TY - CONF
AB - We study the long time evolution of a quantum particle in a Gaussian random environment. We show that in the weak coupling limit the Wigner distribution of the wave function converges to the solution of a linear Boltzmann equation globally in time. The Boltzmann collision kernel is given by the Born approximation of the quantum scattering cross section.
AU - László Erdös
ID - 2711
TI - Linear Boltzmann equation as the weak coupling limit of the random Schrödinger equation
VL - 108
ER -
TY - JOUR
AU - László Erdös
AU - Solovej, Jan P
ID - 2730
IS - 1
JF - Duke Mathematical Journal
TI - Semiclassical eigenvalue estimates for the Pauli operator with strong nonhomogeneous magnetic fields, I: Nonasymptotic Lieb-Thirring-type estimate
VL - 96
ER -
TY - JOUR
AB - Pattern formation in a layer of fluid heated from below is an example of macroscopic ordering in continuous media. Here we show that in a relatively compact experimental version of the problem, a rich and diverse set of stable flows can be found. These flows, many of which are novel, can be categorized and understood in terms of their symmetry properties. This approach shows promise for providing insight into the more complicated fluid motion that occurs as the lateral dimension of the layer is increased.
AU - Björn Hof
AU - Lucas, Peter G
AU - Mullin, Tom P
ID - 2783
IS - 10
JF - Physics of Fluids
TI - Flow state multiplicity in convection
VL - 11
ER -
TY - JOUR
AB - Using an electrospray tandem mass spectrometer as a concentration-sensitive detector, a method has been developed to quantify femtomole amounts of plant growth regulators (i.e. isoprenoid type cytokinins, zeatin, dihydrozeatin, isopentenyladenine and their respective riboside and glucoside analogues) and the second messenger adenosine 3':5'-cyclic monophosphate (3':5'-cAMP). Miniaturisation of the chromatographic setup using capillary high performance liquid chromatographic (HPLC) ion spray mass spectrometry increased the sensitivity to the low femtomole region. Application of automated capillary column switching allowed the introduction of large injection volumes into the HPLC system. Aliquots (25 μL) were injected into one dimension of the HPLC set-up and stacked onto a micro pre-column. By means of mobile phase switching the pre-column was back-flushed to introduce the analytes onto the analytical column. For cytokinin analysis positive electrospray ionisation was used and resulted in 2.5-25 fmol detection limits. Cyclic nucleotides were separated under ion-pair conditions using tetrabutyl ammonium bromide as ion-pair reagent and were detected under negative electrospray ionisation conditions. Here a 25 fmol detection limit was determined. Following this approach, cytokinins and 3':5'-cAMP extracted from only mg amounts of apical shoot meristem and chloroplasts obtained from Nicotiana tabacum cv. Petit Havana SR1 were identified and quantified.
AU - Witters, Erwin
AU - Vanhoutte, Koen
AU - Dewitte, Walter
AU - Macháčková, Ivana
AU - Eva Benková
AU - Van Dongen, Walter
AU - Esmans, Eddy L
AU - Van Onckelen, Henri A
ID - 2864
IS - 3
JF - Phytochemical Analysis
TI - Analysis of cyclic nucleotides and cytokinins in minute plant samples using phase system switching capillary electrospray liquid chromatography tandem mass spectrometry
VL - 10
ER -
TY - JOUR
AB - Although cytokinins (CKs) affect a number of processes connected with chloroplasts, it has never been rigorously proven that chloroplasts contain CKs. We isolated intact chloroplasts from tobacco (Nicotiana tabacum L. cv SR1) and wheat (Triticum aestivum L. cv Ritmo) leaves and determined their CKs by liquid chromatography/tandem mass spectroscopy. Chloroplasts from both species contained a whole spectrum of CKs, including free bases (zeatin and isopentenyladenine), ribosides (zeatin riboside, and isopentenyladenosine), ribotides (isopentenyladenosine-5′-monophosphate, zeatin riboside-5′-monophosphate, and dihydrozeatin riboside-5′-monophosphate), and N-glucosides (zeatin-N 9-glucoside, dihydrozeatin-N 9-glucoside, zeatin-N 7-glucoside, and isopentenyladenine-N-glucosides). In chloroplasts there was a moderately higher relative amount of bases, ribosides, and ribotides than in leaves, and a significantly increased level ofN 9-glucosides of zeatin and dihydrozeatin. Tobacco and wheat chloroplasts were prepared from leaves at the end of either a dark or light period. After a dark period, chloroplasts accumulated more CKs than after a light period. The differences were moderate for free bases and ribosides, but highly significant for glucosides. Tobacco chloroplasts from dark-treated leaves contained zeatin riboside-O-glucoside and dihydrozeatin riboside-O-glucoside, as well as a relatively high CK oxidase activity. These data show that chloroplasts contain a whole spectrum of CKs and the enzymatic activity necessary for their metabolism.
