scholarly journals Fast Parallel Algorithm for Large Fractal Kinetic Models with Diffusion

2018 ◽  
Author(s):  
A. A. Popov ◽  
S.-C. Lee ◽  
P. P. Kuksa ◽  
J. D. Glickson ◽  
A. A. Shestovb
Keyword(s):  
Parallel Algorithm ◽  
Kinetic Models ◽  
Chemical Kinetic ◽  
Mass Action ◽  
Mathematical Treatment ◽  
Complex Dynamic ◽  
Enzyme Model ◽  
Speed Up ◽  
A Cell ◽  
Novel Method

ABSTRACTChemical kinetic simulations are usually based on the law of mass action that applies to behavior of particles in solution. Molecular interactions in a crowded medium as in a cell, however, are not easily described by such conventional mathematical treatment. Fractal kinetics is emerging as a novel method for simulating kinetic reactions in such an environment. To date, there has not been a fast, efficient, and, more importantly, parallel algorithm for such computations. Here, we present an algorithm with several novel features for simulating large (with respect to size and time scale) fractal kinetic models. We applied the fractal kinetic technique and our algorithm to a canonical substrate-enzyme model with explicit phase-separation in the product, and achieved a speed-up of up to 8 times over previous results with reasonably tight bounds on the accuracy of the simulation. We anticipate that this technique and algorithm will have important applications to simulation of intra-cell biochemical reactions with complex dynamic behavior.

scholarly journals A novel method for processing adipose-derived stromal stem cells using a closed cell washing concentration device with a hollow fiber membrane module

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Shinji Hayashi ◽  
Rieko Yagi ◽  
Shuhei Taniguchi ◽  
Masami Uji ◽  
Hidaka Urano ◽  
...  
Keyword(s):  
Stem Cells ◽  
Hollow Fiber ◽  
Hollow Fiber Membrane ◽  
Membrane Module ◽  
Fiber Membrane ◽  
Cell Processing ◽  
Closed Cell ◽  
A Cell ◽  
Novel Method ◽  
Stromal Stem Cells

AbstractCell-assisted lipotransfer (CAL) is an advanced lipoinjection method that uses autologous lipotransfer with addition of a stromal vascular fraction (SVF) containing adipose-derived stromal stem cells (ASCs). The CAL procedure of manual isolation of cells from fat requires cell processing to be performed in clean environment. To isolate cells from fat without the need for a cell processing center, such as in a procedure in an operation theater, we developed a novel method for processing SVF using a closed cell washing concentration device (CCD) with a hollow fiber membrane module. The CCD consists of a sterilized closed circuit, bags and hollow fiber, semi-automatic device and the device allows removal of >99.97% of collagenase from SVF while maintaining sterility. The number of nucleated cells, ASCs and viability in SVF processed by this method were equivalent to those in SVF processed using conventional manual isolation. Our results suggest that the CCD system is as reliable as manual isolation and may also be useful for CAL. This approach will help in the development of regenerative medicine at clinics without a cell processing center.

Dark-Field X-Ray Microscopy of Immunogold-Labeled Cells

1996 ◽  
Vol 2 (2) ◽  
pp. 53-62 ◽  
Author(s):  
Henry N. Chapman ◽  
Jenny Fu ◽  
Chris Jacobsen ◽  
Shawn Williams
Keyword(s):  
Colloidal Gold ◽  
Dark Field Image ◽  
Dark Field ◽  
X Rays ◽  
X Ray ◽  
Scanning Transmission ◽  
A Cell ◽  
Specific Antigens ◽  
Genetic Sequences ◽  
Novel Method

The methods of immunolabeling make visible the presence of specific antigens, proteins, genetic sequences, or functions of a cell. In this paper we present examples of imaging immunolabels in a scanning transmission x-ray microscope using the novel method of dark-field contrast. Colloidal gold, or silver-enhanced colloidal gold, is used as a label, which strongly scatters x-rays. This leads to a high-contrast dark-field image of the label and reduced radiation dose to the specimen. The x-ray images are compared with electron micrographs of the same labeled, unsectioned, whole cell. It is verified that the dark-field x-ray signal is primarily due to the label and the bright-field x-ray signal, showing absorption due to carbon, is largely unaffected by the label. The label can be well visualized even when it is embedded in or laying behind dense material, such as the cell nucleus. The resolution of the images is measured to be 60 nm, without the need for computer processing. This figure includes the x-ray microscope resolution and the accuracy of the label positioning. The technique should be particularly useful for the study of relatively thick (up to 10 μm), wet, or frozen hydrated specimens.

scholarly journals Scaling High-Quality Pairwise Link-Based Similarity Retrieval on Billion-Edge Graphs

