Two Component Heat Diffusion Observed in CMR Manganites

We investigate the low-temperature electron, lattice, and spin dynamics of LaMnO_3 (LMO) and La_0.7Ca_0.3MnO_3 (LCMO) by resonant pump-probe reflectance spectroscopy. Probing the high-spin d-d transition as a function of time delay and probe energy, we compare the responses of the Mott insulator and the double-exchange metal to the photoexcitation. Attempts have previously been made to describe the sub-picosecond dynamics of CMR manganites in terms of a phenomenological three temperature model describing the energy transfer between the electron, lattice and spin subsystems followed by a comparatively slow exponential decay back to the ground state. However, conflicting results have been reported. Here we first show clear evidence of an additional component in the long term relaxation due to film-to-substrate heat diffusion and then develop a modified three temperature model that gives a consistent account for this feature. We confirm our interpretation by using it to deduce the bandgap in LMO. In addition we also model the non-thermal sub-picosecond dynamics, giving a full account of all observed transient features both in the insulating LMO and the metallic LCMO.Comment: 6 pages, 5 figures http://link.aps.org/doi/10.1103/PhysRevB.81.064434 v2: Abstract correcte

Many-body theory for systems with particle conversion: Extending the multiconfigurational time-dependent Hartree method

We derive a multiconfigurational time-dependent Hartree theory for systems with particle conversion. In such systems particles of one kind can convert to another kind and the total number of particles varies in time. The theory thus extends the scope of the available and successful multiconfigurational time-dependent Hartree methods -- which were solely formulated for and applied to systems with a fixed number of particles -- to new physical systems and problems. As a guiding example we treat explicitly a system where bosonic atoms can combine to form bosonic molecules and vise versa. In the theory for particle conversion, the time-dependent many-particle wavefunction is written as a sum of configurations made of a different number of particles, and assembled from sets of atomic and molecular orbitals. Both the expansion coefficients and the orbitals forming the configurations are time-dependent quantities that are fully determined according to the Dirac-Frenkel time-dependent variational principle. Particular attention is paid to the reduced density matrices of the many-particle wavefunction that appear in the theory and enter the equations of motion. There are two kinds of reduced density matrices: particle-conserving reduced density matrices which directly only couple configurations with the same number of atoms and molecules, and particle non-conserving reduced density matrices which couple configurations with a different number of atoms and molecules. Closed-form and compact equations of motion are derived for contact as well as general two-body interactions, and their properties are analyzed and discussed.Comment: 46 page

Time-dependent quantum Monte Carlo: preparation of the ground state

We study one-dimensional (1D) and two-dimensional (2D) Helium atoms using a new time-dependent quantum Monte Carlo (TDQMC) method. The TDQMC method employs random walkers, with a separate guiding wave attached to each walker. The ground state is calculated by a self-consistent solution of complex-time Schroedinger equations for the guiding waves and of equations for the velocity fields of the walkers. Our results show that the many-body wavefunction and the ground state energy of the model atoms are very close to those predicted by the standard diffusion quantum Monte Carlo method. The obtained ground state can further be used to examine correlated time-dependent processes which include, for example, interaction of atoms and molecules with external electromagnetic fields.Comment: 9 pages, 5 figure

Key challenges in designing CHO chassis platforms

Following the success of and the high demand for recombinant protein-based therapeutics during the last 25 years, the pharmaceutical industry has invested significantly in the development of novel treatments based on biologics. Mammalian cells are the major production systems for these complex biopharmaceuticals, with Chinese hamster ovary (CHO) cell lines as the most important players. Over the years, various engineering strategies and modeling approaches have been used to improve microbial production platforms, such as bacteria and yeasts, as well as to create pre-optimized chassis host strains. However, the complexity of mammalian cells curtailed the optimization of these host cells by metabolic engineering. Most of the improvements of titer and productivity were achieved by media optimization and large-scale screening of producer clones. The advances made in recent years now open the door to again consider the potential application of systems biology approaches and metabolic engineering also to CHO. The availability of a reference genome sequence, genome-scale metabolic models and the growing number of various “omics” datasets can help overcome the complexity of CHO cells and support design strategies to boost their production performance. Modular design approaches applied to engineer industrially relevant cell lines have evolved to reduce the time and effort needed for the generation of new producer cells and to allow the achievement of desired product titers and quality. Nevertheless, important steps to enable the design of a chassis platform similar to those in use in the microbial world are still missing. In this review, we highlight the importance of mammalian cellular platforms for the production of biopharmaceuticals and compare them to microbial platforms, with an emphasis on describing novel approaches and discussing still open questions that need to be resolved to reach the objective of designing enhanced modular chassis CHO cell lines.This work has been supported the Federal Ministry for Digital and Economic Affairs (bmwd), the Federal Ministry for Transport, Innovation and Technology (bmvit), the Styrian Business Promotion Agency SFG, the Standortagentur Tirol, Government of Lower Austria and ZIT - Technology Agency of the City of Vienna through the COMET-Funding Program managed by the Austrian Research Promotion Agency FFG. A.H. has been supported by the Portuguese NORTE-08-5369-FSE-000053 operation. Additional funding came from the PhD program BioToP (Biomolecular Technology of Proteins) of the Austrian Science Fund (FWF Project W1224) and MIT-Portugal PhD program (Bioengineering Systems). The funding agencies had no influence on the conduct of this research. Open Access Funding by the University of Vienna.info:eu-repo/semantics/publishedVersio

