Manoj Gopalakrishnan

A systematic study of the photoluminescence quenching efficiencies in P3HT: PCBM blends showed a non-linear dependence on the PCBM concentration. We find a faster decrease in PL emission initially which later flattens out around 1:1 composition which tallies well with sample compositions known to give the best power conversion efficiencies. This implies that the exciton dissociation rates dominate the photocurrent generation in these films. We obtained a maximum of 91% photoluminescence quenching for films with a 1:1 blend ratio. A mean field based phenomenological model is presented, which very well describes our experimental results. The generation of free carriers due to various proposed mechanisms like dissociation and delocalization are collectively considered in the model. The model helps us understand the underlying physics and dependence of the quenching efficiency on parameters like excitation intensities. The proposed model will be useful in predicting the behaviour of exciton dissociation in new organic blends.

Abstract: We study the velocity-force (V-F) relation for a Brownian ratchet consisting of a linear rigid polymer growing against a diffusing barrier, acted upon by a opposing constant force (F). Using a careful mathematical analysis, we derive the V-F relations in the extreme limits of fast and slow barrier diffusion. In the first case, V depends exponentially on the load F, in agreement with the well-known formula proposed by Peskin, Odell and Oster (1993), while the relationship becomes linear in the second case. For a bundle of two filaments growing against a common barrier, equal sharing of load in the corresponding V-F relation is predicted by a mean-field argument in both limits. However, the scaling behaviour of velocity with the number of filaments is different for the two cases. In the limit of large D, the validity of the mean-field approach is tested, and partially supported by a detailed and rigorous analysis. Our principal predictions are also verified in numerical simulations. Graphic abstract: [Figure not available: see fulltext.].

Normal thermal fluctuations of the cell membrane have been studied extensively using high resolution microscopy and focused light, particularly at the peripheral regions of a cell. We use a single probe particle attached non-specifically to the cell-membrane to determine that the power spectral density is proportional to (frequency)-5/3 in the range of 5 Hz to 1 kHz. We also use a new technique to simultaneously ascertain the slope fluctuations of the membrane by relying upon the determination of pitch motion of the birefringent probe particle trapped in linearly polarized optical tweezers. In the process, we also develop the technique to identify pitch rotation to a high resolution using optical tweezers. We find that the power spectrum of slope fluctuations is proportional to (frequency)-1, which we also explain theoretically. We find that we can extract parameters like bending rigidity directly from the coefficient of the power spectrum particularly at high frequencies, instead of being convoluted with other parameters, thereby improving the accuracy of estimation. We anticipate this technique for determination of the pitch angle in spherical particles to high resolution as a starting point for many interesting studies using the optical tweezers. This journal is

When transporting cellular cargoes along the cytoskeletal filament track, motor proteins produce additional frictional drag. This "protein friction"determines the mean speed of a cargo for a given force and the energy dissipated per chemical cycle. Motor protein friction has been measured directly in an optical tweezer experiment, and can also be estimated from the force-velocity curve, close to stall. We present a mathematical and computational study of this phenomenon. In our model, a motor protein is elastically linked to a μm-sized cargo particle, and undergoes tightly coupled, biased random walk-like motion on the microtubule filament, the bias being contributed by nucleotide hydrolysis as well as stretching of the linker "spring", with spring constant κ. The cytoplasm is assumed to be a Newtonian fluid, which exerts a damping force γ V on the cargo moving with velocity V. The effective drag coefficient γeff = F/V is measured in our numerical simulations, where F is the net external force on the cargo, including motor-induced force, near F = 0. The motor friction γm = γeff- γ is predicted theoretically and compared with simulation data for a range of values of κ and γ. The predicted values for small γ are found to be similar to experimental results, though smaller in magnitude. Numerical simulations also show that γm is a weakly increasing function of γ, and is additive when multiple motors are involved in transportation.

