arXiv subjects

Sambarta Chatterjee

Publications and source records attributed to Sambarta Chatterjee.

3 recordsLinked to original sources

arXiv2025

The underappreciated role of nonspecific interactions in the crystallization of DNA-coated colloids

Over the last decade, the field of programmable self-assembly has seen an explosion in the diversity of crystal lattices that can be synthesized from DNA-coated colloidal nanometer- and micrometer-scale particles. The prevailing wisdom has been that a particular crystal structure can be targeted by designing the DNA-mediated interactions, to enforce binding between specific particle pairs, and the particle diameters, to control the packing of the various species. In this article, we show that other ubiquitous nonspecific interactions can play equally important roles in determining the relative stability of different crystal polymorphs and therefore what crystal structure is most likely to form in an experiment. For a binary mixture of same-sized DNA-coated colloidal micrometer-scale particles, we show how changing the magnitudes of nonspecific steric and van der Waals interactions gives rise to a family of binary body-centered tetragonal crystals, including both cesium-chloride and copper-gold crystals. Simulations using pair potentials that account for these interactions reproduce our experimental observations quantitatively, and a theoretical model reveals how a subtle balance between specific and nonspecific forces determines the equilibrium crystal structure. These results highlight the importance of accounting for nonspecific interactions in the crystal-engineering design process.

cond-mat.soft↗

arXiv2024

Multi-objective optimization for targeted self-assembly among competing polymorphs

Most approaches for designing self-assembled materials focus on the thermodynamic stability of a target structure or crystal polymorph. Yet in practice, the outcome of a self-assembly process is often controlled by kinetic pathways. Here we present an efficient machine learning-guided design algorithm to identify globally optimal interaction potentials that maximize both the thermodynamic yield and kinetic accessibility of a target polymorph. We show that optimal potentials exist along a Pareto front, indicating the possibility of a trade-off between the thermodynamic and kinetic objectives. Although the extent of this trade-off depends on the target polymorph and the assembly conditions, we generically find that the trade-off arises from a competition among alternative polymorphs: The most kinetically optimal potentials, which favor the target polymorph on short timescales, tend to stabilize a competing polymorph at longer times. Our work establishes a general-purpose approach for multi-objective self-assembly optimization, reveals fundamental trade-offs between crystallization speed and defect formation in the presence of competing polymorphs, and suggests guiding principles for materials design algorithms that optimize for kinetic accessibility.

cond-mat.soft↗

arXiv2016

Emergence of Dynamic Cooperativity in the Stochastic Kinetics of Fluctuating Enzymes

Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic cooperativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative cooperativity. For fewer enzymes, dynamic cooperativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic cooperativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

physics.chem-ph↗