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We propose a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis, the process of body segmentation during embryonic development, that is invariant across all vertebrate species. This is…
A theoretical treatment of deeply supercooled liquids is difficult because their properties emerge from spatial inhomogeneities that are self-induced, transient, and nanoscopic. I use computer simulations to analyse self-induced static and…
The self-assembly of DNA-coated colloids controlled by enzymatic reactions has the potential to enable the formation of materials with hierarchical organization and switchable configurations. However, the problem of designing such…
This paper presents a novel approach that leverages domain variability to learn representations that are conditionally invariant to unwanted variability or distractors. Our approach identifies both spurious and invariant latent features…
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which…
Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…
We discovered a class of self-similar solutions in nonlinear models describing the formation of morphogen gradients, the concentration fields of molecules acting as spatial regulators of cell differention in developing tissues. These models…
Beyond the genetic code, there is another layer of information encoded as chemical modifications on histone proteins positioned along the DNA. Maintaining these modifications is crucial for survival and identity of cells. How the…
Few questions in condensed matter science have proven as difficult to unravel as the interplay between structure and dynamics in supercooled liquids and glasses. The conundrum: close to the glass transition, the dynamics slow down…
We present a first-principles formalism for studying dynamical heterogeneities in glass forming liquids. Based on the Non-Equilibrium Self-Consistent Generalized Langevin Equation theory, we were able to describe the time-dependent local…
The chromatin folding and the spatial arrangement of chromosomes in the cell play a crucial role in DNA replication and genes expression. An improper chromatin folding could lead to malfunctions and, over time, diseases. For eukaryotes,…
We develop a model the dynamics of human mesenchymal stem cells (hMSCs) and chondrocytes evolving in a nonwoven polyethylene terephtalate (PET) scaffold impregnated with hyaluron and supplied with a differentiation medium. The scaffold and…
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…
Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive…
We use the isoconfigurational (IC) ensemble to show the connection between emerging heterogeneities in the tetrahedral order parameter and the dynamic propensity in a mildly undercooled glass-forming liquid. We observe that spatially…
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…
Driven chemical reactions can control the macroscopic properties of droplets, like their size. Such active droplets are critical in structuring the interior of biological cells. Cells also need to control where and when droplets appear, so…
Supercooled liquids exhibit spatial heterogeneity in the dynamics of their fluctuating atomic arrangements. The length and time scales of the heterogeneous dynamics are central to the glass transition and influence nucleation and growth of…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
Despite the spontaneity of some in vitro protein folding reactions, native folding in vivo often requires the participation of barrel-shaped multimeric complexes known as chaperonins. Although it has long been known that chaperonin…