A. Andersson - Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark

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Name
A. Andersson
Affiliation
Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark
City
Copenhagen
Country
Denmark

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Pub Categories

 
Mathematical Physics (7)
 
Mathematics - Mathematical Physics (7)
 
Mathematics - Probability (6)
 
Mathematics - Numerical Analysis (4)
 
Physics - Superconductivity (4)
 
Quantitative Biology - Molecular Networks (4)
 
Mathematics - Quantum Algebra (3)
 
Mathematics - Operator Algebras (3)
 
Quantum Physics (3)
 
Mathematics - Analysis of PDEs (3)
 
Physics - Statistical Mechanics (2)
 
Physics - Mesoscopic Systems and Quantum Hall Effect (1)
 
Mathematics - K-Theory and Homology (1)
 
Quantitative Biology - Genomics (1)
 
Computer Science - Data Structures and Algorithms (1)
 
Physics - Other (1)
 
Mathematics - Representation Theory (1)
 
Physics - Accelerator Physics (1)
 
High Energy Astrophysical Phenomena (1)
 
Mathematics - Group Theory (1)
 
Physics - Biological Physics (1)
 
High Energy Physics - Experiment (1)

Publications Authored By A. Andersson

In this paper we introduce a Hilbert space-valued Malliavin calculus for Poisson random measures. It is solely based on elementary principles from the theory of point processes and basic moment estimates, and thus allows for a simple treatment of the Malliavin operators. The main part of the theory is developed for general Poisson random measures, defined on a $\sigma$-finite measure space, with minimal conditions. Read More

Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flux Balance Analysis (FBA), by postulating that cells set metabolic fluxes within the allowed stoichiometry so as to maximize their growth. Here, we generalize this framework to single cell level using maximum entropy models from statistical physics. We define and compute, for the core metabolism of Escherichia coli, a joint distribution over all fluxes that yields the experimentally observed growth rate. Read More

In this article we study the differentiability of solutions of parabolic semilinear stochastic evolution equations (SEEs) with respect to their initial values. We prove that if the nonlinear drift coefficients and the nonlinear diffusion coefficients of the considered SEEs are $n$-times continuously Fr\'{e}chet differentiable, then the solutions of the considered SEEs are also $n$-times continuously Fr\'{e}chet differentiable with respect to their initial values. Moreover, a key contribution of this work is to establish suitable enhanced regularity properties of the derivative processes of the considered SEE in the sense that the dominating linear operator appearing in the SEE smoothes the higher order derivative processes. Read More

In this article we establish regularity properties for solutions of infinite dimensional Kolmogorov equations. We prove that if the nonlinear drift coefficients, the nonlinear diffusion coefficients, and the initial conditions of the considered Kolmogorov equations are $n$-times continuously Fr\'{e}chet differentiable, then so are the generalized solutions at every positive time. In addition, a key contribution of this work is to prove suitable enhanced regularity properties for the derivatives of the generalized solutions of the Kolmogorov equations in the sense that the dominating linear operator in the drift coefficient of the Kolmogorov equation regularizes the higher order derivatives of the solutions. Read More

