生物物理
Understanding the mechanisms underlying general anesthesia would be a key step towards understanding consciousness. The process of xenon-induced general anesthesia has been shown to involve electron transfer, and the potency of xenon as a…
To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically…
The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of…
Bacteria can chemotactically migrate up attractant gradients by controlling run-and-tumble motility patterns. In addition to this well-known chemotactic behaviour, several soil and marine bacterial species perform chemokinesis: they adjust…
The Spatial Convolution Model (SCM) analyzes allostery based on the spatial evolution of the docking protein elastic media, whereby convolution of the media in response to wave propagation is solved as a function of Z fluctuations and…
The poor delivery of nanoparticles to target cancer cells hinders their success in the clinical setting. In this work, an alternative target readily available for circulating nanoparticles has been selected to eliminate the need for…
Considering a double-headed Brownian motor moving with both translational and rotational degrees of freedom, we investigate the directed transport properties of the system in a traveling-wave potential. It is found that the traveling wave…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
Several recent experiments, including our own in the fission yeast, S. pombe, have characterized the motions of gene loci within living nuclei by measuring the locus position over time, then proceeding to obtain the statistical properties…
In this paper, we identify optimal swimming strategies for drag-dominated swimmers with a passive elastic joint. We use resistive force theory (RFT) to obtain the dynamics of the system. We then use frequency domain analysis to relate the…
Polymerization of dendritic actin networks underlies important mechanical processes in cell biology such as the protrusion of lamellipodia, propulsion of growth cones in dendrites of neurons, intracellular transport of organelles and…
The method of oncotripsy, first proposed in [S. Heyden and M. Ortiz (2016). Oncotripsy: Targeting cancer cells selectively via resonant harmonic excitation. Journal of the Mechanics and Physics of Solids, 92:164-175], exploits aberrations…
The vertex model is a popular framework for modelling tightly packed biological cells, such as confluent epithelia. Cells are described by convex polygons tiling the plane and their equilibrium is found by minimizing a global mechanical…
In biological systems, the growth of cells, tissues, and organs is influenced by mechanical cues. Locally, cell growth leads to a mechanically heterogeneous environment as cells pull and push their neighbors in a cell network. Despite this…
The ability of bacteria to colonize and grow on different surfaces is an essential process for biofilm development and depends on complex biomechanical interactions between the biofilm and the underlying substrate. Changes in the physical…
Nano-communication has gained significant attention in the last few years, as a means to establish information transfer between future nano-machines. Comparing with other communication techniques for nano-scale (calcium ions signaling,…
The simplest ring oscillator is made from three strongly nonlinear elements repressing each other unidirectionally resulting in the emergence of a limit cycle. A popular implementation of this scheme uses repressive genes in bacteria…
The low efficiency of commercially-used reverse osmosis (RO) membranes has been the main obstacle in seawater desalination application. Here, we report the auspicious performance, through molecular dynamics simulations, of a seawater…
We develop a mathematical model to capture the web dynamics of slingshot spiders (Araneae: Theridiosomatidae), which utilize a tension line to deform their orb webs into conical springs to hunt flying insects. Slingshot spiders are…
Several organelles in eukaryotic cells, including mitochondria and the endoplasmic reticulum, form interconnected tubule networks extending throughout the cell. These tubular networks host many biochemical pathways that rely on proteins…