scholarly journals Temperature and Phase Transferable Bottom-up Coarse-Grained Models

2020 ◽  
Vol 16 (11) ◽  
pp. 6823-6842 ◽  
Author(s):  
Jaehyeok Jin ◽  
Alvin Yu ◽  
Gregory A. Voth
Keyword(s):  
Coarse Grained ◽  
Bottom Up

scholarly journals A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model

2019 ◽  
Vol 151 (4) ◽  
pp. 044111 ◽  
Author(s):  
Tanmoy Sanyal ◽  
Jeetain Mittal ◽  
M. Scott Shell
Keyword(s):  
Coarse Grained ◽  
Bottom Up ◽  
Protein Model

scholarly journals Quantitative Prediction of pH-Controlled Ionization of Oligopeptides

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Weak Acid ◽  
Coarse Grained ◽  
Quantitative Prediction ◽  
Bottom Up ◽  
Coarse Grained Model ◽  
Flexible Polymer ◽  
Acid And Base ◽  
Base Side ◽  
Capillary Zone

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their ionisation response and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Differences in ionisation response between oligopeptides and monomeric amino acids showed that electrostatic interactions between weak acid and base side chains play a key role in oligopeptide ionisation, as predicted by our model. Moreover, by comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the ionisation response and electrophoretic mobilities of various peptide sequences. Ultimately, our model is the first step towards using predictive bottom-up design of responsive ampholytes to tailor their properties as a function of charge and pH.<br>

scholarly journals The Bipolar Logic of Feedforward and Feedback Circuits

2021 ◽  
Author(s):  
Arturo Tozzi
Keyword(s):  
Visual Recognition ◽  
Coarse Grained ◽  
William Of Ockham ◽  
Top Down ◽  
Object Persistence ◽  
Bottom Up ◽  
Bipolar Mode ◽  
External Sources ◽  
Drug Resistant Epilepsy ◽  
Work Up

Instead of the conventional 0 and 1 values, bipolar reasoning uses -1, 0, +1 to describe double-sided judgements in which neutral elements are halfway between positive and negative evaluations (e.g., &ldquo;uncertain&rdquo; lies between &ldquo;impossible&rdquo; and &ldquo;totally sure&rdquo;). We discuss the state-of-the-art in bipolar logics and recall two medieval forerunners, i.e., William of Ockham and Nicholas of Autrecourt, who embodied a bipolar mode of thought that is eminently modern. Starting from the trivial observation that &ldquo;once a wheat sheaf is sealed and tied up, the packed down straws display the same orientation&rdquo;, we work up a new theory of the bipolar nature of networks, suggesting that orthodromic (i.e., feedforward, bottom-up) projections might be functionally coupled with antidromic (i.e., feedback, top-down) projections via the mathematical apparatus of presheaves/globular sets. When an entrained oscillation such as a neuronal spike propagates from A to B, changes in B might lead to changes in A, providing unexpected antidromic effects. Our account points towards the methodological feasibility of novel neural networks in which message feedback is guaranteed by backpropagation mechanisms endowed in the same feedforward circuits. Bottom-up/top-down transmission at various coarse-grained network levels provides fresh insights in far-flung scientific fields such as object persistence, memory reinforcement, visual recognition, Bayesian inferential circuits and multidimensional activity of the brain. Implying that axonal stimulation by external sources might backpropagate and modify neuronal electric oscillations, our theory also suggests testable previsions concerning the optimal location of transcranial magnetic stimulation&rsquo;s coils in patients affected by drug-resistant epilepsy.

scholarly journals Quantitative Prediction of Charge Regulation in Oligopeptides

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Weak Acid ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Quantitative Prediction ◽  
Bottom Up ◽  
Charge Regulation ◽  
Flexible Polymer ◽  
Acid And Base ◽  
Base Side

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their charge regulation and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Our model predicts differences in the charge states between oligopeptides and monomeric amino acids, showing that conformational flexibility and electrostatic interactions between weak acid and base side chains play a key role in the charge regulation. By comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the charge state of various peptide sequences. Ultimately, our model is the first step towards understanding the charge regualtion in flexible disordered proteins, and towards using predictive bottom-up design of responsive ampholytes to tailor their<br>properties as a function of charge and pH.<br>

Implicit-solvent coarse-grained modeling for polymer solutions via Mori-Zwanzig formalism

Soft Matter ◽  
2019 ◽  
Vol 15 (38) ◽  
pp. 7567-7582 ◽  
Author(s):  
Shu Wang ◽  
Zhen Li ◽  
Wenxiao Pan
Keyword(s):  
Polymer Solutions ◽  
Dynamic Properties ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Bottom Up ◽  
System P

We present a bottom-up coarse-graining (CG) method to establish implicit-solvent CG modeling for polymers in solution, which conserves the dynamic properties of the reference microscopic system.

Coarse-grained simulations of cis- and trans-polybutadiene: A bottom-up approach

2017 ◽  
Vol 146 (7) ◽  
pp. 074904 ◽  
Author(s):  
Claire A. Lemarchand ◽  
Marc Couty ◽  
Bernard Rousseau
Keyword(s):  
Coarse Grained ◽  
Bottom Up ◽  
Coarse Grained Simulations ◽  
Cis And Trans

scholarly journals Assessment of an anisotropic coarse-grained model for cis-1,4-polybutadiene: a bottom-up approach

Soft Matter ◽  
2021 ◽  
Author(s):  
Ioannis Tanis ◽  
Bernard Rousseau ◽  
Laurent Soulard ◽  
Claire A. Lemarchand
Keyword(s):  
Polymer Melts ◽  
Coarse Grained ◽  
Bottom Up ◽  
Coarse Grained Model

This work presents a generic anisotropic bottom-up coarse-grained approach for polymer melts and it is tested thoroughly and successfully.

scholarly journals Quantitative Prediction of Charge Regulation in Oligopeptides

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Weak Acid ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Quantitative Prediction ◽  
Bottom Up ◽  
Charge Regulation ◽  
Flexible Polymer ◽  
Acid And Base ◽  
Base Side

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their charge regulation and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Our model predicts differences in the charge states between oligopeptides and monomeric amino acids, showing that conformational flexibility and electrostatic interactions between weak acid and base side chains play a key role in the charge regulation. By comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the charge state of various peptide sequences. Ultimately, our model is the first step towards understanding the charge regualtion in flexible disordered proteins, and towards using predictive bottom-up design of responsive ampholytes to tailor their<br>properties as a function of charge and pH.<br>

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