Related papers: Magnetic Polymer Models for Epigenetics-Driven Chr…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
Single-molecule force-extension experiments have allowed quantitative measurements of the mechanical responses of biomolecules to applied forces explaining their roles in key biological functions. Electrophoretic stretching of charged…
Gene regulatory network (GRN)-based morphogenetic models have recently gained an increasing attention. However, the relationship between microscopic properties of intracellular GRNs and macroscopic properties of morphogenetic systems has…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
Magnetic gels with embedded micro/nano-sized magnetic particles in crosslinked polymer networks can be actuated by external magnetic fields, with changes in their internal microscopic structures and macroscopic mechanical properties. We…
Many morphogenetic processes involve mechanical rearrangement of epithelial tissues that is driven by precisely regulated cytoskeletal forces and cell adhesion. The mechanical state of the cell and intercellular adhesion are not only the…
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
Langevin Dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is…
In this letter we explore how the microscopic dynamics of charge transfer (CT) excitons are influenced by the presence of an external magnetic field in disordered molecular semiconductors. This influence is driven by the dynamic interplay…
Embryogenesis is a multiscale process during which developmental symmetry breaking transitions give rise to complex multicellular organisms. Recent advances in high-resolution live-cell microscopy provide unprecedented insights into the…
Braids composed of two interwoven polymer chains exhibit a buckling transition whose origin has been explained through the onset of plectonemic structures. Here we study, by a combination of simulation and analytics, the dynamics of…
Gene sequences of a deme evolve over time as new chromosome inversions appear in a population via mutations, some of which will replace an existing sequence. The underlying biochemical processes that generates these and other mutations are…
In vivo, eukaryotic cells are embedded in a matrix environment, where they grow and develop. Generally, this extracellular matrix (ECM) is an anisotropic fibrous structure, through which macromolecules and biochemical signaling molecules at…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy and mass spectrometry to dissect…
Morphogen profiles play a vital role in biology by specifying position in embryonic development. However, the factors that influence the shape of a morphogen profile remain poorly understood. Since morphogens should provide precise…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…