Analysis of space-time correlations of diffusive particles in viscoelastic media

Diffusion is the major short-range transport mechanism in living cells. Within individual compartments of a eukaryotic cell, such as the nucleus, mitochondria or the cytosol, biological macromolecules find their targets mostly by thermally driven random motion. For instance, specific access of DNA-binding proteins to their target sequences in the genome occurs through a sequence of three-dimensional diffusion, DNA-binding and one-dimensional search events on the DNA. The DNA/chromatin network in the cell nucleus thus has two effects on protein diffusion: obstruction due to crowding and accelerated association to specific sequences through guided diffusion along the DNA chain. The problem of target finding of proteins in the cell nucleus is only one example of diffusion-controlled reactions in a dense polymer network. Outside the direct relevance for molecular and cellular biology, the study of diffusing particles in viscoelastic media has important applications in many fields of physics. By recording fast image series of two-dimensional sections of live cells, we monitor these diffusion processes in real time and gain better understanding of the underlying physics. The method used is light sheet fluorescence microscopy followed by auto (-cross) correlation analysis. We particularly studied the random motion of chromatin and its interconnection with nucleoplasmic A-type lamins. Utilizing this method, we find that 1. Nucleoplasmic lamin As and chromatin show significant co-mobility, indicating that their motions are interconnected in the nucleus. 2. The random motion of histones H2A within the chromatin network is subdiffusive, i.e. the effective diffusion coefficient decreases for slow timescales. Knocking out lamin A changes the diffusion back to normal. Thus, lamin A influences the dynamics of the entire chromatin network. 3. A-type lamins affect the spatial organisation of chromatin inside the cellular interior. We have also attempted to develop a modelling framework that describes chromatin dynamics within the cell nucleus in the presence and absence of nucleoplasmic A-type lamins. Our conclusion is that lamin A plays a central role in determining the viscoelasticity of the chromatin network and helping to maintain local ordering of interphase chromosomes. These findings enabled us to derive a qualitative description of diffusion based on the viscoelasticity of the cellular environment

Towards a robust criterion of anomalous diffusion

Anomalous-diffusion, the departure of the spreading dynamics of diffusing particles from the traditional law of Brownian-motion, is a signature feature of a large number of complex soft-matter and biological systems. Anomalous-diffusion emerges due to a variety of physical mechanisms, e.g., trapping interactions or the viscoelasticity of the environment. However, sometimes systems dynamics are erroneously claimed to be anomalous, despite the fact that the true motion is Brownian -- or vice versa. This ambiguity in establishing whether the dynamics as normal or anomalous can have far-reaching consequences, e.g., in predictions for reaction- or relaxation-laws. Demonstrating that a system exhibits normal- or anomalous-diffusion is highly desirable for a vast host of applications. Here, we present a criterion for anomalous-diffusion based on the method of power-spectral analysis of single trajectories. The robustness of this criterion is studied for trajectories of fractional-Brownian-motion, a ubiquitous stochastic process for the description of anomalous-diffusion, in the presence of two types of measurement errors. In particular, we find that our criterion is very robust for subdiffusion. Various tests on surrogate data in absence or presence of additional positional noise demonstrate the efficacy of this method in practical contexts. Finally, we provide a proof-of-concept based on diverse experiments exhibiting both normal and anomalous-diffusion.Comment: 13 pages, 6 figures, RevTe

Microarchitected Compliant Scaffolds of Pyrolytic Carbon for 3D Muscle Cell Growth

The integration of additive manufacturing technologies with the pyrolysis of polymeric precursors enables the design-controlled fabrication of architected 3D pyrolytic carbon (PyC) structures with complex architectural details. Despite great promise, their use in cellular interaction remains unexplored. This study pioneers the utilization of microarchitected 3D PyC structures as biocompatible scaffolds for the colonization of muscle cells in a 3D environment. PyC scaffolds are fabricated using micro-stereolithography, followed by pyrolysis. Furthermore, an innovative design strategy using revolute joints is employed to obtain novel, compliant structures of architected PyC. The pyrolysis process results in a pyrolysis temperature- and design-geometry-dependent shrinkage of up to 73%, enabling the geometrical features of microarchitected compatible with skeletal muscle cells. The stiffness of architected PyC varies with the pyrolysis temperature, with the highest value of 29.57 ± 0.78 GPa for 900 °C. The PyC scaffolds exhibit excellent biocompatibility and yield 3D cell colonization while culturing skeletal muscle C2C12 cells. They further induce good actin fiber alignment along the compliant PyC construction. However, no conclusive myogenic differentiation is observed here. Nevertheless, these results are highly promising for architected PyC scaffolds as multifunctional tissue implants and encourage more investigations in employing compliant architected PyC structures for high-performance tissue engineering applications

A new approach to chemicals warehouse risk analysis using computational fluid dynamics simulation and fuzzy Bayesian network

This study aims to assess the risk of chemicals warehouse using a Bayesian networks (BNs) and computational fluid dynamics (CFD). A methodology combining Bow-Tie (BT), fuzzy set theory (FST), and Bayesian network was employed, in which the BT was drawn for chemical spill scenarios. FST was utilized for the estimation of the basic events (BEs) occurrence probability, and the probability of interaction among a set of variables was obtained using BNs. Pool fire scenario radiation heat flux was evaluated using CFD code, fire dynamic simulator (FDS), and the solid flame model (SFM). Fail in forklift brake system (BE1), was the most significant cause for a chemical spill. Based on the CFD model, the heat flux is 31 kW/m2 at a distance of 3.5 m from the fire, decreasing to 6.5 m gradually. The maximum safety distance of 4 m is predicted by the CFD for heat flux that exceeds 12.5 kW/m2; however, SFM predicts approximately 4.5 m. According to the results, the amount of posterior risk is higher than the prior value. The framework presented in the chemicals warehouse for consequence analysis and dynamic risk assessment (DRA) of pool fire could be used for preventing the accidents and domino effects in the chemicals warehouse