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Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…
Chemical autoencoders are attractive models as they combine chemical space navigation with possibilities for de-novo molecule generation in areas of interest. This enables them to produce focused chemical libraries around a single lead…
Biopolymer length regulation is a complex process that involves a large number of subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length…
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…
Metasurfaces play a key role in functionalizing light at the nanoscale. Existing dielectric metasurfaces, however, are often limited to geometric primitives and their usage in emergent hybrid metasurfaces is hampered as confinement of light…
Paediatric Acute Myeloid Leukemia is a complex adaptive ecosystem with high morbidity. Current trajectory inference algorithms struggle to predict causal dynamics in AML progression, including relapse and recurrence risk. We propose a…
A challenging topic in materials engineering is the development of numerical models that can accurately predict material properties with atomistic accuracy, matching the scale and level of detail achieved by experiments. In this regard,…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…
Plasmons in atomically thin materials offer a compelling route to trigger nonlinear light-matter interactions through extreme optical confinement in the two-dimensional (2D) limit. However, optical nonlocality in plasmons is typically…
Plasma membranes appear as deformable systems wherein molecules are free to move and diffuse giving rise to condensed microdomains (composed of ordered lipids, transmembrane proteins and cholesterol) surrounded by disordered lipid…
Biological cells exhibit a hierarchical spatial organization, where various compartments harbor condensates that form by phase separation. Cells can control the emergence of these condensates by affecting compartment size, the amount of the…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration…
Heterogeneity within tumour cell populations is associated with an increase in malignancy and appears to play an important role during cancer metastasis. Using in silico experiments, we study the interplay between collective behaviours and…
A model for a monolayer of two types of particles spontaneously forming ordered patterns is studied by a mesoscopic theory and by MC simulations. We assume hard-cores of the same size for both components, short-range attraction long-range…
In a cellular medium, the plasmic membrane is a place of interactions between the cell and its direct external environment. A classic model describes it as a fluid mosaic. The fluid phase of the membrane allows a lateral degree of freedom…
Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to explore the role of 3D…
Circadian rhythms in mammals are controlled by the neurons located in the suprachiasmatic nucleus of the hypothalamus. In physiological conditions, the system of neurons is very efficiently entrained by the 24-hour light-dark cycle. Most of…
High-throughput preclinical perturbation screens, where the effects of genetic, chemical, or environmental perturbations are systematically tested on disease models, hold significant promise for machine learning-enhanced drug discovery due…
Living cells are characterized by the micrometric confinement of various macromolecules at high concentrations. Using droplets containing binary polymer blends as artificial cells, we previously showed that cell-sized confinement causes…