AU - Eva Benková
AU - Witters, Erwin
AU - Van Dongen, Walter
AU - Kolář, Jan
AU - Motyka, Václav
AU - Brzobohatý, Břetislav
AU - Van Onckelen, Henri A
AU - Macháčková, Ivana
ID - 2865
IS - 1
JF - Plant Physiology
TI - Cytokinins in tobacco and wheat chloroplasts. Occurrence and changes due to light/dark treatment
VL - 121
ER -
TY - JOUR
AU - Kaloshin, Vadim
ID - 8526
IS - 2
JF - The Annals of Mathematics
KW - Statistics
KW - Probability and Uncertainty
KW - Statistics and Probability
SN - 0003-486X
TI - An extension of the Artin-Mazur theorem
VL - 150
ER -
TY - JOUR
AB - Sympatric speciation, the origin of two or more species from a single local population, has almost certainly been involved in formation of several species flocks, and may be fairly common in nature. The most straightforward scenario for sympatric speciation requires disruptive selection favouring two substantially different phenotypes, and consists of the evolution of reproductive isolation between them followed by the elimination of all intermediate phenotypes. Here we use the hypergeometric phenotypic model to show that sympatric speciation is possible even when fitness and mate choice depend on different quantitative traits, so that speciation must involve formation of covariance between these traits. The increase in the number of variable loci affecting fitness facilitates sympatric speciation, whereas the increase in the number of variable loci affecting mate choice has the opposite effect. These predictions may enable more cases of sympatric speciation to be identified.
AU - Kondrashov, Alexey S
AU - Fyodor Kondrashov
ID - 883
IS - 6742
JF - Nature
TI - Interactions among quantitative traits in the course of sympatric speciation
VL - 400
ER -
TY - CONF
AB - Temporal logic comes in two varieties: linear-time temporal logic assumes implicit universal quantification over all paths that are generated by system moves; branching-time temporal logic allows explicit existential and universal quantification over all paths. We introduce a third, more general variety of temporal logic: alternating-time temporal logic offers selective quantification over those paths that are possible outcomes of games, such as the game in which the system and the environment alternate moves. While linear-time and branching-time logics are natural specification languages for closed systems, alternating-time logics are natural specification languages for open systems. For example, by preceding the temporal operator “eventually” with a selective path quantifier, we can specify that in the game between the system and the environment, the system has a strategy to reach a certain state. Also the problems of receptiveness, realizability, and controllability can be formulated as model-checking problems for alternating-time formulas.
Depending on whether we admit arbitrary nesting of selective path quantifiers and temporal operators, we obtain the two alternating-time temporal logics ATL and ATL. We interpret the formulas of ATL and ATL over alternating transition systems. While in ordinary transition systems, each transition corresponds to a possible step of the system, in alternating transition systems, each transition corresponds to a possible move in the game between the system and the environment. Fair alternating transition systems can capture both synchronous and asynchronous compositions of open systems. For synchronous systems, the expressive power of ATL beyond CTL comes at no cost: the model-checking complexity of synchronous ATL is linear in the size of the system and the length of the formula. The symbolic model-checking algorithm for CTL extends with few modifications to synchronous ATL, and with some work, also to asynchronous ATL, whose model-checking complexity is quadratic. This makes ATL an obvious candidate for the automatic verification of open systems. In the case of ATL, the model-checking problem is closely related to the synthesis problem for linear-time formulas, and requires doubly exponential time for both synchronous and asynchronous systems.
