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Single particle cryo-electron microscopy (EM) is an increasingly popular method for determining the 3-D structure of macromolecules from noisy 2-D images of single macromolecules whose orientations and positions are random and unknown. One…
Marine plankton play a crucial role in carbon storage, oxygen production, global climate, and ecosystem function. Planktonic ecosystems are embedded in a Lagrangian patches of water that are continuously moving, stretching, and diluting.…
Collective cell migration plays an essential role in vertebrate development, yet the extent to which dynamically changing microenvironments influence this phenomenon remains unclear. Observations of the distribution of the extracellular…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
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…
Immunohistochemistry (IHC) is essential for assessing specific immune biomarkers like Human Epidermal growth-factor Receptor 2 (HER2) in breast cancer. However, the traditional protocols of obtaining IHC stains are resource-intensive,…
This work deals with the characterisation and modelling of the curing process and its associated volume changes of an epoxy based thermoset resin. Measurements from differential scanning calorimetry (DSC) define the progress of the chemical…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Underwater images are fundamental for studying and understanding the status of marine life. We focus on reducing the memory space required for image storage while the memory space consumption in the collecting phase limits the time lasting…
Evidence accumulated over the past decade provides support for liquid-liquid phase separation as the mechanism underlying the formation of biomolecular condensates, which include not only membraneless organelles such as nucleoli and RNA…
This paper presents a novel approach for denoising Electron Backscatter Diffraction (EBSD) patterns using diffusion models. We propose a two-stage training process with a UNet-based architecture, incorporating an auxiliary regression head…
We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$…
We construct a simple model of a proto-cell that simulates a stochastic dynamics of abstract chemicals on a two-dimensional lattice. We assume that chemicals catalyze their reproduction through interaction with each other, and that between…
Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of…
The lattice gas model of condensation in a heterogeneous pore system, represented by a random graph of cells, is studied using an exact analytical solution. A binary mixture of pore cells with different coordination numbers is shown to…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
Transitions between metabasins in supercooled liquids seem to occur through rapid "democratic" collective particle rearrangements. Here we show that this apparent homogeneous particle motion is a direct consequence of dynamic facilitation.…
The slow dynamics of glass-forming liquids is generally ascribed to the cage-jump motion. In the cage-jump picture, a molecule remains in a cage formed by neighboring molecules, and after a sufficiently long time, it jumps to escape from…
The dynamical arrest of gels is the consequence of a well defined structural phase transition, leading to the formation of a spanning cluster of bonded particles. The dynamical glass transition, instead, is not accompanied by any clear…
A time-domain representation of chromatographic peak shapes is presented as an analytic expression designed for high computational efficiency, which can be used for direct time-domain peak fitting with parameters that represent physical…