Biological Physics
The high fidelity of DNA polymerase is critical for the faithful replication of genomic DNA. Several approaches were proposed to quantify the fidelity of DNA polymerase. Direct measurements of the error frequency of the replication products…
The prediction of protein secondary and tertiary structures from the primary amino acid sequence is both an incredibly important and incredibly difficult problem. Accurate prediction of a protein's native structure can provide critical…
Metastatic cancer cells detect the direction of lymphatic flow by self-communication: they secrete and detect a chemical which, due to the flow, returns to the cell surface anisotropically. The secretion rate is low, meaning detection noise…
Motivated by the mechanics of dynamin-mediated membrane tube fission we analyse the stability of fluid membrane tubes subjected to shear flow in azimuthal direction. We find a novel helical instability driven by the membrane shear flow…
Photosynthesis is remarkable, achieving near unity light harvesting quantum efficiency in spite of dynamic light conditions and noisy physiological environment. Under these adverse conditions, it remains unknown whether there exists a…
We discuss a trajectory of penguins' faeces after the powerful shooting due to their strong rectal pressure. Practically, it is important to see how far faeceses reach when penguins expel them from higher places. Such information is useful…
Structural microvascular alterations and dysfunction serve as key disease indicators of cancer, diabetes, ischemic stroke, neurodegenerative disorders and many other conditions. In vivo visualization of the microvasculature has…
The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and find applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural…
Collective behaviors displayed by groups of social animals are observed frequently in nature. Understanding and predicting the behavior of complex biological systems is dependent on developing effective descriptions and models. While…
Recent advances in DNA sequencing and fluorescence imaging have made it possible to monitor the dynamics of ribosomes actively engaged in messenger RNA (mRNA) translation. Here, we model these experiments within the inhomogeneous totally…
The structural dynamics of a biopolymer is governed by a process of diffusion through its conformational energy landscape. In pulling experiments using optical tweezers, features of the energy landscape can be extracted from the probability…
Cellular behaviors such as migration, division, and differentiation rely on precise timing, and yet the molecular events that govern these behaviors are highly stochastic. We investigate regulatory strategies that decrease the timing noise…
Using Brownian dynamics simulations, the motion of active Brownian particles (ABPs) in the presence of fuel (or 'food') sources is studied. It is an established fact that within confined stationary systems, the activity of ABPs generates…
We study the motion of random walkers with residence time bias between first and subsequent visits to a site, as a model for synthetic molecular walkers composed of coupled DNAzyme legs known as molecular spiders. The mechanism of the…
Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of…
Naively, one expects the information communicated by an enzyme downstream within a signaling network, in which the enzyme is embedded, to grow monotonically with the enzyme's rate of product formation. However, here we observe that this…
Signal propagation over long distances is a ubiquitous feature of multicellular communities. In biofilms of the bacterium Bacillus subtilis, we recently discovered that some, but not all, cells participate in the propagation of an…
Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to…
Confined hydration and conformational flexibility are some of the challenges encountered for the rational design of selective antagonists of G-protein coupled receptors. We present a set of C3-substituted (-)-stepholidine derivatives as…
Collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between…