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An adaptive coarse graining method for signal transduction in three dimensions

Michelle N Archuleta, Jason E McDermott, Jeremy S Edwards, Haluk Resat
2012 Fundamenta Informaticae  
Building upon our earlier studies, we have developed an adaptive coarse-grained Monte Carlo method that can be used to investigate the role of diffusion, clustering and membrane corralling on receptor  ...  association and receptor-adaptor protein complex formation dynamics in three dimensions.  ...  Acknowledgments Authors would like to acknowledge Dionisios Vlachos for insightful discussions on this manuscript. This  ... 
doi:10.3233/fi-2012-720 pmid:24357890 pmcid:PMC3865981 fatcat:xl3hvdz555a75c6luorf54cwli

Mixing and Matching Simulations at Different Resolutions

Manuel N. Melo, Niculae Goga, Alexander de Vries, Herman Berendsen
2014 Biophysical Journal  
A publication introducing D-MetaD method recently appeared in The conversion from coarse-grained to atomistic models is an important step in obtaining insight about atomistic scale processes from coarse-grained  ...  For several applications _ namely those of sampling enhancement _ it is desirable to combine fine-grain (FG) and coarse-grained approaches into a single hybrid approach with an adjustable mixing parameter  ...  The conversion from coarse-grained to atomistic models is an important step in obtaining insight about atomistic scale processes from coarse-grained simulations.  ... 
doi:10.1016/j.bpj.2013.11.3546 fatcat:dkxjx2y4yfdfxbzmsfvdycuxbe

Modeling Multicellular Systems Using Subcellular Elements

T. J. Newman
2005 Mathematical Biosciences and Engineering  
We also discuss efficient algorithms for encoding the model, and give an example of a simulation of an epithelial sheet.  ...  We present here a detailed description of the model, and use successive mean-field approximations to connect it to more coarse-grained approaches, such as discrete cell-based algorithms and coupled partial  ...  The author would like to thank James Glazier, Ramon Grima, John Nagy, Kevin Schmidt, Erick Smith, and Cornelius Weijer for interesting discussions.  ... 
doi:10.3934/mbe.2005.2.613 pmid:20369943 fatcat:isnu6mjqpbaodkkt6cbfceqlpy

Modeling multi-cellular systems using sub-cellular elements [article]

T. J. Newman
2005 arXiv   pre-print
We also discuss efficient algorithms for encoding the model, and give an example of a simulation of an epithelial sheet.  ...  We present here a detailed description of the model, and use successive mean-field approximations to connect it to more coarse-grained approaches, such as discrete cell-based algorithms and coupled partial  ...  The author would like to thank James Glazier, Ramon Grima, John Nagy, Kevin Schmidt, Erick Smith, and Cornelius Weijer for interesting discussions.  ... 
arXiv:q-bio/0504028v1 fatcat:vgznu562tnbhfb3q2kr7h3ohai

A Multivariate Multiscale Fuzzy Entropy Algorithm with Application to Uterine EMG Complexity Analysis

Mosabber Ahmed, Theerasak Chanwimalueang, Sudhin Thayyil, Danilo Mandic
2016 Entropy  
This led to the multiscale entropy (MSE) method in which the multiple scales of input data are first extracted using the so-called "coarse graining" method and SampEn estimates are subsequently calculated  ...  The CMSE value at a given scale was defined as the average of the sample entropies calculated at all the different coarse-grained series in that scale, however, this method also increases the probability  ...  This limits the applicability of coarse graining based MMSE for short data.  ... 
doi:10.3390/e19010002 fatcat:fdinffhyovexzdxxc3bu7tworu

Force Distribution Analysis of Allosteric Mechanisms

Christian Seifert, Frauke Graeter
2011 Biophysical Journal  
In recent years, the development and deployment of coarse grained models for simulations of proteins has taken an enormous flight.  ...  To bring back the detail, yet only where it is needed, we have developed an integrative approach, coupling a Martini Coarse Grained model to an atomistic description of part of the system.  ...  We propose a new model for the signal transduction in the E.Coli(HtpG) and Yeast(Hsp82) homologues of Hsp90.  ... 
doi:10.1016/j.bpj.2010.12.1896 fatcat:vc26iufdwvdujb7p7p2sppsoja

Generalizable Beat-by-Beat Arrhythmia Detection by Using Weakly Supervised Deep Learning

Yang Liu, Qince Li, Runnan He, Kuanquan Wang, Jun Liu, Yongfeng Yuan, Yong Xia, Henggui Zhang
2022 Frontiers in Physiology  
In this work, we propose a weakly supervised deep learning framework for arrhythmia detection (WSDL-AD), which permits training a fine-grained (beat-by-beat) arrhythmia detector with the use of large amounts  ...  performance is evaluated on three independent benchmarks according to the recommendations from the Association for the Advancement of Medical Instrumentation (AAMI).  ...  The coarse-grained annotations usually take much less time and effort than fine-grained annotations.  ... 
doi:10.3389/fphys.2022.850951 pmid:35480046 pmcid:PMC9037749 fatcat:urav5bdoy5dcxmtq46sapessbq

TNT: Text-Conditioned Network with Transductive Inference for Few-Shot Video Classification [article]

Andrés Villa, Juan-Manuel Perez-Rua, Victor Escorcia, Vladimir Araujo, Juan Carlos Niebles, Alvaro Soto
2021 arXiv   pre-print
Current approaches mostly focus on effectively exploiting the temporal dimension in videos to improve learning under low data regimes.  ...  Furthermore, our model follows a transductive setting to improve the task-adaptation ability of the model by using the support textual descriptions and query instances to update a set of class prototypes  ...  Acknowledgements This work was supported in part by the Millennium Institute for Foundational Research on Data (IMFD).  ... 
arXiv:2106.11173v2 fatcat:dgrm6xxutrharom74tcsylfmia

