生物物理
Patient-specific therapies require that cells be manufactured in multiple batches of small volumes, making it a challenge for conventional modes of quality control. The added complexity of inherent variability (even within batches)…
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more…
The response of a fluid to deformation by shear stress is known as shear viscosity. This concept arises from a macroscopic view and was first introduced by Sir Isaac Newton. Nonetheless, a fluid is a series of moving molecules that are…
The long range movement of certain organisms in the presence of a chemoattractant can be governed by long distance runs, according to an approximate Levy distribution. This article clarifies the form of biologically relevant model…
Active diffusion of intracellular components is emerging as an important process in cell biology. This process is mediated by complex assemblies of molecular motors and cytoskeletal filaments that drive force generation in the cytoplasm and…
The most prominent defence of the unicellular parasite Trypanosoma brucei against the host immune system is a dense coat that comprises a variant surface glycoprotein (VSG). Despite the importance of the VSG family, no complete structure of…
Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network.…
Intracellular components explore the cytoplasm via active motor-driven transport in conjunction with passive diffusion. We model the motion of organelles in narrow tubular cells using analytical techniques and numerical simulations to study…
Applying a force to certain supramolecular bonds may initially stabilize them, manifested by a lower dissociation rate. We show that this behavior, known as catch bonding and by now broadly reported in numerous biophysics bonds, is…
Current understanding of how contractility emerges in disordered actomyosin networks of non-muscle cells is still largely based on the intuition derived from earlier works on muscle contractility. This view, however, largely overlooks the…
We introduce a numerical scheme to evolve functional materials that can accomplish a specified mechanical task. In this scheme, the number of solutions, their spatial architectures and the correlations among them can be computed. As an…
The availability of protein is an important factor for the determination of the size of the mitotic spindle. Involved in spindle-size regulation is kinesin-8, a molecular motor and microtubule (MT) depolymerase, which is known to tightly…
We develop a general analytical and numerical framework for estimating intra- and extra-neurite water fractions and diffusion coefficients, as well as neurite orientational dispersion, in each imaging voxel. By employing a set of rotational…
Chemotaxis is a ubiquitous biological phenomenon in which cells detect a spatial gradient of chemoattractant, and then move towards the source. Here we present a position-dependent advection-diffusion model that quantitatively describes the…
In their work [Proc. Natl. Acad. Sci. USA 112 (2015) E5725], Bosse et al. experimentally showed that virus capsid exhibits not only normal diffusion but also anomalous diffusion in nucleus of a living cell. There, it was found that the…
We formulate and solve the locomotion problem for a bio-inspired crawler consisting of two active elastic segments (i.e., capable of changing their rest lengths), resting on three supports providing directional frictional interactions. The…
We study a diagnostic strategy which is based on the anticipation of the diagnostic process by simulation of the dynamical process starting from the initial findings. We show that such a strategy could result in more accurate diagnoses…
We study the surface diffusion of the model cyanobacterium Synechocystis sp. PCC $6803$ during the incipient stages of cell contact with a glass surface in the dilute regime. We observe a twitching motility with alternating immobile…
The Supernova Neutrino Amino Acid Processing model, which uses electron anti-neutrinos and the magnetic field from a source object such as a supernova to selectively destroy one amino acid chirality, is studied for possible sites that would…
The Ground State Dominance Approximation(GSDA) has been extensively used to study the assembly of viral shells. In this work we employ the self-consistent field theory (SCFT) to investigate the adsorption of RNA onto positively charged…