arXiv subjects

Dipanwita Ghanti

Publications and source records attributed to Dipanwita Ghanti.

7 recordsLinked to original sources

arXiv2021

Crowding competes with trapping to enhance interfacial diffusion

Diffusion in the crowded environments of the biological membranes or materials interfaces often involves intermittent binding to surface proteins or defects. To account for this situation we study a 2-dimensional lattice gas in a field of immobilized traps. Using kinetic Monte Carlo simulations, we calculate the effective diffusion coefficient in the long-time limit as a function of the traps and particle densities. We find a remarkable result - an increase of the diffusion coefficient with particle density, an effect that we coin as crowding-enhanced diffusion. We rationalize this result using scaling arguments and the master equation approach.

cond-mat.soft↗

arXiv2018

Molecular force spectroscopy of kinetochore-microtubule attachment {\it in silico}: Mechanical signatures of an unusual catch bond and collective effects

Measurement of the life time of attachments formed by a single microtubule (MT) with a single kinetochore (kt) {\it in-vitro} under force-clamp conditions had earlier revealed a catch-bond-like behavior. In the past the physical origin of this apparently counter-intuitive phenomenon was traced to the nature of the force-dependence of the (de-)polymerization kinetics of the MTs. Here first the same model MT-kt attachment is subjected to external tension that increases linearly with time until rupture occurs. In our {\it force-ramp} experiments {\it in-silico}, the model displays the well known `mechanical signatures' of a catch-bond probed by molecular force spectroscopy. Exploiting this new evidence, we have further strengthened the analogy between MT-kt attachments and common ligand-receptor bonds in spite of the crucial differences in their underlying physical mechanisms. We then extend the formalism to model the stochastic kinetics of an attachment formed by a bundle of multiple parallel microtubules with a single kt considering the effect of rebinding under force-clamp and force-ramp conditions. From numerical studies of the model we predict the trends of variation of the mean life time and mean rupture force with the increasing number of MTs in the bundle. Both the mean life time and the mean rupture force display nontrivial nonlinear dependence on the maximum number of MTs that can attach simultaneously to the same kt.

physics.bio-ph↗

arXiv2018

Fidelity of bacterial translation initiation: a stochastic kinetic model

During the initiation stage of protein synthesis, a ribosomal initiation complex (IC) is assembled on a messenger RNA (mRNA) template. In bacteria, the speed and accuracy of this assembly process are regulated by the complementary activities of three essential initiation factors (IFs). Selection of an authentic N-formylmethionyl-transfer RNA (fMet-tRNA\textsuperscript{fMet}) and the canonical, triplet-nucleotide mRNA start codon are crucial events during assembly of a canonical, ribosomal 70S IC. Mis-initiation due to the aberrant selection of an elongator tRNA or a non-canonical start codon are rare events that result in the assembly of a pseudo 70S IC or a non-canonical 70S IC, respectively. Here, we have developed a theoretical model for the stochastic kinetics of canonical-, pseudo-, and non-canonical 70S IC assembly that includes all of the major steps of the IC assembly process that have been observed and characterized in ensemble kinetic-, single-molecule kinetic-, and structural studies of the fidelity of translation initiation. Specifically, we use the rates of the individual steps in the IC assembly process and the formalism of first-passage times to derive exact analytical expressions for the probability distributions for the assembly of canonical-, pseudo- and non-canonical 70S ICs. In order to illustrate the power of this analytical approach, we compare the theoretically predicted first-passage time distributions with the corresponding computer simulation data. We also compare the mean times required for completion of these assemblies with experimental estimates. In addition to generating new, testable hypotheses, our theoretical model can also be easily extended as new experimental 70S IC assembly data become available, thereby providing a versatile tool for interpreting these data and developing advanced models of the mechanism and regulation of translation initiation.

physics.bio-ph↗

arXiv2017

Strength and stability of active ligand-receptor bonds: a microtubule attached to a wall by molecular motor tethers

