3,587 research outputs found
On defining the Hamiltonian beyond quantum theory
Energy is a crucial concept within classical and quantum physics. An
essential tool to quantify energy is the Hamiltonian. Here, we consider how to
define a Hamiltonian in general probabilistic theories, a framework in which
quantum theory is a special case. We list desiderata which the definition
should meet. For 3-dimensional systems, we provide a fully-defined recipe which
satisfies these desiderata. We discuss the higher dimensional case where some
freedom of choice is left remaining. We apply the definition to example toy
theories, and discuss how the quantum notion of time evolution as a phase
between energy eigenstates generalises to other theories.Comment: Authors' accepted manuscript for inclusion in the Foundations of
Physics topical collection on Foundational Aspects of Quantum Informatio
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A generative inference framework for analysing patterns of cultural change in sparse population data with evidence for fashion trends in LBK culture
Cultural change can be quantified by temporal changes in frequency of different cultural artefacts and it is a central question to identify what underlying cultural transmission processes could have caused the observed frequency changes. Observed changes, however, often describe the dynamics in samples of the population of artefacts, whereas transmission processes act on the whole population. Here we develop a modelling framework aimed at addressing this inference problem. To do so, we firstly generate population structures from which the observed sample could have been drawn randomly and then determine theoretical samples at a later time t2 produced under the assumption that changes in frequencies are caused by a specific transmission process. Thereby we also account for the potential effect of time-averaging processes in the generation of the observed sample. Subsequent statistical comparisons (e.g. using Bayesian inference) of the theoretical and observed samples at t2 can establish which processes could have produced the observed frequency data. In this way, we infer underlying transmission processes directly from available data without any equilibrium assumption. We apply this framework to a dataset describing pottery from settlements of some of the first farmers in Europe (the LBK culture) and conclude that the observed frequency dynamic of different types of decorated pottery is consistent with age-dependent selection, a preference for 'young' pottery types which is potentially indicative of fashion trends
Bilayer manganites: polarons in the midst of a metallic breakdown
The exact nature of the low temperature electronic phase of the manganite
materials family, and hence the origin of their colossal magnetoresistant (CMR)
effect, is still under heavy debate. By combining new photoemission and
tunneling data, we show that in La{2-2x}Sr{1+2x}Mn2O7 the polaronic degrees of
freedom win out across the CMR region of the phase diagram. This means that the
generic ground state is that of a system in which strong electron-lattice
interactions result in vanishing coherent quasi-particle spectral weight at the
Fermi level for all locations in k-space. The incoherence of the charge
carriers offers a unifying explanation for the anomalous charge-carrier
dynamics seen in transport, optics and electron spectroscopic data. The
stacking number N is the key factor for true metallic behavior, as an
intergrowth-driven breakdown of the polaronic domination to give a metal
possessing a traditional Fermi surface is seen in the bilayer system.Comment: 7 pages, 2 figures, includes supplementary informatio
Formation of regulatory modules by local sequence duplication
Turnover of regulatory sequence and function is an important part of
molecular evolution. But what are the modes of sequence evolution leading to
rapid formation and loss of regulatory sites? Here, we show that a large
fraction of neighboring transcription factor binding sites in the fly genome
have formed from a common sequence origin by local duplications. This mode of
evolution is found to produce regulatory information: duplications can seed new
sites in the neighborhood of existing sites. Duplicate seeds evolve
subsequently by point mutations, often towards binding a different factor than
their ancestral neighbor sites. These results are based on a statistical
analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome,
and a comparison set of intergenic regulatory sequence in Saccharomyces
cerevisiae. In fly regulatory modules, pairs of binding sites show
significantly enhanced sequence similarity up to distances of about 50 bp. We
analyze these data in terms of an evolutionary model with two distinct modes of
site formation: (i) evolution from independent sequence origin and (ii)
divergent evolution following duplication of a common ancestor sequence. Our
results suggest that pervasive formation of binding sites by local sequence
duplications distinguishes the complex regulatory architecture of higher
eukaryotes from the simpler architecture of unicellular organisms
DNA intercalator stimulates influenza transcription and virus replication
Influenza A virus uses its host transcription machinery to facilitate viral RNA synthesis, an event that is associated with cellular RNA polymerase II (RNAPII). In this study, various RNAPII transcription inhibitors were used to investigate the effect of RNAPII phosphorylation status on viral RNA transcription. A low concentration of DNA intercalators, such as actinomycin D (ActD), was found to stimulate viral polymerase activity and virus replication. This effect was not observed in cells treated with RNAPII kinase inhibitors. In addition, the loss of RNAPIIa in infected cells was due to the shift of nonphosphorylated RNAPII (RNAPIIa) to hyperphosphorylated RNAPII (RNAPIIo)
Measurement of Epstein-Barr virus DNA load using a novel quantification standard containing two EBV DNA targets and SYBR Green I dye
