arXiv subjects

Ayusman Sen

Publications and source records attributed to Ayusman Sen.

11 recordsLinked to original sources

arXiv2025

Pattern Formation in Isothermal Miscible Protein/Sugar Systems Driven by Marangoni Effects and Evaporation

Through a combination of experiments and modeling, we have demonstrated a novel pattern formation phenomenon in an isothermal miscible fluid system involving simple protein and sugar solutions. We introduced dye-tagged protein solution into a petri dish with sugar solutions, which had higher density than the added protein solution. Initially, the protein spread and became more uniformly distributed at the air-water interface. Subsequently, it concentrated in specific areas to form spiral patterns. We propose that the mechanism involves an interplay between Marangoni effects, evaporation, and airflow. This finding is unexpected as solute Marangoni-related processes are generally characterized by fast spreading (seconds), while the pattern formation in our systems takes several minutes to form. Our work suggests that Turing reaction-diffusion patterns can be replicated by replacing the reaction-induced inhomogeneous solute distribution by evaporation-induced inhomogeneity. In both cases, the fast diffusive or Marangoni spreading of the solute is counteracted by a slower step that serves to reverse the solute homogenization. In showing that dissipative patterns can form in the absence of thermal gradients or chemical reactions, our findings significantly expand the conditions that lead to pattern formation. The insights gained also enhance our ability to manipulate and control fluid motion and surface morphology, with promising implications for many areas such as coating technologies, materials science, and microfluidics.

physics.flu-dyn↗

arXiv2022

Kinetic asymmetry versus dissipation in the evolution of chemical systems as exemplified by single enzyme chemotaxis

Single enzyme chemotaxis is a phenomenon by which a non-equilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise either naturally through metabolism, or experimentally, e.g., by flow of materials through several channels or by use of diffusion chambers with semipermeable membranes. Numerous hypotheses regarding the mechanism of this phenomenon have been proposed. Here we discuss a mechanism based solely on diffusion and chemical kinetics and show that kinetic asymmetry, a difference in the off rates for substrate and for product, and diffusion asymmetry, a difference in the diffusivities of the bound and free forms of the enzyme, are the sole determinates of the direction of chemotaxis. Exploration of these fundamental symmetries that govern nonequilibrium behavior helps to distinguish between possible mechanisms for the evolution of a chemical system from initial to the steady state, and whether the principle that determines the direction a system shifts when exposed to an external energy source is based on thermodynamics, or on kinetics, with the latter being supported by the results of the present paper. Our results show that while dissipation ineluctably accompanies non-equilibrium phenomena, including chemotaxis, systems do not evolve to maximize dissipation, but rather to attain greatest kinetic stability. Chemotactic response to the gradients formed by other enzymes provides a mechanism for forming loose associations known as metabolons. Significantly the direction of the effective force due to these gradients depends on the kinetic asymmetry of the enzyme, and so can be non-reciprocal, where one enzyme is attracted to another enzyme, but the other enzyme is repelled by the one, an important ingredient in the behavior of active matter.

cond-mat.soft↗

arXiv2021

'Fuelled' motion: phoretic motility and collective behaviour of active colloids

Designing microscopic and nanoscopic self-propelled particles and characterising their motion has become a major scientific challenge over the past decades. To this purpose, phoretic effects, namely propulsion mechanisms relying on local field gradients, have been the focus of many theoretical and experimental studies. In this review, we adopt a tutorial approach to present the basic physical mechanisms at stake in phoretic motion, and describe the different experimental works that lead to the fabrication of active particles based on this principle. We also present the collective effects observed in assemblies of interacting active colloids, and the theoretical tools that have been used to describe phoretic and hydrodynamic interactions.

cond-mat.soft↗

arXiv2021

The Relative Diffusivities of Bound and Unbound Protein Can Control Chemotactic Directionality

Enzyme-based systems have been shown to undergo directional motion in response to their substrate gradient. Here, we formulate a kinetic model to analyze the directional movement of an ensemble of protein molecules in response to a gradient of the ligand. A similar analysis has been performed to probe the motion of enzyme molecules in response to a gradient of the substrate under catalytic conditions. In both cases, a net movement up the ligand/substrate gradient is predicted when the diffusivity of the ligand/substrate-bound protein is lower than that of the unbound protein (positive chemotaxis). Conversely, movement down the ligand/substrate gradient is expected when the diffusivity of the ligand/substrate-bound protein is higher than that of the unbound protein (negative chemotaxis). The work underscores the critical importance of measuring the diffusivity of the bound protein and compare it with that of the free protein.

physics.bio-ph↗

arXiv2020

Entanglement and weak interaction driven mobility of small molecules in polymer networks

Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility using a synthetic experimental system of small dye molecules diffusing within a polymer network at short time scales. We find that the diffusion of inert molecules is inhibited by the presence of the polymers. Counter-intuitively, small, hydrophobic molecules display smaller reduction in mobility and also able to diffuse faster through the system by leveraging crowding specific parameters. We explained this phenomenon by developing a de novo model and using these results, we hypothesized that non-specific hydrophobic interactions between the molecules and polymer chains could localize the molecules into compartments of overlapped and entangled chains where they experience microviscosity, rather than macroviscosity. We introduced a characteristic interaction time parameter to quantitatively explain experimental results in the light of frictional effects and molecular interactions. Our model is in good agreement with the experimental results and allowed us to classify molecules into two different mobility categories solely based on interaction. By changing the surface group, polymer molecular weight, and by adding salt to the medium, we could further modulate the mobility and mean square displacements of interacting molecules. Our work has implications in understanding intracellular diffusive transport in microtubule networks and other systems with macromolecular crowding and could lead to transport enhancement in synthetic polymer systems.

