@article{3168, abstract = {The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently, we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper, we prove that this quotienting yields a sufficient condition for weak lumpability (that is to say that the quotient system is still Markovian for a given set of initial distributions) and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system (which means that the conditional probability of being in a given state in the original system knowing that we are in its equivalence class is an invariant of the system). We illustrate the framework on a case study of the epidermal growth factor (EGF)/insulin receptor crosstalk.}, author = {Feret, Jérôme and Henzinger, Thomas A and Koeppl, Heinz and Petrov, Tatjana}, journal = {Theoretical Computer Science}, pages = {137 -- 164}, publisher = {Elsevier}, title = {{Lumpability abstractions of rule based systems}}, doi = {10.1016/j.tcs.2011.12.059}, volume = {431}, year = {2012}, } @article{377, abstract = {The potential to control the composition and crystal phase at the nanometer scale enable the production of nanocrystalline materials with enhanced functionalities and new applications. In the present work, we detail a novel colloidal synthesis route to prepare nanoparticles of the ternary semiconductor Cu2GeSe3 (CGSe) with nanometer-scale control over their crystal phases. We also demonstrate the structural effect on the thermoelectric properties of bottom-up-prepared CGSe nanomaterials. By careful adjustment of the nucleation and growth temperatures, pure orthorhombic CGSe nanoparticles with cationic order or polytypic CGSe nanoparticles with disordered cation positions can be produced. In this second type of nanoparticle, a high density of twins can be created to periodically change the atomic plane stacking, forming a hexagonal wurtzite CGSe phase. The high yield of the synthetic routes reported here allows the production of single-phase and multiphase CGSe nanoparticles in the gram scale, which permits characterization of the thermoelectric properties of these materials. Reduced thermal conductivities and a related 2.5-fold increase of the thermoelectric figure of merit for multiphase nanomaterials compared to pure-phase CGSe are systematically obtained. These results are discussed in terms of the density and efficiency of phonon scattering centers in both types of materials.}, author = {Ibáñez, Maria and Zamani, Reza and Li, Wenhua and Cadavid, Doris and Gorse, Stéphane and Katchoi, Nebll and Shavel, Alexey and López, Antonioo and Morante, Joan and Arbiol, Jordi and Cabot, Andreu}, journal = {Chemistry of Materials}, number = {23}, pages = {4615 -- 4622}, publisher = {American Chemical Society}, title = {{Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials}}, doi = {10.1021/cm303252q}, volume = {24}, year = {2012}, } @article{3846, abstract = {We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A}, journal = {Journal of Computer and System Sciences}, number = {2}, pages = {394 -- 413}, publisher = {Elsevier}, title = {{A survey of stochastic ω regular games}}, doi = {10.1016/j.jcss.2011.05.002}, volume = {78}, year = {2012}, } @article{387, abstract = {In this Letter we present detailed study of the density of states near defects in Bi 2Se 3. In particular, we present data on the commonly found triangular defects in this system. While we do not find any measurable quasiparticle scattering interference effects, we do find localized resonances, which can be well fitted by theory once the potential is taken to be extended to properly account for the observed defects. The data together with the fits confirm that while the local density of states around the Dirac point of the electronic spectrum at the surface is significantly disrupted near the impurity by the creation of low-energy resonance state, the Dirac point is not locally destroyed. We discuss our results in terms of the expected protected surface state of topological insulators. © 2012 American Physical Society.}, author = {Alpichshev, Zhanybek and Biswas, Rudro and Balatsky, Alexander and Analytis, James and Chu, Jiunhaw and Fisher, Ian and Kapitulnik, Aharon}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{STM imaging of impurity resonances on Bi 2Se 3}}, doi = {10.1103/PhysRevLett.108.206402}, volume = {108}, year = {2012}, } @article{3110, abstract = {The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation. }, author = {Dai, Mingqiu and Zhang, Chen and Urszula Kania and Chen, Fang and Xue, Qin and McCray, Tyra and Li, Gang and Qin, Genji and Wakeley, Michelle and Terzaghi, William and Wan, Jianmin and Zhao, Yunde and Xu, Jian and Jirí Friml and Deng, Xing W and Wang, Haiyang}, journal = {Plant Cell}, number = {6}, pages = {2497 -- 2514}, publisher = {American Society of Plant Biologists}, title = {{A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis}}, doi = {10.1105/tpc.112.098905}, volume = {24}, year = {2012}, }