Information Engine in a Nonequilibrium Bath.

Information engines can convert thermal fluctuations of a bath at temperature T into work at rates of order k_{B}T per relaxation time of the system. We show experimentally that such engines, when in contact with a bath that is out of equilibrium, can extract much more work. We place a heavy, micron-scale bead in a harmonic potential that ratchets up to capture favorable fluctuations.

Bayesian Information Engine that Optimally Exploits Noisy Measurements.

We have experimentally realized an information engine consisting of an optically trapped, heavy bead in water. The device raises the trap center after a favorable "up" thermal fluctuation, thereby increasing the bead's average gravitational potential energy. In the presence of measurement noise, poor feedback decisions degrade its performance; below a critical signal-to-noise ratio, the engine shows a phase transition and cannot store any gravitational energy.

Inferring potential landscapes from noisy trajectories of particles within an optical feedback trap.

While particle trajectories encode information on their governing potentials, potentials can be challenging to robustly extract from trajectories. Measurement errors may corrupt a particle's position, and sparse sampling of the potential limits data in higher energy regions such as barriers. We develop a Bayesian method to infer potentials from trajectories corrupted by Markovian measurement noise without assuming prior functional form on the potentials.

Anomalous heating in a colloidal system.

We report anomalous heating in a colloidal system, an experimental observation of the inverse Mpemba effect, where for two initial temperatures lower than the temperature of the thermal bath, the colder of the two systems heats up faster when coupled to the same thermal bath. For an overdamped, Brownian colloidal particle moving in a tilted double-well potential, we find a nonmonotonic dependence of the heating times on the initial temperature of the system. Entropic effects make the inverse Mpemba effect generically weaker-harder to observe-than the usual Mpemba effect (anomalous cooling).

Maximal fluctuation exploitation in Gaussian information engines.

Understanding the connections between information and thermodynamics has been among the most visible applications of stochastic thermodynamics. While recent theoretical advances have established that the second law of thermodynamics sets limits on information-to-energy conversion, it is currently unclear to what extent real systems can achieve the predicted theoretical limits. Using a simple model of an information engine that has recently been experimentally implemented, we explore the limits of information-to-energy conversion when an information engine's benefit is limited to output energy that can be stored.

Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication.

The heterogeneous nature of eukaryotic replication kinetics and the low efficiency of individual initiation sites make mapping the location and timing of replication initiation in human cells difficult. To address this challenge, we have developed optical replication mapping (ORM), a high-throughput single-molecule approach, and used it to map early-initiation events in human cells. The single-molecule nature of our data and a total of >2,500-fold coverage of the human genome on 27 million fibers averaging ∼300 kb in length allow us to identify initiation sites and their firing probability with high confidence.

Maximizing power and velocity of an information engine.

Information-driven engines that rectify thermal fluctuations are a modern realization of the Maxwell-demon thought experiment. We introduce a simple design based on a heavy colloidal particle, held by an optical trap and immersed in water. Using a carefully designed feedback loop, our experimental realization of an "information ratchet" takes advantage of favorable "up" fluctuations to lift a weight against gravity, storing potential energy without doing external work.

Optimal finite-time bit erasure under full control.

We study the finite-time erasure of a one-bit memory consisting of a one-dimensional double-well potential, with each well encoding a memory macrostate. We focus on setups that provide full control over the form of the potential-energy landscape and derive protocols that minimize the average work needed to erase the bit over a fixed amount of time. We allow for cases where only some of the information encoded in the bit is erased.

Finite-Time Landauer Principle.

We study the thermodynamic cost associated with the erasure of one bit of information over a finite amount of time. We present a general framework for minimizing the average work required when full control of a system's microstates is possible. In addition to exact numerical results, we find simple bounds proportional to the variance of the microscopic distribution associated with the state of the bit.

Exponentially faster cooling in a colloidal system.

As the temperature of a cooling object decreases as it relaxes to thermal equilibrium, it is intuitively assumed that a hot object should take longer to cool than a warm one. Yet, some 2,300 years ago, Aristotle observed that "to cool hot water quickly, begin by putting it in the sun". In the 1960s, this counterintuitive phenomenon was rediscovered as the statement that "hot water can freeze faster than cold water" and has become known as the Mpemba effect; it has since been the subject of much experimental investigation and some controversy.

Test of the diffusing-diffusivity mechanism using near-wall colloidal dynamics.

The mechanism of diffusing diffusivity predicts that, in environments where the diffusivity changes gradually, the displacement distribution becomes non-Gaussian, even though the mean-square displacement grows linearly with time. Here, we report single-particle tracking measurements of the diffusion of colloidal spheres near a planar substrate. Because the local effective diffusivity is known, we have been able to carry out a direct test of this mechanism for diffusion in inhomogeneous media.