We develop a stochastic kinetic model of a pre-formed attachment of a mictrotuble (MT) with a cell cortex, in which the MT is tethered to the cell by a group of active motor proteins. Such an attachment is a particularly unique case of ligand-receptor bonds: The MT ligand changes its length (and thus binding sites) with time by polymerization-depolymerization kinetics, while multiple motor receptors tend to walk actively along the MT length. These processes, combined with force-mediated unbinding of the motors, result in an elaborate behavior of the MT connection to the cell cortex. We present results for the strength and lifetime of the system through the well-established force-clamp and force-ramp protocols when external tension is applied to the MT. The simulation results reveal that the MT-cell attachment behaves as a catch-bond or slip-bond depending on system parameters. We provide analytical approximations of the lifetime and discuss implications of our results on in-vitro experiments.

q-bio.SC↗

arXiv2017

A Multispecies Exclusion Model Inspired By Transcriptional Interference

We introduce exclusion models of two distinguishable species of hard rods with their distinct sites of entry and exit under open boundary conditions. In the first model both species of rods move in the same direction whereas in the other two models they move in the opposite direction. These models are motivated by the biological phenomenon known as Transcriptional Interference. Therefore, the rules for the kinetics of the models, particularly the rules for the outcome of the encounter of the rods, are also formulated to mimic those observed in Transcriptional Interference. By a combination of mean-field theory and computer simulation of these models we demonstrate how the flux of one species of rods is completely switched off by the other. Exploring the parameter space of the model we also establish the conditions under which switch-like regulation of two fluxes is possible; from the extensive analysis we discover more than one possible mechanism of this phenomenon.

physics.bio-ph↗

arXiv2015

Mixed molecular motor traffic on nucleic acid tracks: models of transcriptional interference and regulation of gene expression

RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on the ssDNA template. While polymerizing a RNA, the RNAP walks step-by-step on the ssDNA template in a specific direction. Thus, a RNAP can be regarded also as a molecular motor and the sites of start and stop of its walk on the DNA mark the two ends of the genetic message that it transcribes into RNA. Interference of transcription of two overlapping genes is believed to regulate the levels of their expression, i.e., the overall rate of the corresponding RNA synthesis, through suppressive effect of one on the other. Here we model this process as a mixed traffic of two groups of RNAP motors that are characterized by two distinct pairs of start and stop sites. Each group polymerizes identical copies of a RNA while the RNAs polymerized by the two groups are different. These models, which may also be viewed as two interfering totally asymmetric simple exclusion processes, account for all modes of transcriptional interference in spite of their extreme simplicity. A combination of mean-field theory and computer simulation of these models demonstrate the physical origin of the switch-like regulation of the two interfering genes in both co-directional and contra-directional traffic of the two groups of RNAP motors.

physics.bio-ph↗

arXiv2015

Collective cargo hauling by a bundle of parallel microtubules: bi-directional motion caused by load-dependent polymerization and depolymerization

A microtubule (MT) is a hollow tube of approximately 25 nm diameter. The two ends of the tube are dissimilar and are designated as `plus' and `minus' ends. Motivated by the collective push and pull exerted by a bundle of MTs during chromosome segregation in a living cell, we have developed here a much simplified theoretical model of a bundle of parallel dynamic MTs. The plus-end of all the MTs in the bundle are permanently attached to a movable `wall' by a device whose detailed structure is not treated explicitly in our model. The only requirement is that the device allows polymerization and depolymerization of each MT at the plus-end. In spite of the absence of external force and direct lateral interactions between the MTs, the group of polymerizing MTs attached to the wall create a load force against the group of depolymerizing MTs and vice-versa; the load against a group is shared equally by the members of that group. Such indirect interactions among the MTs gives rise to the rich variety of possible states of collective dynamics that we have identified by computer simulations of the model in different parameter regimes. The bi-directional motion of the cargo, caused by the load-dependence of the polymerization kinetics, is a "proof-of-principle" that the bi-directional motion of chromosomes before cell division does not necessarily need active participation of motor proteins.

q-bio.SC↗