2016Oct
Authors: H. E. S. S. Collaboration, H. Abdalla, A. Abramowski, F. Aharonian, F. Ait Benkhali, A. G. Akhperjanian T. Andersson, M. Arrieta, P. Aubert, M. Backes, A. Balzer, M. Barnard, Y. Becherini, J. Becker Tjus, D. Berge S. Bernhard, K. Bernlöhr, R. Blackwell, M. Böttcher, C. Boisson, J. Bolmont, P. Bordas, J. Bregeon, F. Brun, P. Brun, M. Bryan, T. Bulik, M. Capasso, J. Carr S. Casanova, M. Cerruti, N. Chakraborty, R. Chalme-Calvet, R. C. G. Chaves, A. Chen, J. Chevalier, M. Chrétien, S. Colafrancesco, G. Cologna, B. Condon, J. Conrad, Y. Cui, I. D. Davids, J. Decock, B. Degrange, C. Deil, J. Devin, P. deWilt, L. Dirson, A. Djannati-Ataï, W. Domainko, A. Donath, L. O'C. Drury, G. Dubus, K. Dutson, J. Dyks, T. Edwards, K. Egberts, P. Eger, J. -P. Ernenwein, S. Eschbach, C. Farnier, S. Fegan, M. V. Fernandes, A. Fiasson, G. Fontaine, A. Förster, S. Funk, M. Füßling, S. Gabici M. Gajdus, Y. A. Gallant, T. Garrigoux, G. Giavitto, B. Giebels, J. F. Glicenstein, D. Gottschall, A. Goyal, M. -H. Grondin, D. Hadasch, J. Hahn, M. Haupt, J. Hawkes, G. Heinzelmann, G. Henri, G. Hermann, O. Hervet, J. A. Hinton, W. Hofmann, C. Hoischen, M. Holler, D. Horns, A. Ivascenko, A. Jacholkowska, M. Jamrozy, M. Janiak, D. Jankowsky, F. Jankowsky, M. Jingo, T. Jogler, L. Jouvin, I. Jung-Richardt, M. A. Kastendieck, K. Katarzyński, U. Katz, D. Kerszberg, B. Khélifi, M. Kieffer, J. King, S. Klepser, D. Klochkov, W. Kluźniak, D. Kolitzus, Nu. Komin, K. Kosack, S. Krakau, M. Kraus, F. Krayzel, P. P. Krüger, H. Laffon, G. Lamanna, J. Lau, J. -P. Lees, J. Lefaucheur, V. Lefranc, A. Lemière, M. Lemoine-Goumard, J. -P. Lenain, E. Leser, T. Lohse, M. Lorentz, R. Liu, R. López-Coto, I. Lypova, V. Marandon, A. Marcowith, C. Mariaud, R. Marx, G. Maurin, N. Maxted, M. Mayer, P. J. Meintjes, M. Meyer, A. M. W. Mitchell, R. Moderski, M. Mohamed, L. Mohrmann, K. Morå, E. Moulin, T. Murach, M. deNaurois, F. Niederwanger, J. Niemiec, L. Oakes, P. O'Brien, H. Odaka, S. Öttl, S. Ohm, M. Ostrowski, I. Oya, M. Padovani, M. Panter, R. D. Parsons, N. W. Pekeur, G. Pelletier, C. Perennes, P. -O. Petrucci, B. Peyaud, Q. Piel S. Pita, H. Poon, D. Prokhorov, H. Prokoph, G. Pühlhofer, M. Punch, A. Quirrenbach, S. Raab, A. Reimer, O. Reimer, M. Renaud, R. delosReyes, F. Rieger, C. Romoli, S. Rosier-Lees, G. Rowell, B. Rudak, C. B. Rulten, V. Sahakian, D. Salek, D. A. Sanchez, A. Santangelo, M. Sasaki, R. Schlickeiser, F. Schüssler, A. Schulz, U. Schwanke, S. Schwemmer, M. Settimo, A. S. Seyffert, N. Shafi, I. Shilon, R. Simoni, H. Sol, F. Spanier, G. Spengler, F. Spies, Ł. Stawarz, R. Steenkamp, C. Stegmann, F. Stinzing, K. Stycz, I. Sushch, J. -P. Tavernet, T. Tavernier, A. M. Taylor, R. Terrier, L. Tibaldo, D. Tiziani, M. Tluczykont, C. Trichard, R. Tuffs, Y. Uchiyama, D. J. van der Walt, C. vanEldik, C. vanRensburg, B. vanSoelen, G. Vasileiadis, J. Veh, C. Venter, A. Viana, P. Vincent, J. Vink, F. Voisin, H. J. Völk, T. Vuillaume, Z. Wadiasingh, S. J. Wagner, P. Wagner, R. M. Wagner R. White, A. Wierzcholska, P. Willmann, A. Wörnlein, D. Wouters, R. Yang, V. Zabalza, D. Zaborov, M. Zacharias, A. A. Zdziarski, A. Zech, F. Zefi, A. Ziegler, N. Żywucka

