arXiv subjects

Atanu Das

Publications and source records attributed to Atanu Das.

4 recordsLinked to original sources

arXiv2020

Earthquake and Electrochemistry: Unraveling the Unpredictable

Earthquakes are measured using well defined seismic parameters such as seismic moment (Mo), moment magnitude (Mw), and released elastic energy(E). How this tremendous amount of energy is accumulated silently deep inside the earth's crust? The most obvious question in seismic research remains unanswered. We found an inherent and intriguing connection between the released energy in an earthquake and electrochemical potential induced in an ultra-thin metal oxide electrode immersed in an aqueous pH solution, which leads us to understand the origin of the energy accumulation process in an earthquake. A huge electrochemical potential is accumulated from numerous electrochemical cells formed in a unique layer structure of hydrated clay minerals (predominantly smectite), which resulted in a lightning-like discharge in the lithosphere (hypocenter). The subsequent thunder-like massive shockwave is produced, which initiates tectonic plate movement along a fault line, probably through acoustic fluidization (AF), and resulting seismic energy is transmitted as primary wave (P-wave), secondary wave (S-wave), and surface waves. The presence of electrical voltage in the hypocenter directly supports the seismic electric signal (SES), further strengthening the VAN method of earthquake prediction. Our finding is supported by a plethora of research and observation devoted to seismic science. This study will indeed find its significance if immediate action is implemented to monitor the evolution of electrochemical potential, seismic electrical signal (SES), and ionic activity in the fault zone at lithosphere as well as in the ionosphere for predicting an impending earthquake for saving human lives as early as possible.

physics.geo-ph↗

arXiv2020

pH-Sensitive Ultra-thin Oxide-Liquid Metal System: Understanding the Fundamental Sensing Mechanism

The pH response of liquid metal (eutectic GaInSn) in the form of a pendant drop is investigated and the sensitivity of 92.96 mV in the pH range from 4 to 10 is obtained. Unlike the fundamental limit of pH sensitivity of 59.1 mV in an electrolyte-site binding surface, the super-Nernstian pH sensitivity originated from a spontaneous electrochemical reaction associated with an enhanced ionic exchange at the ultra-thin (1-3 nm) Ga2O3-electrolyte interface which is purely driven by thermodynamics, rendering to the lowest system energy possible involving gallate and bi-gallate ions. A unified Nernst equation is derived by introducing an ion-exchange factor x to explain superNernstian pH sensitivity and found a direct link between pH sensitivity and Pourbaix pH-Potential formulations. It is found that Nernstian sensitivity of 59.1 mV occurs only for symmetric ion exchange (x=1) reaction, whereas asymmetric ion exchanges could result in sensitivity far beyond the Nernst sensitivity. Our findings have great scientific significance, which could redefine the conventional concept of the ion sensing mechanism in a solid-state electrochemical sensor and push forward the future development of the 2D oxide-based electrochemical sensor.

physics.app-ph↗

arXiv2013

SOD1 Exhibits Allosteric Frustration to Facilitate Metal Binding Affinity

Superoxide dismutase-1 (SOD1) is a ubiquitous, Cu and Zn binding, free radical defense enzyme whose misfolding and aggregation play a potential key role in amyotrophic lateral sclerosis, an invariably fatal neurodegenerative disease. Over 150 mutations in SOD1 have been identified with a familial form of the disease, but it is presently not clear what unifying features, if any, these mutants share to make them pathogenic. Here, we develop several new computational assays for probing the thermo-mechanical properties of both ALS-associated and rationally-designed SOD1 variants. Allosteric interaction free energies between residues and metals are calculated, and a series of atomic force microscopy experiments are simulated with variable tether positions, to quantify mechanical rigidity "fingerprints" for SOD1 variants. Mechanical fingerprinting studies of a series of C-terminally truncated mutants, along with an analysis of equilibrium dynamic fluctuations while varying native constraints, potential energy change upon mutation, frustratometer analysis, and analysis of the coupling between local frustration and metal binding interactions for a glycine scan of 90 residues together reveal that the apo protein is internally frustrated, that these internal stresses are partially relieved by mutation but at the expense of metal-binding affinity, and that the frustration of a residue is directly related to its role in binding metals. This evidence points to apo SOD1 as a strained intermediate with "self-allostery" for high metal-binding affinity. Thus, the prerequisites for the function of SOD1 as an antioxidant compete with apo state thermo-mechanical stability, increasing the susceptibility of the protein to misfold in the apo state.

q-bio.BM↗

arXiv2012

Mechanical probes of SOD1 predict systematic trends in metal and dimer affinity of ALS-associated mutants

Mutations and oxidative modification in the protein Cu,Zn superoxide dismutase (SOD1) have been implicated in the death of motor neurons in amyotrophic lateral sclerosis (ALS), a presently incurable, invariably fatal neurodegenerative disease. Here we employ steered, all-atom molecular dynamics simulations in implicit solvent to investigate the significance of either mutations or post-translational modifications (PTMs) to SOD1 on metal affinity, dimer stability, and mechanical malleability. The work required to induce moderate structural deformations as a function of sequence index constitutes a "mechanical fingerprint" measuring structural rigidity in the native basin, from which we are able to unambiguously distinguish wild-type (WT) SOD1 from PTM variants, and measure the severity of a given PTM on structural integrity. The cumulative distribution of work values provided a way to cleanly discriminate between SOD1 variants. Disulfide reduction destabilizes dimer stability more than the removal of either metal, but not moreso than the removal of both metals. Intriguingly, we found that disulfide reduction mechanically stabilizes apo SOD1 monomer, underscoring the differences between native basin mechanical properties and equilibrium thermodynamic stabilities, and elucidating the presence of internal stress in the apo state. All PTMs and ALS-associated mutants studied showed an increased tendency to lose either Cu or Zn, and to monomerize- processes known to be critical in the progression of ALS. The valence of Cu strongly modulates its binding free energy. As well, several mutants were more susceptible to loss of metals and monomerization than the disulfide-reduced or apo forms of SOD1. Distance constraints are required to calculate free energies for metal binding and dimer separation, which are validated using thermodynamic cycles.

q-bio.BM↗