Biological Physics
The abstract mathematical rules of artificial neural network (ANN) are implemented through computation using electronic computers, photonics and in-vitro DNA computation. Here we demonstrate the physical realization of ANN in living…
Hyaluronic acid is an abundant polyelectrolyte in the human body that forms extracellular hydrogels in connective tissues. It is essential for regulating tissue biomechanics and cell-cell communication, yet hyaluronan overexpression is…
Fluorescent observation of cells generally suffers from the limited axial resolution due to the elongated point spread function of the microscope optics. Consequently, three-dimensional imaging results in axial resolution being several…
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…
We controlled and observed individual magnetotactic bacteria (Magnetospirillum gryphiswaldense) inside a 5 {\mu}m high microfluidic channel for over four hours. After a period of constant velocity, the duration of which varied between…
Characterization of proteins with intrinsic or unfolded state disorder comprises a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. We introduce a comprehensive Bayesian…
We collaborated with Amgen and spent five years in designing and fabricating next generation multi-well plate imagers based on Fourier ptychographic microscopy (FPM). A 6-well imager (Emsight) and a low-cost parallel microscopic system (96…
We study a system of self-propelled disks that perform run-and-tumble motion, where particles can adopt more than one internal state. One of those internal states can be transmitted to another particle if the particle carrying this state…
The near-surface swimming patterns of bacteria are strongly determined by the hydrodynamic interactions between bacteria and the surface, which trap bacteria in smooth circular trajectories that lead to inefficient surface exploration.…
Molecular specific photonics localization technique, the inverse participation ratio (IPR), is a powerful technique to probe the nanoscale structural alterations due to abnormalities or chronic alcoholism in brain cells using the confocal…
We develop a method to investigate the effect of noise timescales on the first-passage time of nonlinear oscillators. Using Fredholm theory, we derive an exact integral equation for the mean event rate of a leaky-integrate-and-fire…
The spontaneous emergence of collective motion patterns is usually associated with the presence of a velocity alignment mechanism that mediates the interactions among the moving individuals. Despite of this widespread view, it has been…
We study a minimal cognitive flocking model, which assumes that the moving entities navigate using exclusively the available instantaneous visual information. The model consists of active particles, with no memory, that interact by a…
Foerster Resonance Energy Transfer (FRET) allows for the visualization of nanometer-scale distances and distance changes. This sensitivity is regularly achieved in single-molecule experiments in vitro but is still challenging in biological…
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…
Coevolutionary arms races form between interacting populations that constitute each other's environment and respond to mutual changes. This inherently far-from-equilibrium process finds striking manifestations in the adaptive immune system,…
We investigate the phase transition properties of the polymer-Potts model, a chain composed of monomers with magnetic degrees of freedom, with the motivation to study the conformation and mark switching dynamics of chromatin. By the…
Despite their importance in many biological, ecological and physical processes, microorganismal fluid flows under tight confinement have not been investigated experimentally. Strong screening of Stokelets in this geometry suggests that the…
A salient feature of skeletal muscles is their ability to take up an applied slack in a microsecond timescale. Behind this remarkably fast adaptation is a collective folding in a bundle of elastically interacting bistable elements. Since…
In arXiv:1911.06042v1 M. Casiulis et al. study a Hamiltonian model in which rigid rotations of moving clusters give rise to scale-free correlations of velocity and speed. M. Casiulis et al. compare correlations in their model to those…