Studying the temporal variability of BL Lac objects at the highest energies provides unique insights into the extreme physical processes occurring in relativistic jets and in the vicinity of super-massive black holes. To this end, the long-term variability of the BL Lac object PKS 2155-304 is analyzed in the high (HE, 100 MeV < E < 300 GeV) and very high energy (VHE, E > 200 GeV) gamma-ray domain. Over the course of ~9 yr of H. Read More

2016Aug
Authors: The CLIC, CLICdp collaborations, :, M. J. Boland, U. Felzmann, P. J. Giansiracusa, T. G. Lucas, R. P. Rassool, C. Balazs, T. K. Charles, K. Afanaciev, I. Emeliantchik, A. Ignatenko, V. Makarenko, N. Shumeiko, A. Patapenka, I. Zhuk, A. C. Abusleme Hoffman, M. A. Diaz Gutierrez, M. Vogel Gonzalez, Y. Chi, X. He, G. Pei, S. Pei, G. Shu, X. Wang, J. Zhang, F. Zhao, Z. Zhou, H. Chen, Y. Gao, W. Huang, Y. P. Kuang, B. Li, Y. Li, J. Shao, J. Shi, C. Tang, X. Wu, L. Ma, Y. Han, W. Fang, Q. Gu, D. Huang, X. Huang, J. Tan, Z. Wang, Z. Zhao, T. Laštovička, U. Uggerhoj, T. N. Wistisen, A. Aabloo, K. Eimre, K. Kuppart, S. Vigonski, V. Zadin, M. Aicheler, E. Baibuz, E. Brücken, F. Djurabekova, P. Eerola, F. Garcia, E. Haeggström, K. Huitu, V. Jansson, V. Karimaki, I. Kassamakov, A. Kyritsakis, S. Lehti, A. Meriläinen, R. Montonen, T. Niinikoski, K. Nordlund, K. Österberg, M. Parekh, N. A. Törnqvist, J. Väinölä, M. Veske, W. Farabolini, A. Mollard, O. Napoly, F. Peauger, J. Plouin, P. Bambade, I. Chaikovska, R. Chehab, M. Davier, W. Kaabi, E. Kou, F. LeDiberder, R. Pöschl, D. Zerwas, B. Aimard, G. Balik, J. -P. Baud, J. -J. Blaising, L. Brunetti, M. Chefdeville, C. Drancourt, N. Geoffroy, J. Jacquemier, A. Jeremie, Y. Karyotakis, J. M. Nappa, S. Vilalte, G. Vouters, A. Bernard, I. Peric, M. Gabriel, F. Simon, M. Szalay, N. van der Kolk, T. Alexopoulos, E. N. Gazis, N. Gazis, E. Ikarios, V. Kostopoulos, S. Kourkoulis, P. D. Gupta, P. Shrivastava, H. Arfaei, M. K. Dayyani, H. Ghasem, S. S. Hajari, H. Shaker, Y. Ashkenazy, H. Abramowicz, Y. Benhammou, O. Borysov, S. Kananov, A. Levy, I. Levy, O. Rosenblat, G. D'Auria, S. Di Mitri, T. Abe, A. Aryshev, T. Higo, Y. Makida, S. Matsumoto, T. Shidara, T. Takatomi, Y. Takubo, T. Tauchi, N. Toge, K. Ueno, J. Urakawa, A. Yamamoto, M. Yamanaka, R. Raboanary, R. Hart, H. van der