Stochastic modeling of cargo transport by teams of molecular motors

Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directionality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion. An effective theoretical approach, introduced by M\"uller et al., describes the cargo dynamics as a tug-of-war between different kinds of motors. An alternative approach has been suggested recently by Kunwar et al., who considered the coupling between motor and cargo in more detail. Based on this framework we introduce a model considering single motor positions which we propagate in continuous time. Furthermore, we analyze the possible influence of the discrete time update schemes used in previous publications on the system's dynamic.Comment: Cenference proceedings - Traffic and Granular Flow 1

Guardians Ad Litem as Surrogate Parents: Implication for Role Definition and Confidentiality

SALMON (Scalable Ab-initio Light–Mattersimulator for Optics and Nanoscience, http://salmon-tddft.jp) is a software package for the simulation of electron dynamics and optical properties of molecules, nanostructures, and crystalline solids based on first-principles time-dependent density functional theory. The core part of the software is the real-time, real-space calculation of the electron dynamics induced in molecules and solids by an external electric field solving the time-dependent Kohn–Sham equation. Using a weak instantaneous perturbing field, linear response properties such as polarizabilities and photoabsorptions in isolated systems and dielectric functions in periodic systems are determined. Using an optical laser pulse, the ultrafast electronic response that may be highly nonlinear in the field strength is investigated in time domain. The propagation of the laser pulse in bulk solids and thin films can also be included in the simulation via coupling the electron dynamics in many microscopic unit cells using Maxwell’s equations describing the time evolution of the electromagnetic fields. The code is efficiently parallelized so that it may describe the electron dynamics in large systems including up to a few thousand atoms. The present paper provides an overview of the capabilities of the software package showing several sample calculations. Program summary Program Title: SALMON: Scalable Ab-initio Light–Matter simulator for Optics and Nanoscience Program Files doi:http://dx.doi.org/10.17632/8pm5znxtsb.1 Licensing provisions: Apache-2.0 Programming language: Fortran 2003 Nature of problem: Electron dynamics in molecules, nanostructures, and crystalline solids induced by an external electric field is calculated based on first-principles time-dependent density functional theory. Using a weak impulsive field, linear optical properties such as polarizabilities, photoabsorptions, and dielectric functions are extracted. Using an optical laser pulse, the ultrafast electronic response that may be highly nonlinear with respect to the exciting field strength is described as well. The propagation of the laser pulse in bulk solids and thin films is considered by coupling the electron dynamics in many microscopic unit cells using Maxwell’s equations describing the time evolution of the electromagnetic field. Solution method: Electron dynamics is calculated by solving the time-dependent Kohn–Sham equation in real time and real space. For this, the electronic orbitals are discretized on a uniform Cartesian grid in three dimensions. Norm-conserving pseudopotentials are used to account for the interactions between the valence electrons and the ionic cores. Grid spacings in real space and time, typically 0.02 nm and 1 as respectively, determine the spatial and temporal resolutions of the simulation results. In most calculations, the ground state is first calculated by solving the static Kohn–Sham equation, in order to prepare the initial conditions. The orbitals are evolved in time with an explicit integration algorithm such as a truncated Taylor expansion of the evolution operator, together with a predictor–corrector step when necessary. For the propagation of the laser pulse in a bulk solid, Maxwell’s equations are solved using a finite-difference scheme. By this, the electric field of the laser pulse and the electron dynamics in many microscopic unit cells of the crystalline solid are coupled in a multiscale framework

Dicke-Type Energy Level Crossings in Cavity-Induced Atom Cooling: Another Superradiant Cooling

This paper is devoted to energy-spectral analysis for the system of a two-level atom coupled with photons in a cavity. It is shown that the Dicke-type energy level crossings take place when the atom-cavity interaction of the system undergoes changes between the weak coupling regime and the strong one. Using the phenomenon of the crossings we develop the idea of cavity-induced atom cooling proposed by the group of Ritsch, and we lay mathematical foundations of a possible mechanism for another superradiant cooling in addition to that proposed by Domokos and Ritsch. The process of our superradiant cooling can function well by cavity decay and by control of the position of the atom, at least in (mathematical) theory, even if there is neither atomic absorption nor atomic emission of photons.Comment: 15 pages; 8 figure

