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One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
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…
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
The spatial positioning of chromosomes relative to functional nuclear bodies is intertwined with genome functions such as transcription. However, the sequence patterns and epigenomic features that collectively influence chromatin spatial…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The…
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
We study the motion of long polymers (eg DNA) in a gel under the influence of an external force acting locally on small segments of the polymer. In particular, we examine the dependence of the drift velocity on the position where the force…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such…