Design and Optimizing of On-Chip Kinesin Substrates for Molecular Communication

Lab-on-chip devices and point-of-care diagnostic chip devices are composed of many different components such as nanosensors that must be able to communicate with other components within the device. Molecular communication is a promising solution for on-chip communication. In particular, kinesin driven microtubule (MT) motility is an effective means of transferring information particles from one component to another. However, finding an optimal shape for these channels can be challenging. In this paper we derive a mathematical optimization model that can be used to find the optimal channel shape and dimensions for any transmission period. We derive three specific models for the rectangular channels, regular polygonal channels, and regular polygonal ring channels. We show that the optimal channel shapes are the square-shaped channel for the rectangular channel, and circular-shaped channel for the other classes of shapes. Finally, we show that among all 2 dimensional shapes the optimal design choice that maximizes information rate is the circular-shaped channel.Comment: accepted for publication in IEEE Transactions on Nanotechnolog

What pebbles are made of: Interpretation of the V883 Ori disk

Recently, an Atacama Large Millimeter/submillimeter Array (ALMA) observation of the water snow line in the protoplanetary disk around the FU Orionis star V883 Ori was reported. The radial variation of the spectral index at mm-wavelengths around the snow line was interpreted as being due to a pileup of particles interior to the snow line. However, radial transport of solids in the outer disk operates on timescales much longer than the typical timescale of an FU Ori outburst ($10^{1}$--$10^{2}$ yr). Consequently, a steady-state pileup is unlikely. We argue that it is only necessary to consider water evaporation and re-coagulation of silicates to explain the recent ALMA observation of V883 Ori because these processes are short enough to have had their impact since the outburst. Our model requires the inner disk to have already been optically thick before the outburst, and our results suggest that the carbon content of pebbles is low.Comment: Accepted to A&A Letter

Spontaneous fourfold-symmetry breaking driven by electron-lattice coupling and strong correlations in high-TcT_c cuprates

Using dynamical-mean-field theory for clusters, we study the two-dimensional Hubbard model in which electrons are coupled with the orthorhombic lattice distortions through the modulation in the hopping matrix. Instability towards spontaneous symmetry breaking from a tetragonal symmetric phase to an orthorhombic distorted phase is examined as a function of doping and interaction strength. A very strong instability is found in the underdoped pseudogap regime when the interaction strength is large enough to yield the Mott insulating phase at half filling. The symmetry breaking accompanies the recovery of quasiparticle weights along one of the two antinodal directions, leading to the characteristic Fermi arc reconnection. We discuss the implications of our results to the fourfold symmetry breaking reported in systems where the underlying crystal does not have any structural anisotropy.Comment: 6 pages with 4 figure

Detecting signals of weakly first-order phase transitions in two-dimensional Potts models

We investigate the first-order phase transitions of the $q$-state Potts models with $q = 5, 6, 7$, and $8$ on the two-dimensional square lattice, using Monte Carlo simulations. At the very weakly first-order transition of the $q=5$ system, the standard data-collapse procedure for the order parameter, carried out with results for a broad range of system sizes, works deceptively well and produces non-trivial critical exponents different from the trivial values expected for first-order transitions. However, a more systematic study reveals significant drifts in the `pseudo-critical' exponents as a function of the system size. For this purpose, we employ two methods of analysis: the data-collapse procedure with narrow range of the system size, and the Binder-cumulant crossing technique for pairs of system sizes. In both methods, the estimates start to drift toward the trivial values as the system size used in the analysis exceeds a certain `cross-over' length scale. This length scale is remarkably smaller than the correlation length at the transition point for weakly first-order transitions, e.g., less than one tenth for $q=5$, in contrast to the naive expectation that the system size has to be comparable to or larger than the correlation length to observe the correct behavior. The results overall show that proper care is indispensable to diagnose the nature of a phase transition with limited system sizes.Comment: 10 pages, 7 figures. One figure has been replaced to make our claim cleare

Microscopic origin of spin-orbital separation in Sr2CuO3

Recently performed resonant inelastic x-ray scattering experiment (RIXS) at the copper L3 edge in the quasi-1D Mott insulator Sr2CuO3 has revealed a significant dispersion of a single orbital excitation (orbiton). This large and unexpected orbiton dispersion has been explained using the concept of spin-orbital fractionalization in which orbiton, which is intrinsically coupled to the spinon in this material, liberates itself from the spinon due to the strictly 1D nature of its motion. Here we investigate this mechanism in detail by: (i) deriving the microscopic spin-orbital superexchange model from the charge transfer model for the CuO3 chains in Sr2CuO3, (ii) mapping the orbiton motion in the obtained spin-orbital model into a problem of a single hole moving in an effective half-filled antiferromagnetic chain t-J model, and (iii) solving the latter model using the exact diagonalization and obtaining the orbiton spectral function. Finally, the RIXS cross section is calculated based on the obtained orbiton spectral function and compared with the RIXS experiment.Comment: 23 pages, 13 figures; v3 = style and structure improve

