TY - JOUR
AB - We consider the Bogolubov–Hartree–Fock functional for a fermionic many-body system with two-body interactions. For suitable interaction potentials that have a strong enough attractive tail in order to allow for two-body bound states, but are otherwise sufficiently repulsive to guarantee stability of the system, we show that in the low-density limit the ground state of this model consists of a Bose–Einstein condensate of fermion pairs. The latter can be described by means of the Gross–Pitaevskii energy functional.
AU - Bräunlich, Gerhard
AU - Hainzl, Christian
AU - Seiringer, Robert
ID - 1259
IS - 2
JF - Mathematical Physics, Analysis and Geometry
TI - Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit
VL - 19
ER -
TY - JOUR
AB - In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way.
AU - De Martino, Daniele
ID - 1260
IS - 6
JF - International Journal of Modern Physics C
TI - The dual of the space of interactions in neural network models
VL - 27
ER -
TY - JOUR
AB - We consider a non-standard finite-volume discretization of a strongly non-linear fourth order diffusion equation on the d-dimensional cube, for arbitrary . The scheme preserves two important structural properties of the equation: the first is the interpretation as a gradient flow in a mass transportation metric, and the second is an intimate relation to a linear Fokker-Planck equation. Thanks to these structural properties, the scheme possesses two discrete Lyapunov functionals. These functionals approximate the entropy and the Fisher information, respectively, and their dissipation rates converge to the optimal ones in the discrete-to-continuous limit. Using the dissipation, we derive estimates on the long-time asymptotics of the discrete solutions. Finally, we present results from numerical experiments which indicate that our discretization is able to capture significant features of the complex original dynamics, even with a rather coarse spatial resolution.
AU - Maas, Jan
AU - Matthes, Daniel
ID - 1261
IS - 7
JF - Nonlinearity
TI - Long-time behavior of a finite volume discretization for a fourth order diffusion equation
VL - 29
ER -
TY - JOUR
AB - Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.
AU - Mcmahon, Dino
AU - Natsopoulou, Myrsini
AU - Doublet, Vincent
AU - Fürst, Matthias
AU - Weging, Silvio
AU - Brown, Mark
AU - Gogol Döring, Andreas
AU - Paxton, Robert
ID - 1262
IS - 1833
JF - Proceedings of the Royal Society of London Series B Biological Sciences
TI - Elevated virulence of an emerging viral genotype as a driver of honeybee loss
VL - 283
ER -
TY - JOUR
AB - Linking classical microwave electrical circuits to the optical telecommunication band is at the core of modern communication. Future quantum information networks will require coherent microwave-to-optical conversion to link electronic quantum processors and memories via low-loss optical telecommunication networks. Efficient conversion can be achieved with electro-optical modulators operating at the single microwave photon level. In the standard electro-optic modulation scheme, this is impossible because both up- and down-converted sidebands are necessarily present. Here, we demonstrate true single-sideband up- or down-conversion in a triply resonant whispering gallery mode resonator by explicitly addressing modes with asymmetric free spectral range. Compared to previous experiments, we show a 3 orders of magnitude improvement of the electro-optical conversion efficiency, reaching 0.1% photon number conversion for a 10 GHz microwave tone at 0.42 mW of optical pump power. The presented scheme is fully compatible with existing superconducting 3D circuit quantum electrodynamics technology and can be used for nonclassical state conversion and communication. Our conversion bandwidth is larger than 1 MHz and is not fundamentally limited.
AU - Rueda, Alfredo
AU - Sedlmeir, Florian
AU - Collodo, Michele
AU - Vogl, Ulrich
AU - Stiller, Birgit
AU - Schunk, Gerhard
AU - Strekalov, Dmitry
AU - Marquardt, Christoph
AU - Fink, Johannes M
AU - Painter, Oskar
AU - Leuchs, Gerd
AU - Schwefel, Harald
ID - 1263
IS - 6
JF - Optica
TI - Efficient microwave to optical photon conversion: An electro-optical realization
VL - 3
ER -
TY - JOUR
AB - n contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively.
