Filters








145,766 Hits in 3.7 sec

Towards Ensemble Simulation of Complex Systems

Sergey V. Kovalchuk, Alexander V. Boukhanovsky
2015 Procedia Computer Science  
The paper presents an early-stage research which is aimed towards the development of comprehensive conceptual and technological framework for ensemble-based simulation of complex systems.  ...  Formal description of a hybrid model is provided as a core concept for ensemblebased complex system simulation.  ...  The research is performed in Advanced Computing Lab (ITMO University), which is created in the frame of 220 Decree of Russian Government, contract #11.G34.31.0019.  ... 
doi:10.1016/j.procs.2015.05.280 fatcat:57rs76pqxbdi3cylww7ojcpp6u

1P048 Structural ensemble of protein encounter complex revealed by Multiscale Essential Sampling(01B. Protein:Structure & Function,Poster)
1P048 MSESにより明らかになった蛋白質遭遇複合体構造アンサンブル(01B. 蛋白質:構造機能相関,ポスター,日本生物物理学会年会第51回(2013年度))

Satoshi Omori, Kei Moritsugu, Akinori Kidera
2013 Seibutsu Butsuri  
large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ...  The structural ensemble including the encounter complexes successfully reproduced the PRE data. Free energy landscape of the complex formation revealed the role of the encounter complexes.  ...  large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ... 
doi:10.2142/biophys.53.s113_6 fatcat:vxfc6jly4ndqbefbejp4gklqr4

Efficient Simulation of Complex Transition Pathways using a Weighted Ensemble Based String Method

Joshua L. Adelman, Michael Grabe
2013 Biophysical Journal  
From these simulations, accurate estimates of steady state conformational distributions and reaction rates can be obtained, even for systems with complex transition pathways that may involve metastable  ...  The "weighted ensemble" (WE) path sampling method is a rigorous technique for simulating this class of rare transitions.  ...  Supported by NIH grant R01 ES020693. 2578-Pos Board B597 Efficient Simulation of Complex Transition Pathways using a Weighted Ensemble Based String Method Joshua L. Adelman, Michael Grabe.  ... 
doi:10.1016/j.bpj.2012.11.2781 fatcat:ksoconw7fjczhiveqmkt5vmvae

Inactivating mutation in histone deacetylase 3 stabilizes its active conformation

Mehrnoosh Arrar, Cesar Augusto F. de Oliveira, J. Andrew McCammon
2013 Protein Science  
In previous studies, we have shown that binding of DAD and IP4 to HDAC3 significantly restricts its conformational space towards its stable ternary complex conformation, and suggest this to be the active  ...  HDAC3 is activated upon complex formation with both inositol tetraphosphate (IP4) and the deacetylase-activating domain (DAD) of multi-protein nuclear receptor corepressor complexes.  ...  Production MD simulations For each system, three independent simulations were started from different snapshots from the equilibration simulations (taken at arbitrary intervals after density of water box  ... 
doi:10.1002/pro.2317 pmid:23904210 pmcid:PMC3795489 fatcat:ujzr6ngklfga7k2pf3w2tqud6u

Visualization of uncertainty and ensemble data: Exploration of climate modeling and weather forecast data with integrated ViSUS-CDAT systems

Kristin Potter, Andrew Wilson, Peer-Timo Bremer, Dean Williams, Charles Doutriaux, Valerio Pascucci, Chris Johhson
2009 Journal of Physics, Conference Series  
To explore the relationships present in numerical predictions of the atmosphere, ensemble datasets are produced that combine time-and spatially-varying simulations generated using multiple numeric models  ...  Climate scientists and meteorologists are working towards a better understanding of atmospheric conditions and global climate change.  ...  Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04  ... 
doi:10.1088/1742-6596/180/1/012089 fatcat:zpdivospgfanhfaton2c4kbovu

1P046 Metadynamics : Implementation in GENESIS Software Package and Demonstration of the Efficient Computational Simulations of Biomolecules(01B. Protein:Structure & Function,Poster)

Raimondas Galvelis, Yuji Sugita
2013 Seibutsu Butsuri  
large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ...  The structural ensemble including the encounter complexes successfully reproduced the PRE data. Free energy landscape of the complex formation revealed the role of the encounter complexes.  ...  large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ... 
doi:10.2142/biophys.53.s113_4 fatcat:yaeoezh5ebexvpvuk5fk2lyouu

1P047 Dynamical study of capping protein by Motion Tree(01B. Protein:Structure & Function,Poster)
1P047 Motion Treeを利用したcapping proteinの動的構造解析(01B. 蛋白質:構造機能相関,ポスター,日本生物物理学会年会第51回(2013年度))

Motonori Ota, Shuichi Takeda, Yuichiro Maeda, Ryotaro Koike
2013 Seibutsu Butsuri  
large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ...  The structural ensemble including the encounter complexes successfully reproduced the PRE data. Free energy landscape of the complex formation revealed the role of the encounter complexes.  ...  large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ... 
doi:10.2142/biophys.53.s113_5 fatcat:ztswuqbuqbcvjbkqdawevu5gfi

1P045 Efficient sampling for biomolecules by the replica-permutation method(01B. Protein:Structure & Function,Poster)
1P045 レプリカ置換法による生体分子に対する効率的な構造サンプリン(01B. 蛋白質:構造機能相関,ポスター,日本生物物理学会年会第51回(2013年度))

