Talk Session 3

Migration of Active Ring Polymers in Porous Media

Active organisms living inside tight, disordered, porous environments can effectively navigate through their habitat by generating localized forces along their membrane and temporally deforming their shape. To investigate the physical properties that underlie the dynamics of shape-deforming active organisms in the disordered environment, we simulate active ring polymers in two-dimensional random porous media. The dynamics of different systems of active ring polymers has been simulated: flexible, inextensible, and semiflexible. Deformation of flexible and inextensible ring polymers driven by active forces ---in form of expanding and shrinking in the pore space---allow them to navigate smoothly through the disordered micro-environment. In contrast, semiflexible rings undergo transient trapping inside the pore space; the degree of trapping is inversely correlated with the increase in the activity. Migration of active rings in the disordered environment is facilitated by their response to the change in their activity; while flexible rings swell with an increase in activity, inextensible and semiflexible rings monotonically shrink upon increasing the strength of the active force. Our work has direct implications on how shape deforming organisms can navigate through porous environments by generating localized forces along their membrane, and how their membrane stiffness plays a role in their shape deformation.

Using simulated ambiguous NOE-derived distance restraints to design protein switches

Some proteins pose a challenge to the one sequence, one structure dogma proposed by Anfinsen. These proteins contain amino acid sequences which can reversibly switch between different secondary structures. The switching between alternative folds may be driven by interactions of the protein with small ligands or other proteins, by chemical modifications (such as phosphorylation, methylation) or by changed environmental conditions, such as temperature, pH or solvent. De-novo design and detection of such fold switching proteins remains a challenge.

In my talk, I will be discussing an approach which uses simulated ambiguous NOE-derived distance restraints to detect and design amino acid sequences which have the propensity to switch folds. I will discuss some preliminary results and future directions.

Unraveling the role of network motifs to decipher the origin of robust decision making in biological systems

Living cells make precise decisions to opt for proliferation over quiescence or differentiation and survival over apoptosis by considering the given physiological conditions. These decision-making events are highly robust and often orchestrated by regulating the steady-state dynamics of important regulatory genes in a bi-stable manner. Intriguingly, recent studies revealed that in the context of epithelial to mesenchymal transition events and embryonic stem cell regulation, the related biological decision-making happens through even more complicated steady-state dynamics of genes such as tri-stable switches Mushroom and Isola kind of bifurcations. How these complex dynamical features emerge from the complex gene regulatory networks organizing such cellular processes and what are the minimal network motifs to achieve such complex dynamical features, remain elusive. Herein, we employed bifurcation analysis and Waddington’s potential landscape to find out the minimalistic network motifs responsible for giving rise to such complex Mushroom and Isola bifurcations in biological systems. Additionally, we have developed and analyzed a minimalistic network motif that can give rise to tri-stable dynamics for one gene (Oct4) and Mushroom bifurcation for another gene (Nanog) that governs the differentiation dynamics of stem cells. Our systematic bifurcation analysis provides the necessary insights to fine-tune the minimal network motifs that regulate differentiation dynamics. These insights will help to understand complex design principles of biological networks organized by such complex bifurcation features.

Rapid offline O2 detection via inexpensive and non-toxic bio-mimetic metal complex

It is still a challenge for scientists to detect the oxygen saturation in a stream of flowing breathable gas amid the COVID pandemic. The currently available methods/technologies require the use of expensive and complicated instruments or processes that may not be appropriate for a populated country like ours. On the contrary, colorimetric sensing approach because of its easy fabrication, rapid sensing, low-cost, and user-friendly detection with high sensitivity and selectivity. In biology, metalloprotein hemoglobin (Hb) acts as an O2-transporter as it reversibly binds to O2 in the lungs and develops oxy-hemoglobin (Hb-O2). This O2-bound version Hb-O2 (dark brown) can be distinguished easily from the deoxygenated (or non O2-bound) Hb (Maroon) from their distinct color. In this work, we have mimicked the hemoglobin reactivity with a synthetic cobalt (Co)-based metal complex containing a natural amino acid Histidine into a high selective and sensitive colorimetric sensor for different oxygen (O2) concentrations. We observed that this cobalt complex binds reversibly with the oxygen and exhibits distinct colour in solution for different [O2] under benign conditions. Additionally, the electrochemical studies of this complex provided further insight into its moderate catalytic activity towards Oxygen Reduction Reaction (ORR) to generate H2O2 and H2O. Hence, this study sets up another template or provide a prime example for designing the molecular complexes towards oxygen sensing applications by encompassing them with the precisely positioned enzyme-inspired functionalities.

Dimensionality in meta-materials from artificial atoms

Three-dimensional (3D) nanocrystal superlattices (meta-materials) are of immense interest owing to their extraordinary collective properties and potential applications. The dimensionality control of meta-materials is still challenging and no synthetic protocol has been developed so far to tune from 0D-1D-2D-3D. Here, we demonstrate a simple and facile single step chemical route to control the dimensionality of nanocrystal superlattices. Depending on the entire reaction conditions (e.g. solvent concentration, temperature, time and counter ions), we report superlattice of CuxS (x=1, 1.8 and 2) nanocrystals with varying dimensionality. These different morphologies are achieved by using emulsion based technique. The synthesized variants of superstructures seem to be highly stable and there is no disassembly within a solvent (ethanol, hexane and toluene) for a few months and no sonication effect for a few minute. Superstructures generated by this technique have extensive potential for devices fabrication in future because this method addresses several drawbacks associated with previously reported self-assembly methods.

First total synthesis of the conjugation-ready pentasaccharide repeating unit of Plesiomonas shigelloides strain 302-73 (serotype O1) is reported. The complex target pentasaccharide is composed of all-rare amino sugars such as orthogonally functionalized D-bacillosamine, L fucosamine, and L-pneumosamine linked through four consecutive α-linkages. The poor nucleophilicity of axial 4-OH of L-fucosamine and stereoselective glycosylations are the key challenges in the total synthesis, which was completed via a longest linear sequence of 27 steps in 3% overall yield.