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Quasi-cellular systems: stochastic simulation analysis at nanoscale range

Lorenzo Calviello, Pasquale Stano, Fabio Mavelli, Pier Luigi Luisi, Roberto Marangoni
2013 BMC Bioinformatics  
Stochastic simulation is a valuable tool in the study of biochemical reaction at nanoscale range.  ...  Quasi-cellular systems able to produce proteins directly from DNA can be obtained by encapsulating the cell-free transcription/translation system PURESYSTEM(PS) in liposomes.  ...  Acknowledgements The Authors thank Claudio Felicioli for his valuable collaboration in managing the code of the Stochastic Simulator QDC.  ... 
doi:10.1186/1471-2105-14-s7-s7 pmid:23815522 pmcid:PMC3633058 fatcat:xosocvmisrcqrjjt57gqpryoc4

Quasi-cellular systems: stochastic simulation analysis at nanoscale range

L Calviello, P Stano, F Mavelli, PL Luisi, R Marangoni
2012 EMBnet journal  
Stochastic simulation is a valuable tool in the study of biochemical reaction at nanoscale range.  ...  Quasi-cellular systems able to produce proteins directly from DNA can be obtained by encapsulating the cell-free transcription/translation system PURESYSTEM™(PS) in liposomes.  ...  Acknowledgements The Authors thank Claudio Felicioli for his valuable collaboration in managing the code of the Stochastic Simulator QDC.  ... 
doi:10.14806/ej.18.a.399 fatcat:4jarqh24indgxf47bvlctwvfgu

Self-Organizing Systems [chapter]

Wolfgang Banzhaf
2003 Encyclopedia of Physical Science and Technology  
The notion of a graph is, however, more general, and allows other agent-based systems to be simulated.  ...  Explicit simulations of such systems have been considered in the context of "Artificial Chemistries" [46] .  ...  See also -Open Systems -System Modelling -Non-equilibrium systems -Entropy -Cellular Automata -Swarm Intelligence -Biological Development and Evolution -Social Systems -Information Systems -Communication  ... 
doi:10.1016/b0-12-227410-5/00681-5 fatcat:c4cdgyk6wjbizbc7ivbqah75am

Numerical simulation methods in tribology

V.L. Popov, S.G. Psakhie
2007 Tribology International  
and their reintegration into the surfaces at the nanoscale.  ...  The processes on the nanoscale are simulated with the method of Movable Cellular Automata. r ARTICLE IN PRESS 0301-679X/$ -see front matter r  ...  and their reintegration into the surfaces at the nanoscale.  ... 
doi:10.1016/j.triboint.2006.02.020 fatcat:jkpqn4i7orbufpny3zcxjtjpde

Terahertz Band: The Last Piece of RF Spectrum Puzzle for Communication Systems

Hadeel Elayan, Osama Amin, Basem Shihada, Raed M. Shubair, Mohamed-Slim Alouini
2019 IEEE Open Journal of the Communications Society  
Moreover, the recently proposed channel models available for propagation at THz band frequencies are introduced.  ...  As such, in this work, we present an up-to-date review paper to analyze key concepts associated with the THz system architecture.  ...  These involve geometry based stochastic channel models (GSCM) as well as quasi-deterministic models.  ... 
doi:10.1109/ojcoms.2019.2953633 fatcat:sabw2nhimzcixduohzgn4e7nxa

Strategies and Tactics in Multiscale Modeling of Cell-to-Organ Systems

J.B. Bassingthwaighte, H.J. Chizeck, L.E. Atlas
2006 Proceedings of the IEEE  
This is normally accomplished at the risk of limiting the range of adaptability of the model.  ...  Each simplification of lower level complicated function reduces the range of accurate operability at the higher level model, reducing robustness, the ability to respond correctly to dynamic changes in  ...  The range of types of multiscale modeling applications is quite broad, ranging from ecological model aggregation [53] to representations of materials properties at the nanoscale.  ... 
doi:10.1109/jproc.2006.871775 pmid:20463841 pmcid:PMC2867355 fatcat:g5x23zq5qncbxmrotrqjbofuva

Computational modeling of single-cell mechanics and cytoskeletal mechanobiology

Vijay Rajagopal, William R. Holmes, Peter Vee Sin Lee
2017 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
We discuss broad areas of advancement that could accelerate research and understanding of cellular mechanobiology.  ...  Cellular cytoskeletal mechanics plays a major role in many aspects of human health from organ development to wound healing, tissue homeostasis and cancer metastasis.  ...  The quasi-static approximation is routinely used to simulate deformations at iteratively increasing loads, thus removing the velocity and acceleration variables in the equations.  ... 
doi:10.1002/wsbm.1407 pmid:29195023 pmcid:PMC5836888 fatcat:dh5nfwrumrguvid7h2n6ngmzoy

Multiscale-failure criteria of carbon nanotube systems under biaxial tension–torsion

Byeong-Woo Jeong, Jang-Keun Lim, Susan B Sinnott
2007 Nanotechnology  
Our simulations show that the strength of lattice trapping depends on the interaction range of the interatomic force fields.  ...  Through a stability analysis of crack-tip bond separation, the athermal ͑nonthermally activated͒ loads of instantaneous fracture are determined, thereby yielding the estimated lattice trapping range.  ...  ACKNOWLEDGMENT The authors acknowledge startup fund support from the College of Engineering and the Center for Computer-Aided Design ͑CCAD͒ at the University of Iowa.  ... 
doi:10.1088/0957-4484/18/48/485715 fatcat:leh6psovozdxjen2luaf6gzvda

