Effect of the orientational relaxation on the collective motion of patterns formed by self-propelled particles

We investigate the collective behavior of self-propelled particles (SPPs) undergoing competitive processes of pattern formation and rotational relaxation of their self-propulsion velocities. In full accordance with previous work, we observe transitions between different steady states of the SPPs caused by the intricate interplay among the involved effects of pattern formation, orientational order, and coupling between the SPP density and orientation fields. Based on rigorous analytical and numerical calculations, we prove that the rate of the orientational relaxation of the SPP velocity field is the main factor determining the steady states of the SPP system. Further, we determine the boundaries between domains in the parameter plane that delineate qualitatively different resting and moving states. In addition, we analytically calculate the collective velocity $\vec{v}$ of the SPPs and show that it perfectly agrees with our numerical results. We quantitatively demonstrate that $\vec{v}$ does not vanish upon approaching the transition boundary between the moving pattern and homogeneous steady states.Comment: 3 Figure

Thin film evolution equations from (evaporating) dewetting liquid layers to epitaxial growth

In the present contribution we review basic mathematical results for three physical systems involving self-organising solid or liquid films at solid surfaces. The films may undergo a structuring process by dewetting, evaporation/condensation or epitaxial growth, respectively. We highlight similarities and differences of the three systems based on the observation that in certain limits all of them may be described using models of similar form, i.e., time evolution equations for the film thickness profile. Those equations represent gradient dynamics characterized by mobility functions and an underlying energy functional. Two basic steps of mathematical analysis are used to compare the different system. First, we discuss the linear stability of homogeneous steady states, i.e., flat films; and second the systematics of non-trivial steady states, i.e., drop/hole states for dewetting films and quantum dot states in epitaxial growth, respectively. Our aim is to illustrate that the underlying solution structure might be very complex as in the case of epitaxial growth but can be better understood when comparing to the much simpler results for the dewetting liquid film. We furthermore show that the numerical continuation techniques employed can shed some light on this structure in a more convenient way than time-stepping methods. Finally we discuss that the usage of the employed general formulation does not only relate seemingly not related physical systems mathematically, but does as well allow to discuss model extensions in a more unified way

Note on the hydrodynamic description of thin nematic films: strong anchoring model

We discuss the long-wave hydrodynamic model for a thin film of nematic liquid crystal in the limit of strong anchoring at the free surface and at the substrate. We rigorously clarify how the elastic energy enters the evolution equation for the film thickness in order to provide a solid basis for further investigation: several conflicting models exist in the literature that predict qualitatively different behaviour. We consolidate the various approaches and show that the long-wave model derived through an asymptotic expansion of the full nemato-hydrodynamic equations with consistent boundary conditions agrees with the model one obtains by employing a thermodynamically motivated gradient dynamics formulation based on an underlying free energy functional. As a result, we find that in the case of strong anchoring the elastic distortion energy is always stabilising. To support the discussion in the main part of the paper, an appendix gives the full derivation of the evolution equation for the film thickness via asymptotic expansion

Computationally efficient flux variability analysis

<p>Abstract</p> <p>Background</p> <p>Flux variability analysis is often used to determine robustness of metabolic models in various simulation conditions. However, its use has been somehow limited by the long computation time compared to other constraint-based modeling methods.</p> <p>Results</p> <p>We present an open source implementation of flux variability analysis called fastFVA. This efficient implementation makes large-scale flux variability analysis feasible and tractable allowing more complex biological questions regarding network flexibility and robustness to be addressed.</p> <p>Conclusions</p> <p>Networks involving thousands of biochemical reactions can be analyzed within seconds, greatly expanding the utility of flux variability analysis in systems biology.</p

Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication

We aimed at investigating host-virus co-metabolism during SARS-CoV-2 infection. Therefore, we extended comprehensive sex-specific, whole-body organ resolved models of human metabolism with the necessary reactions to replicate SARS-CoV-2 in the lung as well as selected peripheral organs. Using this comprehensive host-virus model, we obtained the following key results: 1. The predicted maximal possible virus shedding rate was limited by isoleucine availability. 2. The supported initial viral load depended on the increase in CD4+ T-cells, consistent with the literature. 3. During viral infection, the whole-body metabolism changed including the blood metabolome, which agreed well with metabolomic studies from COVID-19 patients and healthy controls. 4. The virus shedding rate could be reduced by either inhibition of the guanylate kinase 1 or availability of amino acids, e.g., in the diet. 5. The virus variants differed in their maximal possible virus shedding rates, which could be inversely linked to isoleucine occurrences in the sequences. Taken together, this study presents the metabolic crosstalk between host and virus and emphasises the role of amino acid metabolism during SARS-CoV-2 infection, in particular of isoleucine. As such, it provides an example of how computational modelling can complement more canonical approaches to gain insight into host-virus crosstalk and to identify potential therapeutic strategies.Analytical BioScience

