Coexistence of Multilayered Phases of Confined Water: The Importance of Flexible Confining Surfaces

Flexible nanoscale confinement is critical to understanding the role that bending fluctuations play on biological processes where soft interfaces are ubiquitous or to exploit confinement effects in engineered systems where inherently flexible 2D materials are pervasively employed. Here, using molecular dynamics simulations, we compare the phase behavior of water confined between flexible and rigid graphene sheets as a function of the in-plane density, ρ_2D. We find that both cases show commensurate mono-, bi-, and trilayered states; however, the water phase in those states and the transitions between them are qualitatively different for the rigid and flexible cases. The rigid systems exhibit discontinuous transitions between an (n)-layer and an (n+1)-layer state at particular values of ρ_2D, whereas under flexible confinement, the graphene sheets bend to accommodate an (n)-layer and an (n+1)-layer state coexisting in equilibrium at the same density. We show that the flexible walls introduce a very different sequence of ice phases and their phase coexistence with vapor and liquid phases than that observed with rigid walls. We discuss the applicability of these results to real experimental systems to shed light on the role of flexible confinement and its interplay with commensurability effects.

Improvements to the APBS biomolecular solvation software suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK_a values, and an improved web-based visualization tool for viewing electrostatics.

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators, and students that are more familiar with the APBS framework. © 2016 Wiley Periodicals, Inc.

Role of hydrophilicity and length of diblock arms for determining star polymer physical properties

We present a molecular simulation study of star polymers consisting of 16 diblock copolymer arms bound to a small adamantane core by varying both arm length and the outer hydrophilic block when attached to the same hydrophobic block of poly-δ-valerolactone. Here we consider two biocompatible star polymers in which the hydrophilic block is composed of polyethylene glycol (PEG) or polymethyloxazoline (POXA) in addition to a polycarbonate-based polymer with a pendant hydrophilic group (PC1). We find that the different hydrophilic blocks of the star polymers show qualitatively different trends in their interactions with aqueous solvent, orientational time correlation functions, and orientational correlation between pairs of monomers of their polymeric arms in solution, in which we find that the PEG polymers are more thermosensitive compared with the POXA and PC1 star polymers over the physiological temperature range we have investigated.