A Simple Reverse Mapping Procedure for Coarse-Grained Polymer Models with Rigid Side Groups

2011 ◽  
Vol 44 (13) ◽  
pp. 5520-5526 ◽  
Author(s):  
Azadeh Ghanbari ◽  
Michael C. Böhm ◽  
Florian Müller-Plathe
Keyword(s):  
Coarse Grained ◽  
Mapping Procedure ◽  
Polymer Models ◽  
Reverse Mapping

scholarly journals Energy renormalization for coarse-graining polymers having different segmental structures

2019 ◽  
Vol 5 (4) ◽  
pp. eaav4683 ◽  
Author(s):  
Wenjie Xia ◽  
Nitin K. Hansoge ◽  
Wen-Sheng Xu ◽  
Frederick R. Phelan ◽  
Sinan Keten ◽  
...  
Keyword(s):  
Dynamic Properties ◽  
Interaction Strength ◽  
Configurational Entropy ◽  
Coarse Graining ◽  
Soft Materials ◽  
Polymer Materials ◽  
Coarse Grained ◽  
Art Form ◽  
Polymer Models ◽  
Energy Renormalization

Multiscale coarse-grained (CG) modeling of soft materials, such as polymers, is currently an art form because CG models normally have significantly altered dynamics and thermodynamic properties compared to their atomistic counterparts. We address this problem by exploiting concepts derived from the generalized entropy theory (GET), emphasizing the central role of configurational entropy sc in the dynamics of complex fluids. Our energy renormalization (ER) method involves varying the cohesive interaction strength in the CG models in such a way that dynamic properties related to sc are preserved. We test this ER method by applying it to coarse-graining polymer melts (i.e., polybutadiene, polystyrene, and polycarbonate), representing polymer materials having a relatively low, intermediate, and high degree of glass “fragility”. We find that the ER method allows the dynamics of the atomistic polymer models to be faithfully described to a good approximation by CG models over a wide temperature range.

Predicting the Mobility Increase of Coarse-Grained Polymer Models from Excess Entropy Differences

2020 ◽  
Vol 16 (3) ◽  
pp. 1431-1447 ◽  
Author(s):  
Gustavo G. Rondina ◽  
Michael C. Böhm ◽  
Florian Müller-Plathe
Keyword(s):  
Excess Entropy ◽  
Coarse Grained ◽  
Polymer Models

Highly Cross-Linked Epoxy Resins:  An Atomistic Molecular Dynamics Simulation Combined with a Mapping/Reverse Mapping Procedure

2007 ◽  
Vol 40 (22) ◽  
pp. 8104-8113 ◽  
Author(s):  
Pavel V. Komarov ◽  
Chiu Yu-Tsung ◽  
Chen Shih-Ming ◽  
Pavel G. Khalatur ◽  
Peter Reineker
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Epoxy Resins ◽  
Dynamics Simulation ◽  
Mapping Procedure ◽  
Reverse Mapping

scholarly journals Development of coarse-grained model for a minimal stratum corneum lipid mixture

2021 ◽  
Author(s):  
Parashara Shamaprasad ◽  
Timothy C Moore ◽  
Donna Xia ◽  
Christopher R Iacovella ◽  
Annette L Bunge ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Fatty Acid ◽  
Free Fatty Acid ◽  
Stratum Corneum ◽  
Multiscale Simulation ◽  
Coarse Grained ◽  
Multilayer Structures ◽  
Mapping Procedure ◽  
Lipid Mixture ◽  
Coarse Grained Model

