The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA c...

Proper orthogonal decomposition is a statistical pattern analysis technique for "nding the dominant structures, called the proper orthogonal modes, in an ensemble of spatially distributed data. While the proper orthogonal modes are obtained through a statistical formulation, they can be physically interpreted in the "eld of structural dynamics. The purpose of this paper is thus to provide some ...

TLS (translation/libration/screw) models describe rigid-body vibrational motions of arbitrary objects. A single-group TLS model can be used to approximate the vibration of an entire protein molecule within a crystal lattice. More complex TLS models are broadly applicable to describing inter-domain and other internal vibrational modes of proteins. Such models can be derived and refined from crys...

where n is the forcing function. In our problems, the mass and stiffness matrices are symmetric with the former semidefinite and the latter being positive definite. (We have ignored the damping term for now but it will be relevant in future.) The forcing function n is a product of a vector f that specifies the spatial distribution of the force and a scalar function g(t) that governs the tempora...

The history of ethno-national conflict on the ethnically divided Mediterranean island of Cyprus has decisively marked the communication process between the major stakeholders in the conflict, but most of all, and in a profound way, between the two Cypriot communities, namely, between Greek Cypriots (G/Cs) and Turkish Cypriots (T/Cs). The so-called Green Line, which ethnically divides the capita...

Knowledge management (KM) strategy is the planned or actual coordination of a firm’s major goals and learning, in time, that continually co-align its knowledge-based resources with the environment. This study combined a survey study and system dynamics (SD) simulation to demonstrate an organic KM performance evaluation approach. The survey study was conducted based on a sample of 143 constructi...

The first proton transfer in the bacteriorhodopsin photocycle takes place during the L → M transition. Structural details of the pre proton transfer L intermediate have been investigated using experiments and computations. Here, we assess L-state structural models by performing hybrid quantum mechanical/molecular mechanical molecular dynamics and excitation energy calculations. The computations...

The ability of matrix-assisted pulsed laser evaporation (MAPLE) technique to transfer and deposit high-quality thin organic, bioorganic, and composite films with minimum chemical modification of the target material has been utilized in numerous applications. One of the outstanding problems in MAPLE film deposition, however, is the presence of residual solvent (matrix) codeposited with the polym...

Graph transformation systems can be employed to describe systems with complex structural dynamics which states can be captured by attributed graphs. However, like many other standard computer science models such as automata in their basic form time, continuous behavior, or probabilistic behavior are not supported. In this talk we will report on a number of extensions for graph transformation sy...

The temporal evolution of electron shadow images, formed by the projection of primary femtosecond electron pulses probe over a metal target and perturbed by the transient space-charge field near the target surface induced by the excitation of femtosecond optical pulses pump , is recorded in real time. By quantitatively analyzing the evolution of these shadow images as a function of pump-probe d...