Graaf, G. Eigen, J. Zalieckas, E. Adli, R. Lillestøl, L. Malina, J. Pfingstner, K. N. Sjobak, W. Ahmed, M. I. Asghar, H. Hoorani, S. Bugiel, R. Dasgupta, M. Firlej, T. A. Fiutowski, M. Idzik, M. Kopec, M. Kuczynska, J. Moron, K. P. Swientek, W. Daniluk, B. Krupa, M. Kucharczyk, T. Lesiak, A. Moszczynski, B. Pawlik, P. Sopicki, T. Wojtoń, L. Zawiejski, J. Kalinowski, M. Krawczyk, A. F. Żarnecki, E. Firu, V. Ghenescu, A. T. Neagu, T. Preda, I-S. Zgura, A. Aloev, N. Azaryan, J. Budagov, M. Chizhov, M. Filippova, V. Glagolev, A. Gongadze, S. Grigoryan, D. Gudkov, V. Karjavine, M. Lyablin, A. Olyunin, A. Samochkine, A. Sapronov, G. Shirkov, V. Soldatov, A. Solodko, E. Solodko, G. Trubnikov, I. Tyapkin, V. Uzhinsky, A. Vorozhtov, E. Levichev, N. Mezentsev, P. Piminov, D. Shatilov, P. Vobly, K. Zolotarev, I. Bozovic Jelisavcic, G. Kacarevic, S. Lukic, G. Milutinovic-Dumbelovic, M. Pandurovic, U. Iriso, F. Perez, M. Pont, J. Trenado, M. Aguilar-Benitez, J. Calero, L. Garcia-Tabares, D. Gavela, J. L. Gutierrez, D. Lopez, F. Toral, D. Moya, A. Ruiz Jimeno, I. Vila, T. Argyropoulos, C. Blanch Gutierrez, M. Boronat, D. Esperante, A. Faus-Golfe, J. Fuster, N. Fuster Martinez, N. Galindo Muñoz, I. García, J. Giner Navarro, E. Ros, M. Vos, R. Brenner, T. Ekelöf, M. Jacewicz, J. Ögren, M. Olvegård, R. Ruber, V. Ziemann, D. Aguglia, N. Alipour Tehrani, A. Andersson, F. Andrianala, F. Antoniou, K. Artoos, S. Atieh, R. Ballabriga Sune, M. J. Barnes, J. Barranco Garcia, H. Bartosik, C. Belver-Aguilar, A. Benot Morell, D. R. Bett, S. Bettoni, G. Blanchot, O. Blanco Garcia, X. A. Bonnin, O. Brunner, H. Burkhardt, S. Calatroni, M. Campbell, N. Catalan Lasheras, M. Cerqueira Bastos, A. Cherif, E. Chevallay, B. Constance, R. Corsini, B. Cure, S. Curt, B. Dalena, D. Dannheim, G. De Michele, L. De Oliveira, N. Deelen, J. P. Delahaye, T. Dobers, S. Doebert, M. Draper, F. Duarte Ramos, A. Dubrovskiy, K. Elsener, J. Esberg, M. Esposito, V. Fedosseev, P. Ferracin, A. Fiergolski, K. Foraz, A. Fowler, F. Friebel, J-F. Fuchs, C. A. Fuentes Rojas, A. Gaddi, L. Garcia Fajardo, H. Garcia Morales, C. Garion, L. Gatignon, J-C. Gayde, H. Gerwig, A. N. Goldblatt, C. Grefe, A. Grudiev, F. G. Guillot-Vignot, M. L. Gutt-Mostowy, M. Hauschild, C. Hessler, J. K. Holma, E. Holzer, M. Hourican, D. Hynds, Y. Inntjore Levinsen, B. Jeanneret, E. Jensen, M. Jonker, M. Kastriotou, J. M. K. Kemppinen, R. B. Kieffer, W. Klempt, O. Kononenko, A. Korsback, E. Koukovini