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  • 1
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    Wrong conclusions about non-native plant threats [Biological Sciences] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-06-10
    Description: Conservation scientists and practitioners have long recognized that not all non-native species pose a threat to biodiversity, yet some ecologists still fail to grasp this message (1). The conclusions drawn by Thomas and Palmer (2) that non-native plant species are not a threat to floral diversity in Britain highlight how...
    Keywords: Letters
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Ring-polymer instanton theory of electron transfer in the nonadiabatic limit (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-10-08
    Description: We take the golden-rule instanton method derived in the previous paper [J. O. Richardson, R. Bauer, and M. Thoss, J. Chem. Phys. 143 , 134115 (2015)] and reformulate it using a ring-polymer instanton approach. This gives equations which can be used to compute the rates of electron-transfer reactions in the nonadiabatic (golden-rule) limit numerically within a semiclassical approximation. The multidimensional ring-polymer instanton trajectories are obtained efficiently by minimization of the action. In this form, comparison with Wolynes’ quantum instanton method [P. G. Wolynes, J. Chem. Phys. 87 , 6559 (1987)] is possible and we show that our semiclassical approach is the steepest-descent limit of this method. We discuss advantages and disadvantages of both methods and give examples of where the new approach is more accurate.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    Semiclassical Green’s functions and an instanton formulation of electron-transfer rates in the nonadiabatic limit (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-10-08
    Description: We present semiclassical approximations to Green’s functions of multidimensional systems, extending Gutzwiller’s work to the classically forbidden region. Based on steepest-descent integrals over these functions, we derive an instanton method for computing the rate of nonadiabatic reactions, such as electron transfer, in the weak-coupling limit, where Fermi’s golden-rule can be employed. This generalizes Marcus theory to systems for which the environment free-energy curves are not harmonic and where nuclear tunnelling plays a role. The derivation avoids using the Im  F method or short-time approximations to real-time correlation functions. A clear physical interpretation of the nuclear tunnelling processes involved in an electron-transfer reaction is thus provided. In Paper II [J. O. Richardson, J. Chem. Phys. 143 , 134116 (2015)], we discuss numerical evaluation of the formulae.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Non-oscillatory flux correlation functions for efficient nonadiabatic rate theory (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-08-19
    Description: There is currently much interest in the development of improved trajectory-based methods for the simulation of nonadiabatic processes in complex systems. An important goal for such methods is the accurate calculation of the rate constant over a wide range of electronic coupling strengths and it is often the nonadiabatic, weak-coupling limit, which being far from the Born-Oppenheimer regime, provides the greatest challenge to current methods. We show that in this limit there is an inherent sign problem impeding further development which originates from the use of the usual quantum flux correlation functions, which can be very oscillatory at short times. From linear response theory, we derive a modified flux correlation function for the calculation of nonadiabatic reaction rates, which still rigorously gives the correct result in the long-time limit regardless of electronic coupling strength, but unlike the usual formalism is not oscillatory in the weak-coupling regime. In particular, a trajectory simulation of the modified correlation function is naturally initialized in a region localized about the crossing of the potential energy surfaces. In the weak-coupling limit, a simple link can be found between the dynamics initialized from this transition-state region and an generalized quantum golden-rule transition-state theory, which is equivalent to Marcus theory in the classical harmonic limit. This new correlation function formalism thus provides a platform on which a wide variety of dynamical simulation methods can be built aiding the development of accurate nonadiabatic rate theories applicable to complex systems.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 5
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    Unexpected consequences of a sudden and massive transposon amplification on rice gene expression (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-23
    Description: High-copy-number transposable elements comprise the majority of eukaryotic genomes where they are major contributors to gene and genome evolution. However, it remains unclear how a host genome can survive a rapid burst of hundreds or thousands of insertions because such bursts are exceedingly rare in nature and therefore difficult to observe in real time. In a previous study we reported that in a few rice strains the DNA transposon mPing was increasing its copy number by approximately 40 per plant per generation. Here we exploit the completely sequenced rice genome to determine 1,664 insertion sites using high-throughput sequencing of 24 individual rice plants and assess the impact of insertion on the expression of 710 genes by comparative microarray analysis. We find that the vast majority of transposable element insertions either upregulate or have no detectable effect on gene transcription. This modest impact reflects a surprising avoidance of exon insertions by mPing and a preference for insertion into 5' flanking sequences of genes. Furthermore, we document the generation of new regulatory networks by a subset of mPing insertions that render adjacent genes stress inducible. As such, this study provides evidence for models first proposed previously for the involvement of transposable elements and other repetitive sequences in genome restructuring and gene regulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Naito, Ken -- Zhang, Feng -- Tsukiyama, Takuji -- Saito, Hiroki -- Hancock, C Nathan -- Richardson, Aaron O -- Okumoto, Yutaka -- Tanisaka, Takatoshi -- Wessler, Susan R -- England -- Nature. 2009 Oct 22;461(7267):1130-4. doi: 10.1038/nature08479.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847266" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Flanking Region/genetics ; Alleles ; Arabidopsis/genetics ; Cold Temperature ; DNA Copy Number Variations/genetics ; DNA Transposable Elements/*genetics ; Exons ; Gene Amplification/*genetics ; Gene Dosage/*genetics ; *Gene Expression Regulation, Plant ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames/genetics ; Oryza/*genetics ; Promoter Regions, Genetic/genetics ; Stress, Physiological/genetics ; Transgenes/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Ion-mediated hydrogen-bond rearrangement through tunnelling in the iodide–dihydrate complex (2019)
