scholarly journals Dynamics and rheology of ring-linear blend semidilute solutions in extensional flow. Part I: Modeling and molecular simulations

2021 ◽  
Vol 65 (4) ◽  
pp. 757-777
Author(s):  
Charles D. Young ◽  
Yuecheng Zhou ◽  
Charles M. Schroeder ◽  
Charles E. Sing
Keyword(s):  
Extensional Flow ◽  
Molecular Simulations ◽  
Semidilute Solutions ◽  
Flow Part

scholarly journals Direct observation of DNA dynamics in semidilute solutions in extensional flow

2017 ◽  
Vol 61 (1) ◽  
pp. 151-167 ◽  
Author(s):  
Kai-Wen Hsiao ◽  
Chandi Sasmal ◽  
J. Ravi Prakash ◽  
Charles M. Schroeder
Keyword(s):  
Direct Observation ◽  
Extensional Flow ◽  
Dna Dynamics ◽  
Semidilute Solutions

scholarly journals Dynamics and rheology of ring-linear blend semidilute solutions in extensional flow: Single molecule experiments

2021 ◽  
Vol 65 (4) ◽  
pp. 729-744
Author(s):  
Yuecheng Zhou ◽  
Charles D. Young ◽  
Megan Lee ◽  
Sourya Banik ◽  
Dejie Kong ◽  
...  
Keyword(s):  
Single Molecule ◽  
Extensional Flow ◽  
Semidilute Solutions

scholarly journals Parameter-free prediction of DNA dynamics in planar extensional flow of semidilute solutions

2017 ◽  
Vol 61 (1) ◽  
pp. 169-186 ◽  
Author(s):  
Chandi Sasmal ◽  
Kai-Wen Hsiao ◽  
Charles M. Schroeder ◽  
J. Ravi Prakash
Keyword(s):  
Extensional Flow ◽  
Dna Dynamics ◽  
Semidilute Solutions ◽  
Planar Extensional Flow

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

On the Use of Quantum Thermal Bath in Unimolecular Fragmentation Simulations

2019 ◽  
Author(s):  
Riccardo Spezia ◽  
Hichem Dammak
Keyword(s):  
Degrees Of Freedom ◽  
Molecular Simulations ◽  
Zero Point ◽  
Thermal Bath ◽  
Unimolecular Dissociation ◽  
Point Energy ◽  
Rotational Degrees Of Freedom ◽  
The Difference ◽  
Nuclear Effects

<div> <div> <div> <p>In the present work we have investigated the possibility of using the Quantum Thermal Bath (QTB) method in molecular simulations of unimolecular dissociation processes. Notably, QTB is aimed in introducing quantum nuclear effects with a com- putational time which is basically the same as in newtonian simulations. At this end we have considered the model fragmentation of CH4 for which an analytical function is present in the literature. Moreover, based on the same model a microcanonical algorithm which monitor zero-point energy of products, and eventually modifies tra- jectories, was recently proposed. We have thus compared classical and quantum rate constant with these different models. QTB seems to correctly reproduce some quantum features, in particular the difference between classical and quantum activation energies, making it a promising method to study unimolecular fragmentation of much complex systems with molecular simulations. The role of QTB thermostat on rotational degrees of freedom is also analyzed and discussed. </p> </div> </div> </div>

Ideal shocks in 2-layer flow Part I: Under a rigid lid

2001 ◽  
Vol 53 (2) ◽  
pp. 129-145 ◽  
Author(s):  
Qingfang Jiang ◽  
Ronald B. Smith
Keyword(s):  
Flow Part ◽  
Layer Flow
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