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We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary ...
The stochastic equations of motion for a system of interacting rigid bodies in a solvent are formulated and studied. Three-dimensional bodies of arbitrary shape, with arbitrary couplings between translational and rotational degrees of freedom, as arise in ...
This article is a survey of the present state of the transfer operator approach to the effective dynamics of metastable complex systems, and the variety of algorithms associated with it. We introduce new methods, and we emphasize both the conceptional foun ...
In various single-molecule experiments, a chiral polymer, such as DNA, is simultaneously pulled and twisted. We address an elementary but fundamental question raised by various authors: does the molecule overwind or unwind under tension? We show that withi ...
The most classic approach to the dynamics of an n-dimensional mechanical system constrained by d independent holonomic constraints is to pick explicitly a new set of (n - d) curvilinear coordinatesparametrizingthe manifold of configurations satisfying the ...
A method is described to extract a complete set of sequence-dependent material parameters for rigid base and basepair models of DNA in solution from atomistic molecular dynamics simulations. The method is properly consistent with equilibrium statistical me ...
We consider an elastic chain at thermodynamic equilibrium with a heat bath, and derive an approximation to the probability density function, or pdf, governing the relative location and orientation of the two ends of the chain. Our motivation is to exploit ...
We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algori ...
Given two samples of continuous zero-mean iid Gaussian processes on [0,1], we consider the problem of testing whether they share the same covariance structure. Our study is motivated by the problem of determining whether the mechanical properties of short ...
It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein-DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive ...