The multi-configurational time-dependent Hartree method for bosons: Many-body dynamics of bosonic systems

The evolution of Bose-Einstein condensates is amply described by the time-dependent Gross-Pitaevskii mean-field theory which assumes all bosons to reside in a single time-dependent one-particle state throughout the propagation process. In this work, we go beyond mean-field and develop an essentially-exact many-body theory for the propagation of the time-dependent Schr\"odinger equation of $N$ interacting identical bosons. In our theory, the time-dependent many-boson wavefunction is written as a sum of permanents assembled from orthogonal one-particle functions, or orbitals, where {\it both} the expansion coefficients {\it and} the permanents (orbitals) themselves are {\it time-dependent} and fully determined according to a standard time-dependent variational principle. By employing either the usual Lagrangian formulation or the Dirac-Frenkel variational principle we arrive at two sets of coupled equations-of-motion, one for the orbitals and one for the expansion coefficients. The first set comprises of first-order differential equations in time and non-linear integro-differential equations in position space, whereas the second set consists of first-order differential equations with time-dependent coefficients. We call our theory multi-configurational time-dependent Hartree for bosons, or MCTDHB($M$), where $M$ specifies the number of time-dependent orbitals used to construct the permanents. Numerical implementation of the theory is reported and illustrative numerical examples of many-body dynamics of trapped Bose-Einstein condensates are provided and discussed.Comment: 30 pages, 2 figure

Finite elements and the discrete variable representation in nonequilibrium Green's function calculations. Atomic and molecular models

In this contribution, we discuss the finite-element discrete variable representation (FE-DVR) of the nonequilibrium Green's function and its implications on the description of strongly inhomogeneous quantum systems. In detail, we show that the complementary features of FEs and the DVR allows for a notably more efficient solution of the two-time Schwinger/Keldysh/Kadanoff-Baym equations compared to a general basis approach. Particularly, the use of the FE-DVR leads to an essential speedup in computing the self-energies. As atomic and molecular examples we consider the He atom and the linear version of H$_3^+$ in one spatial dimension. For these closed-shell models we, in Hartree-Fock and second Born approximation, compute the ground-state properties and compare with the exact findings obtained from the solution of the few-particle time-dependent Schr\"odinger equation.Comment: 12 pages, 3 figures, submitted as proceedings of conference "PNGF IV

Exact quantum dynamics of bosons with finite-range time-dependent interactions of harmonic type

The exactly solvable quantum many-particle model with harmonic one- and two-particle interaction terms is extended to include time-dependency. We show that when the external trap potential and finite-range interparticle interaction have a time-dependency the exact solutions of the corresponding time-dependent many-boson Schr\"odinger equation are still available. We use these exact solutions to benchmark the recently developed multiconfigurational time-dependent Hartree method for bosons (MCTDHB) [Phys. Rev. Lett. {\bf 99}, 030402 (2007), Phys. Rev. A {\bf 77}, 033613 (2008)]. In particular, we benchmark the MCTDHB method for: (i) the ground state; (ii) the breathing many-body dynamics activated by a quench scenario where the interparticle interaction strength is suddenly turned on to a finite value; (iii) the non-equilibrium dynamic for driven scenarios where both the trap- and interparticle-interaction potentials are {\it time-dependent}. Excellent convergence of the ground state and dynamics is demonstrated. The great relevance of the self-consistency and time-adaptivity, which are the intrinsic features of the MCTDHB method, is demonstrated by contrasting the MCTDHB predictions and those obtained within the standard full configuration interaction method spanning the Fock space of the same size, but utilizing as one-particle basis set the fixed-shape eigenstates of the one-particle potential. Connections of the model's results to ultra-cold Bose-Einstein condensed systems are addressed.Comment: 31 pages, 5 figure

Recon 2.2: from reconstruction to model of human metabolism.

IntroductionThe human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort generated a consensus reconstruction, several updates have been developed.ObjectivesWe report a new consensus version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing a consensus reconstruction, further key objectives included providing more comprehensive annotation of metabolites and genes, ensuring full mass and charge balance in all reactions, and developing a model that correctly predicts ATP production on a range of carbon sources.MethodsRecon 2.2 has been developed through a combination of manual curation and automated error checking. Specific and significant manual updates include a respecification of fatty acid metabolism, oxidative phosphorylation and a coupling of the electron transport chain to ATP synthase activity. All metabolites have definitive chemical formulae and charges specified, and these are used to ensure full mass and charge reaction balancing through an automated linear programming approach. Additionally, improved integration with transcriptomics and proteomics data has been facilitated with the updated curation of relationships between genes, proteins and reactions.ResultsRecon 2.2 now represents the most predictive model of human metabolism to date as demonstrated here. Extensive manual curation has increased the reconstruction size to 5324 metabolites, 7785 reactions and 1675 associated genes, which now are mapped to a single standard. The focus upon mass and charge balancing of all reactions, along with better representation of energy generation, has produced a flux model that correctly predicts ATP yield on different carbon sources.ConclusionThrough these updates we have achieved the most complete and best annotated consensus human metabolic reconstruction available, thereby increasing the ability of this resource to provide novel insights into normal and disease states in human. The model is freely available from the Biomodels database (http://identifiers.org/biomodels.db/MODEL1603150001)