Literature DB >> 23061853

Pseudo hard-sphere potential for use in continuous molecular-dynamics simulation of spherical and chain molecules.

J Jover1, A J Haslam, A Galindo, G Jackson, E A Müller.   

Abstract

We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for m(c) = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, m(c), approaches a limiting value at reasonably small values, m(c) < 50, as predicted by Wertheim's first order thermodynamic perturbation theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3:1, 5:1, 20:1 over the whole composition range.

Entities:  

Year:  2012        PMID: 23061853     DOI: 10.1063/1.4754275

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  8 in total

1.  Assembly of porous smectic structures formed from interlocking high-symmetry planar nanorings.

Authors:  Carlos Avendaño; George Jackson; Erich A Müller; Fernando A Escobedo
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-18       Impact factor: 11.205

2.  Breakdown of the law of rectilinear diameter and related surprises in the liquid-vapor coexistence in systems of patchy particles.

Authors:  Jorge R Espinosa; Adiran Garaizar; Carlos Vega; Daan Frenkel; Rosana Collepardo-Guevara
Journal:  J Chem Phys       Date:  2019-06-14       Impact factor: 3.488

3.  Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model.

Authors:  Jerelle A Joseph; Jorge R Espinosa; Ignacio Sanchez-Burgos; Adiran Garaizar; Daan Frenkel; Rosana Collepardo-Guevara
Journal:  Biophys J       Date:  2021-02-09       Impact factor: 4.033

4.  Magneto-Mechanical Coupling in Magneto-Active Elastomers.

Authors:  Philipp Metsch; Dirk Romeis; Karl A Kalina; Alexander Raßloff; Marina Saphiannikova; Markus Kästner
Journal:  Materials (Basel)       Date:  2021-01-17       Impact factor: 3.623

5.  Valency and Binding Affinity Variations Can Regulate the Multilayered Organization of Protein Condensates with Many Components.

Authors:  Ignacio Sanchez-Burgos; Jorge R Espinosa; Jerelle A Joseph; Rosana Collepardo-Guevara
Journal:  Biomolecules       Date:  2021-02-14

6.  Elasticity-induced force reversal between active spinning particles in dense passive media.

Authors:  J L Aragones; J P Steimel; A Alexander-Katz
Journal:  Nat Commun       Date:  2016-04-26       Impact factor: 14.919

7.  Size conservation emerges spontaneously in biomolecular condensates formed by scaffolds and surfactant clients.

Authors:  Ignacio Sanchez-Burgos; Jerelle A Joseph; Rosana Collepardo-Guevara; Jorge R Espinosa
Journal:  Sci Rep       Date:  2021-07-27       Impact factor: 4.379

8.  RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins.

Authors:  Ignacio Sanchez-Burgos; Jorge R Espinosa; Jerelle A Joseph; Rosana Collepardo-Guevara
Journal:  PLoS Comput Biol       Date:  2022-02-02       Impact factor: 4.475

  8 in total

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