scholarly journals Coarse-Grained Modeling of Charged Colloidal Suspensions: From Poisson–Boltzmann Theory to Effective Interactions

2014 ◽  
pp. 221-240
Keyword(s):  
Colloidal Suspensions ◽  
Coarse Grained ◽  
Effective Interactions ◽  
Poisson Boltzmann

scholarly journals Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model

2021 ◽  
Vol 8 ◽  
Author(s):  
Chengwei Zhang ◽  
Jing Huang
Keyword(s):  
Atomistic Simulation ◽  
Umbrella Sampling ◽  
Coarse Grained ◽  
Basic Unit ◽  
Time Dimension ◽  
Effective Interactions ◽  
Coarse Grained Model ◽  
Explicit Solvent ◽  
Chromatin Folding ◽  
Free Energy Landscapes

The organization of genomes in space and time dimension plays an important role in gene expression and regulation. Chromatin folding occurs in a dynamic, structured way that is subject to biophysical rules and biological processes. Nucleosomes are the basic unit of chromatin in living cells, and here we report on the effective interactions between two nucleosomes in physiological conditions using explicit-solvent all-atom simulations. Free energy landscapes derived from umbrella sampling simulations agree well with recent experimental and simulation results. Our simulations reveal the atomistic details of the interactions between nucleosomes in solution and can be used for constructing the coarse-grained model for chromatin in a bottom-up manner.

Molecular Modeling Computer Simulations of Organic Polymers: A Novel Computer Simulation Technique to Characterize Nanostructured Materials

2003 ◽  
Vol 788 ◽  
Author(s):  
Sarah G. Schulz ◽  
Hubert Kuhn ◽  
Günter Schmid
Keyword(s):  
Computer Simulations ◽  
Dissipative Particle Dynamics ◽  
Three Dimensional ◽  
Colloidal Suspensions ◽  
Simulation Technique ◽  
Coarse Grained ◽  
Organic Polymer ◽  
Random Forces ◽  
Coarse Grained Simulations ◽  
Immiscible Mixtures

ABSTRACTThe understanding and prediction of complex nanostructured self-assemblies such as colloidal suspensions, micelles, immiscible mixtures, microemulsions, etc., represent a challenge for conventional methods of simulation due to the presence of different time scales in their dynamics.We have recently successfully applied a novel computer simulations technique, Dissipative Particle Dynamics (DPD), to model the behavior of diblockcopolymers at the water/oil interface. With the use of a simple model we have performed simulations of polymer/water/oil systems at different concentrations.We present the results of nanoscale “coarse-grained” simulations with DPD. DPD is a mesoscale simulation technique that has been introduced in order to simulate three-dimensional structures of organic polymer aggregates.In DPD the polymer is modeled using particles which are interacting by conservative, dissipative and random forces. Particles are not regarded as molecules but rather as droplets or nanoclusters of molecules.We have successfully applied this technique to simulate the three-dimensional structures of microemulsions, e.g. the bicontinuous phase of a surfactant in water and oil, in domains of less than 100 nm. The different structures of the polymer/water/oil system were effectively characterized with DPD and are in remarkable agreement with the experiment.The DPD method proofed to be a reliable tool to get a better understanding of the nanostructure of self-assemblies and is therefore applicable to support the often complicated experiments or even to obtain experimentally unavai1able data.

scholarly journals Effective interactions, structure, and isothermal compressibility of colloidal suspensions

2000 ◽  
Vol 113 (11) ◽  
pp. 4799-4807 ◽  
Author(s):  
Marjolein Dijkstra ◽  
René van Roij ◽  
Robert Evans
Keyword(s):  
Isothermal Compressibility ◽  
Colloidal Suspensions ◽  
Effective Interactions

scholarly journals Tuning effective interactions close to the critical point in colloidal suspensions

2012 ◽  
Vol 137 (8) ◽  
pp. 084903 ◽  
Author(s):  
Nicoletta Gnan ◽  
Emanuela Zaccarelli ◽  
Francesco Sciortino
Keyword(s):  
Critical Point ◽  
Colloidal Suspensions ◽  
Effective Interactions
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