Simulating nanoscale functional motions of biomolecules

Simulating Nanoscale Functional Motions of Biomolecules

We are describing efficient dynamics simulation methods for the characterization of functional motion of biomolecules on the nanometer scale. Multivariate statistical methods are widely used to extract and enhance functional collective motions from molecular dynamics (MD) simulations. A dimension reduction in MD is often realized through a principal component analysis or a singular value decomp...

Annotated with a comment on page 811. Simulating nanoscale functional motions of biomolecules

We are describing efficient dynamics simulation methods for the characterization of functional motion of biomolecules on the nanometer scale. Multivariate statistical methods are widely used to extract and enhance functional collective motions from molecular dynamics (MD) simulations. A dimension reduction in MD is often realized through a principal component analysis (PCA) or a singular value ...

Simulating biomolecules in synthetic nanopores

Simulating nanoscale dielectric response.

We introduce a constrained energy functional to describe dielectric response. We demonstrate that the local functional is a generalization of the long-ranged Marcus energy. Our reformulation is used to implement a cluster Monte Carlo algorithm for the simulation of dielectric media. The algorithm avoids solving the Poisson equation and remains efficient in the presence of spatial heterogeneity,...

Magnetic force probe for nanoscale biomolecules.

We present a new technique to measure the mechanical properties of small biomolecules. This technique uses long range repulsive colloidal forces together with magnetic attraction as a force probing tool. The biomolecules are grafted between superparamagnetic particles, which are regularly spaced within long chains maintained by an external magnetic field. Varying the magnetic field results in c...