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- Maya Sen, Rodrigo A. Maillard, +4 authors Carlos Bustamante
- Cell
- 2013

ATP-dependent proteases are vital to maintain cellular protein homeostasis. Here, we study the mechanisms of force generation and intersubunit coordination in the ClpXP protease from E. coli to understand how these machines couple ATP hydrolysis to mechanical protein unfolding. Single-molecule analyses reveal that phosphate release is the force-generating… (More)

- G. J. Peterson, Steve Pressé, Ken A. Dill
- Proceedings of the National Academy of Sciences…
- 2010

We develop a model for the distribution of scientific citations. The model involves a dual mechanism: in the direct mechanism, the author of a new paper finds an old paper A and cites it. In the indirect mechanism, the author of a new paper finds an old paper A only via the reference list of a newer intermediary paper B, which has previously cited A. By… (More)

The variational principles called maximum entropy (MaxEnt) and maximum caliber (MaxCal) are reviewed. MaxEnt originated in the statistical physics of Boltzmann and Gibbs, as a theoretical tool for predicting the equilibrium states of thermal systems. Later, entropy maximization was also applied to matters of information, signal transmission, and image… (More)

- G. Jack Peterson, Steve Pressé, Kristin S. Peterson, Ken A. Dill
- PloS one
- 2012

We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate interactions. (2) Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many… (More)

- Steve Pressé, Julian Lee, Ken A Dill
- The journal of physical chemistry. B
- 2013

Single-molecule data often come in the form of stochastic time trajectories. A key question is how to extract an underlying kinetic model from the data. A traditional approach is to assume some discrete state model, that is, a model topology, and to assume that transitions between states are Markovian. The transition rates are then selected according to… (More)

- Hao Ge, Steve Pressé, Kingshuk Ghosh, Ken A Dill
- The Journal of chemical physics
- 2012

Markov models are widely used to describe stochastic dynamics. Here, we show that Markov models follow directly from the dynamical principle of maximum caliber (Max Cal). Max Cal is a method of deriving dynamical models based on maximizing the path entropy subject to dynamical constraints. We give three different cases. First, we show that if constraints… (More)

- Julian Lee, Steve Pressé
- The Journal of chemical physics
- 2012

The master equation and, more generally, Markov processes are routinely used as models for stochastic processes. They are often justified on the basis of randomization and coarse-graining assumptions. Here instead, we derive nth-order Markov processes and the master equation as unique solutions to an inverse problem. We find that when constraints are not… (More)

Complex feedback systems are ubiquitous in biology. Modeling such systems with mass action laws or master equations requires information rarely measured directly. Thus rates and reaction topologies are often treated as adjustable parameters. Here we present a general stochastic modeling method for small chemical and biochemical systems with emphasis on… (More)

- Steve Pressé, Robert Silbey
- The Journal of chemical physics
- 2006

We consider the sampling problems encountered in computing free-energy differences using Jarzynski's nonequilibrium work relation [Phys. Rev. Lett. 56, 2690 (1997)]. This relation expresses the free-energy change of a system, on which finite-time work is done, as an average over all possible trajectories of the system. This average can then be expressed as… (More)

- Steve Pressé
- 2014

The maximum entropy method—used to infer probabilistic models from data—is a special case of Bayes's model inference prescription which, in turn, is grounded in basic propositional logic. By contrast to the maximum entropy method, the compatibility of nonadditive entropy maximization with Bayes's model inference prescription has never been established. Here… (More)