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A system responding to a stochastic driving signal can be interpreted as computing, by means of its dynamics, an implicit model of the environmental variables. The system's state retains information about past environmental fluctuations, and a fraction of this information is predictive of future ones. The remaining nonpredictive information reflects model… (More)

- Alexander J Mastroianni, David A Sivak, Phillip L Geissler, A Paul Alivisatos
- Biophysical journal
- 2009

We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle x-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average… (More)

A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls… (More)

The wormlike chain model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for elasticity at the 1-10 basepair (bp) scale, which holds particular interest in biological contexts. Here, we examine a class of… (More)

- Patrick R Zulkowski, David A Sivak, Gavin E Crooks, Michael R DeWeese
- Physical review. E, Statistical, nonlinear, and…
- 2012

A deeper understanding of nonequilibrium phenomena is needed to reveal the principles governing natural and synthetic molecular machines. Recent work has shown that when a thermodynamic system is driven from equilibrium then, in the linear response regime, the space of controllable parameters has a Riemannian geometry induced by a generalized friction… (More)

A central endeavor of thermodynamics is the measurement of free energy changes. Regrettably, although we can measure the free energy of a system in thermodynamic equilibrium, typically all we can say about the free energy of a nonequilibrium ensemble is that it is larger than that of the same system at equilibrium. Herein, we derive a formally exact… (More)

- Patrick R. Zulkowski, David A. Sivak, Michael R. DeWeese
- PloS one
- 2013

Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have an interest in optimizing such transitions. Using the Hatano-Sasa Y-value, we extend a recently developed geometrical… (More)

Any organism is embedded in an environment that changes over time. The timescale for and statistics of environmental change, the precision with which the organism can detect its environment, and the costs and benefits of particular protein expression levels all will affect the suitability of different strategies--such as constitutive expression or graded… (More)

A system responding to a stochastic driving signal can be interpreted as computing, by means of its dynamics, an implicit model of the environmental variables. The system's state retains information about past environmental fluctuations, and a fraction of this information is predictive of future ones. The remaining nonpredictive information reflects model… (More)

- David A. Sivak, John D. Chodera, Gavin E. Crooks
- The journal of physical chemistry. B
- 2014

When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad… (More)