AU - Sancho Andrés, Gloria
AU - Soriano Ortega, Esther
AU - Gao, Caiji
AU - Bernabé Orts, Joan
AU - Narasimhan, Madhumitha
AU - Müller, Anna
AU - Tejos, Ricardo
AU - Jiang, Liwen
AU - Friml, Jirí
AU - Aniento, Fernando
AU - Marcote, Maria
ID - 1264
IS - 3
JF - Plant Physiology
TI - Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier
VL - 171
ER -
TY - JOUR
AB - Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical propertiesare modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured "stiffness" of plant ECMs is symmetrically patternedin hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology.
AU - Elsayad, Kareem
AU - Werner, Stephanie
AU - Gallemi Rovira, Marcal
AU - Kong, Jixiang
AU - Guajardo, Edmundo
AU - Zhang, Lijuan
AU - Jaillais, Yvon
AU - Greb, Thomas
AU - Belkhadir, Youssef
ID - 1265
IS - 435
JF - Science Signaling
TI - Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging
VL - 9
ER -
TY - JOUR
AB - Cortical networks exhibit ‘global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ‘prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code.
AU - Chalk, Matthew J
AU - Gutkin, Boris
AU - Denève, Sophie
ID - 1266
IS - 2016JULY
JF - eLife
TI - Neural oscillations as a signature of efficient coding in the presence of synaptic delays
VL - 5
ER -
TY - JOUR
AB - We give a simplified proof of the nonexistence of large nuclei in the liquid drop model and provide an explicit bound. Our bound is within a factor of 2.3 of the conjectured value and seems to be the first quantitative result.
AU - Frank, Rupert
AU - Killip, Rowan
AU - Nam, Phan
ID - 1267
IS - 8
JF - Letters in Mathematical Physics
TI - Nonexistence of large nuclei in the liquid drop model
VL - 106
ER -
TY - JOUR
AU - Milutinovic, Barbara
AU - Kurtz, Joachim
ID - 1268
IS - 4
JF - Seminars in Immunology
TI - Immune memory in invertebrates
VL - 28
ER -
TY - JOUR
AB - Plants are continuously exposed to a myriad of external signals such as fluctuating nutrients availability, drought, heat, cold, high salinity, or pathogen/pest attacks that can severely affect their development, growth, and fertility. As sessile organisms, plants must therefore be able to sense and rapidly react to these external inputs, activate efficient responses, and adjust development to changing conditions. In recent years, significant progress has been made towards understanding the molecular mechanisms underlying the intricate and complex communication between plants and the environment. It is now becoming increasingly evident that hormones have an important regulatory role in plant adaptation and defense mechanisms.
AU - Benková, Eva
ID - 1269
IS - 6
JF - Plant Molecular Biology
TI - Plant hormones in interactions with the environment
VL - 91
ER -
TY - CONF
AB - Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations.
AU - Monk, Travis
AU - Savin, Cristina
AU - Lücke, Jörg
ID - 948
TI - Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
VL - 29
ER -
TY - THES
AB - In this thesis we present a computer-aided programming approach to concurrency. Our approach
helps the programmer by automatically fixing concurrency-related bugs, i.e. bugs that occur
when the program is executed using an aggressive preemptive scheduler, but not when using a
non-preemptive (cooperative) scheduler. Bugs are program behaviours that are incorrect w.r.t.
a specification. We consider both user-provided explicit specifications in the form of assertion
statements in the code as well as an implicit specification. The implicit specification is inferred
from the non-preemptive behaviour. Let us consider sequences of calls that the program makes
to an external interface. The implicit specification requires that any such sequence produced
under a preemptive scheduler should be included in the set of sequences produced under a
non-preemptive scheduler.
We consider several semantics-preserving fixes that go beyond atomic sections typically
explored in the synchronisation synthesis literature. Our synthesis is able to place locks, barriers
and wait-signal statements and last, but not least reorder independent statements. The latter
may be useful if a thread is released to early, e.g., before some initialisation is completed. We
guarantee that our synthesis does not introduce deadlocks and that the synchronisation inserted
is optimal w.r.t. a given objective function.
