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Snigdha Thakur

Publications and source records attributed to Snigdha Thakur.

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Ancilla-mediated fixed-point quantum search using Grover iterations

Grover's quantum search algorithm provides a fundamental quadratic speedup for unstructured datasets, reducing query complexity from $\mathcal{O}(N)$ to $\mathcal{O}(\sqrt{N})$. However, the algorithm's reliance on precise iteration counts leads to the ``soufflé problem,'' where over-rotation results in a sharp decline in success probability. This limitation is particularly restrictive when the number of solution states, $M$, is unknown. In this work, we present an ancilla-mediated fixed-point quantum search algorithm that achieves robust convergence by mapping the solution amplitude to a dedicated ancilla qubit. Unlike existing phase-matching fixed-point methods, our approach utilizes Grover's real-plane reflections, thereby maintaining the intuitive geometric architecture of the original algorithm. We demonstrate that this method achieves a success probability of at least $92.6\%$ with a query complexity of approximately $\mathcal{O}(\sqrt{N/M})$, effectively bridging the gap between standard amplitude amplification and robust fixed-point convergence.

quant-ph

Catalytic Crosstalk: Cooperative Enzyme Dynamics in Artificial Crowded Environments

In cellular environments, enzymes operate under densely crowded conditions that often hinder catalytic efficiency by limiting substrate diffusion and essential conformational dynamics. While reports suggest that crowding can often lead to inhibition of enzyme's catalytic activity, persistent efficiency of cellular biochemistry hints at underlying cooperative mechanisms among these molecules. Here, we experimentally demonstrate catalytic crosstalk between two enzymes - catalase and urease - in artificially crowded environments. Our results reveal that when co-localized in dense media, these enzymes mutually enhance each other's catalytic activity and dynamic behavior. This cooperative interaction leads to a net increase in reaction rates and mobility, suggesting an emergent many-body effect in enzyme assemblies. Modeling enzymes as dimeric active particles, we propose a minimal simulation framework that qualitatively captures the observed synergy. Our findings show that inter-enzyme cooperation can counteract the detrimental effects of crowding, offering insights into how enzymatic efficiency is sustained in complex biological milieu.

cond-mat.soft

Multiscale Phase Separation in Chemophoretic Active Matter

Nonreciprocal interactions in active matter provide interesting structure and dynamics. Here we investigate chemophoretic systems in which nonreciprocity arises from the asymmetric coupling between agents: first species produces certain chemicals and the other phoretically responds to it. This leads to phase separation at varying scales. Our study uncovers a re-entrant steady-state phase diagram as the nature of the coupling changes from chemoattractive to chemorepulsive character. Chemoattraction provides sustained domain growth, leading to macrophase separation via cluster coalescence. Aggregation in the chemorepulsive case, on the other hand, leads to a steady-state situation that displays phase separation only at a microscale, owing to strong caging effect and frequent fragmentation. The overall far-from-steady-state dynamics is quantified via calculations of growth exponents, cluster transition matrices, and mean-squared displacements.

cond-mat.soft

Structured search algorithm: A quantum leap

We introduce a structured quantum search algorithm that leverages entanglement maps and a fixed-point method to minimize oracle query complexity in unsorted datasets. By partitioning qubits into rows based on their entanglement order, the algorithm enables parallel subspace searches, achieving solution identification with at most two oracle calls per row. Experimental results on IBM Kyiv hardware demonstrate successful searches in datasets with up to 5 TB of unsorted data. Our findings indicate that with optimal encoding, the quantum search complexity becomes $\mathcal{O}(1)$, that is, independent of the dataset size $N$, surpassing both classical $\mathcal{O}(N)$ and Grover's $\mathcal{O}(\sqrt{N})$ scaling. Furthermore, the letter hypothesizes a scalable simulation of the said algorithm using classical means.

