130 research outputs found
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 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(), where 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 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)
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