Statistical Physics of Adaptation

Whether by virtue of being prepared in a slowly relaxing, high-free energy initial condition, or because they are constantly dissipating energy absorbed from a strong external drive, many systems subject to thermal fluctuations are not expected to behave in the way they would at thermal equilibrium. Rather, the probability of finding such a system in a given microscopic arrangement may deviate strongly from the Boltzmann distribution, raising the question of whether thermodynamics still has anything to tell us about which arrangements are the most likely to be observed. In this work, we build on past results governing nonequilibrium thermodynamics and define a generalized Helmholtz free energy that exactly delineates the various factors that quantitatively contribute to the relative probabilities of different outcomes in far-from-equilibrium stochastic dynamics. By applying this expression to the analysis of two examples—namely, a particle hopping in an oscillating energy landscape and a population composed of two types of exponentially growing self-replicators—we illustrate a simple relationship between outcome-likelihood and dissipative history. In closing, we discuss the possible relevance of such a thermodynamic principle for our understanding of self-organization in complex systems, paying particular attention to a possible analogy to the way evolutionary adaptations emerge in living things.United States. Air Force Office of Scientific Research (32 CFR 168a

Dissipation Bounds All Steady-State Current Fluctuations

Near equilibrium, small current fluctuations are described by a Gaussian distribution with a linear-response variance regulated by the dissipation. Here, we demonstrate that dissipation still plays a dominant role in structuring large fluctuations arbitrarily far from equilibrium. In particular, we prove a linear-response-like bound on the large deviation function for currents in Markov jump processes. We find that nonequilibrium current fluctuations are always more likely than what is expected from a linear-response analysis. As a small-fluctuations corollary, we derive a recently conjectured uncertainty bound on the variance of current fluctuations.Gordon and Betty Moore Foundation (Grant GBMF4513)Gordon and Betty Moore Foundation (Grant GBMF4343

Case studies in protein folding and adaptation to time-varying fields

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, 2016.Cataloged from PDF version of thesis.Includes bibliographical references (pages 119-128).In this thesis, we use the methods of statistical physics to provide quantitative insights into the behavior of biological systems. In the first half of the thesis, we use equilibrium statistical physics to develop a phenomenological model of how the hydrophobic effect impacts the structure of proteins, and in the second half, we study the phenomenon of adaptation and Darwinian selection from the standpoint of nonequilibrium statistical physics. It has been known for a long time that the hydrophobic effect plays a major role in driving protein folding. However, it has been challenging to translate this understanding into a predictive, quantitative theory of how the full pattern of sequence hydrophobicity in a protein helps to determine its structure. Here, we develop and apply a phenomenological theory of the sequence-structure relationship in globular protein domains. In an effort to optimize parameters for the model, we first analyze the patterns of backbone burial found in single-domain crystal structures and discover that classic hydrophobicity scales derived from bulk physicochemical properties of amino acids are already nearly optimal for prediction of burial using the model. Subsequently, we apply the model to studying structural fluctuations in proteins and establish a means of identifying ligand-binding and protein-protein interaction sites using this approach. In the second half of the thesis, we undertake to address the question of adaptation from the standpoint of physics. Building on past fundamental results in nonequilibrium statistical mechanics, we demonstrate a generalization of the Helmholtz free energy for the finite-time stochastic evolution of driven Newtonian matter. By analyzing this expression, we show a general tendency in a broad class of driven many-particle systems toward self-organization into states formed through reliable absorption and dissipation of work energy from the surrounding environment. We demonstrate how this tendency plays out in the familiar example of Darwinian competition between two exponentially growing self-replicators. Subsequently, we illustrate the more general mechanism by which extra dissipation drives adaptation by analyzing the process of random hopping in driven energy landscapes.by Nikolay Perunov.Ph. D

Single Spoke Cavities for Low-energy Part of CW Linac of Project X.

In the low-energy part of the Project X H-linac three families of 325 MHz SC single spoke cavities will be used, having {beta} = 0.11, 0.21 and 0.4. Single spoke cavity was selected for the linac because of higher r/Q. Results of optimization of all cavities are presented. Results of the beam dynamics optimization for initial stage of the linac with beta=0.11 single spoke cavity are presented at poster MOPEC082 (this conference)