Spatial and temporal cellular responses to single-strand breaks in human cells

DNA single-strand breaks (SSB) are one of the most frequent DNA lesions produced by reactive oxygen species and during DNA metabolism, but the analysis of cellular responses to SSB remains difficult due to the lack of an experimental method to produce SSB alone in cells. By using human cells expressing a foreign UV damage endonuclease (UVDE) and irradiating the cells with UV through tiny pores in membrane filters, we created SSB in restricted areas in the nucleus by the immediate action of UVDE on UV-induced DNA lesions. Cellular responses to the SSB were characterized by using antibodies and fluorescence microscopy. Upon UV irradiation, poly(ADP-ribose) synthesis occurred immediately in the irradiated area. Simultaneously, but dependent on poly(ADP-ribosyl)ation, XRCC1 was translocated from throughout the nucleus, including nucleoli, to the SSB. The BRCT1 domain of XRCC1 protein was indispensable for its poly(ADP-ribose)-dependent recruitment to the SSB. Proliferating cell nuclear antigen and the p150 subunit of chromatin assembly factor 1 also accumulated at the SSB in a detergent-resistant form, which was significantly reduced by inhibition of poly(ADP-ribose) synthesis. Our results show the importance of poly(ADP-ribosyl)ation in sequential cellular responses to SSB

Cosmology from String Theory

We explore the cosmological content of Salam-Sezgin six dimensional supergravity, and find a solution to the field equations in qualitative agreement with observation of distant supernovae, primordial nucleosynthesis abundances, and recent measurements of the cosmic microwave background. The carrier of the acceleration in the present de Sitter epoch is a quintessence field slowly rolling down its exponential potential. Intrinsic to this model is a second modulus which is automatically stabilized and acts as a source of cold dark matter with a mass proportional to an exponential function of the quintessence field (hence realizing VAMP models within a String context). However, any attempt to saturate the present cold dark matter component in this manner leads to unacceptable deviations from cosmological data -- a numerical study reveals that this source can account for up to about 7% of the total cold dark matter budget. We also show that (1) the model will support a de Sitter energy in agreement with observation at the expense of a miniscule breaking of supersymmetry in the compact space; (2) variations in the fine structure constant are controlled by the stabilized modulus and are negligible; (3) ``fifth''forces are carried by the stabilized modulus and are short range; (4) the long time behavior of the model in four dimensions is that of a Robertson-Walker universe with a constant expansion rate (w = -1/3). Finally, we present a String theory background by lifting our six dimensional cosmological solution to ten dimensions.Comment: Version to be published in Physical Review

Quasinormal ringing of acoustic black holes in Laval nozzles: Numerical simulations

Quasinormal ringing of acoustic black holes in Laval nozzles is discussed. The equation for sounds in a transonic flow is written into a Schr\"{o}dinger-type equation with a potential barrier, and the quasinormal frequencies are calculated semianalytically. From the results of numerical simulations, it is shown that the quasinormal modes are actually excited when the transonic flow is formed or slightly perturbed, as well as in the real black hole case. In an actual experiment, however, the purely-outgoing boundary condition will not be satisfied at late times due to the wave reflection at the end of the apparatus, and a late-time ringing will be expressed as a superposition of "boxed" quasinormal modes. It is shown that the late-time ringing damps more slowly than the ordinary quasinormal ringing, while its central frequency is not greatly different from that of the ordinary one. Using this fact, an efficient way for experimentally detecting the quasinormal ringing of an acoustic black hole is discussed.Comment: 9 pages, 8 figures, accepted for publication in Physical Review

Charge-ordering, commensurability and metallicity in the phase diagram of layered Na(x)CoO(2)

The phase diagram of non-hydrated Na(x)CoO(2) has been determined by changing the Na content x using a series of chemical reactions. As x increases from 0.3, the ground state goes from a paramagnetic metal to a charge-ordered insulator (at x=1/2) to a `Curie-Weiss metal' (around 0.70), and finally to a weak-moment magnetically ordered state (x>0.75). The unusual properties of the state at 1/2 (including particle-hole symmetry at low T and enhanced thermal conductivity) are described. The strong coupling between the Na ions and the holes is emphasized.Comment: 4 pages with 3 figures, changed conten