Creation of the selection list for the Experiment Scheduling Program (ESP)

The efforts to develop a procedure to construct selection groups to augment the Experiment Scheduling Program (ESP) are summarized. Included is a User's Guide and a sample scenario to guide in the use of the software system that implements the developed procedures

Entropy and Entanglement in Quantum Ground States

We consider the relationship between correlations and entanglement in gapped quantum systems, with application to matrix product state representations. We prove that there exist gapped one-dimensional local Hamiltonians such that the entropy is exponentially large in the correlation length, and we present strong evidence supporting a conjecture that there exist such systems with arbitrarily large entropy. However, we then show that, under an assumption on the density of states which is believed to be satisfied by many physical systems such as the fractional quantum Hall effect, that an efficient matrix product state representation of the ground state exists in any dimension. Finally, we comment on the implications for numerical simulation.Comment: 7 pages, no figure

Memory B cells and CD8⁺ lymphocytes do not control seasonal influenza A virus replication after homologous re-challenge of rhesus macaques.

This study sought to define the role of memory lymphocytes in the protection from homologous influenza A virus re-challenge in rhesus macaques. Depleting monoclonal antibodies (mAb) were administered to the animals prior to their second experimental inoculation with a human seasonal influenza A virus strain. Treatment with either anti-CD8α or anti-CD20 mAbs prior to re-challenge had minimal effect on influenza A virus replication. Thus, in non-human primates with pre-existing anti-influenza A antibodies, memory B cells and CD8α⁺ T cells do not contribute to the control of virus replication after re-challenge with a homologous strain of influenza A virus

Information capacity of genetic regulatory elements

Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need to perform non-trivial computations that integrate several inputs and affect multiple genes. At the same time, the activities of the regulated genes would fluctuate even if the inputs were held fixed, as a consequence of the intrinsic noise in the system, and such noise must fundamentally limit the reliability of any genetic computation. Here we use information theory to formalize the notion of information transmission in simple genetic regulatory elements in the presence of physically realistic noise sources. The dependence of this "channel capacity" on noise parameters, cooperativity and cost of making signaling molecules is explored systematically. We find that, at least in principle, capacities higher than one bit should be achievable and that consequently genetic regulation is not limited the use of binary, or "on-off", components.Comment: 17 pages, 9 figure

Student Days : March Two-Step

https://digitalcommons.library.umaine.edu/mmb-vp/2532/thumbnail.jp

Information Flow through a Chaotic Channel: Prediction and Postdiction at Finite Resolution

We reconsider the persistence of information under the dynamics of the logistic map in order to discuss communication through a nonlinear channel where the sender can set the initial state of the system with finite resolution, and the recipient measures it with the same accuracy. We separate out the contributions of global phase space shrinkage and local phase space contraction and expansion to the uncertainty in predicting and postdicting the state of the system. Thus, we determine how the amplification parameter, the time lag, and the resolution influence the possibility for communication. A novel representation for real numbers is introduced that allows for a visualization of the flow of information between scales.Comment: 14 pages, 13 figure

Dynamics of the Fisher Information Metric

We present a method to generate probability distributions that correspond to metrics obeying partial differential equations generated by extremizing a functional $J[g^{\mu\nu}(\theta^i)]$, where $g^{\mu\nu}(\theta^i)$ is the Fisher metric. We postulate that this functional of the dynamical variable $g^{\mu\nu}(\theta^i)$ is stationary with respect to small variations of these variables. Our approach enables a dynamical approach to Fisher information metric. It allows to impose symmetries on a statistical system in a systematic way. This work is mainly motivated by the entropy approach to nonmonotonic reasoning.Comment: 11 page

Molecular Dynamics in Hydrogen‐bonded Interactions: A Preliminary Experimentally Determined Harmonic Stretching Force Field for HCN‐‐‐HF

Observation of the 2ν1 overtone band in the hydrogen‐bonded complex HCN‐‐‐HF permits evaluation of the anharmonicity constant X 1 1=−116.9(1) cm− 1 and determination of the anharmonicity corrected fundamental frequency ω1. This information, and available data from previous rovibrational analyses in the common and perdeuterated isotopic species of HCN‐‐‐HF, offer an opportunity for calculation of an approximate stretching harmonic force field. With the assumptions f 1 2=f 2 4=0.0, the remaining force constants (in mdyn/Å) are evaluated as: f 1 1=8.600(20), f 2 2=6.228(9), f 3 3=19.115(40), f 4 4=0.2413(39), f 1 3=0.000(13), f 1 4=0.0343(2), f 2 3=−0.211(6), f 3 4=0.000(2). These compare to f 1 1=9.658(2) in the HF monomer and f 1 1=6.244(3) and f 3 3=18.707(16) in the HCN monomer. These results provide the information necessary to quantitatively assess the applicability of the Cummings and Wood approximation in this hydrogen‐bonded complex and also give an estimate of D e j , the equilibrium distortion constant in the harmonic limit. Comparisons of these experimentally determined parameters with the predictions of a b i n i t i o molecular orbital calculations at several levels of approximation are presented

Specific protein-protein binding in many-component mixtures of proteins

Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein, specific binding in many component mixtures is studied. It is found to be a demanding function in the sense that it demands that the binding sites of the proteins be encoded by long sequences of bits, and the requirement for specific binding then strongly constrains these sequences. This is quantified by the capacity of proteins of a given size (sequence length), which is the maximum number of specific-binding interactions possible in a mixture. This calculation of the maximum number possible is in the same spirit as the work of Shannon and others on the maximum rate of communication through noisy channels.Comment: 13 pages, 3 figures (changes for v2 mainly notational - to be more in line with notation in information theory literature