@article{2192,
  abstract     = {We develop an analytic model of thermal state-to-state rotationally inelastic collisions of asymmetric-top molecules with closed-shell atoms in electric fields and apply it to the Ar-H2O collision system. The predicted cross sections as well as the steric asymmetry of the collisions show at fields up to 150 kV/cm characteristic field-dependent features which can be experimentally tested. Particularly suitable candidates for such tests are the 000 → 220 and 101→ 221 channels, arising from the relaxation of the field-free selection rules due to the hybridization of J states by the field. Averaging over the M' product channels is found to largely obliterate the orientation effects brought about by the field.},
  author       = {Mikhail Lemeshko and Friedrich, Břetislav},
  journal      = {Journal of Physical Chemistry A},
  number       = {52},
  pages        = {15055 -- 15063},
  publisher    = {American Chemical Society},
  title        = {{Model analysis of rotationally inelastic Ar + H2O scattering in an electric field}},
  doi          = {10.1021/jp9051598},
  volume       = {113},
  year         = {2009},
}

@article{2193,
  abstract     = {We show that weakly bound molecules can be probed by "shaking" in a pulsed nonresonant laser field. The field introduces a centrifugal term which expels the highest vibrational level from the potential that binds it. Our numerical simulations applied to the Rb2 and KRb Feshbach molecules indicate that shaking by feasible laser pulses can be used to accurately recover the square of the vibrational wave function and, by inversion, also the long-range part of the molecular potential.},
  author       = {Mikhail Lemeshko and Friedrich, Břetislav},
  journal      = {Physical Review Letters},
  number       = {5},
  publisher    = {American Physical Society},
  title        = {{Probing weakly bound molecules with nonresonant light}},
  doi          = {10.1103/PhysRevLett.103.053003},
  volume       = {103},
  year         = {2009},
}

@article{13414,
  abstract     = {Supraspherical aggregates of crosslinked metal nanoparticles are transformed into pancakes and nanorods by mechanical stresses and shears imparted by macroscopic objects (see image). The dimensions of both types of nanostructures can be controlled by the pressures applied.},
  author       = {Browne, Kevin P. and Klajn, Rafal and Villa, JulieAnn and Grzybowski, Bartosz A.},
  issn         = {1613-6829},
  journal      = {Small},
  keywords     = {Biomaterials, Biotechnology, General Materials Science, General Chemistry},
  number       = {23},
  pages        = {2656--2658},
  publisher    = {Wiley},
  title        = {{Mechanofabrication of pancake and rodlike nanostructures from deformable nanoparticle aggregates}},
  doi          = {10.1002/smll.200900902},
  volume       = {5},
  year         = {2009},
}

@article{13415,
  abstract     = {Systems in which nanoscale components of different types can be captured and/or released from organic scaffolds provide a fertile basis for the construction of dynamic, exchangeable functional materials. In such heterogeneous systems, the components interact with one another by means of programmable, noncovalent bonding interactions. Herein, we describe polymers that capture and release functionalized nanoparticles selectively during redox-controlled aggregation and disaggregation, respectively. The interactions between the polymer and the NPs are mediated by the reversible formation of polypseudorotaxanes, and give rise to architectures ranging from short chains composed of few nanoparticles to extended networks of nanoparticles crosslinked by the polymer. In the latter case, the polymer/nanoparticle aggregates precipitate from solution such that the polymer acts as a selective ‘sponge’ for the capture/release of the nanoparticles of different types.},
  author       = {Klajn, Rafal and Olson, Mark A. and Wesson, Paul J. and Fang, Lei and Coskun, Ali and Trabolsi, Ali and Soh, Siowling and Stoddart, J. Fraser and Grzybowski, Bartosz A.},
  issn         = {1755-4349},
  journal      = {Nature Chemistry},
  keywords     = {General Chemical Engineering, General Chemistry},
  pages        = {733--738},
  publisher    = {Springer Nature},
  title        = {{Dynamic hook-and-eye nanoparticle sponges}},
  doi          = {10.1038/nchem.432},
  volume       = {1},
  year         = {2009},
}

