arXiv subjects

Shivprasad Patil

Publications and source records attributed to Shivprasad Patil.

14 recordsLinked to original sources

arXiv2025

Miniature work-to-work converter engine powered by motor protein

Designing a miniature microscale engine that can override the role of thermal fluctuations has remained elusive and is an important open challenge. Here we provide the design and theoretical framework for a unique information-based engine - a work-to-work converter - comprising a sub-micron size bead and motor protein-microtubule (MT) complex in an optical trap setup. We demonstrate how by implementing a simple motor protein state-dependent feedback protocol of the optical trap stiffness, this engine is able to harness and convert the movement of a motor protein into work output. Unlike other conventional microengines, the fidelity and performance of this engine is determined by the stochasticity of motor (un)binding characteristics. We obtain an analytical form of the work distribution function, average work output and average power output, providing quantitative predictions for engine performance which are validated by stochastic simulations. Remarkably, the average work output per cycle is at least an order of magnitude higher than the thermal fluctuations and supersedes the performance of other microscale engines realized so far.

physics.bio-ph↗

arXiv2022

Direct and simultaneous measurement of the stiffness and internal friction of a single folded protein

The nanomechanical response of a folded single protein, the natural nanomachine responsible for myriad biological processes, provides insight into its function. The conformational flexibility of a folded state, characterized by its viscoelasticity, allows proteins to adopt different shapes to perform their function. Despite efforts, its direct measurement has not been possible so far. We present a direct and simultaneous measurement of the stiffness and internal friction of the folded domains of the protein titin using a special interferometer based atomic force microscope. We analysed the data by carefully separating different contributions affecting the response of the experimental probe to obtain the folded state's viscoelasticity. Above ~ 95 pN of force, the individual immunoglobulins of titin transition from an elastic solid-like native state to a soft viscoelastic intermediate.

physics.bio-ph↗

arXiv2022

Translational diffusion of a fluorescent tracer molecule in nanoconfined water

Diffusion of tracer dye molecules in water confined to nanoscale is an important subject with a direct bearing on many technological applications. It is not yet clear however, if the dynamics of water in hydrophilic as well as hydrophobic nanochannels remains bulk-like. Here, we present diffusion measurement of a fluorescent dye molecule in water confined to nanoscale between two hydrophilic surfaces whose separation can be controlled with a precision of less than a nm. We observe that the fluorescence intensities correlate over a fast($\sim$ 30 $μ$s) and slow ($\sim$ 1000 $μ$s) time components. The slow timescale is due to adsorption of fluorophores to the confining walls and it disappears in presence of 1 M salt. The fast component is attributed to diffusion of dye molecules in the gap and is found to be bulk-like for sub-10 nm separations and indicates that viscosity of water under confinement remains unaltered up to confinement gap as small as $\sim$ 5 nm. Our findings contradict some of the recent measurements of diffusion under nanoconfinement, however they are consistent with many estimates of self-diffusion using molecular dynamics simulations and measurements using neutron scattering experiments.

cond-mat.soft↗

arXiv2021

Elasticity of single flexible polymer chains in good and poor solvents

Force versus extension curves measure entropic elasticity of single polymer chain in force spectroscopy experiments. A Worm-like Chain model is used to describe force extension experiments with an intrinsic chain parameter called persistence length, which is a measure of local bending flexibility. For flexible polymers, there is a discrepancy in estimates of persistence length in various force regimes. For instance, Atomic Force Microscopy (AFM) based pulling experiments report anomaly low values which are also inconsistent with magnetic tweezers experiments. To understand this, we investigate the role of coupling between microscopic force probe and intrinsic elasticity of polyethylene glycol chain in AFM-based experiments. We perform experiments using oscillatory rheology by providing an external excitation of fixed frequency to the probe. We show that a proper quantification of elastic response measured directly by oscillatory technique deviates significantly from conventional force-extension curves. The persistence length obtained by fitting WLC to stiffness extension data matches well with equilibrium tweezers experiments. In addition, for polystyrene chain in poor solvent no deviation in elastic response is observed between oscillatory and constant velocity pulling experiments. However, such deviation is seen for polystyrene in good solvent. We attribute this to hydrophobic interaction between monomers of polystyrene in water. Our results suggest that oscillatory rheology on single polymer chains provide quantitative estimate of its elastic response. The consistency in values of persistence length using magnetic tweezers experiments in low force regime and the AFM experiments in high force regime suggests that WLC is successful in describing the polymer elasticity in the force range typically probed in AFM experiments.

