1,721,117 research outputs found
What Is a Macrostate? Subjective Observations and Objective Dynamics
Full text linkWe consider the question of whether thermodynamic macrostates are objective consequences of dynamics, or subjective reflections of our ignorance of a physical system. We argue that they are both; more specifically, that the set of macrostates forms the unique maximal partition of phase space which 1) is consistent with our observations (a subjective fact about our ability to observe the system) and 2) obeys a Markov process (an objective fact about the system's dynamics). We review the ideas of computational mechanics, an information-theoretic method for finding optimal causal models of stochastic processes, and argue that macrostates coincide with the ``causal states'' of computational mechanics. Defining a set of macrostates thus consists of an inductive process where we start with a given set of observables, and then refine our partition of phase space until we reach a set of states which predict their own future, i.e. which are Markovian. Macrostates arrived at in this way are provably optimal statistical predictors of the future values of our observables
A Statistical Model of translocation of Structured Polypeptide Chains through Nanopores
No full textThe translocation process of a globular protein (ubiquitin) across a cylindrical nanopore is studied via molecular dynamics simulations. The ubiquitin is described by a native-centric model on a CR carbon backbone to investigate the influence of protein-like structural properties on the translocation mechanism. A thermodynamical and kinetic characterization of the process is obtained by studying the statistics of blockage times, the mobility, and the translocation probability as a function of the pulling force F acting in the pore. The transport dynamics occurs when the force exceeds a threshold Fc depending on a free-energy barrier that ubiquitin has to overcome in order to slide along the channel. Such a barrier results from competition of the unfolding energy and the entropy associated with the confinement effects of the pore. We implement appropriate umbrella sampling simulations to compute the free-energy profile as a function of the position of the ubiquitin center of mass inside of the channel (reaction coordinate). This free energy is then used to construct a phenomenological drift-diffusion model in the reaction coordinate which explains and reproduces the behavior of the observables during the translocation
Reductionism, Emergence and Levels of Reality
No full textScientists have always attempted to explain the world in terms of a few unifying principles. In the fifth century B.C. Democritus boldly claimed that reality is simply a collection of indivisible and eternal parts or atoms. Over the centuries his doctrine has remained a landmark, and much progress in physics is due to its distinction between subjective perception and objective reality. This book discusses theory reduction in physics, which states that the whole is nothing more than the sum of its parts: the properties of things are directly determined by their constituent parts. Reductionism deals with the relation between different theories that address different levels of reality, and uses extrapolations to apply that relation in different sciences. Reality shows a complex structure of connections, and the dream of a unified interpretation of all phenomena in several simple laws continues to attract anyone with genuine philosophical and scientific interests. If the most radical reductionist point of view is correct, the relationship between disciplines is strictly inclusive: chemistry becomes physics, biology becomes chemistry, and so on. Eventually, only one science, indeed just a single theory, would survive, with all others merging in the Theory of Everything. Is the current coexistence of different sciences a mere historical venture which will end when the Theory of Everything has been established? Can there be a unified description of nature? Rather than an analysis of full reductionism, this book focuses on aspects of theory reduction in physics and stimulates reflection on related questions: is there any evidence of actual reduction? Are the examples used in the philosophy of science too simplistic? What has been endangered by the search for (the) ultimate truth? Has the dream of reductionist reason created any monsters? Is big science one such monster? What is the point of embedding science Y within science X, if predictions cannot be made on that basis
Linear response of Hamiltonian chaotic systems as a function of the number of degrees of freedom - Reply
Full text linkArticle replying to a comment by Massimo Falcioni and Angelo Vulpiani. The authors discuss research on the linear response theory (LRT)
Comment on ``Universal relation between the Kolmogorov-Sinai Entropy and the thermodynamic entropy in simple liquids
No full textA Comment on the Letter by Mikhail Dzugutor, Erik Aurell, and Angelo Vulpiani, Phys. Rev. Lett. 81, 1762 (1998). The authors of the Letter offer a Reply. © 2000 The American Physical Society
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