Biological Physics
In this article, I advance the idea that physics plays a central role in cell differentiation and makes fundamental contributions to morphogenesis, revealing the totipotent nature of the zygote. Totipotency is a persistent mechanical memory…
Populations of cells regulate gene expression in response to external signals, but their ability to make reliable collective decisions is limited by both intrinsic noise in molecular signaling and variability between individual cells. In…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
Single-molecule spectroscopy (SMS) is an exceptionally sensitive technique, but its inherently limited photon budget produces noisy data that can readily lead to subjective analyses, fitting errors, and reduced statistical power, obscuring…
Simulating spontaneous structural rearrangements in macromolecules with classical Molecular Dynamics (MD) is an outstanding challenge. Conventional supercomputers can access time intervals up to tens of $\mu$s, while many key events occur…
After entering the ear, sound waves propagate as surface waves along the cochlea's basilar membrane. In recent work, we showed numerically that the system supports two types of modes: localized resonant modes, which underpin the modern…
Living systems are made of active materials with microscopic components that work together to perform macroscopic biological tasks. The breakdown of these collective functionalities leads to diseases, which, conversely, could be treated by…
Recent experimental evidence for collective protein vibrations in the terahertz (THz) domain indicates that energy in biomolecular systems can self-organize in an orderly manner, as anticipated by Fr\"ohlich's theory of condensates within a…
Amoeboid motion is a dynamic mode of cell motility essential for processes such as the immune response and wound healing. This review examines recent developments in the mathematical and computational modeling of amoeboid crawling, focusing…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding complexes often have high free energy barriers, which require…
We introduce the concept of Randomly Modulated Gaussian Processes as a unifying framework for modeling, analyzing and classifying anomalous diffusion models in heterogeneous media. This formulation incorporates correlations in the…
This article frames the relation between biology and physics by characterizing the former as a subdiscipline rather than a special case of the latter. To do this, we posit biological physics as the science of living matter in contrast to…
Experience shows that disciplinary science cannot describe life without contradictions. We show that one of the fundamental reasons is the disciplinarity itself: the disciplines deal with a limited set of quantities. This way some 'outlaw'…
Michaelis-Menten kinetics is one of the most recognized models in enzyme kinetics, crucial for the understanding of biochemical reactions in several metabolic processes. In this study, we perform a stochastic analysis of the…
The rapid evolution and global impact of coronaviruses, notably SARS-CoV-1 and SARS-CoV-2, underscore the importance of understanding their molecular mechanisms in detail. This study focuses on the receptor-binding motif (RBM) within the…
Aggregation of the main antenna complex of higher plants, Light-Harvesting Complex II (LHCII), is widely used as an in vitro model for energy-dependent quenching (qE), yet fluorescence reduction in aggregates is frequently interpreted…
Motile cilia drive biological fluid transport through whip-like beating motions that synchronize into metachronal waves. The lengths of these cilia span three orders of magnitude, from microns in human airways to millimeters in ctenophores.…
Using tools from network theory, we analyze the organization of a MYH9-oriented drug-like library in chemical space using a multi-descriptor framework. The dataset is drawn from ZINC, a publicly available database of commercially accessible…
Hibernation is an adaptation to extreme environmental seasonality that has been studied for almost 200 years, but our understanding of the underlying physiological system remains lacking due to the partially observed nature of the system.…