Learn More
Analytical approximations to fundamental equations of continuum electrostatics on simple shapes can lead to computationally inexpensive prescriptions for calculating electrostatic properties of realistic molecules. Here, we derive a closed-form analytical approximation to the Poisson equation for an arbitrary distribution of point charges and a spherical(More)
An ability to efficiently compute the electrostatic potential produced by molecular charge distributions under realistic solvation conditions is essential for a variety of applications. Here, the simple closed-form analytical approximation to the Poisson equation rigorously derived in Part I for idealized spherical geometry is tested on realistic shapes.(More)
The intrinsic stochasticity of gene expression can lead to large variability in protein levels for genetically identical cells. Such variability in protein levels can arise from infrequent synthesis of mRNAs which in turn give rise to bursts of protein expression. Protein expression occurring in bursts has indeed been observed experimentally and recent(More)
Molecular dynamics simulations of unprecedented duration now can provide new insights into biomolecular mechanisms. Analysis of a 1-ms molecular dynamics simulation of the small protein bovine pancreatic trypsin inhibitor reveals that its main conformations have different thermodynamic profiles and that perturbation of a single geometric variable, such as a(More)
The modeling and simulation of macromolecules in solution often benefits from fast analytical approximations for the electrostatic interactions. In our previous work [G. Sigalov et al., J. Chem. Phys. 122, 094511 (2005)], we proposed a method based on an approximate analytical solution of the linearized Poisson-Boltzmann equation for a sphere. In the(More)
Charge hydration asymmetry (CHA) manifests itself in the experimentally observed strong dependence of free energy of ion hydration on the sign of the ion charge. This asymmetry is not consistently accounted for by popular models of solvation; its magnitude varies greatly between the models. While it is clear that CHA is somehow related to charge(More)
Presented here is a quantitative model of the wrapping and unwrapping of the DNA around the histone core of the nucleosome that suggests a mechanism by which this transition can be controlled: alteration of the charge state of the globular histone core. The mechanism is relevant to several classes of posttranslational modifications such as histone(More)
Prospective validation of methods for computing binding affinities can help assess their predictive power and thus set reasonable expectations for their performance in drug design applications. Supramolecular host-guest systems are excellent model systems for testing such affinity prediction methods, because their small size and limited conformational(More)
Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed-up these types(More)
We present a framework for analyzing luminescence regulation during quorum sensing in the bioluminescent bacterium Vibrio harveyi. Using a simplified model for signal transduction in the quorum sensing pathway, we identify key dimensionless parameters that control the system's response. These parameters are estimated using experimental data on luminescence(More)