Biological Physics
Motivation: Engineering high-affinity binders targeting specific antigenic determinants remains a challenging and often daunting task, requiring extensive experimental screening. Computational methods have the potential to accelerate this…
The cystic fibrosis transmembrane conductance regulator (CFTR) is an important membrane protein in vertebrates. The function of CFTR is to transport chloride ions across the cell membrane, which is known to require adenosine triphosphate…
Liquid liquid phase separation (LLPS) of proteins is an intracellular process that is widely used by cells for many purposes. In living cells (in vivo), LLPS occurs in complex and crowded environments. Amino acids (AAs) are vital components…
Active propulsion, as performed by bacteria and Janus particles, in combination with hydrodynamic interaction results in the accumulation of bacteria at a flat wall. However, in microfluidic devices with cylindrical pillars of sufficiently…
The aim of this article is relating the chemical master equation (CME) to the illness-death model for chronic diseases. We show that a recently developed differential equation for the prevalence directly follows from the CME. As an…
Iron (Fe) reduction is one of Earth's most ancient microbial metabolisms, but after atmosphere-ocean oxygenation, this anaerobic process was relegated to niche anoxic environments below the water and soil surface. However, new technologies…
Despite the significance of the high flexibility exhibited by short DNAs, there remains an incomplete understanding of their anomalous persistence length. In this study, we propose a novel approach wherein each fundamental characteristic of…
Tuberculosis (TB) is the world's deadliest infectious disease, with over 1.5 million deaths annually and 10 million new cases reported each year. The causative organism, Mycobacterium tuberculosis (Mtb) can take nearly 40 days to culture, a…
The homeostasis of epithelial tissue relies on a balance between the self-renewal of stem cell populations, cellular differentiation, and loss. Although this balance needs to be tightly regulated to avoid pathologies, such as tumor growth,…
We present EPR-Net, a novel and effective deep learning approach that tackles a crucial challenge in biophysics: constructing potential landscapes for high-dimensional non-equilibrium steady-state (NESS) systems. EPR-Net leverages a nice…
Nanodevices exploiting quantum effects are critically important elements of future quantum technologies (QT), but their real-world performance is strongly limited by decoherence arising from local `environmental' interactions. Compounding…
During colony growth, complex interactions regulate the bacterial orientation, leading to the formation of large-scale ordered structures, including topological defects and microdomains. These structures may benefit bacterial strains,…
Dengue is a viral vector-borne infectious disease that affects many countries worldwide, infecting around 390 million people per year. The main outbreaks occur in subtropical and tropical countries. We study here the influence of climate on…
I review basic concepts in the nonequilibrium physics of small systems, emphasizing single molecule experiments and how they contribute to expanding our current understanding of energy and information.
We demonstrate a deep-learning-based scatterer density estimator (SDE) that processes local speckle patterns of optical coherence tomography (OCT) images and estimates the scatterer density behind each speckle pattern. The SDE is trained…
Mismatch repair is a critical step in DNA replication that occurs after base selection and proofreading, significantly increasing fidelity. However, the mechanism of mismatch recognition has not been established for any repair enzyme.…
A study on primates has established that gyral size is largely independent of overall brain size. Building on this, and other research suggesting that brain gyrification may mitigate the effects of head impacts, our study aims to explore…
Molecular Dynamics (MD) simulations of proteins implicitly contain the information connecting the atomistic molecular structure and proteins' biologically relevant motion, where large-scale fluctuations are deemed to guide folding and…
A physical model for a structured tetrameric pore is studied. The pore is modeled as a device composed of four subunits, each one exhibiting two possible states (open and closed). The pore is located within a membrane that separates two…
Ultrafast lasers, with pulse durations below a few picoseconds, are of significant interest to the industry, offering a cutting-edge approach to enhancing manufacturing processes and enabling the fabrication of intricate components with…