A preliminary version of this paper appeared in the Proceedings of the 38th IEEE Symposium on Foundations of Computer Science (FOCS 1997), pp. 100–109.
AU - Alur, Rajeev
AU - Thomas Henzinger
AU - Kupferman, Orna
ID - 4601
TI - Alternating-time temporal logic
VL - 1536
ER -
TY - CONF
AB - Modular techniques for automatic verification attempt to overcome the state-explosion problem by exploiting the modular structure naturally present in many system designs. Unlike other tasks in the verification of finite-state systems, current modular techniques rely heavily on user guidance. In particular, the user is typically required to construct module abstractions that are neither too detailed as to render insufficient benefits in state exploration, nor too coarse as to invalidate the desired systemproperties. In this paper, we construct abstractmodules automatically, using reachability and controllability information about the concrete modules. This allows us to leverage automatic verification techniques by applying them in layers: first we compute on the state spaces of system components, then we use the results for constructing abstractions, and finally we compute on the abstract state space of the system. Our experimental results indicate that if reachability and controllability information is used in the construction of abstractions, the resulting abstract modules are often significantly smaller than the concrete modules and can drastically reduce the space and time requirements for verification.
AU - Alur, Rajeev
AU - de Alfaro, Luca
AU - Thomas Henzinger
AU - Mang, Freddy Y
ID - 4602
TI - Automating modular verification
VL - 1664
ER -
TY - JOUR
AB - A new paradigm for designing smooth surfaces is described. A finite set of points with weights specifies a closed surface in space referred to as skin. It consists of one or more components, each tangent continuous and free of self-intersections and intersections with other components. The skin varies continuously with the weights and locations of the points, and the variation includes the possibility of a topology change facilitated by the violation of tangent continuity at a single point in space and time. Applications of the skin to molecular modeling and to geometric deformation are discussed.
AU - Herbert Edelsbrunner
ID - 4014
IS - 1
JF - Discrete & Computational Geometry
TI - Deformable smooth surface design
VL - 21
ER -
TY - JOUR
AB - During the development of the zebrafish nervous system both noi, a zebrafish pax2 homolog, and ace, a zebrafish fgf8 homolog, are required for development of the midbrain and cerebellum. Here we describe a dominant mutation, aussicht (aus), in which the expression of noi and ace is upregulated, In aus mutant embryos, ace is upregulated at many sites in the embryo, while Itoi expression is only upregulated in regions of the forebrain and midbrain which also express ace. Subsequent to the alterations in noi and ace expression, aus mutants exhibit defects in the differentiation of the forebrain, midbrain and eyes. Within the forebrain, the formation of the anterior and postoptic commissures is delayed and the expression of markers within the pretectal area is reduced. Within the midbrain, En and wnt1 expression is expanded. In heterozygous aus embryos, there is ectopic outgrowth of neural retina in the temporal half of the eyes, whereas in putative homozygous aus embryos, the ventral retina is reduced and the pigmented retinal epithelium is expanded towards the midline, The observation that ans mutant embryos exhibit widespread upregulation of ace raised the possibility that aus might represent an allele of the ace gene itself. However, by crossing carriers for both aus and ace, we were able to generate homozygous ace mutant embryos that also exhibited the aus phenotype, This indicated that aus is not tightly linked to ace and is unlikely to be a mutation directly affecting the ace locus. However, increased Ace activity may underly many aspects of the aus phenotype and we show that the upregulation of noi in the forebrain of aus mutants is partially dependent upon functional Ace activity. Conversely, increased ace expression in the forebrain of arcs mutants is not dependent upon functional Noi activity. We conclude that aus represents a mutation involving a locus normally required for the regulation of ace expression during embryogenesis.