We dub our solution trace-based synchronisation synthesis and it is loosely based on
counterexample-guided inductive synthesis (CEGIS). The synthesis works by discovering a
trace that is incorrect w.r.t. the specification and identifying ordering constraints crucial to trigger
the specification violation. Synchronisation may be placed immediately (greedy approach) or
delayed until all incorrect traces are found (non-greedy approach). For the non-greedy approach
we construct a set of global constraints over synchronisation placements. Each model of the
global constraints set corresponds to a correctness-ensuring synchronisation placement. The
placement that is optimal w.r.t. the given objective function is chosen as the synchronisation
solution.
We evaluate our approach on a number of realistic (albeit simplified) Linux device-driver
benchmarks. The benchmarks are versions of the drivers with known concurrency-related bugs.
For the experiments with an explicit specification we added assertions that would detect the bugs
in the experiments. Device drivers lend themselves to implicit specification, where the device and
the operating system are the external interfaces. Our experiments demonstrate that our synthesis
method is precise and efficient. We implemented objective functions for coarse-grained and
fine-grained locking and observed that different synchronisation placements are produced for
our experiments, favouring e.g. a minimal number of synchronisation operations or maximum
concurrency.
AU - Tarrach, Thorsten
ID - 1130
TI - Automatic synthesis of synchronisation primitives for concurrent programs
ER -
TY - JOUR
AB - CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network.
AU - Mishra, Rajiv Kumar
AU - Kim, Sooyun
AU - Guzmán, José
AU - Jonas, Peter M
ID - 1432
JF - Nature Communications
TI - Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks
VL - 7
ER -
TY - THES
AB - CA3 pyramidal neurons are thought to pay a key role in memory storage and pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent excitatory synapses. To examine the induction rules of synaptic plasticity at CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute to LTP induction without requirement of a somatic action potential (AP). We next examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3 synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was symmetric and broad, with a half-width of ~150 ms. Consistent with these specific STDP induction properties, post-presynaptic sequences led to a supralinear summation of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage and recall was substantially more robust with symmetric than with asymmetric STDP rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral synapses with distinct induction rules. LTP induced by HFS may be associated with dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic activity induced LTP only if EPSP-AP were temporally very close. Together, these induction mechanisms of synaptiic plasticity may contribute to memory storage in the CA3-CA3 microcircuit at different ranges of activity.
AU - Mishra, Rajiv Kumar
ID - 1396
TI - Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus
ER -
TY - THES
AB - Directed cell migration is a hallmark feature, present in almost all multi-cellular
organisms. Despite its importance, basic questions regarding force transduction
or directional sensing are still heavily investigated. Directed migration of cells
guided by immobilized guidance cues - haptotaxis - occurs in key-processes,
such as embryonic development and immunity (Middleton et al., 1997; Nguyen
et al., 2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues
comprise adhesive ligands, such as collagen and fibronectin (Barczyk et al.,
2009), or chemokines - the main guidance cues for migratory leukocytes
(Middleton et al., 1997; Weber et al., 2013). While adhesive ligands serve as
attachment sites guiding cell migration (Carter, 1965), chemokines instruct
haptotactic migration by inducing adhesion to adhesive ligands and directional
guidance (Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis
of the cellular response to immobilized guidance cues requires in vitro assays
that foster cell migration, offer accurate control of the immobilized cues on a
subcellular scale and in the ideal case closely reproduce in vivo conditions. The
exploration of haptotactic cell migration through design and employment of such
assays represents the main focus of this work.
Dendritic cells (DCs) are leukocytes, which after encountering danger
signals such as pathogens in peripheral organs instruct naïve T-cells and
consequently the adaptive immune response in the lymph node (Mellman and
Steinman, 2001). To reach the lymph node from the periphery, DCs follow
haptotactic gradients of the chemokine CCL21 towards lymphatic vessels
(Weber et al., 2013). Questions about how DCs interpret haptotactic CCL21
gradients have not yet been addressed. The main reason for this is the lack of
an assay that offers diverse haptotactic environments, hence allowing the study
of DC migration as a response to different signals of immobilized guidance cue.
