List of works by Nathan Baker

25-Hydroxycholesterol increases the availability of cholesterol in phospholipid membranes

scientific article

A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential

scientific article

APBSmem: a graphical interface for electrostatic calculations at the membrane

scientific article

Adaptive visual sort and summary of micrographic images of nanoparticles for forensic analysis

conference proceedings item published in 2016

Annotating the structure and components of a nanoparticle formulation using computable string expressions

scientific article

Application of a hemolysis assay for analysis of complement activation by perfluorocarbon nanoparticles

scientific article

Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity

scientific article

Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

scholarly article

Assessing the performance of implicit solvation models at a nucleic acid surface

scientific article published on 7 July 2008

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations.

scientific article

Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies

scientific article published on 14 December 2016

Bayesian model aggregation for ensemble-based estimates of protein pKa values.

scientific article

Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation

scientific article published in February 2002

Biomolecular electrostatics and solvation: a computational perspective

scientific article

CONSTRUCTING SURROGATE MODELS OF COMPLEX SYSTEMS WITH ENHANCED SPARSITY: QUANTIFYING THE INFLUENCE OF CONFORMATIONAL UNCERTAINTY IN BIOMOLECULAR SOLVATION ⬇️

scientific article

Characterization of perfluorooctylbromide-based nanoemulsion particles using atomistic molecular dynamics simulations

scientific article

Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity

scientific article

Computational methods for biomolecular electrostatics

scientific article published on January 2008

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

scientific article published on 20 June 2016

Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis

scientific article

Data-driven parameterization of the generalized Langevin equation

scientific article

Differential geometry based solvation model I: Eulerian formulation

scientific article

Differential geometry based solvation model II: Lagrangian formulation

scientific article

Domain-specific languages for composing signature discovery workflows

Dynamical properties of fasciculin-2.

scientific article published on September 1999

Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach

scientific article published on November 2004

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

scientific article published on June 2006

Electrostatics of nanosystems: application to microtubules and the ribosome

scientific article

Energy Minimization of Discrete Protein Titration State Models Using Graph Theory ⬇️

scientific article published on 18 April 2016

Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations

scientific article published on 16 February 2007

ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format

scientific article

Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers

scientific article

Improvements to the APBS biomolecular solvation software suite

scientific article

Improving implicit solvent simulations: a Poisson-centric view

scientific article

Informatics and standards for nanomedicine technology

journal article published in 2011

Interaction of melittin peptides with perfluorocarbon nanoemulsion particles

scientific article published on 6 December 2011

Iron responsive element RNA flexibility described by NMR and isotropic reorientational eigenmode dynamics

scientific article published in July 2005

Molecular Recognition by Cholesterol Esterase of Active Site Ligands: Structure−Reactivity Effects for Inhibition by Aryl Carbamates and Subsequent Carbamylenzyme Turnover†

scientific article published in 1996

Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways

scientific article

Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects

scientific article published on 25 January 2008

Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer

scientific article published on October 2005

Multi-shell model of ion-induced nucleic acid condensation. ⬇️

scientific article published on April 2016

NanoParticle Ontology for cancer nanotechnology research

scientific article

Nanoinformatics workshop report: current resources, community needs and the proposal of a collaborative framework for data sharing and information integration

journal article published in 2013

Nanoinformatics: developing new computing applications for nanomedicine

scientific article (publication date: June 2012)

Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics ⬇️

scientific article published on 7 May 2015

On the development of protein pKa calculation algorithms.

scientific article

Ontologies for cancer nanotechnology research

scientific article published on January 2009

Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA.

scientific article published on 6 July 2016

Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions.

scientific article published in January 2007

Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies

scientific article

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

scientific article published on 2 November 2016

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

scientific article (publication date: July 2004)

Parameterization of a geometric flow implicit solvation model

scientific article published on 5 December 2012

Perturbations of membrane structure by cholesterol and cholesterol derivatives are determined by sterol orientation

scientific article published on April 2009

Physicochemical signatures of nanoparticle-dependent complement activation

scientific article

Poisson–Boltzmann Methods for Biomolecular Electrostatics

scientific article published on 01 January 2004

Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

scientific article published on March 2007

Probing 3′-ssDNA Loop Formation in E. coli RecBCD/RecBC–DNA Complexes Using Non-natural DNA: A Model for “Chi” Recognition Complexes

article

Progress in the prediction of pKa values in proteins

scientific article published on 15 October 2011

SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome

scientific article published in April 2004

Side-chain oxysterols modulate cholesterol accessibility through membrane remodeling

scientific article

Side-chain oxysterols: from cells to membranes to molecules

scientific article

Simulation of fusion-mediated nanoemulsion interactions with model lipid bilayers

scientific article

Simulations of RNA Interactions with Monovalent Ions

article

Smoothed dissipative particle dynamics model for mesoscopic multiphase flows in the presence of thermal fluctuations ⬇️

scientific article published on 5 August 2016

Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models.

scientific article published in October 2004

Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models?

scientific article published on October 2007

Spermine Condenses DNA, but Not RNA Duplexes

scientific article published on January 2017

Standardizing data

scientific article published on February 2013

Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods

scientific article

The Role of Correlation and Solvation in Ion Interactions with B-DNA

scientific article

The effect of a systematic, personalized computer workstation redesign on musculoskeletal symptoms

abstract published in 2012

The effect of alternative keyboards on discomfort and typing kinematics

final grant report published in 2013

The effectiveness of alternative keyboards at reducing musculoskeletal symptoms at work: a review

conference proceedings item published in 2013

The physical basis of microtubule structure and stability ⬇️

scientific article published on October 1, 2003

The relationship between computer-related discomfort and everyday activities

conference proceedings item published in 2010

The structural basis of cholesterol accessibility in membranes

scientific article published on October 2013

Theoretical and experimental investigations of electrostatic effects on acetylcholinesterase catalysis and inhibition

scientific article published on 01 May 1999

Toward Quantum Computing for High-Energy Excited States in Molecular Systems: Quantum Phase Estimations of Core-Level States

scientific article published on 17 December 2020

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations ⬇️

scientific article published on May 2016

Using physicochemical properties of amino acids to induce graphical models of residue couplings

Variational approach for nonpolar solvation analysis

scientific article

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS

scientific article published on 25 November 2019

Web servers and services for electrostatics calculations with APBS and PDB2PQR

scientific article

Why double-stranded RNA resists condensation

scientific article

iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS).

scientific article

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