Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution.

The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system's electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open-boundary molecular dynamics method that allows for simulation of open systems that can exchange mass and linear momentum with the environment. In our open-boundary molecular dynamics approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.

Deciphering the dynamics of star molecules in shear flow.

This work analyses the rotation of star polymers under shear flow, in melts, and in good solvent dilute solution. The latter is modeled by single molecule Brownian hydrodynamics, while melts are modeled using non-equilibrium molecular dynamics in closed (periodic) boxes and in open boundaries. A Dissipative Particle Dynamics (DPD) thermostat introduces pairwise monomer friction in melts at will, in directions normal and tangent to the monomer-monomer vectors. Although tangential friction is seldom modeled, we show that it is essential to control hydrodynamic effects in melts. We analyze the different sources of molecular angular momentum in solution and melts and distinguish three dynamic regimes as the shear rate [small gamma, Greek, dot above] is increased. These dynamic regimes are related with the disruption of the different relaxation mechanisms of the star in equilibrium. Although strong differences are found between harmonic springs and finitely extensible bonds, above a critical shear rate the star molecule has a "breathing" mode with successive elongations and contractions in the flow direction with frequency Ω. The force balance in the flow direction unveils a relation between Ω and the orientation angle. Using literature results for the tumbling of rings and linear chains, either in melt or in solution, we show that the relation is general. A different "tank-treading" dynamics determines the rotation of monomers around the center of mass of the molecule. We show that the tank-treading frequency does not saturate but keeps increasing with [small gamma, Greek, dot above]. This is at odds with previous studies which erroneously calculated the molecular angular frequency, used as a proxy for tank-treading.

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

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 ωR and a decorrelation rate Γ. We consistently find that Ω coincides with ωR, 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.

Open boundary molecular dynamics of sheared star-polymer melts.

Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt under isothermal conditions are performed to study the rheology and molecular structure of the melt under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes at a fixed shear rate (using the SLLOD dynamics). The OBMD system exchanges mass and momentum with adjacent reservoirs (buffers) where the external pressure tensor is imposed. Insertion of molecules in the buffers is made feasible by implementing there a low resolution model (blob-molecules with soft effective interactions) and then using the adaptive resolution scheme (AdResS) to connect with the bulk MD. Straining with increasing shear stress induces melt expansion and a significantly different redistribution of pressure compared with the closed case. In the open sample, the shear viscosity is also a bit lowered but more stable against the viscous heating. At a given Weissenberg number, molecular deformations and material properties (recoverable shear strain and normal stress ratio) are found to be similar in both setups. We also study the modelling effect of normal and tangential friction between monomers implemented in a dissipative particle dynamics (DPD) thermostat. Interestingly, the tangential friction substantially enhances the elastic response of the melt due to a reduction of the kinetic stress viscous contribution.