In this work, we developed an in vitro assay that enables us to
quantitatively assess DC haptotaxis, by combining precisely controllable
chemokine photo-patterning with physically confining migration conditions. With this tool at hand, we studied the influence of CCL21 gradient properties and
concentration on DC haptotaxis. We found that haptotactic gradient sensing
depends on the absolute CCL21 concentration in combination with the local
steepness of the gradient. Our analysis suggests that the directionality of
migrating DCs is governed by the signal-to-noise ratio of CCL21 binding to its
receptor CCR7. Moreover, the haptotactic CCL21 gradient formed in vivo
provides an optimal shape for DCs to recognize haptotactic guidance cue.
By reconstitution of the CCL21 gradient in vitro we were also able to
study the influence of CCR7 signal termination on DC haptotaxis. To this end,
we used DCs lacking the G-protein coupled receptor kinase GRK6, which is
responsible for CCL21 induced CCR7 receptor phosphorylation and
desensitization (Zidar et al., 2009). We found that CCR7 desensitization by
GRK6 is crucial for maintenance of haptotactic CCL21 gradient sensing in vitro
and confirm those observations in vivo.
In the context of the organism, immobilized haptotactic guidance cues
often coincide and compete with soluble chemotactic guidance cues. During
wound healing, fibroblasts are exposed and influenced by adhesive cues and
soluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,
migrating DCs are exposed to both, soluble chemokines (CCL19 and truncated
CCL21) inducing chemotactic behavior as well as the immobilized CCL21. To
quantitatively assess these complex coinciding immobilized and soluble
guidance cues, we implemented our chemokine photo-patterning technique in a
microfluidic system allowing for chemotactic gradient generation. To validate
the assay, we observed DC migration in competing CCL19/CCL21
environments.
Adhesiveness guided haptotaxis has been studied intensively over the
last century. However, quantitative studies leading to conceptual models are
largely missing, again due to the lack of a precisely controllable in vitro assay. A
requirement for such an in vitro assay is that it must prevent any uncontrolled
cell adhesion. This can be accomplished by stable passivation of the surface. In
addition, controlled adhesion must be sustainable, quantifiable and dose
dependent in order to create homogenous gradients. Therefore, we developed a novel covalent photo-patterning technique satisfying all these needs. In
combination with a sustainable poly-vinyl alcohol (PVA) surface coating we
were able to generate gradients of adhesive cue to direct cell migration. This
approach allowed us to characterize the haptotactic migratory behavior of
zebrafish keratocytes in vitro. Furthermore, defined patterns of adhesive cue
allowed us to control for cell shape and growth on a subcellular scale.
AU - Schwarz, Jan
ID - 1129
TI - Quantitative analysis of haptotactic cell migration
ER -
TY - THES
AB - Motivated by topological Tverberg-type problems in topological combinatorics and by classical
results about embeddings (maps without double points), we study the question whether a finite
simplicial complex K can be mapped into Rd without triple, quadruple, or, more generally, r-fold points (image points with at least r distinct preimages), for a given multiplicity r ≤ 2. In particular, we are interested in maps f : K → Rd that have no global r -fold intersection points, i.e., no r -fold points with preimages in r pairwise disjoint simplices of K , and we seek necessary and sufficient conditions for the existence of such maps.
We present higher-multiplicity analogues of several classical results for embeddings, in particular of the completeness of the Van Kampen obstruction for embeddability of k -dimensional
complexes into R2k , k ≥ 3. Speciffically, we show that under suitable restrictions on the dimensions(viz., if dimK = (r ≥ 1)k and d = rk \ for some k ≥ 3), a well-known deleted product criterion (DPC ) is not only necessary but also sufficient for the existence of maps without global r -fold points. Our main technical tool is a higher-multiplicity version of the classical Whitney trick , by which pairs of isolated r -fold points of opposite sign can be eliminated by local modiffications of the map, assuming codimension d – dimK ≥ 3.
An important guiding idea for our work was that suffciency of the DPC, together with an old
result of Özaydin's on the existence of equivariant maps, might yield an approach to disproving the remaining open cases of the the long-standing topological Tverberg conjecture , i.e., to construct maps from the N -simplex σN to Rd without r-Tverberg points when r not a prime power and
N = (d + 1)(r – 1). Unfortunately, our proof of the sufficiency of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K = σN .