<p>Abstract</p> <p>Background</p> <p>Reactivation of Epstein-Barr virus (EBV) infection may cause serious, life-threatening complications in immunocompromised individuals. EBV DNA is often detected in EBV-associated disease states, with viral load believed to be a reflection of virus activity. Two separate real-time quantitative polymerase chain reaction (QPCR) assays using SYBR Green I dye and a single quantification standard containing two EBV genes, Epstein-Barr nuclear antigen-1 (EBNA-1) and BamHI fragment H rightward open reading frame-1 (BHRF-1), were developed to detect and measure absolute EBV DNA load in patients with various EBV-associated diseases. EBV DNA loads and viral capsid antigen (VCA) IgG antibody titres were also quantified on a population sample.</p> <p>Results</p> <p>EBV DNA was measurable in ethylenediaminetetraacetic acid (EDTA) whole blood, peripheral blood mononuclear cells (PBMCs), plasma and cerebrospinal fluid (CSF) samples. EBV DNA loads were detectable from 8.0 × 10<sup>2 </sup>to 1.3 × 10<sup>8 </sup>copies/ml in post-transplant lymphoproliferative disease (n = 5), 1.5 × 10<sup>3 </sup>to 2.0 × 10<sup>5 </sup>copies/ml in infectious mononucleosis (n = 7), 7.5 × 10<sup>4 </sup>to 1.1 × 10<sup>5 </sup>copies/ml in EBV-associated haemophagocytic syndrome (n = 1), 2.0 × 10<sup>2 </sup>to 5.6 × 10<sup>3 </sup>copies/ml in HIV-infected patients (n = 12), and 2.0 × 10<sup>2 </sup>to 9.1 × 10<sup>4 </sup>copies/ml in the population sample (n = 218). EBNA-1 and BHRF-1 DNA were detected in 11.0% and 21.6% of the population sample respectively. There was a modest correlation between VCA IgG antibody titre and BHRF-1 DNA load (rho = 0.13, p = 0.05) but not EBNA-1 DNA load (rho = 0.11, p = 0.11).</p> <p>Conclusion</p> <p>Two sensitive and specific real-time PCR assays using SYBR Green I dye and a single quantification standard containing two EBV DNA targets, were developed for the detection and measurement of EBV DNA load in a variety of clinical samples. These assays have application in the investigation of EBV-related illnesses in immunocompromised individuals.</p
Monotonicity of Fitness Landscapes and Mutation Rate Control
A common view in evolutionary biology is that mutation rates are minimised.
However, studies in combinatorial optimisation and search have shown a clear
advantage of using variable mutation rates as a control parameter to optimise
the performance of evolutionary algorithms. Much biological theory in this area
is based on Ronald Fisher's work, who used Euclidean geometry to study the
relation between mutation size and expected fitness of the offspring in
infinite phenotypic spaces. Here we reconsider this theory based on the
alternative geometry of discrete and finite spaces of DNA sequences. First, we
consider the geometric case of fitness being isomorphic to distance from an
optimum, and show how problems of optimal mutation rate control can be solved
exactly or approximately depending on additional constraints of the problem.
Then we consider the general case of fitness communicating only partial
information about the distance. We define weak monotonicity of fitness
landscapes and prove that this property holds in all landscapes that are
continuous and open at the optimum. This theoretical result motivates our
hypothesis that optimal mutation rate functions in such landscapes will
increase when fitness decreases in some neighbourhood of an optimum, resembling
the control functions derived in the geometric case. We test this hypothesis
experimentally by analysing approximately optimal mutation rate control
functions in 115 complete landscapes of binding scores between DNA sequences
and transcription factors. Our findings support the hypothesis and find that
the increase of mutation rate is more rapid in landscapes that are less
monotonic (more rugged). We discuss the relevance of these findings to living
organisms
Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site
We introduce a novel method to screen the promoters of a set of genes with
shared biological function, against a precompiled library of motifs, and find
those motifs which are statistically over-represented in the gene set. The gene
sets were obtained from the functional Gene Ontology (GO) classification; for
each set and motif we optimized the sequence similarity score threshold,
independently for every location window (measured with respect to the TSS),
taking into account the location dependent nucleotide heterogeneity along the
promoters of the target genes. We performed a high throughput analysis,
searching the promoters (from 200bp downstream to 1000bp upstream the TSS), of
more than 8000 human and 23,000 mouse genes, for 134 functional Gene Ontology
classes and for 412 known DNA motifs. When combined with binding site and
location conservation between human and mouse, the method identifies with high
probability functional binding sites that regulate groups of biologically
related genes. We found many location-sensitive functional binding events and
showed that they clustered close to the TSS. Our method and findings were put
to several experimental tests. By allowing a "flexible" threshold and combining
our functional class and location specific search method with conservation
between human and mouse, we are able to identify reliably functional TF binding
sites. This is an essential step towards constructing regulatory networks and
elucidating the design principles that govern transcriptional regulation of
expression. The promoter region proximal to the TSS appears to be of central
importance for regulation of transcription in human and mouse, just as it is in
bacteria and yeast.Comment: 31 pages, including Supplementary Information and figure
Predictability of evolutionary trajectories in fitness landscapes
Experimental studies on enzyme evolution show that only a small fraction of
all possible mutation trajectories are accessible to evolution. However, these
experiments deal with individual enzymes and explore a tiny part of the fitness
landscape. We report an exhaustive analysis of fitness landscapes constructed
with an off-lattice model of protein folding where fitness is equated with
robustness to misfolding. This model mimics the essential features of the
interactions between amino acids, is consistent with the key paradigms of
protein folding and reproduces the universal distribution of evolutionary rates
among orthologous proteins. We introduce mean path divergence as a quantitative
measure of the degree to which the starting and ending points determine the
path of evolution in fitness landscapes. Global measures of landscape roughness
are good predictors of path divergence in all studied landscapes: the mean path
divergence is greater in smooth landscapes than in rough ones. The
model-derived and experimental landscapes are significantly smoother than
random landscapes and resemble additive landscapes perturbed with moderate
amounts of noise; thus, these landscapes are substantially robust to mutation.
The model landscapes show a deficit of suboptimal peaks even compared with
noisy additive landscapes with similar overall roughness. We suggest that
smoothness and the substantial deficit of peaks in the fitness landscapes of
protein evolution are fundamental consequences of the physics of protein
folding.Comment: 14 pages, 7 figure
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