Platia, J. W. Kovermann, C-I. Kozsar, I. Kremastiotis, S. Kulis, A. Latina, F. Leaux, P. Lebrun, T. Lefevre, L. Linssen, X. Llopart Cudie, A. A. Maier, H. Mainaud Durand, E. Manosperti, C. Marelli, E. Marin Lacoma, R. Martin, S. Mazzoni, G. Mcmonagle, O. Mete, L. M. Mether, M. Modena, R. M. Münker, T. Muranaka, E. Nebot Del Busto, N. Nikiforou, D. Nisbet, J-M. Nonglaton, F. X. Nuiry, A. Nürnberg, M. Olvegard, J. Osborne, S. Papadopoulou, Y. Papaphilippou, A. Passarelli, M. Patecki, L. Pazdera, D. Pellegrini, K. Pepitone, E. Perez Codina, A. Perez Fontenla, T. H. B. Persson, M. Petrič, F. Pitters, S. Pittet, F. Plassard, R. Rajamak, S. Redford, Y. Renier, S. F. Rey, G. Riddone, L. Rinolfi, E. Rodriguez Castro, P. Roloff, C. Rossi, V. Rude, G. Rumolo, A. Sailer, E. Santin, D. Schlatter, H. Schmickler, D. Schulte, N. Shipman, E. Sicking, R. Simoniello, P. K. Skowronski, P. Sobrino Mompean, L. Soby, M. P. Sosin, S. Sroka, S. Stapnes, G. Sterbini, R. Ström, I. Syratchev, F. Tecker, P. A. Thonet, L. Timeo, H. Timko, R. Tomas Garcia, P. Valerio, A. L. Vamvakas, A. Vivoli, M. A. Weber, R. Wegner, M. Wendt, B. Woolley, W. Wuensch, J. Uythoven, H. Zha, P. Zisopoulos, M. Benoit, M. Vicente Barreto Pinto, M. Bopp, H. H. Braun, M. Csatari Divall, M. Dehler, T. Garvey, J. Y. Raguin, L. Rivkin, R. Zennaro, A. Aksoy, Z. Nergiz, E. Pilicer, I. Tapan, O. Yavas, V. Baturin, R. Kholodov, S. Lebedynskyi, V. Miroshnichenko, S. Mordyk, I. Profatilova, V. Storizhko, N. Watson, A. Winter, J. Goldstein, S. Green, J. S. Marshall, M. A. Thomson, B. Xu, W. A. Gillespie, R. Pan, M. A Tyrk, D. Protopopescu, A. Robson, R. Apsimon, I. Bailey, G. Burt, D. Constable, A. Dexter, S. Karimian, C. Lingwood, M. D. Buckland, G. Casse, J. Vossebeld, A. Bosco, P. Karataev, K. Kruchinin, K. Lekomtsev, L. Nevay, J. Snuverink, E. Yamakawa, V. Boisvert, S. Boogert, G. Boorman, S. Gibson, A. Lyapin, W. Shields, P. Teixeira-Dias, S. West, R. Jones, N. Joshi, R. Bodenstein, P. N. Burrows, G. B. Christian, D. Gamba, C. Perry, J. Roberts, J. A. Clarke, N. A. Collomb, S. P. Jamison, B. J. A. Shepherd, D. Walsh, M. Demarteau, J. Repond, H. Weerts, L. Xia, J. D. Wells, C. Adolphsen, T. Barklow, M. Breidenbach, N. Graf, J. Hewett, T. Markiewicz, D. McCormick, K. Moffeit, Y. Nosochkov, M. Oriunno, N. Phinney, T. Rizzo, S. Tantawi, F. Wang, J. Wang, G. White, M. Woodley

