生物物理
Transcription of the genetic message encoded chemically in the sequence of the DNA template is carried out by a molecular machine called RNA polymerase (RNAP). Backward or forward slippage of the nascent RNA with respect to the DNA template…
We introduce a self-consistent multi-species kinetic theory based on the structure of the narrow voltage-gated potassium channel. Transition rates depend on a complete energy spectrum with contributions including the dehydration amongst…
In MR elastography it is common to use an elastic model for the tissue's response in order to properly interpret the results. More complex models such as viscoelastic, fractional viscoelastic, poroelastic, or poroviscoelastic ones are also…
Actin cables are linear cytoskeletal structures that serve as tracks for myosin-based intracellular transport of vesicles and organelles in both yeast and mammalian cells. In a yeast cell undergoing budding, cables are in constant dynamic…
Assuming a steady-state condition within a cell, metabolic fluxes satisfy an under-determined linear system of stoichiometric equations. Characterizing the space of fluxes that satisfy such equations along with given bounds (and possibly…
In this paper, scalable Whole Slide Imaging (sWSI), a novel high-throughput, cost-effective and robust whole slide imaging system on both Android and iOS platforms is introduced and analyzed. With sWSI, most mainstream smartphone connected…
We study a generic one-dimensional model for an intracellular cargo driven by N motor proteins against an external applied force. The model includes motor-cargo and motor-motor interactions. The cargo motion is described by an over-damped…
Solid-state nanopores are promising tools for single molecule detection of both DNA and proteins. In this study, we investigate the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of such…
Refractive index of tubulin is an important parameter underlying fundamental electromagnetic and biophysical properties of microtubules - protein fibers essential for several cell functions including cell division. Yet, the only…
We present a novel illumination control technique for optical diffraction tomography (ODT). Various spatial frequencies of beam illumination were controlled by displaying time-averaged sinusoidal patterns using a digital micromirror device…
In biological membranes, alpha-tocopherols ({\alpha}-toc; vitamin E) protect polyunsaturated lipids from free radicals. Although the interactions of {\alpha}-toc with non-oxidized lipid bilayers have been studied, their on oxidized bilayers…
Electron paramagnetic resonance spectroscopy in combination with site-directed spin-labeling is a very powerful tool for elucidating the structure and organization of biomolecules. Gd$^{3+}$ complexes have recently emerged as a new class of…
The biological function of protein assemblies was conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it was found that some assemblies contain long…
Allostery plays a fundament role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two…
Bacterial migration through confined spaces is critical for several phenomena like: biofilm formation, bacterial transport in soils, and bacterial therapy against cancer . In the present work, \textit{E. coli} (strain K12-MG1655 WT)…
We present a hydrodynamic theory to describe shear flows in developing epithelial tissues. We introduce hydrodynamic fields corresponding to state properties of constituent cells as well as a contribution to overall tissue shear flow due to…
Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which…
In this article, we introduce a novel backward method to model stochastic gene expression and protein level dynamics. The protein amount is regarded as a diffusion process and is described by a backward stochastic differential equation…
Advances in time resolved spectroscopy have provided new insight into the energy transmission in natural photosynthetic complexes. Novel theoretical tools and models are being developed in order to explain the experimental results. We…
In order to keep their cohesiveness during locomotion gregarious animals must make collective decisions. Many species boast complex societies with multiple levels of communities. A common case is when two dominant levels exist, one…