Diffusion-Based Noise Analysis for Molecular Communication in Nanonetworks

Massimiliano Pierobon, Ian F. Akyildiz
2011 IEEE Transactions on Signal Processing  
Molecular communication (MC) is a promising bioinspired paradigm, in which molecules are used to encode, transmit and receive information at the nanoscale.  ...  The reference diffusion-based MC system for this analysis is the physical end-to-end model introduced in a previous work by the same authors.  ...  However, the analysis of the system is limited to a numerical evaluation of the simulation results using communication engineering parameters [e.g., the signal-to-noise ratio (SNR)].  ... 
doi:10.1109/tsp.2011.2114656 fatcat:yuxr7tkg4zh7rgoys3ll6izyna

Super-Resolution Microscopy Reveals Protein Spatial Reorganization in Early Innate Immune Responses

Jesse S. Aaron, Bryan Carson, Jerilyn Timlin
2011 Biophysical Journal  
This enables us to accurately investigate the interplay of at least three differently labeled cellular components [1].  ...  In order to expand the regime of applications to high-resolution colocalization studies we designed a setup which allows for STED imaging of up to three different labels (quasi-)simultaneously.  ...  Spectral CARS data sets were generated by imaging tissue sections at consecutive Raman shifts in the CH 2 stretching vibrational range.  ... 
doi:10.1016/j.bpj.2010.12.2135 fatcat:wj73plpscrecneuofishjsp334

Out-of-equilibrium dynamics of classical and quantum complex systems

Leticia F. Cugliandolo
2013 Comptes rendus. Physique  
It is illusionary to attempt to give, at least at this stage, a complete description of all non-equilibrium situations.  ...  Whenever the external or internal parameters of a physical system are varied its subsequent relaxation to equilibrium may be either impossible or take very long times.  ...  Topological defects proliferate in the disordered phase and they bind in pairs in the one with quasi long-range order and correlation functions that decay algebraically.  ... 
doi:10.1016/j.crhy.2013.09.004 fatcat:ucckrnge35aebktsh35c4vmika

A Review of Statistical Methods for Quality Improvement and Control in Nanotechnology

Jye-Chyi Lu, Shuen-Lin Jeng, Kaibo Wang
2009 Journal of QualityTechnology  
This paper reviews some instances where statistical methods have been used in nanoscale applications.  ...  Because measurements with complicated data patterns are frequently seen in experiments in nanotechnology, the collection, analysis, and modeling Vol. 41, No. 2, April 2009 FIGURE 7.  ...  At random times, the system switches from state on (or up) to state off (or down) and vice versa.  ... 
doi:10.1080/00224065.2009.11917770 fatcat:izaiqisx6nftpdmqvceghmjpgq

Shining New Light on the Structural Determinants of Cardiac Couplon Function: Insights From Ten Years of Nanoscale Microscopy

Izzy Jayasinghe, Alexander H. Clowsley, Oscar de Langen, Sonali S. Sali, David J. Crossman, Christian Soeller
2018 Frontiers in Physiology  
In particular, super-resolution and tomographic electron micrographs have revised and refined the classical views of the nanoscale geometries of couplons, t-tubules and the organisation of the principal  ...  More recently, we characterised the morphological differences between the t-tubular systems in a range of mammalian species .  ...  In addition to the above features, a handful of new observations of couplon and cellular remodelling now call for further investigation with the use of nanoscale imaging methods.  ... 
doi:10.3389/fphys.2018.01472 pmid:30405432 pmcid:PMC6204384 fatcat:6ieeujy7rfh4jbhnpexex3gvmu

Ultrastructural anatomy of nodes of Ranvier in the peripheral nervous system as revealed by STED microscopy

Elisa D'Este, Dirk Kamin, Francisco Balzarotti, Stefan W. Hell
2016 Proceedings of the National Academy of Sciences of the United States of America  
We used stimulated emission depletion (STED) superresolution microscopy to analyze the nanoscale organization of 12 glial and axonal proteins at the nodes of Ranvier of teased sciatic nerve fibers.  ...  At paranodes, both axonal proteins (betaII spectrin, Caspr) and glial proteins (neurofascin-155, ankyrin B) form periodic quasi-one-dimensional arrangements, with a high degree of interdependence between  ...  This work was supported through the Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) in Göttingen.  ... 
doi:10.1073/pnas.1619553114 pmid:28003466 pmcid:PMC5240729 fatcat:kgokag5i2bftlpnkj2cggvitce

Self-Assembly Kinetics of Microscale Components: A Parametric Evaluation

Jose M. Carballo, Nathan B. Crane
2015 Journal of microelectromechanical systems  
the rate at which stochastic interactions occur.  ...  At the microscale, stochastic interactions occur at a much slower rate. Generally, components need to travel longer distances, and do so at much slower speeds (Nathan B.  ...  APPENDIX C: MATLAB SCRIPTS C.1 Matlab Script for Image Analysis and Part-Location Recognition %% Apply Scaling/Alignment to Pickup Locations npi=IAnalysis.number_parts_per_image; C=Pickup.raw(2:(npi  ... 
doi:10.1109/jmems.2014.2354137 fatcat:w2nffzdiorfxnpquwycc3yrzei
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