arXiv subjects

Aakash Basu

Publications and source records attributed to Aakash Basu.

5 recordsLinked to original sources

arXiv2020

Searching for sequence features that control DNA flexibility

Modern genomics experiments measure functional behaviors for many thousands of DNA sequences. We suggest that, especially when these sequences are chosen at random, it is natural to compute correlation functions between sequences and measured behaviors. In simple models for the dependence of DNA flexibility on sequence, for example, correlation functions can be interpreted directly as interaction parameters. Analysis of recent experiments shows that this is surprisingly effective, leading directly to extraction of distinct features for DNA flexibility and predictions that are as accurate as more complex models. This approach follows the conventional use of correlation functions in statistical physics and connects the search for relevant DNA sequence features to the search for relevant stimulus features in the analysis of sensory neurons.

physics.bio-ph↗

arXiv2008

Intra-cellular traffic: bio-molecular motors on filamentary tracks

Molecular motors are macromolecular complexes which use some form of input energy to perform mechanical work. The filamentary tracks, on which these motors move, are made of either proteins (e.g., microtubules) or nucleic acids (DNA or RNA). Often, many such motors move simultaneously on the same track and their collective properties have superficial similarities with vehicular traffic on highways. The models we have developed provide ``unified'' description: in the low-density limit, a model captures the transport properties of a single motor while, at higher densities the same model accounts for the collective spatio-temporal organization of interacting motors. By drawing analogy with vehicular traffic, we have introduced novel quantities for characterizing the nature of the spatio-temporal organization of molecular motors on their tracks. We show how the traffic-like intracellular collective phenomena depend on the mechano-chemistry of the corresponding individual motors.

physics.bio-ph↗

arXiv2007

Modeling protein synthesis from a physicist's perspective: a toy model

Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell biology, important quantitative models of protein synthesis have been reported in research journals devoted to statistical physics and related interdisciplinary topics. From the perspective of a physicist, protein synthesis is the classical transport of interacting ribosomes on a messenger RNA (mRNA) template that dictates the sequence of the amino acids on the protein. We discuss appropriate simplification of the models and methods. In particular, we develop and analyze a simple toy model using some elementary techniques of non-equilibrium statistical mechanics and predict the average rate of protein synthesis and the spatial organization of the ribosomes in the steady state.

physics.bio-ph↗

arXiv2006

Delay times and detector times for optical pulses traversing plasmas and negative refractive media

We show that arrival times for electromagnetic pulses measured through the rate of absorption in an ideal impedance matched detector are equivalent to the arrival times using the average flow of optical energy as proposed by Peatross {\it et al.} [ Phys. Rev. Lett. {\bf 84}, 2370 (2000)]. We then investigate the transport of optical pulses through dispersive media with negative dielectric permittivity and negative refractive index choosing the geometry such that no resonant effects come into play. For evanescent waves, the definitions of the group delay and the reshaping delay get interchanged in comparison to propagating waves. The total delay times for the evanescent waves can be negative in an infinite plasma medium even for broad-band pulses. The total time is, however, positive for broad band pulses in the presence of an interface when the radiation is detected outside the plasma. We find evidence of the Hartman effect for pulses when the distance traversed in the plasma is much smaller than the free space pulse length. We also show that for a negative refractive index medium(NRM) with $ε(ω)$ = $μ(ω)$ the reshaping delay for propagating waves is identically zero. The total delay time in NRM is otherwise dominated by the reshaping delay time, and for broad band pulses in NRM the total delay time is subluminal.

cond-mat.mtrl-sci↗

arXiv2006

Traffic of interacting ribosomes: effects of single-machine mechano-chemistry on protein synthesis

Many ribosomes simultaneously move on the same messenger RNA (mRNA), each separately synthesizing the protein coded by the mRNA. Earlier models of ribosome traffic represent each ribosome by a ``self-propelled particle'' and capture the dynamics by an extension of the totally asymmetric simple exclusion process (TASEP). In contrast, here we develope a theoretical model that not only incorporates the mutual exclusions of the interacting ribosomes, but also describes explicitly the mechano-chemistry of each of these individual cyclic machines during protein synthesis. Using analytical and numerical techniques of non-equilibrium statistical mechanics, we analyze this model and illustrate its power by making experimentally testable predictions on the rate of protein synthesis in real time and the density profile of the ribosomes on some mRNAs in E-Coli.

physics.bio-ph↗