arXiv subjects

Teresa Head-Gordon

Publications and source records attributed to Teresa Head-Gordon.

57 records · Page 4Linked to original sources

arXiv2016

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 Poisson Boltzmann equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, 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.

q-bio.BM↗

arXiv2007

Representability problems for coarse-grained water potentials

The use of an effective intermolecular potential often involves a compromise between more accurate, complex functional forms and more tractable simple representations. To study this choice in detail, we systematically derive coarse-grained isotropic pair potentials that accurately reproduce the oxygen-oxygen radial distribution function of the TIP4P-Ew water model at state points over density ranges from 0.88-1.30g/cc and temperature ranges from 235K-310K. Although by construction these effective potentials correctly represent the isothermal compressibility of TIP4P-Ew water, they do not accurately resolve other thermodynamic properties such as the virial pressure, the internal energy or thermodynamic anomalies. Because at a given state point the pair potential that reproduces the pair structure is unique, we have therefore explicitly demonstrated that it is impossible to simultaneously represent the pair-structure and several key equilibrium thermodynamic properties of water with state-point dependent radially symmetric pair potentials. We argue that such representability problems are related to, but different from, more widely acknowledged transferability problems, and discuss in detail the implications this has for the modeling of water and other liquids by coarse-grained potentials. Nevertheless, regardless of thermodynamic inconsistencies, the state-point dependent effective potentials for water do generate structural and dynamical anomalies.

cond-mat.stat-mech↗

arXiv2003

Hydration Water Dynamics and Instigation of Protein Structural Relaxation

The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron scattering (QENS) and molecular dynamics simulation to investigate hydration water dynamics near a greatly simplified protein surface. We consider the hydration water dynamics near the completely deuterated N-acetyl-leucine-methylamide (NALMA) solute, a hydrophobic amino acid side chain attached to a polar blocked polypeptide backbone, as a function of concentration between 0.5M-2.0M, under ambient conditions. In this Communication, we focus our results of hydration dynamics near a model protein surface on the issue of how enzymatic activity is restored once a critical hydration level is reached, and provide a hypothesis for the molecular mechanism of the solvent motion that is required to trigger protein structural relaxation when above the hydration transition.

q-bio.BM↗