Directional Locomotion of C. elegans in the Absence of External Stimuli

Margherita Peliti, John S. Chuang, Shai Shaham, Jill C. Bettinger
2013 PLoS ONE  
This directional behavior requires sensory neurons, but appears to be independent of known sensory signal-transduction pathways.  ...  Furthermore, we find that such trajectories cannot be accounted for by simple random, isotropic models of animal locomotion.  ...  Acknowledgments We thank Francis Corson for suggesting to us the 'mirror' null model, Max Heiman and David Jordan for technical advice, Yun Lu for electron microscopy, Sharon White for media preparation  ... 
doi:10.1371/journal.pone.0078535 pmid:24223821 pmcid:PMC3818405 fatcat:txj6g4rvyvdevlxjzdh7bqdclq

Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes

Stuart Collins, Michail Stamatakis, Dionisios G Vlachos
2010 BMC Bioinformatics  
It can be downloaded, printed and distributed freely for any purposes (see copyright notice below). Articles in BMC journals are listed in PubMed and archived at PubMed Central.  ...  Like all articles in BMC journals, this peer-reviewed article was published immediately upon acceptance.  ...  For example, it could also be conceivably expanded to three dimensions and applied to a whole new class of systems.  ... 
doi:10.1186/1471-2105-11-218 pmid:20429923 pmcid:PMC2868014 fatcat:wtpkdm7wangubbrvouo5ffpsd4

Can a Reduced Dimension Interface Model be More Computationally Effective than a Docking Algorithm?

Chia-Cheng Liu, Esfandiar A. Khatiblou, Jun Zhou, Steven M. Kreuzer, Joel D. Marquez, Tess J. Moon
2010 Biophysical Journal  
By summing interactions from whole regions of the solute molecule, this method solves problems that appear as nonadditivities in traditional g A approaches.  ...  fast to compute as g A methods.  ...  Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic / Coarse-Grained Multiscale Simulations Andreas Heyden.  ... 
doi:10.1016/j.bpj.2009.12.2104 fatcat:vbpwcw3yereytfuzwcue3v5quu

Interactions of Bio-Inspired Membranes with Peptides and Peptide-Mimetic Nanoparticles

Michael Sebastiano, Xiaolei Chu, Fikret Aydin, Leebyn Chong, Meenakshi Dutt
2015 AIMS Materials Science  
Via Dissipative Particle Dynamics (DPD) and implicit solvent coarse-grained (CG) Molecular Dynamics (MD) we examine the interaction of an amphiphilic cell-penetrating peptide PMLKE and its synthetic counterpart  ...  We use the DPD technique to investigate the interaction of peptide-mimetic nanoparticles, or nanopins, with a three-component membrane.  ...  Acknowledgments The authors would like to thank Jia Li for assistance in providing data for running portion of the simulations.  ... 
doi:10.3934/matersci.2015.3.303 fatcat:7lh63khxbrhd3eh3apzvizmmh4

Adaptive Multiscale Molecular Dynamics of Macromolecular Fluids

Steven O. Nielsen, Preston B. Moore, Bernd Ensing
2010 Physical Review Letters  
Until now, adaptive atomistic-coarse-grain (A/CG) molecular dynamics simulations have had very limited applicability because the on-the-fly CG !  ...  We illustrate the method with adaptive multiscale simulations of liquid hexane and of a dilute polymer solution in a theta solvent.  ...  In this Letter, we present a hybrid molecular dynamics method that implements the adaptive A/CG coupling for general molecular systems in an efficient manner.  ... 
doi:10.1103/physrevlett.105.237802 pmid:21231504 fatcat:2t7dn6y33jatzf7nmyoq7selha

Insights into intercellular receptor-ligand binding kinetics in cell communication

Chenyi An, Xiaohuan Wang, Fan Song, Jinglei Hu, Long Li
2022 Frontiers in Bioengineering and Biotechnology  
Cell-cell communication is crucial for cells to sense, respond and adapt to environmental cues and stimuli.  ...  Meanwhile, we introduce modeling methods together with experiment technologies developed for dealing with issues at different scales.  ...  In comparison, the coarse-grained MC method has advantages in both computing scale and efficiency.  ... 
doi:10.3389/fbioe.2022.953353 pmid:35837553 pmcid:PMC9273785 fatcat:4meri62khzcvded4mp7pnbyrp4

INFERENCE OF FUNCTIONAL NETWORKS OF CONDITION-SPECIFIC RESPONSE - A CASE STUDY OF QUIESCENCE IN YEAST

SUSHMITA ROY, TERRAN LANE, MARGARET WERNER-WASHBURNE, DIEGO MARTINEZ
2008 Biocomputing 2009  
The recent generation of microarray datasets for these cells 4 , gives us the first opportunity to infer a functional network that provides a fine-grained characterization of yeast quiescence.  ...  Finally, SNF1, which is crucial for quiescence, occurs exclusively among quiescent network hubs, while non-quiescent network hubs are enriched in human disease causing homologs. 12:58 Proceedings Trim  ...  Furthermore, subgraph genes that are not annotated with signal transduction (SPG3, PFK2), are all important for stationary phase.  ... 
doi:10.1142/9789812836939_0006 fatcat:ueeapm3z5jazxl5kfwhlrljvxa
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