides in the cardiac myofibril, using homogenization theory and atomistic thin filament models from the Protein Data Bank. Our results demonstrate considerable anisotropy in ATP and ADP diffusion constants that is consistent with experimental measurements and dependent on lattice spacing and myofilament overlap. A reaction-diffusion model of the half-sarcomere further suggests that diffusional anisotropy may lead to modest adenine nucleotide gradients in the myoplasm under physiological conditions

Dynamic two-axis curvature measurement using multicore fiber Bragg gratings interrogated by arrayed waveguide gratings

We describe the use of arrayed waveguide gratings (AWGs) in the interrogation of fiber Bragg gratings (FBGs) for dynamic strain measurement. The ratiometric AWG output was calibrated in a static deflection experiment over a ±200 με range. Dynamic strain measurement was demonstrated with a FBG in a conventional single-mode fiber mounted on the surface of a vibrating cantilever and on a piezoelectric actuator, giving a resolution of 0.5 με at 2.4 kHz. We present results of this technique extended to measure the dynamic differential strain between two FBG pairs within a multicore fiber. An arbitrary cantilever oscillation of the multicore fiber was determined from curvature measurements in two orthogonal axes at 1125 Hz with a resolution of 0.05 m-1. © 2006 Optical Society of America

Apolipoprotein E Genotype-Dependent Nutrigenetic Effects to Prebiotic Inulin for Modulating Systemic Metabolism and Neuroprotection in Mice via Gut-Brain Axis

OBJECTIVE: The goal of the study was to identify the potential nutrigenetic effects to inulin, a prebiotic fiber, in mice with different human apolipoprotein E (APOE) genetic variants. Specifically, we compared responses to inulin for the potential modulation of the systemic metabolism and neuroprotection via gut-brain axis in mice with human APOE ϵ3 and ϵ4 alleles. METHOD: We performed experiments with young mice expressing the human APOE3 (E3FAD mice and APOE4 gene (E4FAD mice). We fed mice with either inulin or control diet for 16 weeks starting from 3 months of age. We determined gut microbiome diversity and composition using16s rRNA sequencing, systemic metabolism using in vivo MRI and metabolomics, and blood–brain barrier (BBB) tight junction expression using Western blot. RESULTS: In both E3FAD and E4FAD mice, inulin altered the alpha and beta diversity of the gut microbiome, increased beneficial taxa of bacteria and elevated cecal short chain fatty acid and hippocampal scyllo-inositol. E3FAD mice had altered metabolism related to tryptophan and tyrosine, while E4FAD mice had changes in the tricarboxylic acid cycle, pentose phosphate pathway, and bile acids. Differences were found in levels of brain metabolites related to oxidative stress, and levels of Claudin-1 and Claudin-5 BBB tight junction expression. DISCUSSION: We found that inulin had many similar beneficial effects in the gut and brain for both E3FAD and E4FAD mice, which may be protective for brain functions and reduce risk for neurodegeneration. . E3FAD and E4FAD mice also had distinct responses in several metabolic pathways, suggesting an APOE-dependent nutrigenetic effects in modulating systemic metabolism and neuroprotection