The ideal trefoil knot

The most tight conformation of the trefoil knot found by the SONO algorithm is presented. Structure of the set of its self-contact points is analyzed.Comment: 11 pages, 8 figure

Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties

Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes' blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.Comment: 12 pages, 10 figure

Reduced P300 amplitude during retrieval on a spatial working memory task in a community sample of adolescents who report psychotic symptoms.

BACKGROUND: Deficits in working memory are widely reported in schizophrenia and are considered a trait marker for the disorder. Event-related potentials (ERPs) and imaging data suggest that these differences in working memory performance may be due to aberrant functioning in the prefrontal and parietal cortices. Research suggests that many of the same risk factors for schizophrenia are shared with individuals from the general population who report psychotic symptoms. METHODS: Forty-two participants (age range 11--13 years) were divided into those who reported psychotic symptoms (N = 17) and those who reported no psychotic symptoms, i.e. the control group (N = 25). Behavioural differences in accuracy and reaction time were explored between the groups as well as electrophysiological correlates of working memory using a Spatial Working Memory Task, which was a variant of the Sternberg paradigm. Specifically, differences in the P300 component were explored across load level (low load and high load), location (positive probe i.e. in the same location as shown in the study stimulus and negative probe i.e. in a different location to the study stimulus) and between groups for the overall P300 timeframe. The effect of load was also explored at early and late timeframes of the P300 component (250-430 ms and 430-750 ms respectively). RESULTS: No between-group differences in the behavioural data were observed. Reduced amplitude of the P300 component was observed in the psychotic symptoms group relative to the control group at posterior electrode sites. Amplitude of the P300 component was reduced at high load for the late P300 timeframe at electrode sites Pz and POz. CONCLUSIONS: These results identify neural correlates of neurocognitive dysfunction associated with population level psychotic symptoms and provide insights into ERP abnormalities associated with the extended psychosis phenotype

The Shapes of Tight Composite Knots

We present new computations of tight shapes obtained using the constrained gradient descent code RIDGERUNNER for 544 composite knots with 12 and fewer crossings, expanding our dataset to 943 knots and links. We use the new data set to analyze two outstanding conjectures about tight knots, namely that the ropelengths of composite knots are at least 4\pi-4 less than the sums of the prime factors and that the writhes of composite knots are the sums of the writhes of the prime factors.Comment: Summary text file of tight knot lengths and writhing numbers stored in anc/ropelength_data.txt. All other data freely available at http:://www.jasoncantarella.com/ and through Data Conservanc

Repulsive Forces Between Looping Chromosomes Induce Entropy-Driven Segregation

One striking feature of chromatin organization is that chromosomes are compartmentalized into distinct territories during interphase, the degree of intermingling being much smaller than expected for linear chains. A growing body of evidence indicates that the formation of loops plays a dominant role in transcriptional regulation as well as the entropic organization of interphase chromosomes. Using a recently proposed model, we quantitatively determine the entropic forces between chromosomes. This Dynamic Loop Model assumes that loops form solely on the basis of diffusional motion without invoking other long-range interactions. We find that introducing loops into the structure of chromatin results in a multi-fold higher repulsion between chromosomes compared to linear chains. Strong effects are observed for the tendency of a non-random alignment; the overlap volume between chromosomes decays fast with increasing loop number. Our results suggest that the formation of chromatin loops imposes both compartmentalization as well as order on the system without requiring additional energy-consuming processes

The Electrical Activity of a Denervated Ear

The electrical response from the cochlea of a cat which had previously been denervated by intracranial crushing of the auditory nerve was submitted to a lengthy study, the results of which may be summarized as follows:- The responses to acoustical stimulation derived from electrodes placed on the round window margin and in the chin muscles were studied by means of an amplifier and cathode ray oscillograph, in the usual way. Transient stimuli whose polarity could be reversed were employed to demonstrate the absence of any electrical component of neural origin such as is invariably present in a normal ear. In all other respects, however, the responses were unaffected, and both threshold contours (the so-called “electrical audiogram”) and equal response contours for approximately pure-tone stimuli demonstrated close comparability with those for normal ears. Harmonic analysis of the cochlear response yielded results departing from the normal only in such respects as would be expected in view of the complete absence of nervous component in the analysed wave. From these data, it is argued that this animal presented a case in which normal electrical responses were obtained from the peripheral organ, despite virtually complete degeneration of the auditory nerve, and, it follows, complete unilateral deafness. Subsequent histological examination confirmed these observations, and it is urged, therefore, that the validity of the view that the cochlear response provides an index of the hearing ability of an animal, as is sometimes stated, is open to question. Additionally, this experiment finally discredits the hypothesis that the cochlear response itself is, in any sense, neural in origin; it further indicates the necessity for caution in the interpretation of results obtained from normal ears, where the cochlear response, however derived, is in some degree adulterated by the simultaneous presence of an action potential component. </jats:p