cond-mat.soft↗

arXiv2020

3-D Printed Swimming Microtori for Cargo Transport and Flow Manipulation

Through billions of years of evolution, microorganisms mastered unique swimming behaviors to thrive in complex fluid environments. Limitations in nanofabrication have thus far hindered the ability to design and program synthetic swimmers with the same abilities. Here we encode multi-behavioral responses in artificial swimmers such as microscopic, self-propelled tori using nanoscale 3D printing. We show experimentally and theoretically that the tori continuously transition between two primary swimming modes in response to a magnetic field. The tori also manipulate and transport other artificial swimmers, bimetallic nanorods, as well as passive colloidal particles. In the first behavioral mode, the tori accumulate and transport nanorods; in the second mode, nanorods align along the tori's self-generated streamlines. Our results indicate that such shape-programmed microswimmers have the potential to manipulate biological active matter, e.g. bacteria or cells.

physics.flu-dyn↗

arXiv2018

A Theory of Enzyme Chemotaxis: Comparison Between Experiment and Model

Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with high substrate concentration, termed chemotaxis. While a variety of enzymes has been shown to undergo chemotaxis, there remains a lack of quantitative understanding of the phenomenon. Here, we provide a general expression for the active movement of an enzyme in a concentration gradient of its substrate. The proposed model takes into account both the substrate-binding and catalytic turnover step, as well as the enhanced diffusion effect. We have experimentally measured the chemotaxis of a fast and a slow enzyme: urease under catalytic conditions, and hexokinase for both full catalysis and for simple non-catalytic substrate binding. There is good agreement between the proposed model and the experiments. The model is general, has no adjustable parameters, and only requires three experimentally defined constants to quantify chemotaxis: enzyme-substrate binding affinity (Kd), Michaelis-Menten constant (KM) and level of diffusion enhancement in the associated substrate (α).

physics.bio-ph↗

arXiv2017

Distinguishing Advective and Powered Motion in Self-Propelled Colloids

Self-powered motion in catalytic colloidal particles provides a compelling example of active matter, i.e. systems that engage in single-particle and collective behavior far from equilibrium. The long-time, long-distance behavior of such systems is of particular interest, since it connects their individual micro-scale behavior to macro-scale phenomena. In such analyses, it is important to distinguish motion due to subtle advective effects -- which also has long time scales and length scales -- from phenomena that derive from intrinsically powered motion. Here, we develop a methodology to analyze the statistical properties of the translational and rotational motions of powered colloids to distinguish, for example, active chemotaxis from passive advection by bulk flow.

cond-mat.soft↗

arXiv2017

Exothermicity is not a necessary condition for enhanced diffusion of enzymes

Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We perform measurements on the endothermic and relatively slow enzyme aldolase, which also shows substrate-induced enhanced diffusion. We propose a new physical paradigm, which reveals that the diffusion coefficient of a model enzyme hydrodynamically coupled to its environment increases significantly when undergoing changes in conformational fluctuations in a substrate-dependent manner, and is independent of the overall turnover rate of the underlying enzymatic reaction. Our results show that substrate-induced enhanced diffusion of enzyme molecules can be explained within an equilibrium picture, and that the exothermicity of the catalyzed reaction is not a necessary condition for the observation of this phenomenon.

physics.bio-ph↗

arXiv2014

Enhanced brightness and photostability of cyanine dyes by supramolecular containment

Ultrasensitive detection and real-time monitoring of biological processes can benefit significantly from the improved brightness and photostability of the popular organic dyes such as cyanines. Here, using a model cyanine dye, Cy3, we demonstrate that brightness and photostability of the dye is significantly altered when trapped in a molecular container, e.g. cucurbit[n]urils (CB[n]) and cyclodextrins (CD).Through computational modeling, we predicted that Cy3 forms a stable inclusion complex with three different hosts, CB[7], beta-CD, and methyl-beta-CD, which was further confirmed by single-molecule diffusion measurements using fluorescence correlation spectroscopy. The effect of supramolecular encapsulation on Cy3 photophysical properties was found to be highly host-specific. Up to three-fold increase in brightness of Cy3 was observed when the dye was trapped in methyl-beta-CD, due to an increase in both dye absorption and quantum yield. Steady-state and time-resolved spectroscopy of the various complexes revealed that host polarizability and restricted mobility of the dye in the host both contribute to the observed increase in molecular brightness. Furthermore, entrapment of the dye molecule in CDs resulted in a marked increase in dye photostability, whereas the dye degraded more rapidly in CB[7]. These results suggest that the changes in photophysical properties of the dye afforded by supramolecular encapsulation are highly dependent on the host molecule. The reported improvement in brightness and photostability together with the excellent biocompatibility of cyclodextrins makes supramolecular encapsulation a viable strategy for routine dye enhancement.

q-bio.BM↗

arXiv2005

Design and Test of a Carbon-Tolerant Alkaline Fuel Cell

This paper presents new results which may constitute a breakthrough in the effort to develop fuel cells truly suitable for use in cars and trucks. For decades, researchers have known that the alkaline fuel cell (AFC) is much cheaper to make, more efficient and more durable than the more popular PEM fuel cell; however, "carbon poisoning" (either from CO2 in air or from contaminants in reformed methanol) causes big problems in the kind of oxygen-hydrogen AFC commonly used in space. This paper reports successful tests of a technique for coating the electrodes with polystyrene which, in conjunction with older common-sense techniques, appears to solve the problem. This kind of design is applicable to cars run on hydrogen fuel, on reformed methanol or even direct methanol. Developing a test methodology was a major part of the work. A foreword by one of the sponsors at NSF discusses the larger importance of this work for energy security and the environment.

physics.chem-ph↗