2022 ◽  
Vol 40 (4) ◽  
pp. 1-45
Author(s):  
Weiren Yu ◽  
Julie McCann ◽  
Chengyuan Zhang ◽  
Hakan Ferhatosmanoglu
Keyword(s):  
Web Search ◽  
Similarity Score ◽  
High Quality ◽  
Deterministic Method ◽  
Large Graphs ◽  
Guaranteed Accuracy ◽  
Semantic Difference ◽  
Speed Up ◽  
Novel Method ◽  
Search Quality

SimRank is an attractive link-based similarity measure used in fertile fields of Web search and sociometry. However, the existing deterministic method by Kusumoto et al. [ 24 ] for retrieving SimRank does not always produce high-quality similarity results, as it fails to accurately obtain diagonal correction matrix  D . Moreover, SimRank has a “connectivity trait” problem: increasing the number of paths between a pair of nodes would decrease its similarity score. The best-known remedy, SimRank++ [ 1 ], cannot completely fix this problem, since its score would still be zero if there are no common in-neighbors between two nodes. In this article, we study fast high-quality link-based similarity search on billion-scale graphs. (1) We first devise a “varied- D ” method to accurately compute SimRank in linear memory. We also aggregate duplicate computations, which reduces the time of [ 24 ] from quadratic to linear in the number of iterations. (2) We propose a novel “cosine-based” SimRank model to circumvent the “connectivity trait” problem. (3) To substantially speed up the partial-pairs “cosine-based” SimRank search on large graphs, we devise an efficient dimensionality reduction algorithm, PSR # , with guaranteed accuracy. (4) We give mathematical insights to the semantic difference between SimRank and its variant, and correct an argument in [ 24 ] that “if D is replaced by a scaled identity matrix (1-Ɣ)I, their top-K rankings will not be affected much”. (5) We propose a novel method that can accurately convert from Li et al.  SimRank ~{S} to Jeh and Widom’s SimRank S . (6) We propose GSR # , a generalisation of our “cosine-based” SimRank model, to quantify pairwise similarities across two distinct graphs, unlike SimRank that would assess nodes across two graphs as completely dissimilar. Extensive experiments on various datasets demonstrate the superiority of our proposed approaches in terms of high search quality, computational efficiency, accuracy, and scalability on billion-edge graphs.

Magnetic nanoparticles for the measurement of cell mechanics using force-induced remnant magnetization spectroscopy

Nanoscale ◽  
2020 ◽  
Vol 12 (27) ◽  
pp. 14573-14580
Author(s):  
Min Xu ◽  
Xueyan Feng ◽  
Feng Feng ◽  
Hantao Pei ◽  
Ruping Liu ◽  
...  
Keyword(s):  
Magnetic Nanoparticles ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cell Mechanics ◽  
Magnetic Nanoparticle ◽  
Adhesion Force ◽  
Force Spectroscopy ◽  
Remnant Magnetization ◽  
A Cell ◽  
Novel Method

Interactions of magnetic nanoparticles with cells were investigated from a cell mechanics perspective, and magnetic nanoparticle-based force spectroscopy was developed as a novel method to measure the adhesion force among various cancer cell lines.

Restrictions on chemical kinetic models

1976 ◽  
Vol 65 (1) ◽  
pp. 284-292 ◽  
Author(s):  
David Wallwork ◽  
Alan S. Perelson
Keyword(s):  
Kinetic Models ◽  
Chemical Kinetic

scholarly journals Arabidopsis plants perform arithmetic division to prevent starvation at night

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Antonio Scialdone ◽  
Sam T Mugford ◽  
Doreen Feike ◽  
Alastair Skeffington ◽  
Philippa Borrill ◽  
...  
Keyword(s):  
Biological System ◽  
Kinetic Models ◽  
Starch Content ◽  
Chemical Kinetic ◽  
Light Period ◽  
Starch Degradation ◽  
Degradation Pathways ◽  
Night Time ◽  
Expected Time ◽  
Time Period

Photosynthetic starch reserves that accumulate in Arabidopsis leaves during the day decrease approximately linearly with time at night to support metabolism and growth. We find that the rate of decrease is adjusted to accommodate variation in the time of onset of darkness and starch content, such that reserves last almost precisely until dawn. Generation of these dynamics therefore requires an arithmetic division computation between the starch content and expected time to dawn. We introduce two novel chemical kinetic models capable of implementing analog arithmetic division. Predictions from the models are successfully tested in plants perturbed by a night-time light period or by mutations in starch degradation pathways. Our experiments indicate which components of the starch degradation apparatus may be important for appropriate arithmetic division. Our results are potentially relevant for any biological system dependent on a food reserve for survival over a predictable time period.

Computer Construction of Detailed Chemical Kinetic Models for Gas-Phase Reactors

2001 ◽  
Vol 40 (23) ◽  
pp. 5362-5370 ◽  
Author(s):  
W. H. Green ◽  
P. I. Barton ◽  
B. Bhattacharjee ◽  
D. M. Matheu ◽  
D. A. Schwer ◽  
...  
Keyword(s):  
Gas Phase ◽  
Kinetic Models ◽  
Chemical Kinetic ◽  
Detailed Chemical
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