AU - Heisenberg, Carl-Philipp J
AU - Brennan, Caroline
AU - Wilson, Stephen
ID - 4204
IS - 10
JF - Development
TI - Zebrafish aussicht mutant embryos exhibit widespread overexpression of ace (fgf8) and coincident defects in CNS development
VL - 126
ER -
TY - JOUR
AB - Reproductive isolation between two taxa may be due to endogenous selection, which is generated by incompatibilities between the respective genomes, to exogenous selection, which is generated by differential adaptations to alternative environments, or to both. The continuing debate over the relative importance of either mode of selection has highlighted the need for unambiguous data on the fitness of hybrid genotypes. The hybrid zone between the fire-bellied toad (Bombina bombina) and the yellow-bellied toad (B. variegata) in central Europe involves adaptation to different environments, but evidence of hybrid dysfunction is equivocal. In this study, we followed the development under laboratory conditions of naturally laid eggs collected from a transect across the Bombina hybrid zone in Croatia. Fitness was significantly reduced in hybrid populations: Egg batches from the center of the hybrid zone showed significantly higher embryonic and larval mortality and higher frequencies of morphological abnormalities relative to either parental type. Overall mortality from day of egg collection to three weeks after hatching reached 20% in central hybrid populations, compared to 2% in pure populations. There was no significant difference in fitness between two parental types. Within hybrid populations, there was considerable variation in fitness, with some genotypes showing no evidence of reduced viability. We discuss the implications of these findings for our understanding of barriers to gene flow between species.
AU - Kruuk, Loeske E
AU - Gilchrist, Jason S
AU - Nicholas Barton
ID - 4277
IS - 5
JF - Evolution; International Journal of Organic Evolution
TI - Hybrid dysfunction in fire-bellied toads (Bombina)
VL - 53
ER -
TY - JOUR
AB - In this article we describe the structure of a hybrid zone in Argyll, Scotland, between native red deer (Cervus elaphus) and introduced Japanese sika deer (Cervus nippon), on the basis of a genetic analysis using 11 microsatellite markers and mitochondrial DNA. In contrast to the findings of a previous study of the same population, we conclude that the deer fall into two distinct genetic classes, corresponding to either a sika-like or red- like phenotype. Introgression is rare at any one locus, but where the taxa overlap up to 40% of deer carry apparently introgressed alleles. While most putative hybrids are heterozygous at only one locus, there are rare multiple heterozygotes, reflecting significant linkage disequilibrium within both sika- and red-like populations. The rate of backcrossing into the sika population is estimated as H = 0.002 per generation and into red, H = 0.001 per generation. On the basis of historical evidence that red deer entered Kintyre only recently, a diffusion model evaluated by maximum likelihood shows that sika have increased at ~9.2% yr-1 from low frequency and disperse at a rate of ~3.7 km yr-1. Introgression into the red-like population is greater in the south, while introgression into sika varies little along the transect. For both sika- and red-like populations, the degree of introgression is 30-40% of that predicted from the rates of current hybridization inferred from linkage disequilibria; however, in neither case is this statistically significant evidence for selection against introgression.
AU - Goodman, Simon J
AU - Nicholas Barton
AU - Swanson, Graeme M
AU - Abernethy, Kate
AU - Pemberton, Josephine M
ID - 4279
IS - 1
JF - Genetics
TI - Introgression through rare hybridisation: A genetic study of a hybrid zone between red and sika deer (genus Cervus), in Argyll, Scotland
VL - 152
ER -
TY - THES
AB - Model checking algorithms for the verification of reactive systems proceed by a systematic and exhaustive exploration of the system state space. They do not scale to large designs because of the state explosion problem --the number of states grows exponentially with the number of components in the design. Consequently, the model checking problem is PSPACE-hard in the size of the design description. This dissertation proposes three novel techniques to combat the state explosion problem.
One of the most important advances in model checking in recent years has been the discovery of symbolic methods, which use a calculus of expressions, such as binary decision diagrams, to represent the state sets encountered during state space exploration. Symbolic model checking has proved to be effective for verifying hardware designs. Traditionally, symbolic checking of temporal logic specifications is performed by backward fixpoint reasoning with the operator Pre. Backward reasoning can be wasteful since unreachable states are explored. We suggest the use of forward fixpoint reasoning based on the operator Post. We show how all linear temporal logic specifications can be model checked symbolically by forward reasoning. In contrast to backward reasoning, forward reasoning performs computations only on the reachable states.