    Springer Nature
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    Publication Date: 2019
    Print ISSN: 1755-4330
    Electronic ISSN: 1755-4349
    Topics: Chemistry and Pharmacology
    Published by Springer Nature
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  • 7
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    Derivation of instanton rate theory from first principles (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-03-18
    Description: Instanton rate theory is used to study tunneling events in a wide range of systems including low-temperature chemical reactions. Despite many successful applications, the method has never been obtained from first principles, relying instead on the “Im  F ” premise. In this paper, the same expression for the rate of barrier penetration at finite temperature is rederived from quantum scattering theory [W. H. Miller, S. D. Schwartz, and J. W. Tromp, J. Chem. Phys. 79 , 4889 (1983)] using a semiclassical Green’s function formalism. This justifies the instanton approach and provides a route to deriving the rate of other processes.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 8
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    [Report] Concerted hydrogen-bond breaking by quantum tunneling in the water hexamer prism (2016)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2016-03-18
    Description: The nature of the intermolecular forces between water molecules is the same in small hydrogen-bonded clusters as in the bulk. The rotational spectra of the clusters therefore give insight into the intermolecular forces present in liquid water and ice. The water hexamer is the smallest water cluster to support low-energy structures with branched three-dimensional hydrogen-bond networks, rather than cyclic two-dimensional topologies. Here we report measurements of splitting patterns in rotational transitions of the water hexamer prism, and we used quantum simulations to show that they result from geared and antigeared rotations of a pair of water molecules. Unlike previously reported tunneling motions in water clusters, the geared motion involves the concerted breaking of two hydrogen bonds. Similar types of motion may be feasible in interfacial and confined water. Authors: Jeremy O. Richardson, Cristóbal Pérez, Simon Lobsiger, Adam A. Reid, Berhane Temelso, George C. Shields, Zbigniew Kisiel, David J. Wales, Brooks H. Pate, Stuart C. Althorpe
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-12-21
    Description: We report the complete mitochondrial genome sequence of the flowering plant Amborella trichopoda. This enormous, 3.9-megabase genome contains six genome equivalents of foreign mitochondrial DNA, acquired from green algae, mosses, and other angiosperms. Many of these horizontal transfers were large, including acquisition of entire mitochondrial genomes from three green algae and one moss. We propose a fusion-compatibility model to explain these findings, with Amborella capturing whole mitochondria from diverse eukaryotes, followed by mitochondrial fusion (limited mechanistically to green plant mitochondria) and then genome recombination. Amborella's epiphyte load, propensity to produce suckers from wounds, and low rate of mitochondrial DNA loss probably all contribute to the high level of foreign DNA in its mitochondrial genome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rice, Danny W -- Alverson, Andrew J -- Richardson, Aaron O -- Young, Gregory J -- Sanchez-Puerta, M Virginia -- Munzinger, Jerome -- Barry, Kerrie -- Boore, Jeffrey L -- Zhang, Yan -- dePamphilis, Claude W -- Knox, Eric B -- Palmer, Jeffrey D -- R01-GM-76012/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 20;342(6165):1468-73. doi: 10.1126/science.1246275.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Indiana University, Bloomington, IN 47405, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24357311" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Bryophyta/classification/genetics ; Chlorophyta/classification/genetics ; DNA, Mitochondrial/*genetics ; *Gene Transfer, Horizontal ; *Genome, Plant ; Membrane Fusion ; *Mitochondrial Dynamics ; Molecular Sequence Data ; Phylogeny ; Tracheobionta/classification/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Concerted hydrogen-bond breaking by quantum tunneling in the water hexamer prism (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-03-19
    Description: The nature of the intermolecular forces between water molecules is the same in small hydrogen-bonded clusters as in the bulk. The rotational spectra of the clusters therefore give insight into the intermolecular forces present in liquid water and ice. The water hexamer is the smallest water cluster to support low-energy structures with branched three-dimensional hydrogen-bond networks, rather than cyclic two-dimensional topologies. Here we report measurements of splitting patterns in rotational transitions of the water hexamer prism, and we used quantum simulations to show that they result from geared and antigeared rotations of a pair of water molecules. Unlike previously reported tunneling motions in water clusters, the geared motion involves the concerted breaking of two hydrogen bonds. Similar types of motion may be feasible in interfacial and confined water.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Richardson, Jeremy O -- Perez, Cristobal -- Lobsiger, Simon -- Reid, Adam A -- Temelso, Berhane -- Shields, George C -- Kisiel, Zbigniew -- Wales, David J -- Pate, Brooks H -- Althorpe, Stuart C -- New York, N.Y. -- Science. 2016 Mar 18;351(6279):1310-3. doi: 10.1126/science.aae0012.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. Department of Chemistry, Durham University, South Road Durham DH1 3LE, UK. ; Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, VA 22903, USA. ; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. ; Dean's Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, PA 17837, USA. ; Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warszawa, Poland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26989250" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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