In 2015, Frick [16] found a very elegant way to overcome this \codimension 3 obstacle" and
to construct the first counterexamples to the topological Tverberg conjecture for all parameters(d; r ) with d ≥ 3r + 1 and r not a prime power, by a reduction1 to a suitable lower-dimensional skeleton, for which the codimension 3 restriction is satisfied and maps without r -Tverberg points exist by Özaydin's result and sufficiency of the DPC.
In this thesis, we present a different construction (which does not use the constraint method) that yields counterexamples for d ≥ 3r , r not a prime power.
AU - Mabillard, Isaac
ID - 1123
TI - Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture
ER -
TY - THES
AB - Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species
boundaries, is a major evolutionary force shaping microbial genomes that facilitates
adaptation to new environments as well as resistance to antimicrobial drugs. As such,
understanding the mechanisms and constraints that determine the outcomes of HGT
events is crucial to understand the dynamics of HGT and to design better strategies to
overcome the challenges that originate from it.
Following the insertion and expression of a newly transferred gene, the success of an
HGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,
predicting the impact of HGT on the genetic composition of a population critically
depends on the distribution of fitness effects (DFE) of horizontally transferred genes.
However, to date, we have little knowledge of the DFE of newly transferred genes, and
hence little is known about the shape and scale of this distribution.
It is particularly important to better understand the selective barriers that determine
the fitness effects of newly transferred genes. In spite of substantial bioinformatics
efforts to identify horizontally transferred genes and selective barriers, a systematic
experimental approach to elucidate the roles of different selective barriers in defining
the fate of a transfer event has largely been absent. Similarly, although the fact that
environment might alter the fitness effect of a horizontally transferred gene may seem
obvious, little attention has been given to it in a systematic experimental manner.
In this study, we developed a systematic experimental approach that consists of
transferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an
Escherichia coli host, and estimating the fitness effects of these transferred genes at a
constant expression level by performing competition assays against the wild type.
In chapter 2, we performed one-to-one competition assays between a mutant strain
carrying a transferred gene and the wild type strain. By using flow cytometry we
estimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these
fitness effects could be predicted by any of the intrinsic properties of the genes, namely,
functional category, degree of complexity (protein-protein interactions), GC content,
codon usage and length. Our analyses revealed that the functional category and length
of the genes act as potential selective barriers. Finally, using the same procedure with
the endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is
the most prominent selective barrier to HGT.
In chapter 3, using the same set of genes we investigated the role of environment on the
success of HGT events. Under six different environments with different levels of stress
we performed more complex competition assays, where we mixed all 44 mutant strains
carrying transferred genes with the wild type strain. To estimate the fitness effects of
genes relative to wild type we used next generation sequencing. We found that the DFEs
of horizontally transferred genes are highly dependent on the environment, with
abundant gene–by-environment interactions. Furthermore, we demonstrated a
relationship between average fitness effect of a gene across all environments and its
environmental variance, and thus its predictability. Finally, in spite of the fitness effects
of genes being highly environment-dependent, we still observed a common shape of
DFEs across all tested environments.
AU - Acar, Hande
ID - 1121
TI - Selective barriers to horizontal gene transfer
ER -
TY - THES
AB - Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.
In the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).
In the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment.
AU - Tugrul, Murat
ID - 1131
TI - Evolution of transcriptional regulatory sequences
ER -
TY - THES
AB - Natural environments are never constant but subject to spatial and temporal change on
all scales, increasingly so due to human activity. Hence, it is crucial to understand the
impact of environmental variation on evolutionary processes. In this thesis, I present
three topics that share the common theme of environmental variation, yet illustrate its
effect from different perspectives.
First, I show how a temporally fluctuating environment gives rise to second-order
selection on a modifier for stress-induced mutagenesis. Without fluctuations, when
populations are adapted to their environment, mutation rates are minimized. I argue
that a stress-induced mutator mechanism may only be maintained if the population is
repeatedly subjected to diverse environmental challenges, and I outline implications of
the presented results to antibiotic treatment strategies.
Second, I discuss my work on the evolution of dispersal. Besides reproducing
known results about the effect of heterogeneous habitats on dispersal, it identifies
spatial changes in dispersal type frequencies as a source for selection for increased
propensities to disperse. This concept contains effects of relatedness that are known
to promote dispersal, and I explain how it identifies other forces selecting for dispersal
and puts them on a common scale.
