Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting

Patrick B. Warren and Rosalind J. Allen

Parameter sensitivity analysis is effective in the building and analysis of biochemical network models, but requires multiple simulations for perturbed values of the parameters when used in stochastic simulations. This paper describes the use of trajectory reweighting to derive a method for computing sensitivity coefficients in stochastic simulations without explicitly perturbing the parameter values, which avoids the need for repeated simulations.

J. Chem. Phys. 136, 104106 (2012)

Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme

Susmita Roy, Biman Jana, and Biman Bagchi

Dimethyl sulfoxide (DMSO) can have many effects on proteins such as stabilizing, denaturing, or inhibiting them depending on the concentration of DMSO. The authors use atomistic molecular dynamic simulations of Hen Egg White Lysozyme (HEWL) in solutions of water and DMSO to determine how the lysozyme changes with increasing DMSO concentration.

J. Chem. Phys. 136, 115103 (2012)

From protein denaturant to protectant: Comparative molecular dynamics study of alcohol∕protein interactions

Qiang Shao, Yubo Fan, Lijiang Yang, and Yi Qin Gao

The authors study how alcohols with varied hydrophobicity and different numbers of hydrophilic groups exert effects on the structure of the model polypeptide, BBA5 by using molecular dynamics simulations. Alcohols can denature or protect proteins and this study aids in the understanding of the molecular mechanisms.

J. Chem. Phys. 136, 115101 (2012)

Trapping of excess electrons at the microhydrated protonated amino groups in proteins

Wenchao Li, Zhenwei Zhang, Hongfang Yang, Xiuxiu Wu, Jinxiang Liu, and Yuxiang Bu

An excess electron in a condensed phase of a microhydrated protonated amino group in proteins is studied using a combined first-principles calculation and a molecular dynamics simulation. The study can be a basis for considering increasingly larger peptide fragments and charge migration mechanisms.

J. Chem. Phys. 136, 105101 (2012)

Kinetic pathways to peptide aggregation on surfaces: The effects of β-sheet propensity and surface attraction

Alex Morriss-Andrews and Joan-Emma Shea

The kinetics of peptide aggregation on a solid surface is studied using molecular dynamics simulations with a coarse-grained peptide representation. This work builds on previous work which examined the equilibrium structures of the system and provides details of aggregate growth mechanisms on scales inaccessible to either experiment or atomistic simulations.

J. Chem. Phys. 136, 065103 (2012)

Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

Zaixing Yang, Zhigang Wang, Xingling Tian, Peng Xiu, and Ruhong Zhou

The authors investigate the binding of three aromatic residue analogues and benzene to single-walled carbon nanotubes in the gas phase through π-π interactions by using both quantum mechanical and molecular mechanical approaches.

J. Chem. Phys. 136, 025103 (2012)

Amyloid-β peptide structure in aqueous solution varies with fragment size

Olivia Wise-Scira, Liang Xu, Taizo Kitahara, George Perry, and Orkid Coskuner

A report on the structural and thermodynamic properties of the Aβ16, Aβ28, and Aβ42 peptides in an aqueous solution environment. The paper presents results from replica exchange molecular dynamics simulations along with thermodynamic calculations for investigating the conformational free energies, secondary and tertiary structures of the Aβ16, Aβ28, and Aβ42 peptides.

J. Chem. Phys. 135, 205101 (2011)

Polymerization of actin filaments coupled with adenosine triphosphate hydrolysis: Brownian dynamics and theoretical analysis

Kunkun Guo, Wenjia Xiao, and Dong Qiu

Polymerization dynamics of single actin filaments coupled with ATP hydrolysis is investigated via both theoretical analysis and Brownian dynamics simulations. In the present study, both ATP cap length and length diffusivity are studied as a function of the free ATP-actin monomer concentrations, C_{T, cr}.

J. Chem. Phys. 135, 105101 (2011)

Influence of mobile DNA-protein-DNA bridges on DNA configurations: Coarse-grained Monte-Carlo simulations

Renko de Vries

Using Monte-Carlo simulations, the influence of (non-interacting) mobile DNA-protein-DNA bridges on the configurations of a 1000 bp piece of linear DNA, for both homogeneous DNA and DNA with an intrinsic planar bend is investigated. Results are compared to experimental data on the bacterial nucleoid protein H-NS that forms DNA-protein-DNA bridges.The results illustrate the importance of quantifying the various effects on DNA configurations that have been proposed for proteins that bind DNA sequence independently. 

J. Chem. Phys. 135, 125104 (2011)

Thermodynamics of twisted DNA with solvent interaction

Marco Zoli

The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation.

J. Chem. Phys. 135, 115101 (2011)