软凝聚态物质
We present a Brownian dynamics simulation of the bacterial Stirling engine studied by Krishnamurthy et al., Nat. Phys. 12, 1134 (2016). In their experimental setup, an overdamped colloid in an optical trap with time-modulated stiffness…
Recent developments in topological mechanics have demonstrated the ability of Maxwell lattices to effectively focus stress along domain walls between differently polarized domains. The focusing ability can be exploited to protect the…
Accurate constitutive models and corresponding mechanical property values for the meninges are important for predicting mechanical damage to brain tissue due to traumatic brain injury. The meninges are often oversimplified in current finite…
The stability of water against cavitation under negative pressures is a phenomenon known for considerable discrepancies between theoretical predictions and experimental observations. Using a combination of molecular dynamics simulations and…
We present an innovative template-free water-based sol-gel method to produce uniform mesoporous silica beads of millimeter size, which have tunable size, stiffness and porosity, and could be used for adsorption applications. Our protocol…
Active, responsive, nonequilibrium materials, at the forefront of materials engineering, offer dynamical restructuring, mobility and other complex life-like properties. Yet, this enhanced functionality comes with significant amplification…
We use a continuum, two-fluid approach to study a mixture of two active nematic fluids. Even in the absence of thermodynamically-driven ordering, for mixtures of different activities we observe turbulent microphase separation, where domains…
Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of linear…
Understanding the relationship between the microscopic structure and topology of a material and its macroscopic properties is a fundamental challenge across a wide range of systems. Here, we investigate the viscoelasticity of DNA nanostar…
Knots are deeply entangled with every branch of science. One of the biggest open challenges in knot theory is to formalise a knot invariant that can unambiguously and efficiently distinguish any two knotted curves. Additionally, the…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
In spite of the nanoscale and single-molecule insights into how nucleoid associated proteins (NAPs) interact with DNA, their role in modulating the mesoscale viscoelasticity of the entangled genome in vivo has been overlooked so far. By…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Crystallization of biological molecules has high potential to solve some challenges in drug manufacturing. Thus, understanding the process is critical to efficiently adapting crystallization to biopharmaceutical manufacturing. This article…
Lipid bilayers often form high-curvature configurations due to self-assembly conditions or certain biological processes. However, particle-based simulations of lipid membranes are predominantly of flat lipid membranes because planar…
We use extensive molecular dynamics simulations to calculate thermal conductivity and thermal diffusivity in two common molten salts, LiF and KCl. Our analysis includes the total thermal conductivity and intrinsic conductivity involving…
Two-dimensional (2D) mechanical models of confluent tissues have related the mechanical state of a monolayer of cells to the average perimeter length of the cell cross sections, predicting floppiness or rigidity of the material. For the…
The structure and dynamics of fluids confined in nanoporous media differ from those in bulk, which can be probed using NMR relaxation measurements. We here show, using atomistic molecular dynamics simulations of water in a slit nanopore,…