Third, I analyse genetic variances of phenotypic traits under multivariate stabilizing
selection. For the case of constant environments, I generalize known formulae of
equilibrium variances to multiple traits and discuss how the genetic variance of a focal
trait is influenced by selection on background traits. I conclude by presenting ideas and
preliminary work aiming at including environmental fluctuations in the form of moving
trait optima into the model.
AU - Novak, Sebastian
ID - 1125
TI - Evolutionary proccesses in variable emvironments
ER -
TY - THES
AU - Morri, Maurizio
ID - 1124
TI - Optical functionalization of human class A orphan G-protein coupled receptors
ER -
TY - JOUR
AB - Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function.
AU - Tarlungeanu, Dora-Clara
AU - Deliu, Elena
AU - Dotter, Christoph
AU - Kara, Majdi
AU - Janiesch, Philipp
AU - Scalise, Mariafrancesca
AU - Galluccio, Michele
AU - Tesulov, Mateja
AU - Morelli, Emanuela
AU - Sönmez, Fatma
AU - Bilgüvar, Kaya
AU - Ohgaki, Ryuichi
AU - Kanai, Yoshikatsu
AU - Johansen, Anide
AU - Esharif, Seham
AU - Ben Omran, Tawfeg
AU - Topcu, Meral
AU - Schlessinger, Avner
AU - Indiveri, Cesare
AU - Duncan, Kent
AU - Caglayan, Ahmet
AU - Günel, Murat
AU - Gleeson, Joseph
AU - Novarino, Gaia
ID - 1183
IS - 6
JF - Cell
TI - Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder
VL - 167
ER -
TY - JOUR
AB - Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion.
AU - Leithner, Alexander F
AU - Eichner, Alexander
AU - Müller, Jan
AU - Reversat, Anne
AU - Brown, Markus
AU - Schwarz, Jan
AU - Merrin, Jack
AU - De Gorter, David
AU - Schur, Florian
AU - Bayerl, Jonathan
AU - De Vries, Ingrid
AU - Wieser, Stefan
AU - Hauschild, Robert
AU - Lai, Frank
AU - Moser, Markus
AU - Kerjaschki, Dontscho
AU - Rottner, Klemens
AU - Small, Victor
AU - Stradal, Theresia
AU - Sixt, Michael K
ID - 1321
JF - Nature Cell Biology
TI - Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes
VL - 18
ER -
TY - JOUR
AB - During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.
AU - Sako, Keisuke
AU - Pradhan, Saurabh
AU - Barone, Vanessa
AU - Inglés Prieto, Álvaro
AU - Mueller, Patrick
AU - Ruprecht, Verena
AU - Capek, Daniel
AU - Galande, Sanjeev
AU - Janovjak, Harald L
AU - Heisenberg, Carl-Philipp J
ID - 1100
IS - 3
JF - Cell Reports
TI - Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation
VL - 16
ER -
TY - CONF
AB - We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir
AU - Ibsen-Jensen, Rasmus
AU - Pavlogiannis, Andreas
ID - 1437
TI - Algorithms for algebraic path properties in concurrent systems of constant treewidth components
VL - 20-22
ER -
TY - CONF
AB - We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs.
AU - Chatterjee, Krishnendu
AU - Fu, Hongfei
AU - Goharshady, Amir
ID - 1386
TI - Termination analysis of probabilistic programs through Positivstellensatz's
VL - 9779
ER -
TY - JOUR
AB - A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. Finite-valued constraint languages contain functions that take on rational costs and general-valued constraint languages contain functions that take on rational or infinite costs. An instance of the problem is specified by a sum of functions from the language with the goal to minimise the sum. This framework includes and generalises well-studied constraint satisfaction problems (CSPs) and maximum constraint satisfaction problems (Max-CSPs).