cond-mat.soft↗

arXiv2021

Validity of point-mass model in off-resonance dynamic atomic force microscopy

The quantitative measurement of viscoelasticity of nano-scaleentities is an important goal of nanotechnology research and there is considerable progress with advent of dynamic Atomic Force Microscopy. The hydrodynamics of cantilever, the force sensor in AFM measurements, plays a pivotal role in quantitative estimates of nano-scale viscoelasticity. The point-mass model,wherein the AFM cantilever is approximated as a point mass with mass-less spring is widely used in dynamic AFM analysis and its validity, particularly in liquid environments, is debated. It is suggested that the cantilever must be treated as a continuous rectangular beam to obtain accurate estimates of nano-scale viscoelasticity of materials it is probing. Here, we derived equations, which relate stiffness and damping coefficient of the material under investigation to measured parameters, by approximating cantilever as a point mass and also considering the full geometric details. These equations are derived for both tip-excited as well as base excited cantilevers. We have performed off-resonance dynamic atomic force spectroscopy on a single protein molecule to investigate the validity of widely used point-mass model. We performed measurements with AFMs equipped with different cantilever excitation methods as well as detection schemes to measure cantilever response. The data was analyzed using both, continuous-beam model and the point-mass model. We found that both models yield same results when the experiments are performed in truly off-resonance regime with small amplitudes and the cantilever stiffness is much higher than the interaction stiffness. Our findings suggest that a simple point-mass approximation based model is adequate to describe the dynamics, provided care is taken while performing experiments so that the approximations used in these models are valid.

cond-mat.soft↗

arXiv2020

Non-van der Waals honeycomb antiferromagnet SrRu$_2$O$_6$ down to a few layers

The current family of experimentally realized two-dimensional magnetic materials consist of 3$d$ transition metals with very weak spin-orbit coupling. In contrast, we report a new platform in a chemically bonded and layered 4$d$ oxide, with strong electron correlations and competing spin-orbit coupling. We synthesize ultra-thin sheets of SrRu$_2$O$_6$ using scalable liquid exfoliation. These exfoliated sheets are characterized by complementary experimental and theoretical techniques. The thickness of the nano-sheets varies between three to five monolayers, and within the first-principles calculations, we show that antiferromagnetism survives in these ultra-thin layers. Experimental data suggest that exfoliation occurs from the planes perpendicular to the $c$-axis as the intervening hexagonal Sr-lattice separates the two-dimensional magnetic honeycomb Ru-layers. The high-resolution transmission electron microscope images indicate that the average inter-atomic spacing between the Ru-layers is slightly reduced, which agrees with the present calculations. The signatures of rotational stacking of the nanosheets are also observed. Such new two-dimensional platform offers enormous possibilities to explore emergent properties that appear due to the interplay between magnetism, strong correlations and spin-orbit coupling. Moreover, these effects can be further tuned as a function of layer thickness.

cond-mat.str-el↗

arXiv2020

Elastic response of poly(ethylene glycol) polymer chains studied using dynamic atomic force microscopy

Stretching response of polymer chains under external force is crucial in understanding polymer dynamics under equilibrium and non-equilibrium conditions. Here we measure the elastic response of poly(ethylene glycol) using a lock-in based amplitude modulation-AFM with sub-angstrom amplitude in both low and high frequency regime. Appropriate analysis that takes into account the cantilever geometry and hydrodynamic loading effects of oscillating cantilever in liquid, relates X signal of lock-in amplifier linearly to stiffness.Stiffness data extracted from X signal was compared with stiffness from derivative of conventional "static" force extension curves. For stiffness data from X signal, fitting to standard entropic model of WLC gives a physically meaningful value of persistense length and also follows scaling behaviour of WLC. Entropy dominated conformational transition with its characteristic V-shaped signature was observed at arount 250 pN. Accurate measurement of stiffness enabled us in understanding the thermodynamics of conformational changes.

cond-mat.soft↗

arXiv2020

A new method for measurement and quantification of tracer diffusion in nanoconfined liquids

We report development of a novel instrument to measure tracer diffusion in water under nano-scale confinement. A direct optical access to the confinement region, where water is confined between a tapered fiber and a flat substrate, is made possible by coating the probe with metal and opening a small aperture( 0.1 $μ$m to 1 $μ$m) at its end. A well-controlled cut using an ion beam ensures desired lateral confinement area as well as adequate illumination of the confinement gap. The probe is mounted on a tuning-fork based force sensor to control the separation between the probe and the substrate with nm precision. Fluctuations in fluorescence intensity due to diffusion of a dye molecule in water confined between probe and the sample are recorded using a confocal arrangement with a single photon precision. A Monte-Carlo method is developed to determine the diffusion coefficient from the measured autocorrelation of intensity fluctuations which accommodates the specific geometry of confinement and the illumination profile. The instrument allows measurement of diffusion laws under confinement. We found that the diffusion of a tracer molecule is slowed down by more than ten times for the probe-substrate separations of 5 nm and below.

cond-mat.soft↗

arXiv2017

The effect of boundary slippage and nonlinear rheological response on flow of nanoconfined water