The Compact Linear Collider (CLIC) is a multi-TeV high-luminosity linear e+e- collider under development. For an optimal exploitation of its physics potential, CLIC is foreseen to be built and operated in a staged approach with three centre-of-mass energy stages ranging from a few hundred GeV up to 3 TeV. The first stage will focus on precision Standard Model physics, in particular Higgs and top-quark measurements. Read More

In this article we develop a framework for studying parabolic semilinear stochastic evolution equations (SEEs) with singularities in the initial condition and singularities at the initial time of the time-dependent coefficients of the considered SEE. We use this framework to establish existence, uniqueness, and regularity results for mild solutions of parabolic semilinear SEEs with singularities at the initial time. We also provide several counterexample SEEs that illustrate the optimality of our results. Read More

We consider the question whether electromagnetism can be derived from quantum physics of measurements. It turns out that this is possible, both for quantum and classical electromagnetism, if we use more recent innovations such as smearing of observables and simultaneous measurability. In this way we justify the use of von Neumann-type measurement models for physical processes. Read More

In this paper the numerical approximation of stochastic differential equations satisfying a global monotonicity condition is studied. The strong rate of convergence with respect to the mean square norm is determined to be $\frac{1}{2}$ for the two-step BDF-Maruyama scheme and for the backward Euler-Maruyama method. In particular, this is the first paper which proves a strong convergence rate for a multi-step method applied to equations with possibly superlinearly growing drift and diffusion coefficient functions. Read More

For a unital completely positive map $\Phi$ ("quantum channel") governing the time propagation of a quantum system, the Stinespring representation gives an enlarged system evolving unitarily. We argue that the Stinespring representations of each power $\Phi^m$ of the single map together encode the structure of the original quantum channel and provides an interaction-dependent model for the bath. The same bath model gives a "classical limit" at infinite time $m\to\infty$ in the form of a noncommutative "manifold" determined by the channel. Read More

We use operator algebras and operator theory to obtain new result concerning Berezin quantization of compact K\"ahler manifolds. Our main tool is the notion of subproduct systems of finite-dimensional Hilbert spaces, which enables all involved objects, such as the Toeplitz operators, to be very conveniently expressed in terms of shift operators compressed to a subspace of full Fock space. This subspace is not required to be contained in the symmetric Fock space, so from finite-dimensional matrix algebras we can construct noncommutative manifolds with extra structure generalizing that of a projective variety endowed with a positive Hermitian line bundle and a canonical K\"ahler metric in the class of the line bundle. Read More

A unital completely positive map governing the time evolution of a quantum system is usually called a quantum channel, and it can be represented by a tuple of operators which are then referred to as the Kraus operators of the channel. We look at states of the system whose correlations with respect to the channel have a certain symmetry. Then we show that detailed balance holds if the Kraus operators satisfy a very interesting algebraic relation which plays an important role in the representation theory of any compact quantum group. Read More

We prove a weak error estimate for the approximation in space and time of a semilinear stochastic Volterra integro-differential equation driven by additive space-time Gaussian noise. We treat this equation in an abstract framework, in which parabolic stochastic partial differential equations are also included as a special case. The approximation in space is performed by a standard finite element method and in time by an implicit Euler method combined with a convolution quadrature. Read More

We study quantum phase slips (QPS) in ultrathin superconducting wires. Starting from an effective one-dimensional microscopic model, which includes electromagnetic fluctuations, we map the problem to a (1+1)-dimensional gas of interacting instantons. We introduce a method to calculate the tunneling amplitude of quantum phase slips directly from Monte Carlo simulations. Read More

With an action $\alpha$ of $\mathbb{R}^n$ on a $C^*$-algebra $A$ and a skew-symmetric $n\times n$ matrix $\Theta$ one can consider the Rieffel deformation $A_\Theta$ of $A$, which is a $C^*$-algebra generated by the $\alpha$-smooth elements of $A$ with a new multiplication. The purpose of this paper is to obtain explicit formulas for $K$-theoretical quantities defined by elements of $A_\Theta$. We assume that there is a densely defined trace on $A$, invariant under the action. Read More

