Related papers: RSC remodeling of oligo-nucleosomes: an atomic for…
regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal…
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the…
We review recent efforts to detect small numbers of nuclear spins using magnetic resonance force microscopy. Magnetic resonance force microscopy (MRFM) is a scanning probe technique that relies on the mechanical measurement of the weak…
A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
Atomic force microscopy (AFM) can be used to characterise several aspects of the surface degradation and reinforcement mechanisms of zirconia based ceramics, such as crack propagation, martensitic relief formation, grains pull-out and…
Automated cell detection and localization from microscopy images are significant tasks in biomedical research and clinical practice. In this paper, we design a new cell detection and localization algorithm that combines deep convolutional…
Microscopic optical potentials have been successful in describing nucleon-nucleus and nucleus-nucleus scattering. Some essential ingredients of the framework, however, have not been examined in detail. Applicability of the microscopic…
ATP-dependent chromatin remodeling enzymes (CRE) are bio-molecular motors in eukaryotic cells. These are driven by a chemical fuel, namely, adenosine triphosphate (ATP). CREs actively participate in many cellular processes that require…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
Comparative genomics methods are widely used to aid the functional annotation of non coding DNA regions. However, aligning non coding sequences requires new algorithms and strategies, in order to take into account extensive rearrangements…
Apart from being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. The detailed knowledge of this code contrasts the…
In ferromagnetic (FM) metal/organic semiconductor (OSC) heterostructures charge transfer can occur which leads to induction of magnetism in the non-magnetic OSC. This phenomenon has been described by the change in the density of states in…
Critical experimental design issues connecting energy transduction and inheritable information within a protocell are explored and elucidated. The protocell design utilizes a photo-driven energy transducer (a ruthenium complex) to turn…
Background and Objectives: The mechanics of the nucleus depends on cellular structures and architecture, and impact a number of diseases. Nuclear mechanics is yet rather complex due to heterogeneous distribution of dense heterochromatin and…
Atomic force microscopy (AFM) is a mechanical profiling technique that allows to image surfaces with atomic resolution. Recent progress in reducing the noise of this technique has led to a resolution level where previously undetectable…
Osteoclastic resorption of bone plays a central role in both osteoporosis and bone metastasis. A reliable in vitro assay that simulates osteoclastic resorption in vivo would significantly speed up the process of devel-oping effective…
With the invention of scanning probe techniques, direct imaging of single atoms and molecules became possible. Today, scanning tunnelling microscopy (STM) routinely provides angstrom-scale image resolution. At the same time, however, STM…
Nucleosome core particle is a dynamic structure -- DNA may transiently peel off the histone octamer surface due to thermal fluctuations or the action of chromatin remodeling enzymes. Partial DNA unwrapping enables easier access of…
Atomic Force Microscopy (AFM) has a great potential as a tool to characterize mechanical and morphological properties of living cells; these properties have been shown to correlate with cells' fate and patho-physiological state in view of…