Our main result is a precise algebraic characterisation of valued constraint languages whose instances can be solved exactly by the basic linear programming relaxation (BLP). For a general-valued constraint language Γ, BLP is a decision procedure for Γ if and only if Γ admits a symmetric fractional polymorphism of every arity. For a finite-valued constraint language Γ, BLP is a decision procedure if and only if Γ admits a symmetric fractional polymorphism of some arity, or equivalently, if Γ admits a symmetric fractional polymorphism of arity 2.
Using these results, we obtain tractability of several novel and previously widely-open classes of VCSPs, including problems over valued constraint languages that are: (1) submodular on arbitrary lattices; (2) bisubmodular (also known as k-submodular) on arbitrary finite domains; (3) weakly (and hence strongly) tree-submodular on arbitrary trees.
AU - Kolmogorov, Vladimir
AU - Thapper, Johan
AU - Živný, Stanislav
ID - 2271
IS - 1
JF - SIAM Journal on Computing
TI - The power of linear programming for general-valued CSPs
VL - 44
ER -
TY - JOUR
AB - Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.
AU - Engel, Jakob
AU - Schmalhorst, Philipp S
AU - Kruger, Anke
AU - Muller, Christina
AU - Buettner, Falk
AU - Routier, Françoise
ID - 802
IS - 12
JF - Glycobiology
TI - Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis
VL - 25
ER -
TY - JOUR
AU - Kiermaier, Eva
AU - Sixt, Michael K
ID - 1686
IS - 6252
JF - Science
TI - Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection
VL - 349
ER -
TY - JOUR
AB - Guided cell movement is essential for development and integrity of animals and crucially involved in cellular immune responses. Leukocytes are professional migratory cells that can navigate through most types of tissues and sense a wide range of directional cues. The responses of these cells to attractants have been mainly explored in tissue culture settings. How leukocytes make directional decisions in situ, within the challenging environment of a tissue maze, is less understood. Here we review recent advances in how leukocytes sense chemical cues in complex tissue settings and make links with paradigms of directed migration in development and Dictyostelium discoideum amoebae.
AU - Sarris, Milka
AU - Sixt, Michael K
ID - 1687
IS - 10
JF - Current Opinion in Cell Biology
TI - Navigating in tissue mazes: Chemoattractant interpretation in complex environments
VL - 36
ER -
TY - JOUR
AB - We estimate the selection constant in the following geometric selection theorem by Pach: For every positive integer d, there is a constant (Formula presented.) such that whenever (Formula presented.) are n-element subsets of (Formula presented.), we can find a point (Formula presented.) and subsets (Formula presented.) for every i∈[d+1], each of size at least cdn, such that p belongs to all rainbowd-simplices determined by (Formula presented.) simplices with one vertex in each Yi. We show a super-exponentially decreasing upper bound (Formula presented.). The ideas used in the proof of the upper bound also help us to prove Pach’s theorem with (Formula presented.), which is a lower bound doubly exponentially decreasing in d (up to some polynomial in the exponent). For comparison, Pach’s original approach yields a triply exponentially decreasing lower bound. On the other hand, Fox, Pach, and Suk recently obtained a hypergraph density result implying a proof of Pach’s theorem with (Formula presented.). In our construction for the upper bound, we use the fact that the minimum solid angle of every d-simplex is super-exponentially small. This fact was previously unknown and might be of independent interest. For the lower bound, we improve the ‘separation’ part of the argument by showing that in one of the key steps only d+1 separations are necessary, compared to 2d separations in the original proof. We also provide a measure version of Pach’s theorem.
AU - Karasev, Roman
AU - Kynčl, Jan
AU - Paták, Pavel
AU - Patakova, Zuzana
AU - Tancer, Martin
ID - 1688
IS - 3
JF - Discrete & Computational Geometry
TI - Bounds for Pach's selection theorem and for the minimum solid angle in a simplex
VL - 54
ER -
TY - CONF
AB - We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. We demonstrate our approach on an illustrative case study.
