Folding of small knotted proteins: Insights from a mean field coarse-grained model

2015 ◽  
Vol 143 (24) ◽  
pp. 243121 ◽  
Author(s):  
Saeed Najafi ◽  
Raffaello Potestio
Keyword(s):  
Mean Field ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Knotted Proteins

scholarly journals A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

2014 ◽  
Vol 20 (8) ◽  
Author(s):  
Adam Liwo ◽  
Maciej Baranowski ◽  
Cezary Czaplewski ◽  
Ewa Gołaś ◽  
Yi He ◽  
...  
Keyword(s):  
Mean Field ◽  
Coarse Grained ◽  
Biological Macromolecules ◽  
Coarse Grained Model

scholarly journals Coarse-Grained Modelling and Temperature Effect on the Morphology of PS-b-PI Copolymer

Polymers ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1008 ◽  
Author(s):  
Natthiti Chiangraeng ◽  
Vannajan Sanghiran Lee ◽  
Piyarat Nimmanpipug
Keyword(s):  
Density Functional ◽  
Spatial Organization ◽  
Mean Field ◽  
Md Simulations ◽  
Coarse Grained ◽  
Functional Theory ◽  
Coarse Grained Model ◽  
Mesoscopic Models ◽  
Aggregate Morphology ◽  
Mesoscopic Simulations

Spontaneous spatial organization behavior and the aggregate morphology of polystyrene-block-polyisoprene (PS-b-PI) copolymer were investigated. Molecular dynamic (MD) and mesoscopic simulations using the dynamic of mean field density functional theory (DDF) were adopted to investigate the morphology changes exhibited by this block copolymer (BCP). In the mesoscopic simulations, several atoms in repeating units were grouped together into a bead representing styrene or isoprene segments as a coarse-grained model. Inter-bead interactions and essential parameters for mesoscopic models were optimized from MD simulations. Study indicated that morphology alternations can be induced in this system at annealing temperature of 393, 493, and 533 K. From our simulations, lamellar, bicontinuous, and hexagonally packed cylindrical equilibrium morphologies were achieved. Our simulated morphologies agree well with the reported experimental evidence at the selected temperature. The process of aggregate formation and morphology evolution were concretely clarified.

Grand-Reaction Method for Simulations of Ionization Equilibria and Ion Partitioning in a Broad Range of pH and Ionic Strength

2019 ◽  
Author(s):  
Jonas Landsgesell ◽  
Oleg Rud ◽  
Pascal Hebbeker ◽  
Raju Lunkad ◽  
Peter Košovan ◽  
...  
Keyword(s):  
Mean Field ◽  
Coarse Grained ◽  
Reactive System ◽  
Acid Base ◽  
Buffer Solution ◽  
Reaction Method ◽  
Ionization Equilibria ◽  
Coarse Grained Simulations ◽  
Ph Range ◽  
Weak Polyelectrolytes

We introduce the grand-reaction method for coarse-grained simulations of acid-base equilibria in a system coupled to a reservoir at a given pH and concentration of added salt. It can be viewed as an extension of the constant-pH method and the reaction ensemble, combining explicit simulations of reactions within the system, and grand-canonical exchange of particles with the reservoir. Unlike the previously introduced methods, the grand-reaction method is applicable to acid-base equilibria in the whole pH range because it avoids known artifacts. However, the method is more general, and can be used for simulations of any reactive system coupled to a reservoir of a known composition. To demonstrate the advantages of the grand-reaction method, we simulated a model system: A solution of weak polyelectrolytes in equilibrium with a buffer solution. By carefully accounting for the exchange of all constituents, the method ensures that all chemical potentials are equal in the system and in the multi-component reservoir. Thus, the grand-reaction method is able to predict non-monotonic swelling of weak polyelectrolytes as a function of pH, that has been known from mean-field predictions and from experiments but has never been observed in coarse-grained simulations. Finally, we outline possible extensions and further generalizations of the method, and provide a set of guidelines to enable safe usage of the method by a broad community of users.<br><br>

scholarly journals Mean-Field Models for EEG/MEG: From Oscillations to Waves

2021 ◽  
Author(s):  
Áine Byrne ◽  
James Ross ◽  
Rachel Nicks ◽  
Stephen Coombes
Keyword(s):  
Gap Junction ◽  
Large Scale ◽  
Mean Field ◽  
Coarse Grained ◽  
Neural Mass Model ◽  
Neuron Network ◽  
Mass Model ◽  
Mean Field Model ◽  
Neural Mass ◽  
The Rich

AbstractNeural mass models have been used since the 1970s to model the coarse-grained activity of large populations of neurons. They have proven especially fruitful for understanding brain rhythms. However, although motivated by neurobiological considerations they are phenomenological in nature, and cannot hope to recreate some of the rich repertoire of responses seen in real neuronal tissue. Here we consider a simple spiking neuron network model that has recently been shown to admit an exact mean-field description for both synaptic and gap-junction interactions. The mean-field model takes a similar form to a standard neural mass model, with an additional dynamical equation to describe the evolution of within-population synchrony. As well as reviewing the origins of this next generation mass model we discuss its extension to describe an idealised spatially extended planar cortex. To emphasise the usefulness of this model for EEG/MEG modelling we show how it can be used to uncover the role of local gap-junction coupling in shaping large scale synaptic waves.

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