Satoru Itoh, Hisashi Okumura
2013 Seibutsu Butsuri  
large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ...  The structural ensemble including the encounter complexes successfully reproduced the PRE data. Free energy landscape of the complex formation revealed the role of the encounter complexes.  ...  large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ... 
doi:10.2142/biophys.53.s113_3 fatcat:fcyv5zte3ffl3amsmwxhrkhmeu

1P043 Computational design of short peptide inhibitors of protein-protein interactions in intracellular signaling mediated by CRK-SH2(01B. Protein:Structure & Function,Poster)

Junya Yamagishi, Noriaki Okimoto, Takuma Kasai, Atsushi Suenaga, Mariko Okada, Akira Imamoto, Makoto Taiji
2013 Seibutsu Butsuri  
large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ...  The structural ensemble including the encounter complexes successfully reproduced the PRE data. Free energy landscape of the complex formation revealed the role of the encounter complexes.  ...  large systems and complex phenomena (i.e. folding, binding, chemical reactions, etc.).  ... 
doi:10.2142/biophys.53.s113_1 fatcat:yjlj4xb465e6tedcjp7dq7r4c4

Reconstruction of the Most Probable Folding Transition Path from All-Atom Replica Exchange Simulations, using the Dynamic String Method

Camilo A. Jimenez-Cruz, Angel E. Garcia
2013 Biophysical Journal  
From these simulations, accurate estimates of steady state conformational distributions and reaction rates can be obtained, even for systems with complex transition pathways that may involve metastable  ...  The "weighted ensemble" (WE) path sampling method is a rigorous technique for simulating this class of rare transitions.  ...  Supported by NIH grant R01 ES020693. 2578-Pos Board B597 Efficient Simulation of Complex Transition Pathways using a Weighted Ensemble Based String Method Joshua L. Adelman, Michael Grabe.  ... 
doi:10.1016/j.bpj.2012.11.2784 fatcat:zicgixufkzduril6zqd4sqkhpe

Loos: A Tool for Making New Tools for Analyzing Molecular Simulations

Tod D. Romo, Alan Grossfield
2013 Biophysical Journal  
From these simulations, accurate estimates of steady state conformational distributions and reaction rates can be obtained, even for systems with complex transition pathways that may involve metastable  ...  The "weighted ensemble" (WE) path sampling method is a rigorous technique for simulating this class of rare transitions.  ...  Supported by NIH grant R01 ES020693. 2578-Pos Board B597 Efficient Simulation of Complex Transition Pathways using a Weighted Ensemble Based String Method Joshua L. Adelman, Michael Grabe.  ... 
doi:10.1016/j.bpj.2012.11.2783 fatcat:gibfjivs65hyhij5tjebqgypsy

A Robust Framework for Adaptive Multiscale Modeling of Biopolymers using Highy Parallelizable Methods

Imad Khan
2013 Biophysical Journal  
From these simulations, accurate estimates of steady state conformational distributions and reaction rates can be obtained, even for systems with complex transition pathways that may involve metastable  ...  The "weighted ensemble" (WE) path sampling method is a rigorous technique for simulating this class of rare transitions.  ...  Supported by NIH grant R01 ES020693. 2578-Pos Board B597 Efficient Simulation of Complex Transition Pathways using a Weighted Ensemble Based String Method Joshua L. Adelman, Michael Grabe.  ... 
doi:10.1016/j.bpj.2012.11.2782 fatcat:rqpboni5wbgdjcnomnyfdpulrq

Optimized ensemble Monte Carlo simulations of dense Lennard-Jones fluids

Simon Trebst, Emanuel Gull, Matthias Troyer
2005 Journal of Chemical Physics  
Equilibration of the simulated fluid is improved by sampling an optimized histogram in radial coordinates that shifts statistical weight towards the entropic barriers between the shells of the liquid.  ...  We apply the recently developed adaptive ensemble optimization technique to simulate dense Lennard-Jones fluids and a particle-solvent model by broad-histogram Monte Carlo techniques.  ...  The free-energy landscapes of complex systems are characterized by many local minima that are separated by entropic barriers.  ... 
doi:10.1063/1.2121709 pmid:16351275 fatcat:sakevdzidjeq5iqqt2iimpbnpa

Study Of Functional Relevant Conformational Mobility Of Β-2 Adrenoreceptor By Means Of Molecular Dynamics Simulation

G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan
2014 Zenodo  
Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity.  ...  On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state.  ...  ACKNOWLEDGMENT This work was carried out with the financial support of Russian Foundation for Basic Research (grant No. 14-04-01198).  ... 
doi:10.5281/zenodo.1091102 fatcat:zwhodbmfxfelff3y55l5fjxdli

A Conceptual Approach to Complex Model Management with Generalized Modelling Patterns and Evolutionary Identification [article]

Sergey V. Kovalchuk, Oleg G. Metsker, Anastasia A. Funkner, Ilia O. Kisliakovskii, Nikolay O. Nikitin, Anna V. Kalyuzhnaya, Danila A. Vaganov, Klavdiya O. Bochenina
2018 arXiv   pre-print
Complex systems' modeling and simulation are powerful ways to investigate a multitude of natural phenomena providing extended knowledge on their structure and behavior.  ...  Growing complexity of such composite model leads to the need of specific approaches for management of such model. This need extends where the model itself becomes a complex system.  ...  Introduction Today the area of modeling and simulation of complex systems evolves rapidly.  ... 
arXiv:1809.04656v1 fatcat:wyss4tmwtzdsjmjqhhcpsfidle
« Previous Showing results 1 — 15 out of 145,766 results