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Felberg, Lisa E.

Publications and source records attributed to Felberg, Lisa E..

6 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

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, ρ2D. 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 ρ2D, 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.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses 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 manuscript, 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 pKa values, and an improved web-based visualization tool for viewing electrostatics.

Biomedical applications↗
DOE OSTI2017

Effect of Hydrophobic Core Topology and Composition on the Structure and Kinetics of Star Polymers: A Molecular Dynamics Study

We present a molecular dynamics study of the effect of core chemistry on star polymer structural and kinetic properties. This work serves to validate the choice of a model adamantane core used in previous simulations to represent larger star polymeric systems in an aqueous environment, as well as to explore how the choice of size and core chemistry using a dendrimer or nanogel core may affect these polymeric nanoparticle systems, particularly with respect to thermosensitivity and solvation properties that are relevant for applications in drug loading and delivery.

Carr, Amber C.↗
DOE OSTI2016

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

Here, 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.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Structural transition of nanogel star polymers with pH by controlling PEGMA interactions with acid or base copolymers

We use small angle X-ray scattering (SAXS) to characterise a class of star diblock polymers with a nanogel core on which the outer block arms are comprised of random copolymers of temperature sensitive PEGMA with pH sensitive basic (PDMAEMA) and acidic (PMAA) monomers. The acquired SAXS data show that many of the nanogel star polymers undergo a sharp structural transition over a narrow range of pH, but with unexpectedly large shifts in the apparent pKa with respect to that of the acidic or basic monomer unit, the linear polymer form or even an alternate star polymer with a tightly cross-linked core chemistry. We have demonstrated a distinct and quantifiable structural response for the nanogel star copolymers by altering the core or by pairing the monomers PDMAEMA–PEGMA and PMAA–PEGMA to achieve structural transitions that have typically been observed in stars through changes in arm length and number.

74 ATOMIC AND MOLECULAR PHYSICS↗