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

Soft Matter
Ioannis TanisClaire A Lemarchand

Abstract

The spherical representation usually utilized for the coarse-grained particles of soft matter systems is an assumption and pertinent studies have shown that both structural and dynamical properties can depend on anisotropic effects. On these grounds, we develop coarse-grained equations of motion which take into account explicitly the anisotropy of the beads. As a first step, this model incorporates only conservative terms. Inclusion of the dissipative and random terms is in principle possible but is beyond the scope of this study. The translational dynamics of the beads is tracked using the position and momentum of their center of mass, while their rotational dynamics is modeled by representing their orientation through the use of quaternions, similarly to the case of rigid bodies. The associated force and torque controlling the motion are derived from atomistic molecular dynamics (MD) simulations via a bottom-up approach and define a coarse-grained potential. The assumptions of the model are clearly stated and checked for a reference system of a cis-1,4-polybutadiene melt. In particular, the choice of the angular velocity as a slow variable is justified by comparing its dynamics to atomic vibrations. The accuracy of this appro...Continue Reading

References

Jul 1, 1996·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·D J CleaverM P Neal
Apr 17, 2001·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·J B MailletB L Holian
Nov 20, 2002·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Florian Müller-Plathe
Aug 20, 2003·Journal of Computational Chemistry·Dirk ReithFlorian Müller-Plathe
May 13, 2006·The Journal of Chemical Physics·M BabadiM R Ejtehadi
Sep 1, 2006·The Journal of Chemical Physics·Pavel A Golubkov, Pengyu Ren
Feb 18, 2010·Faraday Discussions·Carmen HijónRafael Delgado-Buscalioni
Mar 29, 2011·Physical Chemistry Chemical Physics : PCCP·Pep Español, Ignacio Zúñiga
Apr 3, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Anand Srivastava, Somnath Ghosh
Sep 14, 2013·The Journal of Chemical Physics·W G Noid
Sep 4, 2015·The Journal of Chemical Physics·Alain Dequidt, Jose G Solano Canchaya
Oct 30, 2015·Soft Matter·Zhan-Wei LiZhao-Yan Sun
Nov 18, 2015·Journal of Chemical Theory and Computation·Thomas K HaxtonStephen Whitelam
Nov 13, 2012·Journal of Chemical Theory and Computation·G MaurelP Malfreyt
Sep 3, 2016·The Journal of Chemical Physics·Clement LawRobert L Jack
Feb 24, 2017·The Journal of Chemical Physics·Claire A LemarchandBernard Rousseau
Apr 24, 2017·The Journal of Chemical Physics·Pep Español, Patrick B Warren
Jun 17, 2019·The Journal of Chemical Physics·C A LemarchandN Pineau
Aug 29, 2019·ACS Omega·Kévin KempferPatrice Malfreyt

❮ Previous
Next ❯

Citations

Jun 3, 2021·International Journal of Molecular Sciences·Xiaoyong Cao, Pu Tian

❮ Previous
Next ❯

Software Mentioned

MPI
STAMP

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.