scholarly journals A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature

2021 ◽  
Vol 154 (4) ◽  
pp. 044105
Author(s):  
Jaehyeok Jin ◽  
Alexander J. Pak ◽  
Yining Han ◽  
Gregory A. Voth
Keyword(s):  
Low Temperature ◽  
Structural Properties ◽  
Coarse Grained ◽  
Many Body ◽  
Bottom Up ◽  
Coarse Grained Model ◽  
Water Bottom

Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide

2018 ◽  
Vol 20 (36) ◽  
pp. 23386-23396 ◽  
Author(s):  
Pu Du ◽  
Steven W. Rick ◽  
Revati Kumar
Keyword(s):  
Coarse Grained ◽  
Many Body ◽  
Coarse Grained Model

Coarse-grained model of DMA, containing the basic motif of the peptoid backbone, based on short ranged many-body ranged interactions.

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 Concentration-dependent swelling and structure of ionic microgels: simulation and theory of a coarse-grained model

Soft Matter ◽  
2018 ◽  
Vol 14 (22) ◽  
pp. 4530-4540 ◽  
Author(s):  
Tyler J. Weyer ◽  
Alan R. Denton
Keyword(s):  
Structural Properties ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Coarse Grained Model

Swelling and structural properties of ionic microgel suspensions are described by a coarse-grained model that includes elastic and electrostatic interactions.

A minimal coarse-grained model for the low-frequency normal mode analysis of icosahedral viral capsids

Soft Matter ◽  
2020 ◽  
Vol 16 (14) ◽  
pp. 3443-3455 ◽  
Author(s):  
M. Martín-Bravo ◽  
J. M. Gomez Llorente ◽  
J. Hernández-Rojas
Keyword(s):  
Structural Properties ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Low Frequency ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Viral Capsids ◽  
Mode Spectrum ◽  
Coarse Grained Model

A minimal coarse-grained model unveils relevant structural properties of icosahedral viral capsids when fitted to reproduce their low-frequency normal-mode spectrum.

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 pH-Controlled Ionization of Oligoampholytes

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 Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

2015 ◽  
Vol 142 (23) ◽  
pp. 234901 ◽  
Author(s):  
Benedict E. K. Snodin ◽  
Ferdinando Randisi ◽  
Majid Mosayebi ◽  
Petr Šulc ◽  
John S. Schreck ◽  
...  
Keyword(s):  
Structural Properties ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Salt Dependence
Sign in / Sign up

Export Citation Format

Share Document