Efficiency fluctuations and noise induced refrigerator-to-heater transition in information engines

Understanding noisy information engines is a fundamental problem of non-equilibrium physics, particularly in biomolecular systems agitated by thermal and active fluctuations in the cell. By the generalized second law of thermodynamics, the efficiency of these engines is bounded by the mutual information passing through their noisy feedback loop. Yet, direct measurement of the interplay between mutual information and energy has so far been elusive. To allow such examination, we explore here the entire phase-space of a noisy colloidal information engine, and study efficiency fluctuations due to the stochasticity of the mutual information and extracted work. We find that the average efficiency is maximal for non-zero noise level, at which the distribution of efficiency switches from bimodal to unimodal, and the stochastic efficiency often exceeds unity. We identify a line of anomalous, noise-driven equilibrium states that defines a refrigerator-to-heater transition, and test the generalized integral fluctuation theorem for continuous engines

Long reach cantilevers for sub-cellular force measurements

Maneuverable, high aspect ratio poly 3-4 ethylene dioxythiophene (PEDOT) fibers are fabricated for use as cellular force probes that can interface with individual pseudopod adhesive contact sites without forming unintentional secondary contacts to the cell. The straight fibers have lengths between 5 and 40 μm and spring constants in the 0.07-23.2 nN μm-1 range. The spring constants of these fibers were measured directly using an atomic force microscope (AFM). These AFM measurements corroborate determinations based on the transverse vibrational resonance frequencies of the fibers, which is a more convenient method. These fibers are employed to characterize the time dependent forces exerted at adhesive contacts between apical pseudopods of highly migratory D. discoideum cells and the PEDOT fibers, finding an average terminal force of 3.1 ± 2.7 nN and lifetime of 23.4 ± 18.5 s to be associated with these contacts

Forces at Individual Pseudopod-Filament Adhesive Contacts

On-chip cellular force sensors are fabricated from cantilever poly(3,4-ethylene dioxythiophene) filaments that visibly deflect under forces exerted at individual pseudopod-filament adhesive contacts. The shape of the deflected filaments and their ∼3 nN/μm spring constants are predicted by cantilever rod theory. Pulling forces exerted by Dictyostelium discoideumcells at these contacts are observed to reach ∼20 nN without breaking the contact

Acceleration of enzymatic catalysis by active hydrodynamic fluctuations

Cells are teeming with biochemical nano-machines whose vigorous activity generates strong hydrodynamic fluctuations. The authors revamp transition-state theory to account for the effect of this active noise and find that it may significantly accelerate the turnover rate of enzymes, thus proposing a physical picture of enzymatic catalysis as a collective process with long-range hydrodynamic coupling. The cellular milieu is teeming with biochemical nano-machines whose activity is a strong source of correlated non-thermal fluctuations termed active noise. Essential elements of this circuitry are enzymes, catalysts that speed up the rate of metabolic reactions by orders of magnitude, thereby making life possible. Here, we examine the possibility that active noise in the cell, or in vitro, affects enzymatic catalytic rate by accelerating or decelerating the crossing rate of energy barriers during the reaction. Considering hydrodynamic perturbations induced by biochemical activity as a source of active noise, we evaluate their impact on the enzymatic cycle using a combination of analytic and numerical methods. Our estimates show that the fast component of the active noise spectrum may significantly enhance the turnover rate of enzymes, while reactions remain practically unaffected by the slow noise spectrum. Revisiting the physics of barrier crossing under the influence of active hydrodynamic fluctuations suggests that the biochemical activity of macromolecules such as enzymes is coupled to active noise. Thus, we propose that enzymatic catalysis is a collective, many-body process in which enzymes may affect each other's activity via long-range hydrodynamic interaction, with potential impact on biochemical networks in living and artificial systems alike

Nano-fabrication of cellular force sensors and surface coatings via dendritic solidification

