J. M. Deutsch
[This is the unpublished supplemental information from 1989 to the paper: J.M. Deutsch, "Quantum statistical mechanics in a closed system." Phys. Rev. A, 43(4), 2046 (1991).] A closed quantum mechanical system does not necessarily give time…
Cosmological boundary conditions for particles and fields are often discussed as a Cauchy problem, in which configurations and conjugate momenta are specified on an "initial" time slice. But this is not the only way to specify boundary…
In the past several years, observational entropy has been developed as both a (time-dependent) quantum generalization of Boltzmann entropy, and as a rather general framework to encompass classical and quantum equilibrium and non-equilibrium…
Does regulation in the genome use collective behavior, similar to the way the brain or deep neural networks operate? Here I make the case for why having a genomic network capable of a high level of computation would be strongly selected…
We develop the framework of classical Observational entropy, which is a mathematically rigorous and precise framework for non-equilibrium thermodynamics, explicitly defined in terms of a set of observables. Observational entropy can be seen…
In this paper, we investigate and compare two well-developed definitions of entropy relevant for describing the dynamics of isolated quantum systems: bipartite entanglement entropy and observational entropy. In a model system of interacting…
We investigate the detailed properties of Observational entropy, introduced by \v{S}afr\'{a}nek et al. [Phys. Rev. A 99, 010101 (2019)] as a generalization of Boltzmann entropy to quantum mechanics. This quantity can involve multiple…
We extend classical coarse-grained entropy, commonly used in many branches of physics, to the quantum realm. We find two coarse-grainings, one using measurements of local particle numbers and then total energy, and the second using local…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
We study the diffusion of a linear polymer in the presence of permeable membranes without excluded volume interactions, using scaling theory and Monte Carlo simulations. We find that the average time it takes for a chain with polymerization…
The majority of mammalian genomic transcripts do not directly code for proteins and it is currently believed that most of these are not under evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and its strong…
Biophysics is a subject that is spread over many disciplines and transcends the skills and knowledge of the individual student. This makes it challenging both to teach and to learn. Educational materials are described to aid in teaching…
We study self avoiding random walks in an environment where sites are excluded randomly, in two and three dimensions. For a single polymer chain, we study the statistics of the time averaged monomer density and show that these are well…
In a number of experimental situations, single polymer molecules can be suspended in a vacuum. Here collisions between such molecules are considered. The limit of high collision velocity is investigated numerically for a variety of…
It is argued that a typical many body energy eigenstate has a well defined thermodynamic entropy and that individual eigenstates possess thermodynamic characteristics analogous to those of generic isolated systems. We examine large systems…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
We analyze experimental observations of microtubules undergoing small fluctuations about a "balance point" when mixed in solution of two different kinesin motor proteins, KLP61F and Ncd. It has been proposed that the microtubule movement is…
The statistical mechanics of a linear non-interacting polymer chain with a large number of monomers is considered with fixed angular momentum. The radius of gyration for a linear polymer is derived exactly by functional integration. This…
The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics…
We study stress relaxation in bi-disperse entangled polymer solutions. Shorter chains embedded in a majority of longer ones are known to be oriented by coupling to them. We analyze the mechanism for this both by computer simulation and…