@article{13416,
  abstract     = {The reversible molecular template-directed self-assembly of gold nanoparticles (AuNPs), a process which relies solely on noncovalent bonding interactions, has been demonstrated by high-resolution transmission electron microscopy (HR-TEM). By employing a well-known host−guest binding motif, the AuNPs have been systemized into discrete dimers, trimers, and tetramers. These nanoparticulate twins, triplets, and quadruplets, which can be disassembled and reassembled either chemically or electrochemically, can be coalesced into larger, permanent polygonal structures by thermal treatment using a focused HR-TEM electron beam.},
  author       = {Olson, Mark A. and Coskun, Ali and Klajn, Rafal and Fang, Lei and Dey, Sanjeev K. and Browne, Kevin P. and Grzybowski, Bartosz A. and Stoddart, J. Fraser},
  issn         = {1530-6992},
  journal      = {Nano Letters},
  keywords     = {Mechanical Engineering, Condensed Matter Physics, General Materials Science, General Chemistry, Bioengineering},
  number       = {9},
  pages        = {3185--3190},
  publisher    = {American Chemical Society},
  title        = {{Assembly of polygonal nanoparticle clusters directed by reversible noncovalent bonding interactions}},
  doi          = {10.1021/nl901385c},
  volume       = {9},
  year         = {2009},
}

@article{13417,
  abstract     = {Mission Impossible: Metal nanoparticles (NPs) coated with photoresponsive ligands are used as “inks” for self-erasing “paper” whereby light-induced self-assembly of the NPs is transduced into local color changes (see picture). Depending on the degree of self-assembly, multicolor images can be written using only one type of NP ink. Duration of image erasure is regulated by the surface concentration of photoactive groups and can range from seconds to days.},
  author       = {Klajn, Rafal and Wesson, Paul J. and Bishop, Kyle J. M. and Grzybowski, Bartosz A.},
  issn         = {1521-3773},
  journal      = {Angewandte Chemie International Edition},
  keywords     = {General Chemistry, Catalysis},
  number       = {38},
  pages        = {7035--7039},
  publisher    = {Wiley},
  title        = {{Writing self-erasing images using metastable nanoparticle “inks”}},
  doi          = {10.1002/anie.200901119},
  volume       = {48},
  year         = {2009},
}

@article{13418,
  abstract     = {In traditional photoconductors1,2,3, the impinging light generates mobile charge carriers in the valence and/or conduction bands, causing the material’s conductivity to increase4. Such positive photoconductance is observed in both bulk and nanostructured5,6 photoconductors. Here we describe a class of nanoparticle-based materials whose conductivity can either increase or decrease on irradiation with visible light of wavelengths close to the particles’ surface plasmon resonance. The remarkable feature of these plasmonic materials is that the sign of the conductivity change and the nature of the electron transport between the nanoparticles depend on the molecules comprising the self-assembled monolayers (SAMs)7,8 stabilizing the nanoparticles. For SAMs made of electrically neutral (polar and non-polar) molecules, conductivity increases on irradiation. If, however, the SAMs contain electrically charged (either negatively or positively) groups, conductivity decreases. The optical and electrical characteristics of these previously undescribed inverse photoconductors can be engineered flexibly by adjusting the material properties of the nanoparticles and of the coating SAMs. In particular, in films comprising mixtures of different nanoparticles or nanoparticles coated with mixed SAMs, the overall photoconductance is a weighted average of the changes induced by the individual components. These and other observations can be rationalized in terms of light-induced creation of mobile charge carriers whose transport through the charged SAMs is inhibited by carrier trapping in transient polaron-like states9,10. The nanoparticle-based photoconductors we describe could have uses in chemical sensors and/or in conjunction with flexible substrates.},
  author       = {Nakanishi, Hideyuki and Bishop, Kyle J. M. and Kowalczyk, Bartlomiej and Nitzan, Abraham and Weiss, Emily A. and Tretiakov, Konstantin V. and Apodaca, Mario M. and Klajn, Rafal and Stoddart, J. Fraser and Grzybowski, Bartosz A.},
  issn         = {1476-4687},
  journal      = {Nature},
  keywords     = {Multidisciplinary},
  number       = {7253},
  pages        = {371--375},
  publisher    = {Springer Nature},
  title        = {{Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles}},
  doi          = {10.1038/nature08131},
  volume       = {460},
  year         = {2009},
}

