生物物理
The spike protein (SP) of SARS-CoV-2 is the major molecular target for making diagnostic tests, vaccines, and therapeutic development. We used a combination of transmission electron microscopy (TEM) and surface enhanced Raman microscopy…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
We consider the problem of olfactory searches in a turbulent environment. We focus on agents that respond solely to odor stimuli, with no access to spatial perception nor prior information about the odor. We ask whether navigation to a…
About 4 billion years ago, the Earth probably fulfilled the environmental conditions necessary to favour the transition from primitive chemistry to life. Based on a theoretical hairpin duplication origin of tRNAs and their putative…
Mathematical modeling can offer valuable insights into the behavior of biological systems upon treatment. Different mathematical models have been designed to predict the efficacy of hyperthermia (HT), radiotherapy (RT), or their…
The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat…
The natural vibrational frequencies of biological particles such as viruses and bacteria encode critical information about their mechanical and biological states as they interact with their local environment and undergo structural…
The Escherichia coli chemoreceptors form an extensive array that achieves cooperative and adaptive sensing of extracellular signals. The receptors control the activity of histidine kinase CheA, which drives a nonequilibrium…
When confronted with an undesired cell population, such as bacterial infections or tumors, we seek the most effective treatment, designed to eliminate the population as rapidly as possible. A common practice is to monitor the cells…
In the present paper we deal with nonlinear dynamics of microtubules (MTs). The structure and role of MTs in cells are explained. One model explaining MT dynamics is explained. Solutions of the crucial nonlinear differential equation depend…
The Gillespie algorithm is commonly used to simulate and analyze complex chemical reaction networks. Here, we leverage recent breakthroughs in deep learning to develop a fully differentiable variant of the Gillespie algorithm. The…
With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a…
Magnetotactic bacteria (MTB) are a diverse group of microorganisms whose movement can be directed via a magnetic field, which makes them attractive for applications in medicine and microfluidics. One of their key properties is the magnetic…
A large number of magnetic sensors, like superconducting quantum interference devices, optical pumping and nitrogen vacancy magnetometers, were shown to satisfy the energy resolution limit. This limit states that the magnetic sensitivity of…
The revival mechanism in dormant bacteria is a puzzling and open issue. We propose a model of information diffusion on a regular grid where agents represent bacteria and their mutual interactions implement quorum sensing. Agents may have…
We demonstrate that confinement geometry can act as a rectifier in passive diffusion, optimally accelerating first-passage rates beyond free diffusion. Using analytic theory based on the Fick-Jacobs approach and Brownian dynamics…
Incorporating cells within active biomaterial scaffolds is a promising strategy to develop forefront materials that can autonomously sense, respond, and alter the scaffold in response to environmental cues or internal cell circuitry. Using…
Super-Resolution Microscopy (SRM) is emerging as a powerful and innovative tool for imaging, characterizing, and understanding the structure of Extracellular Vesicles (EVs). By addressing the need for single-particle analysis with the high…
Tissue homeostasis, the biological process of maintaining a steady state in tissue via control of cell proliferation, death, and metabolic function, is essential for the development, growth, maintenance, and proper function of living…
We use the helicoidal Peyrard-Bishop model of DNA in the current work. We solve a dynamical equation of motion using a continuum approximation, resulting in kink-solitary waves that travel along the chain. We demonstrate that, whereas…