Changes in the chemical configuration of alloyed nanoparticle (NP) catalysts induced by adsorbates under working conditions, such as reversal in core-shell preference, are crucial to understand and design NP functionality. We extend the cluster expansion method to predict the configurational thermodynamics of alloyed NPs with adsorbates based on density functional theory data. Exemplified with ...

The packing of the genomic DNA in the living cell is essential for its biological function. While individual aspects of the genome architecture, such as DNA and nucleosome structure or the arrangement of chromosome territories are well studied, much information is missing for a unified description of cellular DNA at all its structural levels. Computer modeling can contribute to such a descripti...

Mitotic chromosomes are the iconic structures into which the genome is packaged to ensure its accurate segregation during mitosis. Although they have appeared on countless journal cover illustrations, there remains no consensus on how the chromatin fiber is packaged during mitosis. In fact, work in recent years has both added to existing controversies and sparked new ones. By contrast, there ha...

Mössbauer spectroscopy (MS) is not a routine method for the evaluation of the concentration of iron in samples. Due to its great advantage of being a method which does not destroy the sample, it is used when one is dealing with hardly available material, like extraterrestrial samples (e.g., meteorites, lunar soil) or with biological samples, which after the Mössbauer spectroscopy measurements m...

The relatively high co-occurrence of Parkinson's disease (PD) and melanoma has been established by a large number of epidemiological studies. However, a clear biological explanation for this finding is still lacking. Ultra-violet radiation (UVR)-induced skin melanin synthesis is a defense mechanism against UVR-induced damage relevant to the initiation of melanoma, whereas, increased neuromelani...

1. Synaptosomes Kiebler et al [1] was the first group to describe the use of a discontinuous iodixanol gradient in the isolation of dendritic spines from mouse hippocampus. The gradient comprised four layers of 9%, 12.5%, 15% and 25% (w/v) iodixanol (equivalent to densities of 1.076, 1.095, 1.105 and 1.152 g/ml); the densest solution contained the material pelleted from the hippocampal homogena...

The spatial organization of genes and chromosomes plays an important role in the regulation of several DNA processes. However, the principles and forces underlying this nonrandom organization are mostly unknown. Despite its small dimension, and thanks to new imaging and biochemical techniques, studies of the budding yeast nucleus have led to significant insights into chromosome arrangement and ...

Proteins that bind DNA so as to reduce its end-to-end length can be dissociated by application of force. The thermodynamics of this process are discussed, with special attention to the case of histones bound to DNA (i.e., a string of nucleosomes, or chromatin fiber). The histone octamer is predicted to be driven off chromatin fiber for tensions >2 piconewtons.

DNA spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core, are ubiquitous in nature. We develop a general theory describing the nonequilibrium behavior of DNA spools under linear tension. Two puzzling and seemingly unrelated recent experimental findings, the sudden quantized unwrapping of nucleosomes and that of DNA toroidal condensates under tension...