Molecular dynamics simulations of mixtures of the ceramide N-(tetracosanoyl)-sphingosine (NS), cholesterol, and a free fatty acid are performed to gain a molecular-level understanding of the structure of the lipids found in the stratum corneum layer of skin. A new coarse-grained model for cholesterol, developed using the multistate iterative Boltzmann inversion method, is compatible with previously developed coarse-grained forcefields for ceramide NS, free fatty acid, and water, and validated against atomistic simulations of these lipids using the CHARMM force field. Self-assembly simulations of multilayer structures using these coarse-grained force fields are performed, revealing that a large fraction of the ceramides adopt extended conformations, which cannot occur in the bilayer structures typically studied using simulation. Cholesterol fluidizes the membrane by promoting packing defects and it is observed that an increase in cholesterol content reduces the bilayer height, due to an increase in interdigitation of the C24 lipid tails, consistent with experimental observations. Through the use of a simple reverse-mapping procedure, a self-assembled coarse-grained multilayer system is used to construct an equivalent structure with atomistic resolution. Simulations of this atomistic structure are found to closely agree with experimentally derived neutron scattering length density profiles. Significant interlayer hydrogen bonding is observed in the inner layers of the atomistic multilayer structure that are not found in the outer layers in contact with water or in equivalent bilayer structures. These results identify several significant differences in the structure and hydrogen bonding of multilayer structures as compared to the more commonly studied bilayer systems, and, as such, highlight the importance of simulating multilayer structures for more accurate comparisons with experiment. These results also provide validation of the efficacy of the coarse-grained forcefields and the framework for multiscale simulation.

Extensive nodal involvement increases the positivity of blue nodes in the axillary reverse mapping procedure in patients with breast cancer

2012 ◽  
Vol 106 (1) ◽  
pp. 89-93 ◽  
Author(s):  
Isabel T. Rubio ◽  
Isaac Cebrecos ◽  
Vicente Peg ◽  
Antonio Esgueva ◽  
Cesar Mendoza ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Nodal Involvement ◽  
Mapping Procedure ◽  
Axillary Reverse Mapping ◽  
Reverse Mapping

scholarly journals Effects of Sequence Composition and Patterning on the Structure and Dynamics of Intrinsically Disordered Proteins

2020 ◽  
Author(s):  
Andrei Vovk ◽  
Anton Zilman
Keyword(s):  
Amino Acid ◽  
Intrinsically Disordered Proteins ◽  
Amino Acid Sequences ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Radius Of Gyration ◽  
Sequence Composition ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Polymer Models

AbstractUnlike the well defined structures of classical natively folded proteins, Intrinsically Disordered Proteins (IDP) and Intrinsically Disordered Regions (IDR) dynamically span large conformational and structural ensembles. This dynamic disorder impedes the study of the relationship between the amino acid sequences of the IDPs and their spatial structures, dynamics, and function. Multiple experimental and theoretical evidence points in many cases to the overall importance of the general properties of the amino acid sequence of the IPDs rather than their precise atomistic details. However, while different experimental techniques can probe aspects of the IDP conformations, often different techniques or conditions offer seemingly contradictory results. Using coarse-grained polymer models informed by experimental observations, we investigate the effects of several key variables on the dimensions and the dynamics of IDPs. The coarse-grained simulations are in a good agreement with the results of atomistic MD. We show that the sequence composition and patterning are well reflected in the global conformational variables such as the radius of gyration and hydrodynamic radius, while the end-to-end distance and dynamics are highly sequence specific. We identify the conditions that allow mapping of highly heterogeneous sequences of IDPs onto averaged minimal polymer models. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for further development of appropriate mesoscopic models of IDPs.

scholarly journals An investigation of free-energy-averaged (coarse-grained) potentials for fluid adsorption on heterogeneous solid surfaces

2019 ◽  
Vol 21 (46) ◽  
pp. 25558-25568 ◽  
Author(s):  
Srikanth Ravipati ◽  
Amparo Galindo ◽  
George Jackson ◽  
Andrew J. Haslam
Keyword(s):  
Free Energy ◽  
Solid Surface ◽  
Body Fluid ◽  
Solid Surfaces ◽  
Coarse Grained ◽  
Heterogeneous Surfaces ◽  
Mapping Procedure ◽  
Adsorption On Heterogeneous Surfaces ◽  
Heterogeneous Solid

A FEA mapping procedure for providing coarse-grained, two-body fluid–solid potentials (describing the interaction between a fluid molecule and a solid surface) is investigated, and adapted to allow study of adsorption on heterogeneous surfaces.

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