quant-ph

Critical role of the motor density and distribution on polar active polymers

Polar polymer activity is a fundamental mechanism behind a large number of cellular dynamical processes. The number and location of the active sites on the polymer backbone play a central role in their dynamics and conformational properties. Globular conformations for high motor densities change to stretched ones for the more realistic moderate or low density of motors, with a self-propelled polymer velocity non-monotonically related to the motor density. A small difference in the position of the first motor, or the motor distribution, can also dramatically modify the polymer typical conformations

cond-mat.soft

Active chiral rotors: hydrodynamics and chemotaxis

An active chiral rotor is a spherical object that can generate chiral flows in a fluid by rotating about an axis. For example, if the flow around the upper hemisphere of the chiral rotor is in a clockwise direction, then the flow in the lower hemisphere is in the anti-clockwise direction, and vice versa. In this paper, we aim to study the combined behaviour of hydrodynamically interacting chiral rotors in the presence of an external chemical gradient. While a single isolated rotor is stationary in a fluid, a pair of rotors can move in linear or circular paths as they hydrodynamically interact with each other. It is observed that the emergent linear or circular trajectories depend on the type of rotors and the orientation of their rotation axes. The dynamics of the rotors are altered in a more complex environment, such as in an external chemical field. Interestingly, we observe two types of motion: chemotaxis and anti-chemotaxis. While in the anti-chemotaxis case, both rotors are driving away from the target, in the chemotaxis case, one of the rotors successfully reaches the chemical target. This study helps to understand the collective behavior of self-propelled microorganisms and artificial swimmers.

cond-mat.soft

Diffusiophoretic Brownian dynamics: characterization of hydrodynamic effects for an active chemoattractive polymer

The phoretic Brownian dynamics method is shown here to be an effective approach to simulate the properties of colloidal chemophoretic based systems. The method is then optimized to allow for the comparison with results from multiparticle collision dynamics, a hydrodynamic method with explicit solvent, which can also be employed in the case of chemoattractive polymers. In order to obtain a good match of the conformational equilibrium properties of the models without and with explicit solvent, we propose a modified version of the phoretic Brownian dynamics accounting for the explicit solvent induced swelling. In the presence of activity, chemoattractive polymers show a transition to a compact globular state and hydrodynamics have a non-trivial influence in the polymer collapse times. The phoretic Brownian method can then be applied to much longer polymers, which allows the observation of a non-monotonous growth of both, the radius of gyration and the relaxation time with polymer length, for such chemoattractive active polymers.

cond-mat.soft

Role of viscoelasticity on the dynamics and aggregation of chemically active sphere-dimers

The impact of complex media on the dynamics of active swimmers has gained a thriving interest in the research community for their prominent applications in various fields. This paper investigates the effect of viscoelasticity on the dynamics and aggregation of chemically powered sphere-dimers by using a coarse-grained hybrid mesoscopic simulation technique. The sphere-dimers perform active motion by virtue of the concentration gradient around the swimmer's surface, produced by the chemical reaction at one end of the dimer. We observe that the fluid elasticity enhances translational and rotational motion of a single dimer, however for a pair of dimers, the clustering in a particular alignment is more pronounced. In case of multiple dimers, the kinetics of cluster formation along with their propulsive nature are presented in detail. The key factors influencing the enhanced motility and the aggregation of dimers are the concentration gradients, hydrodynamic coupling and the microstructures present in the system.

cond-mat.soft

Active Particles in Explicit Solvent: Dynamics of clustering for alignment interaction

We study dynamics of clustering in systems containing active particles that are immersed in an explicit solvent. For this purpose we have adopted a hybrid simulation method, consisting of molecular dynamics and multi-particle collision dynamics. In our model, overlap-avoiding passive interaction of an active particle with another active particle or a solvent particle has been taken care of via variants of Lennard-Jones potential. Dynamic interaction among the active particles has been incorporated via the Vicsek-like self-propulsion that facilitates clustering. We quantify the effects of activity and importance of hydrodynamics on the dynamics of clustering via variations of relevant system parameters. We work with low overall density of active particles. For this the morphology consists of disconnected clusters, the mechanism of growth switching among particle diffusion, diffusive coalescence and ballistic aggregation, depending upon the presence or absence of active and hydrodynamic interactions. Corresponding growth laws have been quantified and discussed in the background of appropriate theoretical pictures. Our results suggest that multi-particle collision dynamics is an effective method for investigation of hydrodynamic phenomena even in active matter systems.