Reducing relative termination to dependency pair problems

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-21401-6_11Relative termination, a generalized notion of termination, has been used in a number of different contexts like proving the confluence of rewrite systems or analyzing the termination of narrowing. In this paper, we introduce a new technique to prove relative termination by reducing it to dependency pair problems. To the best of our knowledge, this is the first significant contribution to Problem #106 of the RTA List of Open Problems. The practical significance of our method is illustrated by means of an experimental evaluation.Germán Vidal is partially supported by the EU (FEDER) and the Spanish Ministerio de Economía y Competitividad under grant TIN2013-44742-C4-R and by the Generalitat Valenciana under grant PROMETEOII201/013. Akihisa Yamadais supported by the Austrian Science Fund (FWF): Y757Iborra, J.; Nishida, N.; Vidal Oriola, GF.; Yamada, A. (2015). Reducing relative termination to dependency pair problems. En Automated Deduction - CADE-25. Springer. 163-178. https://doi.org/10.1007/978-3-319-21401-6_11S163178Alarcón, B., Lucas, S., Meseguer, J.: A dependency pair framework for A $$\vee$$ C-termination. In: Ölveczky, P.C. (ed.) WRLA 2010. LNCS, vol. 6381, pp. 35–51. Springer, Heidelberg (2010)Arts, T., Giesl, J.: Termination of term rewriting using dependency pairs. Theor. Comput. Sci. 236(1–2), 133–178 (2000)Arts, T., Giesl, J.: A collection of examples for termination of term rewriting using dependency pairs. Technical report AIB-2001-09, RWTH Aachen (2001)Baader, F., Nipkow, T.: Term Rewriting and All That. Cambridge University Press, Cambridge (1998)Dershowitz, N.: Termination of rewriting. J. Symb. Comput. 3(1&2), 69–115 (1987)Endrullis, J., Waldmann, J., Zantema, H.: Matrix interpretations for proving termination of term rewriting. J. Autom. Reasoning 40(2–3), 195–220 (2008)Geser, A.: Relative termination. Dissertation, Fakultät für Mathematik und Informatik, Universität Passau, Germany (1990)Giesl, J., Kapur, D.: Dependency pairs for equational rewriting. In: Middeldorp, A. (ed.) RTA 2001. LNCS, vol. 2051, pp. 93–107. Springer, Heidelberg (2001)Giesl, J., Schneider-Kamp, P., Thiemann, R.: AProVE 1.2: automatic termination proofs in the dependency pair framework. In: Furbach, U., Shankar, N. (eds.) IJCAR 2006. LNCS (LNAI), vol. 4130, pp. 281–286. Springer, Heidelberg (2006)Giesl, J., Thiemann, R., Schneider-Kamp, P., Falke, S.: Mechanizing and improving dependency pairs. J. Autom. Reasoning 37(3), 155–203 (2006)Hirokawa, N., Middeldorp, A.: Polynomial interpretations with negative coefficients. In: Buchberger, B., Campbell, J. (eds.) AISC 2004. LNCS (LNAI), vol. 3249, pp. 185–198. Springer, Heidelberg (2004)Hirokawa, N., Middeldorp, A.: Dependency pairs revisited. In: van Oostrom, V. (ed.) RTA 2004. LNCS, vol. 3091, pp. 249–268. Springer, Heidelberg (2004)Hirokawa, N., Middeldorp, A.: Decreasing diagrams and relative termination. J. Autom. Reasoning 47(4), 481–501 (2011)Hullot, J.M.: Canonical forms and unification. CADE-5. LNCS, vol. 87, pp. 318–334. Springer, Heidelberg (1980)Iborra, J., Nishida, N., Vidal, G.: Goal-directed and relative dependency pairs for proving the termination of narrowing. In: De Schreye, D. (ed.) LOPSTR 2009. LNCS, vol. 6037, pp. 52–66. Springer, Heidelberg (2010)Kamin, S., Lévy, J.J.: Two generalizations of the recursive path ordering (1980, unpublished note)Klop, J.W.: Term rewriting systems: a tutorial. Bull. Eur. Assoc. Theor. Comput. Sci. 32, 143–183 (1987)Koprowski, A., Zantema, H.: Proving liveness with fairness using rewriting. In: Gramlich, B. (ed.) FroCos 2005. LNCS (LNAI), vol. 3717, pp. 232–247. Springer, Heidelberg (2005)Koprowski, A.: TPA: termination proved automatically. In: Pfenning, F. (ed.) RTA 2006. LNCS, vol. 4098, pp. 257–266. Springer, Heidelberg (2006)Korp, M., Sternagel, C., Zankl, H., Middeldorp, A.: Tyrolean termination tool 2. In: Treinen, R. (ed.) RTA 2009. LNCS, vol. 5595, pp. 295–304. Springer, Heidelberg (2009)Lankford, D.: Canonical algebraic simplification in computational logic. Technical report ATP-25, University of Texas (1975)Liu, J., Dershowitz, N., Jouannaud, J.-P.: Confluence by critical pair analysis. In: Dowek, G. (ed.) RTA-TLCA 2014. LNCS, vol. 8560, pp. 287–302. Springer, Heidelberg (2014)Nishida, N., Sakai, M., Sakabe, T.: Narrowing-based simulation of term rewriting systems with extra variables. ENTCS 86(3), 52–69 (2003)Nishida, N., Vidal, G.: Termination of narrowing via termination of rewriting. Appl. Algebra Eng. Commun. Comput. 21(3), 177–225 (2010)Ohlebusch, E.: Advanced Topics in Term Rewriting. Springer-Verlag, London (2002)Thiemann, R., Allais, G., Nagele, J.: On the formalization of termination techniques based on multiset orderings. In: RTA 2012. LIPIcs, vol. 15, pp. 339–354. Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2012)Vidal, G.: Termination of narrowing in left-linear constructor systems. In: Garrigue, J., Hermenegildo, M.V. (eds.) FLOPS 2008. LNCS, vol. 4989, pp. 113–129. Springer, Heidelberg (2008)Yamada, A., Kusakari, K., Sakabe, T.: Nagoya termination tool. In: Dowek, G. (ed.) RTA-TLCA 2014. LNCS, vol. 8560, pp. 466–475. Springer, Heidelberg (2014)Yamada, A., Kusakari, K., Sakabe, T.: A unified ordering for termination proving. Sci. Comput. Program. (2014). doi: 10.1016/j.scico.2014.07.009Zantema, H.: Termination of term rewriting by semantic labelling. Fundamenta Informaticae 24(1/2), 89–105 (1995)Zantema, H.: Termination. In: Bezem, M., Klop, J.W., de Vrijer, R. (eds.) Term Rewriting Systems. Cambridge Tracts in Theoretical Computer Science, vol. 55, pp. 181–259. Cambridge University Press, Cambridge (2003