@article{13419,
  abstract     = {Reaction-diffusion (RD) processes initiated from the surfaces of mesoscopic particles can fabricate complex core-and-shell structures. The propagation of a sharp RD front selectively removes metal colloids or nanoparticles from the supporting gel or polymer matrix. Once fabricated, the core structures can be processed “remotely” via galvanic replacement reactions, and the composite particles can be assembled into open-lattice crystals.},
  author       = {Wesson, Paul J. and Soh, Siowling and Klajn, Rafal and Bishop, Kyle J. M. and Gray, Timothy P. and Grzybowski, Bartosz A.},
  issn         = {1521-4095},
  journal      = {Advanced Materials},
  keywords     = {Mechanical Engineering, Mechanics of Materials, General Materials Science},
  number       = {19},
  pages        = {1911--1915},
  publisher    = {Wiley},
  title        = {{“Remote” fabrication via three-dimensional reaction-diffusion: Making complex core-and-shell particles and assembling them into open-lattice crystals}},
  doi          = {10.1002/adma.200802964},
  volume       = {21},
  year         = {2009},
}

@article{13420,
  abstract     = {Weakly protected metal nanoparticles (MNPs) are used as precursors for the preparation of catenane- and pseudorotaxane-decorated NPs of various compositions (gold, palladium, platinum). When attached to the surface of MNPs, the molecular switches retain their switching abilities. The redox potentials of these switches depend on and can be regulated by the composition of the mixed self-assembled monolayers covering the MNPs.},
  author       = {Klajn, Rafal and Fang, Lei and Coskun, Ali and Olson, Mark A. and Wesson, Paul J. and Stoddart, J. Fraser and Grzybowski, Bartosz A.},
  issn         = {1520-5126},
  journal      = {Journal of the American Chemical Society},
  keywords     = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis},
  number       = {12},
  pages        = {4233--4235},
  publisher    = {American Chemical Society},
  title        = {{Metal nanoparticles functionalized with molecular and supramolecular switches}},
  doi          = {10.1021/ja9001585},
  volume       = {131},
  year         = {2009},
}

@article{13421,
  abstract     = {Side-chain poly[2]catenanes at the click of a switch! A bistable side-chain poly[2]catenane has been synthesized and found to form hierarchical self-assembled hollow superstructures of nanoscale dimensions in solution. Molecular electromechanical switching (see picture) of the material is demonstrated, and the ground-state equilibrium thermodynamics and switching kinetics are examined as the initial steps towards processible molecular-based electronic devices and nanoelectromechanical systems.},
  author       = {Olson, Mark A. and Braunschweig, Adam B. and Fang, Lei and Ikeda, Taichi and Klajn, Rafal and Trabolsi, Ali and Wesson, Paul J. and Benítez, Diego and Mirkin, Chad A. and Grzybowski, Bartosz A. and Stoddart, J. Fraser},
  issn         = {1521-3773},
  journal      = {Angewandte Chemie International Edition},
  keywords     = {General Chemistry, Catalysis},
  number       = {10},
  pages        = {1792--1797},
  publisher    = {Wiley},
  title        = {{A bistable poly[2]catenane forms nanosuperstructures}},
  doi          = {10.1002/anie.200804558},
  volume       = {48},
  year         = {2009},
}

@inbook{164,
  abstract     = {Let g be a cubic polynomial with integer coefficients and n>9 variables, and assume that the congruence g=0 modulo p^k is soluble for all prime powers p^k. We show that the equation g=0 has infinitely many integer solutions when the cubic part of g defines a projective hypersurface with singular locus of dimension <n-10. The proof is based on the Hardy-Littlewood circle method.},
  author       = {Browning, Timothy D and Heath Brown, Roger},
  booktitle    = {Analytic Number Theory: Essays in honour of Klaus Roth},
  pages        = {75 -- 90},
  publisher    = {Cambridge University Press},
  title        = {{Integral points on cubic hypersurfaces}},
  year         = {2009},
}

@inproceedings{165,
  abstract     = {We survey the state of affairs for the distribution of ℚ-rational points on non-singular del Pezzo surfaces of low degree, highlighting the recent resolution of Manin's conjecture for a non-singular del Pezzo surface of degree 4 by la Bretèche and Browning.},
  author       = {Timothy Browning},
  editor       = {Aoki, Takashi and Kanemitsu, Shigeru and Liu, Jianya},
  pages        = {1 -- 18},
  publisher    = {World Scientific Publishing},
  title        = {{Resent progress on the quantitative arithmetic of del Pezzo surfaces}},
  doi          = {https://doi.org/10.1142/9789814289924_0001},
  volume       = {6},
  year         = {2009},
}

@inbook{168,
  abstract     = {The arithmetic of ternary diagonal equation is considered for degree d >1, with the outcome that the set of coefficients for which the equation admits a non-zero integer solution is shown to have density zero.},
  author       = {Timothy Browning and Dietmann, Rainer},
  booktitle    = {Quadratic Forms - algebra, arithmetic and geometry},
  pages        = {99 -- 106},
  publisher    = {American Mathematical Society},
  title        = {{Solubility of Fermat equations}},
  doi          = {http://dx.doi.org/10.1090/conm/493},
  volume       = {493},
  year         = {2009},
}