Direct measurement of weakly nonequilibrium system entropy is consistent with Gibbs-Shannon form.

Stochastic thermodynamics extends classical thermodynamics to small systems in contact with one or more heat baths. It can account for the effects of thermal fluctuations and describe systems far from thermodynamic equilibrium. A basic assumption is that the expression for Shannon entropy is the appropriate description for the entropy of a nonequilibrium system in such a setting.

When memory pays: Discord in hidden Markov models.

When is keeping a memory of observations worthwhile? We use hidden Markov models to look at phase transitions that emerge when comparing state estimates in systems with discrete states and noisy observations. We infer the underlying state of the hidden Markov models from the observations in two ways: through naive observations, which take into account only the current observation, and through Bayesian filtering, which takes the history of observations into account. Defining a discord order parameter to distinguish between the different state estimates, we explore hidden Markov models with various numbers of states and symbols and varying transition-matrix symmetry.

Feedback traps for virtual potentials.

Feedback traps are tools for trapping and manipulating single charged objects, such as molecules in solution. An alternative to optical tweezers and other single-molecule techniques, they use feedback to counteract the Brownian motion of a molecule of interest. The trap first acquires information about a molecule's position and then applies an electric feedback force to move the molecule.

Erasure without Work in an Asymmetric Double-Well Potential.

According to Landauer's principle, erasing a memory requires an average work of at least kTln2 per bit. Recent experiments have confirmed this prediction for a one-bit memory represented by a symmetric double-well potential. Here, we present an experimental study of erasure for a memory encoded in an asymmetric double-well potential.

Replication timing is regulated by the number of MCMs loaded at origins.

Replication timing is a crucial aspect of genome regulation that is strongly correlated with chromatin structure, gene expression, DNA repair, and genome evolution. Replication timing is determined by the timing of replication origin firing, which involves activation of MCM helicase complexes loaded at replication origins. Nonetheless, how the timing of such origin firing is regulated remains mysterious.

High-precision test of Landauer's principle in a feedback trap.

We confirm Landauer's 1961 hypothesis that reducing the number of possible macroscopic states in a system by a factor of 2 requires work of at least kTln2. Our experiment uses a colloidal particle in a time-dependent, virtual potential created by a feedback trap to implement Landauer's erasure operation. In a control experiment, similar manipulations that do not reduce the number of system states can be done reversibly.

Note: Split PID control--two sensors can be better than one.

The traditional proportional-integral-derivative (PID) algorithm for regulation suffers from a tradeoff: placing the sensor near the sample being regulated ensures that its steady-state temperature matches the desired setpoint. However, the propagation delay (lag) between heater and sample can limit the control bandwidth. Moving the sensor closer to the heater reduces the lag and increases the bandwidth but introduces offsets and drifts into the temperature of the sample.

Virtual potentials for feedback traps.

The recently developed feedback trap can be used to create arbitrary virtual potentials, to explore the dynamics of small particles or large molecules in complex situations. Experimentally, feedback traps introduce several finite time scales: There is a delay between the measurement of a particle's position and the feedback response, the feedback response is applied for a finite update time, and a finite camera exposure integrates motion. We show how to incorporate such timing effects into the description of particle motion.

Conductive probe AFM study of Pt-thiol and Au-thiol contacts in metal-molecule-metal systems.

The charge transport mechanism between 1,8-octanedithiol (ODT, C(8)H(16)S(2)H(2)) and platinum and gold electrodes is studied by breaking bonds between single ODT molecules and atomic metal junctions using conductive probe atomic force microscopy. Histograms of conductance values show peaks that are obscured by background processes that differ from the metal-molecule-metal conduction path of interest. We introduce a new method to reduce greatly such backgrounds by dividing by a 1-octanethiol (OMT, C(8)H(17)SH) reference histogram, without data selection.

Regulation of DNA replication within the immunoglobulin heavy-chain locus during B cell commitment.

The temporal order of replication of mammalian chromosomes appears to be linked to their functional organization, but the process that establishes and modifies this order during cell differentiation remains largely unknown. Here, we studied how the replication of the Igh locus initiates, progresses, and terminates in bone marrow pro-B cells undergoing B cell commitment. We show that many aspects of DNA replication can be quantitatively explained by a mechanism involving the stochastic firing of origins (across the S phase and the Igh locus) and extensive variations in their firing rate (along the locus).

Replication timing and its emergence from stochastic processes.

The temporal organization of DNA replication has puzzled cell biologists since before the mechanism of replication was understood. The realization that replication timing correlates with important features, such as transcription, chromatin structure and genome evolution, and is misregulated in cancer and aging has only deepened the fascination. Many ideas about replication timing have been proposed, but most have been short on mechanistic detail.