Thermodynamics of Writhe in DNA Minicircles from Molecular Dynamics Simulations
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Sequence dependent mechanics of DNA is believed to play a central role in the functioning of the cell through the expression of genetic information. Nucleosome positioning, gene regulation, DNA looping and packaging within the cell are only some of the pro ...
Network models have been used to study the underlying processes and principles of biological systems for decades, providing many insights into the complexity of life. Biological systems require a constant flow of free energy to drive these processes that o ...
When adsorbing guest molecules, the porous metal-organic framework MIL-53(Cr) may vary its cell parameters drastically while retaining its crystallinity. A first approach to the thermodynamic analysis of this "framework breathing" consists of comparing the ...
2013
Water is ubiquitous in the biosphere, and the difficulty of rigorously treating the effects of aqueous solvation currently limits the widespread use of computational methods in many areas of environmental chemistry. We propose an approach to benchmark calc ...
2015
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Chloramines, bromamines, and bromochloramines are halogen-containing oxidants that arise from the reaction between ammonia and hypohalous acids during the disinfection of drinking and wastewaters. Although involved in the formation of toxic disinfection by ...
cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated fre ...
The oxidation of ground-state (singlet) and triplet Ru(bpy)(3) were studied by full quantum-mechanical (QM) and mixed quantum/classical (QM/MM) molecular dynamics simulations. Both approaches provide reliable results for the redox potentials of the t ...
We study the thermodynamics of cubic Ti1-xAlxN using a unified cluster expansion approach for the alloy problem. The purely configurational part of the alloy Hamiltonian is expanded in terms of concentration- and volume-dependent effective cluster interact ...
DNA damages induced by oxidative intrastrand cross-links have been the subject of intense research during the past decade. Yet, the currently available experimental protocols used to isolate such lesions only allow to get structural information about linke ...
2012
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In cells, DNA is routinely subjected to significant levels of bending and twisting. In some cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it transitions into non-canonical structural conformations that are c ...