@article{1718,
  abstract     = {Morphogens act as graded positional cues to control cell fate specification in many developing tissues. This concept, in which a signaling gradient regulates differential gene expression in a concentration-dependent manner, has received considerable experimental support. Nevertheless, several recent studies have challenged the straightforward model of morphogen activity. In particular, the observation that pattern formation is a dynamic process has raised questions about the influence of time on morphogen activity. Here we propose that the spatiotemporal dynamics of the cellular response to a morphogen gradient depend on a combination of temporal alterations to the morphogen gradient itself, the dynamics of its signal transduction and downstream interactions between target genes.},
  author       = {Kutějová, Eva and Briscoe, James and Anna Kicheva},
  journal      = {Current Opinion in Genetics & Development},
  number       = {4},
  pages        = {315 -- 322},
  publisher    = {Elsevier},
  title        = {{Temporal dynamics of patterning by morphogen gradients}},
  doi          = {10.1016/j.gde.2009.05.004},
  volume       = {19},
  year         = {2009},
}

@article{1720,
  abstract     = {How morphogen gradients are formed in target tissues is a key question for understanding the mechanisms of morphological patterning. Here, we review different mechanisms of morphogen gradient formation from theoretical and experimental points of view. First, a simple, comprehensive overview of the underlying biophysical principles of several mechanisms of gradient formation is provided. We then discuss the advantages and limitations of different experimental approaches to gradient formation analysis.},
  author       = {Wartlick, Ortrud and Anna Kicheva and González-Gaitán, Marcos A},
  journal      = {Cold Spring Harbor perspectives in biology},
  number       = {3},
  publisher    = {Cold Spring Harbor Laboratory Press},
  title        = {{Morphogen gradient formation }},
  doi          = {10.1101/cshperspect.a001255},
  volume       = {1},
  year         = {2009},
}

@inproceedings{18726,
  abstract     = {The high sensitivity of JWST will open a new window on the end of the cosmological dark ages. Small stellar clusters, with a stellar mass of several × 106 M⊙, and low-mass black holes (BHs), with a mass of several $× 105 M⊙ should be directly detectable out to redshift z = 10, and individual supernovae (SNe) and gamma ray burst GRB afterglows are bright enough to be visible beyond this redshift. Dense primordial gas, in the process of collapsing from large scales to form protogalaxies, may also be possible to image through diffuse recombination line emission, possibly even before stars or BHs are formed. In this article, I discuss the key physical processes that are expected to have determined the sizes of the first star–clusters and black holes, and the prospect of studying these objects by direct detections with JWST and with other instruments. The direct light emitted by the very first stellar clusters and intermediate-mass black holes at z > 10 will likely fall below JWST’s detection threshold. However, JWST could reveal a decline at the faint-end of the high-redshift luminosity function, and thereby shed light on radiative and other feedback effects that operate at these early epochs. JWST will also have the sensitivity to detect individual SNe from beyond z = 10. In a dedicated survey lasting for several weeks, thousands of SNe could be detected at z > 6, with a redshift distribution extending to the formation of the very first stars at z ≳ 15. Using these SNe as tracers may be the only method to map out the earliest stages of the cosmic star–formation history. Finally, we point out that studying the earliest objects at high redshift will also offer a new window on the primordial power spectrum, on ∼100 times smaller scales than probed by current large-scale structure data.},
  author       = {Haiman, Zoltán},
  booktitle    = {Astrophysics and Space Science Proceedings},
  isbn         = {9781402094569},
  issn         = {1570-6605},
  pages        = {385--418},
  publisher    = {Springer Nature},
  title        = {{Observing the first stars and black holes}},
  doi          = {10.1007/978-1-4020-9457-6_15},
  year         = {2009},
}