Heuristics that improve algorithms for application domains, such as symbolic methods for hardware designs, are useful but not enough to make model checking feasible on industrial designs. Currently, exhaustive state exploration is possible only on designs with about 50-100 boolean state variables. Assume-guarantee verification attempts to combat the state explosion problem by using the principle of "divide and conquer," where the components of the implementation are analyzed one at a time. Typically, an implementation component refines its specification only when its inputs are suitably constrained by other components in the implementation. The assume-guarantee principle states that instead of constraining the inputs by implementation components, it is sound to constrain them by the corresponding specification components, which can be significantly smaller. We extend the assume-guarantee proof rule to deal with the case where the specification operates at a coarser time scale than the implementation. Using our model checker Mocha, which implements this methodology, we verify VGI, a parallel DSP processor chip with 64 compute processors each containing approximately 800 state variables and 30K gates.
Our third contribution is a systematic model checking methodology for verifying the abstract shared-memory interface of sequential consistency on multiprocessor systems with three parameters --number of processors, number of memory locations, and number of data values. Sequential consistency requires that some interleaving of the local temporal orders of read/write events at different processors be a trace of serial memory. Therefore, it suffices to construct a non-interfering serializer that watches and reorders read/write events so that a trace of serial memory is obtained. While in general such a serializer must be unbounded even for fixed values of the parameters --checking sequential consistency is undecidable!-- we show that the paradigmatic class of snoopy cache coherence protocols has finite-state serializers. In order to reduce the arbitrary-parameter problem to the fixed-parameter problem, we develop a novel framework for induction over the number of processors and use the notion of a serializer to reduce the problem of verifying sequential consistency to that of checking language inclusion between finite state machines.
AU - Qadeer, Shaz
ID - 4411
TI - Algorithms and Methodology for Scalable Model Checking
ER -
TY - JOUR
AB - Rectangular hybrid automata model digital control programs of analog plant environments. We study rectangular hybrid automata where the plant state evolves continuously in real-numbered time, and the controller samples the plant state and changes the control state discretely, only at the integer points in time. We prove that rectangular hybrid automata have finite bisimilarity quotients when all control transitions happen at integer times, even if the constraints on the derivatives of the variables vary between control states. This is in contrast with the conventional model where control transitions may happen at any real time, and already the reachability problem is undecidable. Based on the finite bisimilarity quotients, we give an exponential algorithm for the symbolic sampling-controller synthesis of rectangular automata. We show our algorithm to be optimal by proving the problem to be EXPTIME-hard. We also show that rectangular automata form a maximal class of systems for which the sampling-controller synthesis problem can be solved algorithmically.
AU - Thomas Henzinger
AU - Kopke, Peter W
ID - 4442
IS - 1-2
JF - Theoretical Computer Science
TI - Discrete-time control for rectangular hybrid automata
VL - 221
ER -
TY - CONF
AB - We describe the formal specification and verification of the VGI parallel DSP chip [1], which contains 64 compute processors with ~30K gates in each processor. Our effort coincided in time with the “informal” verification stage of the chip. By interacting with the designers, we produced an abstract but executable specification of the design which embodies the programmer's view of the system. Given the size of the design, an automatic check that even one of the 64 processors satisfies its specification is well beyond the scope of current verification tools. However, the check can be decomposed using assume-guarantee reasoning. For VGI, the implementation and specification operate at different time scales: several steps of the implementation correspond to a single step in the specification. We generalized both the assume-guarantee method and our model checker MOCHA to allow compositional verification for such applications. We used our proof rule to decompose the verification problem of the VGI chip into smaller proof obligations that were discharged automatically by MOCHA. Using our formal approach, we uncovered and fixed subtle bugs that were unknown to the designers.
AU - Thomas Henzinger
AU - Liu, Xiaojun
AU - Qadeer,Shaz
AU - Rajamani, Sriram K
ID - 4480
TI - Formal specification and verification of a dataflow processor array
ER -
TY - CONF
AB - In shared-memory multiprocessors sequential consistency offers a natural tradeoff between the flexibility afforded to the implementor and the complexity of the programmer’s view of the memory. Sequential consistency requires that some interleaving of the local temporal orders of read/write events at different processors be a trace of serial memory. We develop a systematic methodology for proving sequential consistency for memory systems with three parameters —number of processors, number of memory locations, and number of data values. From the definition of sequential consistency it suffices to construct a non-interfering observer that watches and reorders read/write events so that a trace of serial memory is obtained. While in general such an observer must be unbounded even for fixed values of the parameters —checking sequential consistency is undecidable!— we show that for two paradigmatic protocol classes—lazy caching and snoopy cache coherence—there exist finite-state observers. In these cases, sequential consistency for fixed parameter values can thus be checked by language inclusion between finite automata.