We introduce a new family of refined Sobolev-Malliavin spaces that capture the integrability in time of the Malliavin derivative. We consider duality in these spaces and derive a Burkholder type inequality in a dual norm. The theory we develop allows us to prove weak convergence with essentially optimal rate for numerical approximations in space and time of semilinear parabolic stochastic evolution equations driven by Gaussian additive noise. Read More

Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the same genome, a process referred to as binning, remains a major informatics challenge. Here we present CONCOCT, a computer program that combines three types of information - sequence composition, coverage across multiple sample, and read-pair linkage - to automatically bin contigs into genomes. Read More

A set of semi-analytical techniques based on Fourier analysis is used to solve wave scattering problems in variously shaped waveguides with varying normal admittance boundary conditions. Key components are newly developed conformal mapping methods, wave splitting, Fourier series expansions in eigen-functions to non-normal operators, the building block method or the cascade technique, Dirichlet-to-Neumann operators, and reformulation in terms of stable differential equations for reflection and transmission matrices. For an example the results show good correspondence with a finite element method solution to the same problem in the low and medium frequency domain. Read More

We describe rigorous quantum measurement theory in the Heisenberg picture by applying operator deformation techniques previously used in noncommutative quantum field theory. This enables the conventional observables (represented by unbounded operators) to play a role also in the more general setting. Read More

We find the weak rate of convergence of the spatially semidiscrete finite element approximation of the nonlinear stochastic heat equation. Both multiplicative and additive noise is considered under different assumptions. This extends an earlier result of Debussche in which time discretization is considered for the stochastic heat equation perturbed by white noise. Read More

We revisit the scaling properties of the resistivity and the current-voltage characteristics at and below the Berezinskii-Kosterlitz-Thouless transition, both in zero and nonzero magnetic field. The scaling properties are derived by integrating the renormalization group flow equations up to a scale where they can be reliably matched to simple analytic expressions. The vortex fugacity turns out to be dangerously irrelevant for these quantities below Tc, thereby altering the scaling behavior. Read More

We study heat transport and thermoelectric effects in two-dimensional superconductors in a magnetic field. These are modeled as granular Josephson-junction arrays, forming either regular or random lattices. We employ two different models for the dynamics, relaxational model-A dynamics or resistively and capacitively shunted Josephson junction (RCSJ) dynamics. Read More

We study the Nernst effect due to vortex motion in two-dimensional granular superconductors using simulations with Langevin or resistively shunted Josephson-junction dynamics. In particular, we show that the geometric frustration of both regular and irregular granular materials can lead to thermally driven transport of vortices from colder to hotter regions, resulting in a sign reversal of the Nernst signal. We discuss the underlying mechanisms of this anomalous behavior in terms of heat transport by mobile vacancies in an otherwise pinned vortex lattice. Read More

We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in the bacterium E. coli, and compare it with the corresponding system in H. pylori which uses purely transcriptional regulation. Read More

2006Sep
Affiliations: 1Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark, 2Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark, 3Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark, 4Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark, 52*, 61*

Iron is an essential trace-element for most organisms. However, because high concentration of free intracellular iron is cytotoxic, cells have developed complex regulatory networks that keep free intracellular iron concentration at optimal range, allowing the incorporation of the metal into iron-using enzymes and minimizing damage to the cell. We built a mathematical model of the network that controls iron uptake and usage in the bacterium Escherichia coli to explore the dynamics of iron flow. Read More

The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple signal molecules that exist in its environment. A key part of this overall system of molecular regulation is therefore the interface between the genetic and the metabolic network. A motif that occurs very often at this interface is a negative feedback loop used to regulate the level of the signal molecules. Read More

We introduce exponential search trees as a novel technique for converting static polynomial space search structures for ordered sets into fully-dynamic linear space data structures. This leads to an optimal bound of O(sqrt(log n/loglog n)) for searching and updating a dynamic set of n integer keys in linear space. Here searching an integer y means finding the maximum key in the set which is smaller than or equal to y. Read More