arXiv subjects

Shatruhan Singh Rajput

Publications and source records attributed to Shatruhan Singh Rajput.

4 recordsLinked to original sources

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↗

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↗