Open boundary molecular dynamics of sheared star-polymer melts

Sablić, Jurij; Praprotnik, Matej; Delgado‐Buscalioni, Rafael

doi:10.1039/c5sm02604k

Cited by 39 publications

(60 citation statements)

References 102 publications

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“…Current efforts are also focusing on combining AdResS and advance sampling techniques, e.g., metadynamics 63 . Another direction of AdResS development is considering simulations of open grand-canonical systems 64 , e.g., the grand-canonical (GC)-AdResS 65, 66 and open boundary molecular dynamics (OBMD) approaches 67, 68 . To properly model the hexagonal to orthorhombic phase transition all of these techniques would need to be combined.…”

Section: Methodsmentioning

confidence: 99%

“…The whole DNA array is at all times modeled at full atomistic resolution, but since the region outside the semipermeable walls is used only as a solution reservoir, it can be modeled with the coarse-grained resolution, acting in a similar way as a buffer in an OBMD simulation 67, 68 . We perform our multiscale simulations, with a length of 22 ns (2 ns equilibration followed by 20 ns production runs) for each system or 900 ns of production runs in total, employing AdResS.…”

Section: Methodsmentioning

confidence: 99%

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Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Zavadlav

Podgornik

Praprotnik

2017

Sci Rep

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While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Zavadlav

Podgornik

Praprotnik

2017

Sci Rep

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“…We have recently completed a series of works on star polymer dynamics 19,26,27 . This series started by a study of the effect of open boundaries compared with closed systems in the rheology of melts under shear (simulations using Open Boundary Molecular Dynamics (OBMD) [26][27][28] permits to fix the pressure load and shear stress, instead of the density and shear velocity). As a continuation of such work, we studied the dynamics of stars in solution and melt 19 and observed that the tank-treading frequency of monomers around the molecule's CoM, ω R , was completely different from the "apparent" angular velocity obtained from the standard (lab-frame) analysis ω.…”

Section: Introductionmentioning

confidence: 99%

Application of the Eckart frame to soft matter: rotation of star polymers under shear flow

2017

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The Eckart co-rotating frame is used to analyze the dynamics of star polymers under shear flow, either in melt or solution and with different types of bonds. This formalism is compared with the standard approach used in many previous studies on polymer dynamics, where an apparent angular velocity ω is obtained from the relation between the tensor of inertia and angular momentum. A common mistake is to interpret ω as the molecular rotation frequency, which is only valid for rigid-body rotation. The Eckart frame, originally formulated to analyze the infrared spectra of small molecules, dissects different kinds of displacements: vibrations without angular momentum, pure rotation, and vibrational angular momentum (leading to a Coriolis cross-term). The Eckart frame co-rotates with the molecule with an angular frequency Ω obtained from the Eckart condition for minimal coupling between rotation and vibration. The standard and Eckart approaches are compared with a straight description of the star's dynamics taken from the time autocorrelation of the monomer positions moving around the molecule's center of mass. This is an underdamped oscillatory signal, which can be described by a rotation frequency ω and a decorrelation rate Γ. We consistently find that Ω coincides with ω, which determines the characteristic tank-treading rotation of the star. By contrast, the apparent angular velocity ω < Ω does not discern between pure rotation and molecular vibrations. We believe that the Eckart frame will be useful to unveil the dynamics of semiflexible molecules where rotation and deformations are entangled, including tumbling, tank-treading motions and breathing modes.

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“…To perform a truly open grand-canonical molecular simulations one should take recourse to the open boundary molecular dynamics (OBMD) [57,116,[136][137][138] that permits simulations directly in the grand-canonical ensemble. The OBMD method combines features of AdResS and open MD [139,140], which enable the exchange of energy, momentum, and matter with the external environment through the imposed arbitrary time-dependent external pressure tensor.…”

Section: Discussionmentioning

confidence: 99%

Molecular Dynamics Simulation of High Density DNA Arrays

2018

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Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine) counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and consequently identify the most important contribution to the DNA-DNA interactions at high DNA densities.

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Open boundary molecular dynamics of sheared star-polymer melts

Cited by 39 publications

References 102 publications

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Application of the Eckart frame to soft matter: rotation of star polymers under shear flow

Molecular Dynamics Simulation of High Density DNA Arrays

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