Biological Physics
The mechanical behaviour of solid biological tissues has long been described using models based on classical continuum mechanics. However, the classical continuum theories of elasticity and viscoelasticity cannot easily capture the…
The comprehension of tumor growth is a intriguing subject for scientists. New researches has been constantly required to better understand the complexity of this phenomenon. In this paper, we pursue a physical description that account for…
Understanding the operation of biological molecular motors, nanoscale machines that transduce electrochemical energy into mechanical work, is enhanced by bottom-up strategies to synthesize novel motors.
Physical thermodynamic and kinetic, chemical and biological reasoning restrict the spatial dimensions of living cells and confine them to between one and one hundred micrometers. Cells should necessarily be macroscopic, dissipative objects,…
Unlike other tissue types, like epithelial tissue, which consist of cells with a much more homogeneous structure and function, the nervous tissue spans in a complex multilayer environment whose topographical features display a large…
This paper proposes a neuronal circuitry layout and synaptic plasticity principles that allow the (pyramidal) neuron to act as a "combinatorial switch". Namely, the neuron learns to be more prone to generate spikes given those combinations…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
We have earlier reported the MOLSDOCK technique to perform rigid receptor/flexible ligand docking. The method uses the MOLS method, developed in our laboratory. In this paper we report iMOLSDOCK, the 'flexible receptor' extension we have…
Point-wise localization of individual fluorophores is a critical step in super-resolution microscopy and single particle tracking. Although the methods are limited by the accuracy in localizing individual flourophores, this point-wise…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
We present a study on the evolution of the Fenna-Matthews-Olson bacterial photosynthetic pigment-protein complex. This protein complex functions as an antenna. It transports absorbed photons - excitons - to a reaction center where…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
In spite of many years of research, the mechanism of avian magnetoreception remains a mystery due to its seemingly insurmountable intricacies. Recently Xie and colleagues proposed that IscA1 can act as a protein biocompass due to the…
The transfer of mechanical signals through cells is a complex phenomenon. To uncover a new mechanotransduction pathway, we study the frequency-dependent transport of mechanical stimuli by single microtubules and small networks in a…
The response of lipid bilayers to osmotic stress is an important part of cellular function. Previously, in [Oglecka et al. 2014], we reported that cell-sized giant unilamellar vesicles (GUVs) exposed to hypotonic media, respond to the…
Collective motion of cells is common in many physiological processes, including tissue development, repair, and tumor formation. Recent experiments have shown that certain malignant cancer cells form clusters in a chemoattractant gradient,…
By developing a molecular dynamics model of bacterial chemotaxis, we present the first investigation of tracer statistics in bacterial suspensions where chemotactic effects are considered. We demonstrate that the non-Gaussian statistics of…
Here we reveal details of the interaction between human lysozyme proteins, both native and fibrils, and their water environment by intense terahertz time domain spectroscopy. With the aid of a rigorous dielectric model, we determine the…
Sub-diffraction resolution imaging has played a pivotal role in biological research by visualizing key, but previously unresolvable, sub-cellular structures. Unfortunately, applications of far-field sub-diffraction resolution are currently…
We present a weakly coupled map lattice model for patterning that explores the effects exerted by weakening the local dynamic rules on model biological and artificial networks composed of two-state building blocks (cells). To this end, we…