Biological Physics
We introduce a model for the global optimization problem of nectar harvesting by flower visitors, e.g., nectar-feeding bats, as a generalization of the (multiple) traveling-salesperson problem (TSP). The model includes multiple independent…
One of the greatest challenges in biophysical models of translation is to identify coding sequences features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to…
Circadian clocks are biochemical oscillators that allow organisms to estimate the time of the day. These oscillators are inherently noisy due to the discrete nature of the reactants and the stochastic character of their interactions. To…
We study stochastic dynamics of a point and extended inclusion within a one dimensional confined active viscoelastic gel. We show that the dynamics of a point inclusion can be described by a Langevin equation with a confining potential and…
A discrete electrostatic/diffusion model has been developed to describe the selective permeation of ion channels, based on ionic Coulomb blockade (ICB) and quantised dehydration (QD). It has been applied to describe selectivity phenomena…
In this Account, we discuss a variety of static and dynamic chiral plasmonic nanostructures enabled by DNA nanotechnology. In the category of static plasmonic systems, we first show chiral plasmonic nanostructures based on spherical AuNPs,…
We demonstrate hierarchical assembly of plasmonic toroidal metamolecules, which exhibit tailored optical activity in the visible spectral range. Each metamolecule consists of four identical origami-templated helical building blocks. Such…
Deterministic placement and dynamic manipulation of individual plasmonic nanoparticles with nanoscale precision feature an important step towards active nanoplasmonic devices with prescribed levels of performance and functionalities at…
We study the force generation by a set of parallel actin filaments growing against an elastic membrane. The elastic membrane tries to stay flat and any deformation from this flat state, either caused by thermal fluctuations or due to…
We study the dynamical regimes demonstrated by a pair of identical 3-element ring oscillators (reduced version of synthetic 3-gene genetic Repressilator) coupled using the design of the "quorum sensing (QS)" process natural for…
Curvature in biological membranes can be generated by a variety of different molecular mechanisms such as protein scaffolding, lipid or protein asymmetry, cytoskeletal forces, etc. These mechanisms have the net effect of generating stresses…
During the alphavirus lifecycle, a nucleocapsid core buds through the cell membrane to acquire an outer envelope of lipid membrane and viral glycoproteins. However, the presence of a nucleocapsid core is not required for assembly of…
A significant part of the proteome is composed of intrinsically-disordered proteins (IDPs). These proteins do not fold into a well-defined structure and behave like ordinary polymers. In this work we consider IDPs which have the tendency to…
Magnetic nanoparticles are promising systems for biomedical applications and in particular for Magnetic Fluid Hyperthermia, a promising therapy that utilizes the heat released by such systems to damage tumor cells. We present an…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
Axons transmit action potentials with high fidelity and minimal jitter. This unique capability is likely the result of the spatiotemporal arrangement of sodium channels along the axon. Super-resolution microscopy recently revealed that the…
The infection pathway of virus in living cell is of interest from the viewpoint of the physics of diffusion. Here, recent developments about a diffusion theory for the infection pathway of an adeno-associated virus in cytoplasm of a living…
Double-stranded DNA may contain mismatched base pairs beyond the Watson-Crick pairs guanine-cytosine and adenine-thymine. Such mismatches bear adverse consequences for human health. We utilize molecular dynamics and metadynamics computer…
We investigate the effect of stress fluctuations on the stochastic dynamics of an inclusion embedded in a viscous gel. We show that, in non-equilibrium systems, stress fluctuations give rise to an effective attraction towards the boundaries…
We develop a biophysically realistic model of the nematode C. elegans that includes: (i) its muscle structure and activation, (ii) key connectomic activation circuitry, and (iii) a weighted and time-dynamic proprioception. In combination,…