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Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…
We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$…
A fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. In many cases, pattern formation is driven by the positional information determined by both the gradient of maternal factors and hard-wired…
Although somatic mutations are the main contributor to cancer, underlying germline alterations may increase the risk of cancer, mold the somatic alteration landscape and cooperate with acquired mutations to promote the tumor onset and/or…
Breast cancer continues to be a significant cause of mortality among women globally. Timely identification and precise diagnosis of breast abnormalities are critical for enhancing patient prognosis. In this study, we focus on improving the…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA…
We comment on the paper "Dark Matter collisions with the Human Body" by K. Freese and C. Savage (Phys. Lett. B 717, 25 (2012) [arXiv:1204.1339]) and describe a dark matter model for which the results of the previous paper do not quite…
Structure determination is necessary to identify unknown organic molecules, such as those in natural products, forensic samples, the interstellar medium, and laboratory syntheses. Rotational spectroscopy enables structure determination by…
Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes. However, the similarities of such signatures across different cancer types have not been strong enough to conclude…
In this survey article, a variety of systems modeling tumor growth are discussed. In accordance with the hallmarks of cancer, the described models incorporate the primary characteristics of cancer evolution. Specifically, we focus on…
Quantum Chromodynamics is an established part of the Standard Model and an essential part of the toolkit for searching for new physics at high-energy colliders. I present a status report on the theory of QCD and review some of the important…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
This paper reviews the new highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The paper highlights several relevant examples of recent advances in the field and provides a roadmap…
Mankind has not yet explained dark matter, the accelerating expansion of the Universe, the 'knee' and 'ankle' of the cosmic ray energy spectrum graph, the low star formation rates of low surface brightness (LSB) dwarf galaxies, the ignition…
The problem of the onset and growth of solid tumour in homogeneous tissue is regarded using an approach based on local interaction between the tumoral and the sane tissue cells. The characteristic sizes and growth rates of spherical…
Quantum Chromodynamics (QCD) is generally assumed to be the fundamental theory underlying nuclear physics. In recent years there is progress towards investigating the nucleon structure from first principles of QCD. Although this structure…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…