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)

Thermodynamic study of benzocaine insertion into different lipid bilayers

J. J. López Cascales, S. D. Oliveira Costa, and R. D. Porasso

By use of molecular dynamics simulations, the authors study  the thermodynamic behavior of a local anesthetics during its insertion process into a lipid bilayers, as a function of the lipid composition of the membrane. Thus, for first time the entropy and enthalpy profile associated to this process from the bulk aqueous solution to the interior of a membrane is presented.

J. Chem. Phys. 135, 135103 (2011) | Read the press release.

Simulations of the confinement of ubiquitin in self-assembled reverse micelles

Jianhui Tian and Angel E. García

The authors conducted extensive molecular dynamics simulations on a self-assembled protein-RM system which is composed of AOT surfactants, water, a single folded ubiquitin, ions (Na+ and Cl-), and iso-octane. These simulations provided information about the location of the ubiquitin inside RM, the interaction between ubiquitin and surfactants, and the hydration structure and the protein dynamical changes of the encapsulated ubiquitin, when compared with ubiquitin in bulk water.

J. Chem. Phys. 134, 225101 (2011)