cond-mat.soft

Formation of self-propelling clusters starting from randomly dispersed Brownian particles

We present a simple chemical strategy for the formation of a self-propelling cluster via the process of capture and assembly of passive colloids on the surface of a chemically active colloid. The two species of colloids that are isotropic and Brownian otherwise interact to form propelling cluster. With the help of coarse-grained numerical simulations, we show that a chemically active colloid can induce diffusiophoretic motility to nearby chemically inert colloids towards itself. This propulsion and then self-assembly can then lead to the formation of active cluster. We observe the formation of propelling dimers, trimers, tetramers, etc. depending on the chemical activity and size of the colloids.

physics.bio-ph

Biased random walks with finite mean first passage time

A power-law distance-dependent biased random walk model with a tuning parameter ($σ$) is introduced in which finite mean first passage times are realizable if $σ$ is less than a critical value $σ_c$. We perform numerical simulations in $1$-dimension to obtain $σ_c \sim 1.14$. The three-dimensional version of this model is related to the phenomenon of chemotaxis. Diffusiophoretic theory supplemented with coarse-grained simulations establish the connection with the specific value of $σ= 2$ as a consequence of in-built solvent diffusion. A variant of the one-dimensional power-law model is found to be applicable in the context of a stock investor devising a strategy for extricating their portfolio out of loss.

cond-mat.stat-mech

Diffusiophoretically induced interactions between chemically active and inert particles

In the presence of a chemically active particle, a nearby chemically inert particle can respond to a concentration gradient and move by diffusiophoresis. The nature of the motion is studied for two cases: first, a fixed reactive sphere and a moving inert sphere, and second, freely moving reactive and inert spheres. The continuum reaction-diffusion and Stokes equations are solved analytically for these systems and microscopic simulations of the dynamics are carried out. Although the relative velocities of the spheres are very similar in the two systems, the local and global structures of streamlines and the flow velocity fields are found to be quite different. For freely moving spheres, when the two spheres approach each other the flow generated by the inert sphere through diffu- siophoresis drags the reactive sphere towards it. This leads to a self-assembled dimer motor that is able to propel itself in solution. The fluid flow field at the moment of dimer formation changes direction. The ratio of sphere sizes in the dimer influences the characteristics of the flow fields, and this feature suggests that active self-assembly of spherical colloidal particles may be manipulated by sphere-size changes in such reactive systems.

cond-mat.soft

Anisotropic universe with anisotropic sources

We analyze the state space of a Bianchi-I universe with anisotropic sources. Here we consider an extended state space which includes null geodesics in this background. The evolution equations for all the state observables are derived. Dynamical systems approach is used to study the evolution of these equations. The asymptotic stable fixed points for all the evolution equations are found. We also check our analytic results with numerical analysis of these dynamical equations. The evolution of the state observables are studied both in cosmic time and using a dimensionless time variable. Then we repeat the same analysis with a more realistic scenario, adding the isotropic (dust like dark) matter and a cosmological constant (dark energy) to our anisotropic sources, to study their co-evolution. The universe now approaches a de~Sitter space asymptotically dominated by the cosmological constant. The cosmic microwave background anisotropy maps due to shear are also generated in this scenario, assuming that the universe contains anisotropic matter along with the usual (dark) matter and vacuum (dark) energy since decoupling. We find that they contribute dominantly to the CMB quadrupole. We also constrain the current level of anisotropy and also search for any cosmic preferred axis present in the data. We use the Union~2 Supernovae data to this extent. An anisotropy axis close to the mirror symmetry axis seen in the cosmic microwave background data from Planck probe is found.

gr-qc

Autonomous movement of chemically powered vesicle

A mechanism for self propulsion of deformable vesicle has been proposed, vesicle moves by sensing the self-generated chemical gradient. Like many molecular motors they suffer strong perturbations from the environment in which they move as a result of thermal fluctuations and do not rely on inertia for their propulsion. Motion of the vesicle is driven by an asymmetric distribution of reaction products. The propulsive velocity of the device is calculated as well as the scale of the velocity fluctuations. We present the simulation results on velocity of vesicle, reorientation of vesicle, and shape transformation of vesicles.

physics.bio-ph