Sequence-Dependent Dynamics of Synthetic and Endogenous RSSs in V(D)J Recombination

Developing lymphocytes of jawed vertebrates cleave and combine distinct gene segments to assemble antigen–receptor genes. This process called V(D)J recombination that involves the RAG recombinase binding and cutting recombination signal sequences (RSSs) composed of conserved heptamer and nonamer sequences flanking less well-conserved 12- or 23-bp spacers. Little quantitative information is known about the contributions of individual RSS positions over the course of the RAG–RSS interaction. We employ a single-molecule method known as tethered particle motion to track the formation, lifetime and cleavage of individual RAG–12RSS–23RSS paired complexes (PCs) for numerous synthetic and endogenous 12RSSs. We reveal that single-bp changes, including in the 12RSS spacer, can significantly and selectively alter PC formation or the probability of RAG-mediated cleavage in the PC. We find that some rarely used endogenous gene segments can be mapped directly to poor RAG binding on their adjacent 12RSSs. Finally, we find that while abrogating RSS nicking with Ca²⁺ leads to substantially shorter PC lifetimes, analysis of the complete lifetime distributions of any 12RSS even on this reduced system reveals that the process of exiting the PC involves unidentified molecular details whose involvement in RAG–RSS dynamics are crucial to quantitatively capture kinetics in V(D)J recombination

Complexity Bounds for Ordinal-Based Termination

`What more than its truth do we know if we have a proof of a theorem in a given formal system?' We examine Kreisel's question in the particular context of program termination proofs, with an eye to deriving complexity bounds on program running times. Our main tool for this are length function theorems, which provide complexity bounds on the use of well quasi orders. We illustrate how to prove such theorems in the simple yet until now untreated case of ordinals. We show how to apply this new theorem to derive complexity bounds on programs when they are proven to terminate thanks to a ranking function into some ordinal.Comment: Invited talk at the 8th International Workshop on Reachability Problems (RP 2014, 22-24 September 2014, Oxford

Measuring surface-area-to-volume ratios in soft porous materials using laser-polarized xenon interphase exchange NMR

We demonstrate a minimally invasive nuclear magnetic resonance (NMR) technique that enables determination of the surface-area-to-volume ratio (S/V) of soft porous materials from measurements of the diffusive exchange of laser-polarized 129Xe between gas in the pore space and 129Xe dissolved in the solid phase. We apply this NMR technique to porous polymer samples and find approximate agreement with destructive stereological measurements of S/V obtained with optical confocal microscopy. Potential applications of laser-polarized xenon interphase exchange NMR include measurements of in vivo lung function in humans and characterization of gas chromatography columns.Comment: 14 pages of text, 4 figure

Cilia at the node of mouse embryos sense fluid flow for left-right determination via Pkd2

Unidirectional fluid flow plays an essential role in the breaking of left-right (L-R) symmetry in mouse embryos, but it has remained unclear how the flow is sensed by the embryo. We report that the Ca2+ channel Polycystin-2 (Pkd2) is required specifically in the perinodal crown cells for sensing the nodal flow. Examination of mutant forms of Pkd2 shows that the ciliary localization of Pkd2 is essential for correct L-R patterning. Whereas Kif3a mutant embryos, which lack all cilia, failed to respond to an artificial flow, restoration of primary cilia in crown cells rescued the response to the flow. Our results thus suggest that nodal flow is sensed in a manner dependent on Pkd2 by the cilia of crown cells located at the edge of the node.CREST of the Japan Science and Technology Corporation; NIH [P30 DK090744]; Human Frontier Science Program [ST00246/2003C]; Deutsche Forschungsgemeinschaft [PE 853/2]; Japan Society for the Promotion of Science; American Heart Association [R10682]info:eu-repo/semantics/publishedVersio

Ethyl 2-(7-oxo-3,5-diphenyl-1,4-diaze­pan-2-yl)acetate

In the title compound, C21H24N2O3, the diazepane ring adopts a chair conformation. The central diazepane ring forms dihedral angles 67.80 (7) and 72.29 (5)° with the two benzene rings. The eth­oxy­carbonyl group is disordered over two conformations with site-occupancy factors of 0.643 (5) and 0.357 (5). In the crystal, inversion dimers linked by pairs of N—H⋯O hydrogen bonds generate R 2 2(8) loops