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

<p>Abstract</p> <p>Background</p> <p>Well-curated and validated network reconstructions are extremely valuable tools in systems biology. Detailed metabolic reconstructions of mammals have recently emerged, including human reconstructions. They raise the question if the various successful applications of microbial reconstructions can be replicated in complex organisms.</p> <p>Results</p> <p>We mapped the published, detailed reconstruction of human metabolism (Recon 1) to other mammals. By searching for genes homologous to Recon 1 genes within mammalian genomes, we were able to create draft metabolic reconstructions of five mammals, including the mouse. Each draft reconstruction was created in compartmentalized and non-compartmentalized version via two different approaches. Using gap-filling algorithms, we were able to produce all cellular components with three out of four versions of the mouse metabolic reconstruction. We finalized a functional model by iterative testing until it passed a predefined set of 260 validation tests. The reconstruction is the largest, most comprehensive mouse reconstruction to-date, accounting for 1,415 genes coding for 2,212 gene-associated reactions and 1,514 non-gene-associated reactions.</p> <p>We tested the mouse model for phenotype prediction capabilities. The majority of predicted essential genes were also essential in vivo. However, our non-tissue specific model was unable to predict gene essentiality for many of the metabolic genes shown to be essential in vivo. Our knockout simulation of the lipoprotein lipase gene correlated well with experimental results, suggesting that softer phenotypes can also be simulated.</p> <p>Conclusions</p> <p>We have created a high-quality mouse genome-scale metabolic reconstruction, iMM1415 (<it>Mus Musculus</it>, 1415 genes). We demonstrate that the mouse model can be used to perform phenotype simulations, similar to models of microbe metabolism. Since the mouse is an important experimental organism, this model should become an essential tool for studying metabolic phenotypes in mice, including outcomes from drug screening.</p

Fingering Instabilities in Dewetting Nanofluids

The growth of fingering patterns in dewetting nanofluids (colloidal solutions of thiol-passivated gold nanoparticles) has been followed in real time using contrast-enhanced video microscopy. The fingering instability on which we focus here arises from evaporatively-driven nucleation and growth a nanoscopically thin "precursor" solvent film behind the macroscopic contact line. We find that well-developed isotropic fingering structures only form for a narrow range of experimental parameters. Numerical simulations, based on a modification of the Monte Carlo approach introduced by Rabani et al. [Nature 426, 271 (2003)], reproduce the patterns we observe experimentally

Coulomb Correlations and Magnetic Anisotropy in ordered L10L1_0 CoPt and FePt alloys

We present results of the magneto-crystalline anisotropy energy (MAE) calculations for chemically ordered $L1_0$ CoPt and FePt alloys taking into account the effects of strong electronic correlations and spin-orbit coupling. The local spin density + Hubbard U approximation (LSDA+U) is shown to provide a consistent picture of the magnetic ground state properties when intra-atomic Coulomb correlations are included for both 3$d$ and 5$d$ elements. Our results demonstrate significant and complex contribution of correlation effects to large MAE of these material.Comment: revised version; 4 pages, 2 figure

Chiral skyrmions in thin magnetic films: new objects for magnetic storage technologies?

Axisymmetric magnetic lines of nanometer sizes (chiral vortices or skyrmions) have been predicted to exist in a large group of noncentrosymmetric crystals more than two decades ago. Recently these magnetic textures have been directly observed in nanolayers of cubic helimagnets and monolayers of magnetic metals. We develop a micromagnetic theory of chiral skyrmions in thin magnetic layers for magnetic materials with intrinsic and induced chirality. Such particle-like and stable micromagnetic objects can exist in broad ranges of applied magnetic fields including zero field. Chiral skyrmions can be used as a new type of highly mobile nanoscale data carriers