Detecting vapour bubbles in simulations of metastable water

International audienceThe investigation of cavitation in metastable liquids with molecular simulations requires an appropriate definition of the volume of the vapour bubble forming within the metastable liquid phase. Commonly used approaches for bubble detection exhibit two significant flaws: first, when applied to water they often identify the voids within the hydrogen bond network as bubbles thus masking the signature of emerging bubbles and, second, they lack thermodynamic consistency. Here, we present two grid-based methods, the M-method and the V-method, to detect bubbles in metastable water specifically designed to address these shortcomings. The M-method incorporates information about neighbouring grid cells to distinguish between liquid- and vapour-like cells, which allows for a very sensitive detection of small bubbles and high spatial resolution of the detected bubbles. The V-method is calibrated such that its estimates for the bubble volume correspond to the average change in system volume and are thus thermodynamically consistent. Both methods are computationally inexpensive such that they can be used in molecular dynamics and Monte Carlo simulations of cavitation. We illustrate them by computing the free energy barrier and the size of the critical bubble for cavitation in water at negative pressure

MetaAvatar: Learning Animatable Clothed Human Models from Few Depth Images

In this paper, we aim to create generalizable and controllable neural signed distance fields (SDFs) that represent clothed humans from monocular depth observations. Recent advances in deep learning, especially neural implicit representations, have enabled human shape reconstruction and controllable avatar generation from different sensor inputs. However, to generate realistic cloth deformations from novel input poses, watertight meshes or dense full-body scans are usually needed as inputs. Furthermore, due to the difficulty of effectively modeling pose-dependent cloth deformations for diverse body shapes and cloth types, existing approaches resort to per-subject/cloth-type optimization from scratch, which is computationally expensive. In contrast, we propose an approach that can quickly generate realistic clothed human avatars, represented as controllable neural SDFs, given only monocular depth images. We achieve this by using meta-learning to learn an initialization of a hypernetwork that predicts the parameters of neural SDFs. The hypernetwork is conditioned on human poses and represents a clothed neural avatar that deforms non-rigidly according to the input poses. Meanwhile, it is meta-learned to effectively incorporate priors of diverse body shapes and cloth types and thus can be much faster to fine-tune, compared to models trained from scratch. We qualitatively and quantitatively show that our approach outperforms state-of-the-art approaches that require complete meshes as inputs while our approach requires only depth frames as inputs and runs orders of magnitudes faster. Furthermore, we demonstrate that our meta-learned hypernetwork is very robust, being the first to generate avatars with realistic dynamic cloth deformations given as few as 8 monocular depth frames.Comment: 17 pages, 9 figures. Project page: https://neuralbodies.github.io/metavatar

qqqbar to qqqbar and qqbarqbar to qqbarqbar Elastic Scatterings and Thermalization of Quark Matter and Antiquark Matter

Thermalization of quark matter and antiquark matter is studied with quark-quark-antiquark as well as quark-antiquark-antiquark elastic scatterings. Squared amplitudes of qqqbar to qqqbar and qqbarqbar to qqbarqbar at order alpha_s^4 are derived in perturbative QCD. Solved by a new technique, solutions of transport equations with the squared amplitudes indicate that the scatterings qqqbar to qqqbar and qqbarqbar to qqbarqbar shorten the thermalization time of quark matter and antiquark matter. It is emphasized that three-parton and other multi-parton scatterings become important at the high parton number density achieved in RHIC Au-Au collisions.Comment: 14 pages, 5 figures, Late

Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

<p>Abstract</p> <p>Background</p> <p>Recent advances in massively parallel sequencing have increased the depth at which T cell receptor (TCR) repertoires can be probed by >3log10, allowing for saturation sequencing of immune repertoires. The resolution of this sequencing is dependent on its accuracy, and direct assessments of the errors formed during high throughput repertoire analyses are limited.</p> <p>Results</p> <p>We analyzed 3 monoclonal TCR from TCR transgenic, Rag^-/-mice using Illumina^®sequencing. A total of 27 sequencing reactions were performed for each TCR using a trifurcating design in which samples were divided into 3 at significant processing junctures. More than 20 million complementarity determining region (CDR) 3 sequences were analyzed. Filtering for lower quality sequences diminished but did not eliminate sequence errors, which occurred within 1-6% of sequences. Erroneous sequences were pre-dominantly of correct length and contained single nucleotide substitutions. Rates of specific substitutions varied dramatically in a position-dependent manner. Four substitutions, all purine-pyrimidine transversions, predominated. Solid phase amplification and sequencing rather than liquid sample amplification and preparation appeared to be the primary sources of error. Analysis of polyclonal repertoires demonstrated the impact of error accumulation on data parameters.</p> <p>Conclusions</p> <p>Caution is needed in interpreting repertoire data due to potential contamination with mis-sequence reads. However, a high association of errors with phred score, high relatedness of erroneous sequences with the parental sequence, dominance of specific nt substitutions, and skewed ratio of forward to reverse reads among erroneous sequences indicate approaches to filter erroneous sequences from repertoire data sets.</p

