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 structural and dynamic dataset which is currently unavailable from experiment. A consortium of laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing information not only on all 10 unique base pair steps, but also on all possible nearest-neighbor effects on these steps. These results are derived from simulations of 50–100 ns on 39 different DNA oligomers in explicit solvent and using a physiological salt concentration. We demonstrate that the simulations are converged in terms of helical and backbone parameters. The results show that nearest-neighbor effects on base pair steps are very significant, implying that dinucleotide models are insufficient for predicting sequence-dependent behavior. Flanking base sequences can notably lead to base pair step parameters in dynamic equilibrium between two conformational sub-states. Although this study only provides limited data on next-nearest-neighbor effects, we suggest that such effects should be analyzed before attempting to predict the sequence-dependent behavior of DNA.

We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters.

Ever since the discovery of the nucleosome in 1974, scientists have stumbled upon discrete particles in which DNA is wrapped around histone complexes of different stoichiometries: octasomes, hexasomes, tetrasomes, "split" half-nucleosomes, and, recently, bona fide hemisomes. Do all these particles exist in vivo? Under what conditions? What is their physiological significance in the complex DNA transactions in the eukaryotic nucleus? What are their dynamics? This review summarizes research spanning more than three decades and provides a new meaning to the term "nucleosome." The nucleosome can no longer be viewed as a single static entity: rather, it is a family of particles differing in their structural and dynamic properties, leading to different functionalities.

Numerical experiments are performed on a 36,000-atom protein᎐DNA᎐water simulation to ascertain the effectiveness of two devices for reducing the time spent computing long-range electrostatics interactions. It is shown for Verlet-Irr-RESPA multiple time stepping, which is based on approximating long-range forces as widely separated impulses, that a long time step of 5 fs results in a dramatic energy drift and that this is reduced by using an even larger long time step. It is also shown that the use of as many as six terms in a fast multipole algorithm approximation to long-range electrostatics still fails to prevent significant energy drift even though four digits of accuracy is obtained.

We theoretically discuss an implementation of a Sagnac interferometer with cold atoms. In contrast to currently existing schemes our protocol does not rely on any free propagation of atoms. Instead it is based on superpositions of fully confined atoms and state-dependent transport along a closed path. Using Ramsey sequences for an atomic clock, the accumulated Sagnac phase is encoded in the resulting population imbalance between two internal (clock) states. Using minimal models for the above protocol we analytically quantify limitations arising from atomic dynamics and finite temperature. We discuss an actual implementation of the interferometer with adiabatic radio-frequency potentials that is inherently robust against common mode noise as well as phase noise from the reference oscillator.PACS numbers: 07.60. Ly, 03.75.Dg The Sagnac effect enables interferometric measurements of rotation with high precision [1]. For example, the large Wettzell laser gyroscope achieves a theoretical resolution of 10. Interferometers based on matterwaves instead of light promise resolution enhancement by orders of magnitude that scales with particle mass [3], see [4] for a recent review. Despite the immense challenges in achieving similar particle flux and interferometer areas as with photons, atomic gyroscopes [5,6] have reached performance levels that should enable applications in fundamental physics, geodesy, seismology, or inertial navigation. Atom interferometers [7] have been demonstrated with record sensitivities below 10 −9 rad/ √ s [8, 9] outperforming commercial navigation sensors by orders of magnitude. Recent experiments aim at geodetic [10] and navigational applications combining multi-axis measurements of acceleration and rotation [11,12]. Since free falling atoms require large apparatus size, ring shaped traps and guided interferometers have been proposed [13][14][15][16] and demonstrated [17][18][19][20][21][22] for a variety of geometries and levels of sophistication, e.g., using soliton dynamics in Bose-Einstein condensates to enhance sensitivity by non-linear interactions or to prevent wavepacket dispersion [23][24][25].So far, the paradigm for matter wave Sagnac interferometry relies on DeBroglie waves and thus on free propagation of atoms either in free fall or within waveguides. However, the Sagnac effect can be expressed as a propertime difference experienced by two observers moving in opposite directions along closed paths and has indeed been measured with atomic clocks flown around Earth [26]. Inspired by this, we investigate an interferometer comprised of a single atomic clock. It uses the acquired phase shift between atoms in two different internal clock (spin) states that are each fully confined in atom traps but separately displaced. This approach offers a high degree of control over atomic motion, removing velocity dependent effects and phase front and interferometric stability requirements of laser beams. It improves con- Figure 1: Experimental sequence depicted in an inertial frame. Starting wit...