Harmonically confined, semiflexible polymer in a channel: response to a stretching force and spatial distribution of the endpoints

We consider an inextensible, semiflexible polymer or worm-like chain which is confined in the transverse direction by a parabolic potential and subject to a longitudinal force at the ends, so that the polymer is stretched out and backfolding is negligible. Simple analytic expressions for the partition function, valid in this regime, are obtained for chains of arbitrary length with a variety of boundary conditions at the ends. The spatial distribution of the end points or radial distribution function is also analyzed.Comment: 14 pages including figure

Minimizing magnetic fields for precision experiments

An increasing number of measurements in fundamental and applied physics rely on magnetically shielded environments with sub nano-Tesla residual magnetic fields. State of the art magnetically shielded rooms (MSRs) consist of up to seven layers of high permeability materials in combination with highly conductive shields. Proper magnetic equilibration is crucial to obtain such low magnetic fields with small gradients in any MSR. Here we report on a scheme to magnetically equilibrate MSRs with a 10 times reduced duration of the magnetic equilibration sequence and a significantly lower magnetic field with improved homogeneity. For the search of the neutron's electric dipole moment, our finding corresponds to a linear improvement in the systematic reach and a 40 % improvement of the statistical reach of the measurement. However, this versatile procedure can improve the performance of any MSR for any application.Comment: 5 pages, 4 figure

The pre-WDVV ring of physics and its topology

We show how a simplicial complex arising from the WDVV (Witten-Dijkgraaf-Verlinde-Verlinde) equations of string theory is the Whitehouse complex. Using discrete Morse theory, we give an elementary proof that the Whitehouse complex $\Delta_n$ is homotopy equivalent to a wedge of $(n-2)!$ spheres of dimension $n-4$. We also verify the Cohen-Macaulay property. Additionally, recurrences are given for the face enumeration of the complex and the Hilbert series of the associated pre-WDVV ring.Comment: 13 pages, 4 figures, 2 table

Dragging a polymer chain into a nanotube and subsequent release

We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves the tube. MC simulations were performed for a self-avoiding lattice model with a biased chain growth algorithm, the pruned-enriched Rosenbluth method. The nanotube is a long channel opened at one end and its diameter $D$ is much smaller than the size of the polymer coil in solution. We analyze the following characteristics as functions of the chain end position $x$ inside the tube: the free energy of confinement, the average end-to-end distance, the average number of imprisoned monomers, and the average stretching of the confined part of the chain for various values of $D$ and for the number of monomers in the chain, $N$. We show that when the chain end is dragged by a certain critical distance $x^*$ into the tube, the polymer undergoes a first-order phase transition whereby the remaining free tail is abruptly sucked into the tube. This is accompanied by jumps in the average size, the number of imprisoned segments, and in the average stretching parameter. The critical distance scales as $x^*\sim ND^{1-1/\nu}$. The transition takes place when approximately 3/4 of the chain units are dragged into the tube. The theory presented is based on constructing the Landau free energy as a function of an order parameter that provides a complete description of equilibrium and metastable states. We argue that if the trapped chain is released with all monomers allowed to fluctuate, the reverse process in which the chain leaves the confinement occurs smoothly without any jumps. Finally, we apply the theory to estimate the lifetime of confined DNA in metastable states in nanotubes.Comment: 13pages, 14figure

A Tool to Recover Scalar Time-Delay Systems from Experimental Time Series

We propose a method that is able to analyze chaotic time series, gained from exp erimental data. The method allows to identify scalar time-delay systems. If the dynamics of the system under investigation is governed by a scalar time-delay differential equation of the form $dy(t)/dt = h(y(t),y(t-\tau_0))$, the delay time $\tau_0$ and the functi on $h$ can be recovered. There are no restrictions to the dimensionality of the chaotic attractor. The method turns out to be insensitive to noise. We successfully apply the method to various time series taken from a computer experiment and two different electronic oscillators

Amplified stretch of bottlebrush-coated DNA in nanofluidic channels

The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.Singapore-MIT Alliance for Research and TechnologyNational Science Foundation (U.S.

Statics and dynamics of single DNA molecules confined in nanochannels

The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics

Staying true with the help of others: doxastic self-control through interpersonal commitment

I explore the possibility and rationality of interpersonal mechanisms of doxastic self-control, that is, ways in which individuals can make use of other people in order to get themselves to stick to their beliefs. I look, in particular, at two ways in which people can make interpersonal epistemic commitments, and thereby willingly undertake accountability to others, in order to get themselves to maintain their beliefs in the face of anticipated “epistemic temptations”. The first way is through the avowal of belief, and the second is through the establishment of collective belief. I argue that both of these forms of interpersonal epistemic commitment can function as effective tools for doxastic self-control, and, moreover, that the control they facilitate should not be dismissed as irrational from an epistemic perspective

Heme ligation and redox chemistry in two bacterial thiosulfate dehydrogenase (TsdA) enzyme

Thiosulfate dehydrogenases (TsdA) are bidirectional bacterial di-heme enzymes that catalyze the interconversion of tetrathionate and thiosulfate at measurable rates in both directions. In contrast to our knowledge of TsdA activities, information on the redox properties in the absence of substrates is rather scant. To address this deficit, we combined magnetic circular dichroism (MCD) spectroscopy and protein film electrochemistry (PFE) in a study to resolve heme ligation and redox chemistry in two representative TsdAs. We examined the TsdAs from Campylobacter jejuni, a micro-aerobe human pathogen, and from the purple sulfur bacterium Allochromatium vinosum. In these organisms, the enzyme functions as a tetrathionate reductase and a thiosulfate oxidase respectively. The active site Heme 1 in both enzymes has His/Cys− ligation in the ferric and ferrous states and the midpoint potentials (Em) of the corresponding redox transformations are similar, −185 mV versus standard hydrogen electrode (SHE). However, fundamental differences are observed in the properties of the second, electron transferring, Heme 2. In C. jejuni TsdA Heme 2 has His/Met ligation and an Em of +172 mV. In A. vinosum TsdA, Heme 2 reduction triggers a switch from His/Lys ligation (Em, −129 mV) to His/Met (Em,+266 mV) but the rates of interconversion are such that His/Lys ligation would be retained during turnover. In summary, our findings have unambiguously assigned Em values to defined axial ligand sets in TsdAs, specified the rates of Heme 2 ligand exchange in the A. vinosum enzyme, and provided information relevant to describing their catalytic mechanism(s)