@inbook{18735,
  abstract     = {The high sensitivity of JWST will open a new window on the end of the cosmological dark ages. Small stellar clusters, with a stellar mass of several × 106 M⊙, and low-mass black holes (BHs), with a mass of several $× 105 M⊙ should be directly detectable out to redshift z = 10, and individual supernovae (SNe) and gamma ray burst GRB afterglows are bright enough to be visible beyond this redshift. Dense primordial gas, in the process of collapsing from large scales to form protogalaxies, may also be possible to image through diffuse recombination line emission, possibly even before stars or BHs are formed. In this article, I discuss the key physical processes that are expected to have determined the sizes of the first star–clusters and black holes, and the prospect of studying these objects by direct detections with JWST and with other instruments. The direct light emitted by the very first stellar clusters and intermediate-mass black holes at z > 10 will likely fall below JWST’s detection threshold. However, JWST could reveal a decline at the faint-end of the high-redshift luminosity function, and thereby shed light on radiative and other feedback effects that operate at these early epochs. JWST will also have the sensitivity to detect individual SNe from beyond z = 10. In a dedicated survey lasting for several weeks, thousands of SNe could be detected at z > 6, with a redshift distribution extending to the formation of the very first stars at z ≳ 15. Using these SNe as tracers may be the only method to map out the earliest stages of the cosmic star–formation history. Finally, we point out that studying the earliest objects at high redshift will also offer a new window on the primordial power spectrum, on ∼100 times smaller scales than probed by current large-scale structure data.},
  author       = {Haiman, Zoltán},
  booktitle    = {Astrophysics in the Next Decade},
  editor       = {Thronson, Harley A. and Stiavelli, Massimo and Tielens, Alexander},
  isbn         = {9781402094569},
  issn         = {1570-6605},
  pages        = {385--418},
  publisher    = {Springer Nature},
  title        = {{Observing the First Stars and Black Holes}},
  doi          = {10.1007/978-1-4020-9457-6_15},
  year         = {2009},
}

@article{1971,
  abstract     = {Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 Å resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several α-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines.},
  author       = {Berrisford, John M and Leonid Sazanov},
  journal      = {Journal of Biological Chemistry},
  number       = {43},
  pages        = {29773 -- 29783},
  publisher    = {American Society for Biochemistry and Molecular Biology},
  title        = {{Structural basis for the mechanism of respiratory complex I}},
  doi          = {10.1074/jbc.M109.032144},
  volume       = {284},
  year         = {2009},
}

@article{4357,
  abstract     = {Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying adaptation to a common selective environment are parallel within and between species is interesting because it sheds light on the degree of evolutionary constraints. If parallel evolution is perfect, then the implication is that forces such as functional constraints, epistasis, and pleiotropy play an important role in shaping the outcomes of adaptive evolution. In addition, population genetic theory predicts that the probability of parallel evolution will decline with an increase in the number of adaptive solutions-if a single adaptive solution exists, then parallel evolution will be observed among highly divergent species. For this reason, it is predicted that close relatives-which likely overlap more in the details of their adaptive solutions-will show more parallel evolution. By adapting three related bacteriophage species to a novel environment we find (1) a high rate of parallel genetic evolution at orthologous nucleotide and amino acid residues within species, (2) parallel beneficial mutations do not occur in a common order in which they fix or appear in an evolving population, (3) low rates of parallel evolution and convergent evolution between species, and (4) the probability of parallel and convergent evolution between species is strongly effected by divergence.},
  author       = {Jonathan Bollback and Huelsenbeck, John P},
  journal      = {Genetics},
  number       = {1},
  pages        = {225 -- 234},
  publisher    = {Genetics Society of America},
  title        = {{Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence}},
  doi          = {10.1534/genetics.107.085225},
  volume       = {181},
  year         = {2009},
}

@inproceedings{4360,
  abstract     = {Motivated by applications in software verification, we explore automated reasoning about the non-disjoint combination of theories of infinitely many finite structures, where the theories share set variables and set operations. We prove a combination theorem and apply it to show the decidability of the satisfiability problem for a class of formulas obtained by applying propositional connectives to formulas belonging to: 1) Boolean Algebra with Presburger Arithmetic (with quantifiers over sets and integers), 2) weak monadic second-order logic over trees (with monadic second-order quantifiers), 3) two-variable logic with counting quantifiers (ranging over elements), 4) the Bernays-Schönfinkel-Ramsey class of first-order logic with equality (with ∃ * ∀ * quantifier prefix), and 5) the quantifier-free logic of multisets with cardinality constraints.},
  author       = {Wies, Thomas and Piskac, Ruzica and Kuncak, Viktor},
  booktitle    = {7th International Symposium on Frontiers of Combining Systems},
  location     = {Trento, Italy},
  pages        = {366 -- 382},
  publisher    = {Springer},
  title        = {{Combining theories with shared set operations}},
  doi          = {10.1007/978-3-642-04222-5_23},
  volume       = {5749},
  year         = {2009},
}