Bacteria such as Escherichia coli move about in a series of runs and tumbles: while a run state (straight motion) entails all the flagellar motors spinning in counterclockwise (CCW) mode, a tumble is caused by a shift in the state of one or more motors to clockwise (CW) spinning mode. In the presence of an attractant gradient in the environment, runs in the favourable direction are extended, and this results in a net drift of the organism in the direction of the gradient. Existing theoretical predictions for the drift velocity are limited to exponentially distributed run durations. However, recent experimental observations strongly suggest that the CCW and CW intervals have gamma, rather than exponential distributions. We present a path-integral method which can be used to compute various quantities of interest for the run and tumble walk, with and without chemotaxis, for arbitrary distributions of run and tumble intervals, as power series expansions in the gradient. The effectiveness of the method is demonstrated by deriving a number of existing results for the mean-squared displacement (including motion with directional persistence and algebraically distributed run times) and also chemotactic drift (with exponentially distributed run intervals) in a systematic way, starting from a set of general formulae. New results for chemotactic drift velocity for gamma-distributed run and tumble intervals are then derived, in the limit of weak gradients. Finally, by making use of available experimental data, we make testable predictions for the dependence of the drift velocity on the clockwise bias of the flagellar motor.

We study the normal fluctuations of an MCF-7 cell membrane and calibrate the optical trap to detect pitch motion to get information about the rocking motion of a birefringent particle. We could show both theoretically and experimentally that the Z power spectrum has a power-law behavior of (frequency)-5/3, and We find that the power spectrum of slope fluctuations is proportional to (frequency)-1. We could extract parameters like bending rigidity directly from the power spectrum fitting parameters in 5 Hz to 1 kHz range. Our method was powerful enough to identify pitch rotation for a spherical birefringent particle to a high resolution using optical tweezers.

In the intracellular environment, the intrinsic dynamics of microtubule filaments is often hindered by the presence of barriers of various kind, such as kinetochore complexes and cell cortex, which impact their polymerisation force and dynamical properties such as catastrophe frequency. We present a theoretical study of the effect of a forced barrier, also subjected to thermal noise, on the statistics of catastrophe events in a single microtubule as well as a 'bundle' of two parallel microtubules. For microtubule dynamics, which includes growth, detachment, hydrolysis and the consequent dynamic instability, we employ a one-dimensional discrete stochastic model. The dynamics of the barrier is captured by over-damped Langevin equation, while its interaction with a growing filament is assumed to be hard-core repulsion. A unified treatment of the continuum dynamics of the barrier and the discrete dynamics of the filament is realized using a hybrid Fokker-Planck equation. An explicit mathematical formula for the force-dependent catastrophe frequency of a single microtubule is obtained by solving the above equation, under some assumptions. The prediction agrees well with results of numerical simulations in the appropriate parameter regime. More general situations are studied via numerical simulations. To investigate the extent of 'load-sharing' in a microtubule bundle, and its impact on the frequency of catastrophes, the dynamics of a two-filament bundle is also studied. Here, two parallel, non-interacting microtubules interact with a common, forced barrier. The equations for the two-filament model, when solved using a mean-field assumption, predicts equal sharing of load between the filaments. However, numerical results indicate the existence of a wide spectrum of load-sharing behaviour, which is characterized using a dimensionless parameter.

Zero-order ultrasensitivity (ZOU) is a long known and interesting phenomenon in enzyme networks. Here, a substrate is reversibly modified by two antagonistic enzymes (a 'push-pull' system) and the fraction in modified state undergoes a sharp switching from near-zero to near-unity at a critical value of the ratio of the enzyme concentrations, under saturation conditions. ZOU and its extensions have been studied for several decades now, ever since the seminal paper of Goldbeter and Koshland (1981); however, a complete probabilistic treatment, important for the study of fluctuations in finite populations, is still lacking. In this paper, we study ZOU using a modular approach, akin to the total quasi-steady state approximation (tQSSA). This approach leads to a set of Fokker-Planck (drift-diffusion) equations for the probability distributions of the intermediate enzyme-bound complexes, as well as the modified/unmodified fractions of substrate molecules. We obtain explicit expressions for various average fractions and their fluctuations in the linear noise approximation (LNA). The emergence of a 'critical point' for the switching transition is rigorously established. New analytical results are derived for the average and variance of the fractional substrate concentration in various chemical states in the near-critical regime. For the total fraction in the modified state, the variance is shown to be a maximum near the critical point and decays algebraically away from it, similar to a second-order phase transition. The new analytical results are compared with existing ones as well as detailed numerical simulations using a Gillespie algorithm. © 2013 Elsevier Ltd.