Doctor of PhilosophyDepartment of PhysicsBret N. FlandersDirected electrochemical nanowire assembly (DENA) is a method for fabricating nano-structured materials via electrochemical dendritic solidification. This thesis presents two new applications of nano-structured materials that are fabricated via the DENA methodology: cellular force sensors to probe adhesive sites on living cells and single-crystalline metallic dendrites as surface coating materials. Fast migrating cells like D. discoideum, leukocytes, and breast cancer cells migrate by attachment and detachment of discrete adhesive contacts, known as actin foci, to the substrate where the cell transmits traction forces. Despite their importance in migration, the physics by which actin foci bind and release substrates is poorly understood. This gap is largely due to the compositional complexity of actin foci in living cells and to a lack of technique for directly probing these sub-cellular structures. Recent theoretical work predicts these adhesive structures to depend on the density of adhesion receptors in the contact sites, the receptor-substrate potential, and cell-medium surface tension. This thesis describes the fabrication of sub-microscopic force sensors composed of poly(3,4-ethylene dioxythiophene) fibers that can interface directly with sub-cellular targets such as actin foci. The spring constants of these fibers are in the range of 0.07-430 nN m-1. These fibers were used to characterize the strength and lifetime of adhesion between the single adhesive contacts of D. discoideum cells and the fibers, finding an average force of 3.1 ± 2.7 nN and lifetime of 23.4 ± 18.5 s. This capability is significant because direct measurement of these properties will be necessary to measure the cell-medium surface tension and to characterize the receptor-substrate potential in the next (future) stage of this project. The fabrication of smart materials that are capable of the high dynamic range structural reconfiguration would lead to their use to confer hydrophobic, lipophobic, and anti-corrosive character to substrates in a regenerative manner. As a step towards this goal, we have extended the DENA method to enable repetitive growth and dissolution of metallic dendrites to substrates. The experimental parameters that control this process are the frequency and duty cycle of the alternating voltage signal that initiates the dendritic growth

Bona fide stochastic resonance under nonGaussian active fluctuations

We report on the experimental observation of stochastic resonance (SR) in a nonGaussian active bath without any periodic modulation. A Brownian particle hopping in a nanoscale double-well potential under the influence of nonGaussian correlated noise, with mean interval tau(P) and correlation time tau(c), shows a series of equally-spaced peaks in the residence time distribution at integral multiples of tau(P). The strength of the first peak is found to be maximum when the mean residence time (tau)(d) matches the double condition, 4 tau(c) asymptotic to tau(P) asymptotic to(tau)(d)/2, demonstrating a new type of bona fide SR. The experimental findings agree with a simple model that explains the emergence of SR without periodic modulation of the double-well potential. Additionally, we show that generic SR under periodic modulation, known to degrade in strongly correlated continuous noise, is recovered by the discrete nonGaussian kicks

Colossal power extraction from active cyclic Brownian information engines

Brownian information engines can extract work from thermal fluctuations by utilizing information. So far, the studies on Brownian information engines consider the system in a thermal bath; however, many processes in nature occur in a nonequilibrium setting, such as the suspensions of self-propelled microorganisms or cellular environments called an active bath. Here, we introduce an archetypal model for Maxwell-demon type cyclic Brownian information engine operating in a Gaussian correlated active bath. The active engine can extract more work than its thermal counterpart, exceeding the bound set by the second law of information thermodynamics. We obtain a general integral fluctuation theorem for the active engine that includes additional mutual information gained from the active bath with a unique effective temperature. This effective description modifies the second law and provides a new upper bound for the extracted work. Unlike the passive information engine operating in a thermal bath, the active information engine extracts colossal power that peaks at the finite cycle period. Our study provides fundamental insights into the design and functioning of synthetic and biological submicron motors in active baths under measurement and feedback control

Transport and Diffusion Enhancement in Experimentally Realized Non-Gaussian Correlated Ratchets

Living cells are known to generate non-Gaussian active fluctuations significantly larger than thermal fluctuations owing to various active processes. Understanding the effect of these active fluctuations on various physicochemical processes, such as the transport of molecular motors, is a fundamental problem in nonequilibrium physics. Therefore, we experimentally and numerically studied an active Brownian ratchet comprising a colloidal particle in an optically generated asymmetric periodic potential driven by non-Gaussian noise having finite-amplitude active bursts, each arriving at random and decaying exponentially. We find that the particle velocity is maximum for relatively sparse bursts with finite correlation time and non-Gaussian distribution. These occasional kicks, which produce Brownian yet non-Gaussian diffusion, are more efficient for transport and diffusion enhancement of the particle than the incessant kicks of active Ornstein???Uhlenbeck noise

Optical tweezers as a mathematically driven spatio-temporal potential generator

The ability to create and manipulate spatio-temporal potentials is essential in the diverse fields of science and technology. Here, we introduce an optical feedback trap system based on high precision position detection and ultrafast feedback control of a Brownian particle in the optical tweezers to generate spatio-temporal virtual potentials of the desired shape in a controlled manner. As an application, we study the nonequilibrium fluctuation dynamics of the particle in a time-varying virtual harmonic potential and validate the Crooks fluctuation theorem in the highly nonequilibrium condition