The flow of water confined to nanometer-sized pores is central to a wide range of subjects from biology to nanofluidic devices. Despite its importance, a clear picture about nanoscale fluid dynamics is yet to emerge. Here we measured dissipation in less than 20 nm thick water films and it was found to decrease for both wetting and non-wetting confining surfaces. The fitting of Carreau-Yasuda model of shear thinning to our measurements implies that flow is non-Newtonian and for wetting surfaces the no-slip boundary condition is valid. On the contrary, for non-wetting surfaces boundary slippage occurs with slip lengths of the order of few nm. The findings suggest that both, the wettability of the confining surfaces and nonlinear rheological response of water molecules under nano-confinement play a dominant role in transport properties.

cond-mat.soft↗

arXiv2016

Excess area dependent scaling behavior of nano-sized membrane tethers

Thermal fluctuations in cell membranes manifest as an excess area (${\cal A}_{\rm ex}$) which governs a multitude of physical process at the sub-micron scale. We present a theoretical framework, based on an in silico tether pulling method, which may be used to reliably estimate ${\cal A}_{\rm ex}$ in live cells. The tether forces estimated from our simulations compare well with our experimental measurements for tethers extracted from ruptured GUVs and HeLa cells. We demonstrate the significance and validity of our method by showing that all our calculations along with experiments of tether extraction in 15 different cell types collapse onto two unified scaling relationships mapping tether force, tether radius, bending stiffness $κ$, and membrane tension $σ$. We show that $R_{\rm bead}$, the size of the wetting region, is an important determinant of the radius of the extracted tether, which is equal to $ξ=\sqrt{κ/2σ}$ (a characteristic length scale of the membrane) for $R_{\rm bead}<ξ$, and is equal to $R_{\rm bead}$ for $R_{\rm bead}>ξ$. We also find that the estimated excess area follows a linear scaling behavior that only depends on the true value of ${\cal A}_{\rm ex}$ for the membrane, based on which we propose a self-consistent technique to estimate the range of excess membrane areas in a cell.

physics.bio-ph↗

arXiv2013

A new tuning fork-based instrument for oscillatory shear rheology of nano-confined liquids

We present a new method to measure rheological response of liquids confined to nano-scale which exhibit a considerable slow-down in dynamics compared to bulk liquids. The method relies on using a robust force sensor that has a sensitivity to measure shear forces in the range of 1 to 10 nN and a stiffness of 55000 N/m to avoid thermal noise. Off-resonance operation ensures application of a range of shear frequencies . This range is higher than the inverse of the system's mechanical relaxation time and allows the measurement of non-linear effects emerging due to significant "slow down" in dynamics upon confinement. The instrument is a step forward towards resolving the controversies about the nature of nano-confined liquids.

cond-mat.soft↗

arXiv2012

Direct evidence of photo-ionization causing luminescence "off" state in CdTe Quantum dots

We present a direct experimental evidence of photo-ionized CdTe quantum dot core having luminescence "off" state at band-edge photo-excitation. We use the autocorrelation of fluorescence fluctuations from dilute colloidal solution of CdTe quantum dots in a diffraction limited detection volume to determine their photo-ionization probability. The ionization probability is in the same order of magnitude (\approx10-6) as the CdSe and CdSe/ZnS core/shell quantum dots. Further, we measured the ionization/ neutralization rates (\approx104 s-1) after addition of β-mercaptanol and found that ionization rate is enhanced by two orders of magnitude after the addition. However, a comparable neutralization rate enhances the light emission quantum yield. The ionization/ neutralization at microsecond time scales puts an upper limit on achieving better quantum yield by thiol addition. The results also indicate that the dominant ionization mechanism at band-edge excitation is tunneling.

cond-mat.mes-hall↗

arXiv2010

Dynamic Solidification in Nanoconfined Water Films

The mechanical properties of nanoconfined water layers are still poorly understood and continue to create considerable controversy, despite their importance for biology and nanotechnology. Here, we report on dynamic nanomechanical measurements of water films compressed down to a few single molecular layers. We show that the mechanical properties of nanoconfined water layers change dramatically with their dynamic state. In particular, we observed a sharp transition from viscous to elastic response even at extremely slow compression rates, indicating that mechanical relaxation times increase dramatically once water is compressed to less than 3-4 molecular layers.

cond-mat.soft↗

arXiv2005

Solid or Liquid ? - Kinetically induced phase transition of a confined liquid

There has been long-standing debate about the physical state and possible phase transformations of confined liquids. In this report we show that a model confined liquid can behave both as a Newtonian liquid with very little change in its dynamics or as a pseudo-solid depending solely on the {\it rate} of approach of the confining surfaces. Thus, the confined liquid does {\it not} exhibit any confinement induced solidification in thermodynamic equilibrium. Instead, solidification is induced kinetically, when the two confining surfaces are approached with a minimum critical rate. This critical rate is surprisingly slow, of the order of 6 Å/s, explaining the frequent observation of confinement induced solidification.

cond-mat.soft↗