Related papers: How human-derived brain organoids are built differ…
Organoids are prototypes of human organs derived from cultured human stem cells. They provide a reliable and accurate experimental model to study the physical mechanisms underlying the early developmental stages of human organs…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
Brain organoids recapitulate a number of brain properties, including neuronal diversity. However, do they recapitulate brain structure? Using a hydrodynamic description for cell nuclei as particles interacting initially via an effective,…
The aim of this paper is to give an overview of brain organoid computing, its characteristics, challenges, as well as possible advantages for future applications in the field of artificial intelligence. An important part is the extensive…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
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…
There are many experimental data indicating the correlations of the changes in high level of organization of chromatin in human cells and changes in the state of the whole organism related to disease, state of tiredness or aging. In our…
The human connectome represents a network map of the brain's wiring diagram and the pattern into which its connections are organized is thought to play an important role in cognitive function. The generative rules that shape the topology of…
Chromatin is repeatedly deformed in vivo during transcription, nuclear remodeling, and confined migration - yet how mechanical response varies from locus to locus, and how it relates to epigenetic state, remains unclear. We develop a theory…
Structural connectivity in the brain is typically studied by reducing its observation to a single spatial resolution. However, the brain possesses a rich architecture organized over multiple scales linked to one another. We explored the…
The study of organoids, artificially grown cell aggregates with the functionality and small-scale anatomy of real organs, is one of the most active areas of research in biology and biophysics, yet the basic physical origins of their…
The relation between large-scale brain structure and function is an outstanding open problem in neuroscience. We approach this problem by studying the dynamical regime under which realistic spatio-temporal patterns of brain activity emerge…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
The brain is immensely complex, with diverse components and dynamic interactions building upon one another to orchestrate a wide range of functions and behaviors. Understanding patterns of these complex interactions and how they are…
Chromatin is a complex of DNA and specific proteins forming an intermediary level of organization of eukaryotic genomes, between double-stranded DNA and chromosome. Within a generic modeling of the chromatin assembly, we investigate the…
The spatial organization of chromatin within the nucleus plays a crucial role in gene expression and genome function. However, the quantitative relationship between this organization and nuclear biochemical processes remains under debate.…
A complete understanding of the brain requires an integrated description of the numerous scales of neural organization. It means studying the interplay of genes, synapses, and even whole brain regions which ultimately leads to different…
In this essay we elaborate on recent evidence demonstrating the presence of a second order phase transition in human brain dynamics and discuss its consequences for theoretical approaches to brain function. We review early evidence of…