Biological Physics
The MARTINI coarse-grained (CG) force field is used to test the ability of CG models to simulate ionic transport through protein nanopores. The ionic conductivity of CG ions in solution was computed and compared with experimental results.…
This work attempts to understand the mechanism of simultaneous electrodeformation and electroporation in Giant Unilamellar Vesicles (GUVs) using a minimal analytical model. In the small deformation limit, the coupled electroporation,…
Lyme disease, caused by the bacterium Borrelia burgdorferi, is a significant public health concern in North America, with approximately 500,000 cases reported annually in the United States. The dissemination of B. burgdorferi from the…
Cells frequently employ extracellular vesicles, or exosomes, to signal across long distances and coordinate collective actions. Exosomes diffuse slowly, can be actively degraded, and contain stochastic amounts of molecular cargo. These…
The variation of the oxygen enhancement ratio (OER) across Linear Energy Transfer (LET) currently lacks a comprehensive mechanistic interpretation and a mechanistic model. Our earlier research revealed a significant correlation between the…
Zoonotic pathogens represent a growing global risk, yet the speed of adaptive immune activation across mammalian species remains poorly understood. Despite orders-of-magnitude differences in size and metabolic rate, we show that the time to…
Active flexible filaments form the classical continuum framework for modelling the locomotion of spermatozoa and algae driven by the periodic oscillation of flagella. This framework also applies to the locomotion of various artificial…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
Limbless animals such as snakes, limbless lizards, worms, eels, and lampreys move their slender, long bodies in three dimensions to traverse diverse environments. Accurately quantifying their continuous body's 3-D shape and motion is…
Nanoscale chromatin domains, variously termed nucleosome clutches, nanodomains, or packing domains, have emerged as fundamental architectural units of the mammalian genome during interphase and mitosis. Unlike cohesin-dependent loops or…
Many swimming bacteria naturally inhabit confined environments, yet how confinement influences their swimming behaviors remains unclear. Here, we combine experiments, continuum modeling and particle-based simulations to investigate…
Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to explore the role of 3D…
Soil is a complex, dynamic material, with physical properties that depend on its biological content. We propose a cellular automaton model for self-organizing soil structure, where soil aggregates and serves as food for microbial species.…
Life is an exergonic chemical reaction. Many individual reactions in metabolism entail slightly endergonic steps that are coupled to free energy release, typically as ATP hydrolysis, in order to go forward. ATP is almost always supplied by…
Transcranial ultrasound stimulation (TUS) is an emerging technology for non-invasive brain stimulation. The International Transcranial Ultrasonic Stimulation Safety and Standards consortium (ITRUSST) has established consensus on…
Neuronal circuits arise as axons and dendrites extend, navigate, and connect to target cells. Axonal growth, in particular, integrates deterministic guidance from substrate mechanics and geometry with stochastic fluctuations generated by…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
Carbon quantum dots (CQDs) are known for their antibacterial properties and ability to inhibit bacteria growth. In the current study, we observed a dopant and concentration-dependency on the antibacterial effect of CQDs. High concentrations…
F$_1$-ATPase (F$_1$) is central to cellular energy transduction. Forcibly rotated by another motor F$_\mathrm{o}$, F$_1$ catalyzes ATP synthesis by converting mechanical work into chemical free energy stored in the molecule ATP. The details…
This work demonstrates biological detection of a low concentration of O3 by measuring electrochemical impedances of tissues in tobacco and tomato plants located indoor and outdoor. The lower range of generated ozone in the O3-air mix is…