Superior Lithium Storage Capacity of α‐MnS Nanoparticles Embedded in S‐Doped Carbonaceous Mesoporous Frameworks

Herein, a Mn‐based metal–organic framework is used as a precursor to obtain well‐defined α‐MnS/S‐doped C microrod composites. Ultrasmall α‐MnS nanoparticles (3–5 nm) uniformly embedded in S‐doped carbonaceous mesoporous frameworks (α‐MnS/SCMFs) are obtained in a simple sulfidation reaction. As‐obtained α‐MnS/SCMFs shows outstanding lithium storage performance, with a specific capacity of 1383 mAh g−1 in the 300th cycle or 1500 mAh g−1 in the 120th cycle (at 200 mA g−1) using copper or nickel foil as the current collector, respectively. The significant (pseudo)capacitive contribution and the stable composite structure of the electrodes result in impressive rate capabilities and outstanding long‐term cycling stability. Importantly, in situ X‐ray diffraction measurements studies on electrodes employing various metal foils/disks as current collector reveal the occurrence of the conversion reaction of CuS at (de)lithiation process when using copper foil as the current collector. This constitutes the first report of the reaction mechanism for α‐MnS, eventually forming metallic Mn and Li2S. In situ dilatometry measurements demonstrate that the peculiar structure of α‐MnS/SCMFs effectively restrains the electrode volume variation upon repeated (dis)charge processes. Finally, α‐MnS/SCMFs electrodes present an impressive performance when coupled in a full cell with commercial LiMn1/3Co1/3Ni1/3O2 cathodes

Event by Event Analysis and Entropy of Multiparticle Systems

The coincidence method of measuring the entropy of a system, proposed some time ago by Ma, is generalized to include systems out of equilibrium. It is suggested that the method can be adapted to analyze multiparticle states produced in high-energy collisions.Comment: 13 pages, 2 figure

Characterizing groundwater flow and heat transport in fractured rock using Fiber-Optic Distributed Temperature Sensing

International audienceWe show how fully distributed space-time measurements with Fiber-Optic Distributed Temperature Sensing (FO-DTS) can be used to investigate groundwater flow and heat transport in fractured media. Heat injection experiments are combined with temperature measurements along fiber-optic cables installed in boreholes. Thermal dilution tests are shown to enable detection of cross-flowing fractures and quantification of the cross flow rate. A cross borehole thermal tracer test is then analyzed to identify fracture zones that are in hydraulic connection between boreholes and to estimate spatially distributed temperature breakthrough in each fracture zone. This provides a significant improvement compared to classical tracer tests, for which concentration data are usually integrated over the whole abstraction borehole. However, despite providing some complementary results, we find that the main contributive fracture for heat transport is different to that for a solute tracer

Nucleosomes in serum of patients with early cerebral stroke

Background: Nucleosomes are cell death products that are elevated in serum of patients with diseases that are associated with massive cell destruction. We investigated the kinetics of circulating nucleosomes after cerebral stroke and their correlation with the clinical status. Methods: In total, we analyzed nucleosomes by ELISA in sera of 63 patients with early stroke daily during the first week after onset. For correlation with the clinical pathology, patients were grouped into those with medium to slight functional impairment (Barthel Index BI >= 50) and those with severe functional impairment (BI = 50 showed a continuous increase in nucleosomes until day 5 (median: 523 arbitrary units, AU) followed by a slow decline. In contrast, patients with BI = 50 (497 AU; p = 0.031). Concerning the infarction volume, nucleosomes showed significant correlations for the concentrations on day 3 (r = 0.43; p = 0.001) and for the area under the curve (r = 0.34; p = 0.016). Conclusion: Even if nucleosomes are nonspecific cell death markers, their release into serum after cerebral stroke correlates with the gross functional status as well as with the infarction volume and can be considered as biochemical correlative to the severity of stroke. Copyright (c) 2006 S. Karger AG, Basel

Photoluminescent arginine‐functionalized polycitrate with enhanced cell activity and hemocompatibility for live cell bioimaging

Development of biodegradable and highly biocompatible polymer with intrinsical photoluminescence and high photostability for real‐time live cell bioimaging has attracted much attention recently. Here, a biodegradable and amphiphilic poly (citrate)‐co‐poly (ethylene glycol) (PEG) grafted with arginine (PCGA) polymer with intrinsical fluorescence was synthesized for targeted live cell bioimaging. The physicochemical structure, photoluminescent properties, hemocompatibility, cytotoxicity, and fluorescent bioimaging studies in live cells were determined in detail. PCGA showed a significantly high hemocompatibility, low cytotoxicity, and excellent photostability, which allows for imaging the live cells attachment and proliferation. Furthermore, PCGA could efficiently enhance cell attachment and proliferation due to the presence of arginine, suggesting their high cellular biocompatibility. Importantly, PCGA could selectively stain the lysosome in cells. Our results demonstrated that the amino acid‐based polymer functionalization may be an important strategy to develop multifunctional biomaterials with enhanced biocompatibility for targeted bioimaging, cancer therapy, and regenerative medicine. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 3175–3184, 2018.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146603/1/jbma36512.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146603/2/jbma36512_am.pd