In order to reduce the arbitrary-parameter problem to the fixed-parameter problem, we develop a novel framework for induction over the number of processors. Classical induction schemas, which are based on process invariants that are inductive with respect to an implementation preorder that preserves the temporal sequence of events, are inadequate for our purposes, because proving sequential consistency requires the reordering of events. Hence we introduce merge invariants, which permit certain reorderings of read/write events. We show that under certain reasonable assumptions about the memory system, it is possible to conclude sequential consistency for any number of processors, memory locations, and data values by model checking two finite-state lemmas about process and merge invariants: they involve two processors each accessing a maximum of three locations, where each location stores at most two data values. For both lazy caching and snoopy cache coherence we are able to discharge the two lemmas using the model checker MOCHA.
AU - Thomas Henzinger
AU - Qadeer,Shaz
AU - Rajamani, Sriram K
ID - 4484
TI - Verifying sequential consistency on shared-memory multiprocessor systems
VL - 1633
ER -
TY - CONF
AB - In order to study control problems for hybrid systems, we generalize hybrid automata to hybrid games —say, controller vs. plant. If we specify the continuous dynamics by constant lower and upper bounds, we obtain rectangular games. We show that for rectangular games with objectives expressed in Ltl (linear temporal logic), the winning states for each player can be computed, and winning strategies can be synthesized. Our result is sharp, as already reachability is undecidable for generalizations of rectangular systems, and optimal —singly exponential in the size of the game structure and doubly exponential in the size of the Ltl objective. Our proof systematically generalizes the theory of hybrid systems from automata (single-player structures) [9] to games (multi-player structures): we show that the successively more general infinite-state classes of timed, 2D rectangular, and rectangular games induce successively weaker, but still finite, quotient structures called game bisimilarity, game similarity, and game trace equivalence. These quotients can be used, in particular, to solve the Ltl control problem.
AU - Thomas Henzinger
AU - Horowitz, Benjamin
AU - Majumdar, Ritankar S
ID - 4485
TI - Rectangular hybrid games
VL - 1664
ER -
TY - CONF
AB - Refinement checking is used to verify implementations against more abstract specifications. Assume-guarantee reasoning is used to decompose refinement proofs in order to avoid state-space explosion. In previous approaches, specifications are forced to operate on the same time scale as the implementation. This may lead to unnatural specifications and inefficiencies in verification. We introduce a novel methodology for decomposing refinement proofs of temporally abstract specifications, which specify implementation requirements only at certain sampling instances in time. Our new assume-guarantee rule allows separate refinement maps for specifying functionality and timing.We present the theory for the correctness of our methodology, and illustrate it using a simple example. Support for sampling and the generalized assume-guarantee rule have been implemented in the model checker Mocha and successfully applied to verify the VGI multiprocessor dataflow chip with 6 million transistors.
AU - Thomas Henzinger
AU - Qadeer,Shaz
AU - Rajamani, Sriram K
ID - 4487
TI - Assume-guarantee refinement between different time scales
VL - 1633
ER -
TY - JOUR
AB - We present a formal model for concurrent systems. The model represents synchronous and asynchronous components in a uniform framework that supports compositional (assume-guarantee) and hierarchical (stepwise-refinement) design and verification. While synchronous models are based on a notion of atomic computation step, and asynchronous models remove that notion by introducing stuttering, our model is based on a flexible notion of what constitutes a computation step: by applying an abstraction operator to a system, arbitrarily many consecutive steps can be collapsed into a single step. The abstraction operator, which may turn an asynchronous system into a synchronous one, allows us to describe systems at various levels of temporal detail. For describing systems at various levels of spatial detail, we use a hiding operator that may turn a synchronous system into an asynchronous one. We illustrate the model with diverse examples from synchronous circuits, asynchronous shared-memory programs, and synchronous message-passing protocols.
AU - Alur, Rajeev
AU - Thomas Henzinger
ID - 4582
IS - 1
JF - Formal Methods in System Design
TI - Reactive modules
VL - 15
ER -