AU - Svoreňová, Mária
AU - Kretinsky, Jan
AU - Chmelik, Martin
AU - Chatterjee, Krishnendu
AU - Cěrná, Ivana
AU - Belta, Cǎlin
ID - 1689
T2 - Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control
TI - Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games
ER -
TY - CONF
AB - A number of powerful and scalable hybrid systems model checkers have recently emerged. Although all of them honor roughly the same hybrid systems semantics, they have drastically different model description languages. This situation (a) makes it difficult to quickly evaluate a specific hybrid automaton model using the different tools, (b) obstructs comparisons of reachability approaches, and (c) impedes the widespread application of research results that perform model modification and could benefit many of the tools. In this paper, we present Hyst, a Hybrid Source Transformer. Hyst is a source-to-source translation tool, currently taking input in the SpaceEx model format, and translating to the formats of HyCreate, Flow∗, or dReach. Internally, the tool supports generic model-to-model transformation passes that serve to both ease the translation and potentially improve reachability results for the supported tools. Although these model transformation passes could be implemented within each tool, the Hyst approach provides a single place for model modification, generating modified input sources for the unmodified target tools. Our evaluation demonstrates Hyst is capable of automatically translating benchmarks in several classes (including affine and nonlinear hybrid automata) to the input formats of several tools. Additionally, we illustrate a general model transformation pass based on pseudo-invariants implemented in Hyst that illustrates the reachability improvement.
AU - Bak, Stanley
AU - Bogomolov, Sergiy
AU - Johnson, Taylor
ID - 1690
TI - HYST: A source transformation and translation tool for hybrid automaton models
ER -
TY - CONF
AB - We consider a case study of the problem of deploying an autonomous air vehicle in a partially observable, dynamic, indoor environment from a specification given as a linear temporal logic (LTL) formula over regions of interest. We model the motion and sensing capabilities of the vehicle as a partially observable Markov decision process (POMDP). We adapt recent results for solving POMDPs with parity objectives to generate a control policy. We also extend the existing framework with a policy minimization technique to obtain a better implementable policy, while preserving its correctness. The proposed techniques are illustrated in an experimental setup involving an autonomous quadrotor performing surveillance in a dynamic environment.
AU - Svoreňová, Mária
AU - Chmelik, Martin
AU - Leahy, Kevin
AU - Eniser, Hasan
AU - Chatterjee, Krishnendu
AU - Cěrná, Ivana
AU - Belta, Cǎlin
ID - 1691
T2 - Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control
TI - Temporal logic motion planning using POMDPs with parity objectives: Case study paper
ER -
TY - CONF
AB - Computing an approximation of the reachable states of a hybrid system is a challenge, mainly because overapproximating the solutions of ODEs with a finite number of sets does not scale well. Using template polyhedra can greatly reduce the computational complexity, since it replaces complex operations on sets with a small number of optimization problems. However, the use of templates may make the over-approximation too conservative. Spurious transitions, which are falsely considered reachable, are particularly detrimental to performance and accuracy, and may exacerbate the state explosion problem. In this paper, we examine how spurious transitions can be avoided with minimal computational effort. To this end, detecting spurious transitions is reduced to the well-known problem of showing that two convex sets are disjoint by finding a hyperplane that separates them. We generalize this to owpipes by considering hyperplanes that evolve with time in correspondence to the dynamics of the system. The approach is implemented in the model checker SpaceEx and demonstrated on examples.
AU - Frehse, Goran
AU - Bogomolov, Sergiy
AU - Greitschus, Marius
AU - Strump, Thomas
AU - Podelski, Andreas
ID - 1692
SN - 978-1-4503-3433-4
T2 - Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control
TI - Eliminating spurious transitions in reachability with support functions
ER -
TY - JOUR
AB - Quantum interference between energetically close states is theoretically investigated, with the state structure being observed via laser spectroscopy. In this work, we focus on hyperfine states of selected hydrogenic muonic isotopes, and on how quantum interference affects the measured Lamb shift. The process of photon excitation and subsequent photon decay is implemented within the framework of nonrelativistic second-order perturbation theory. Due to its experimental interest, calculations are performed for muonic hydrogen, deuterium, and helium-3. We restrict our analysis to the case of photon scattering by incident linear polarized photons and the polarization of the scattered photons not being observed. We conclude that while quantum interference effects can be safely neglected in muonic hydrogen and helium-3, in the case of muonic deuterium there are resonances with close proximity, where quantum interference effects can induce shifts up to a few percent of the linewidth, assuming a pointlike detector. However, by taking into account the geometry of the setup used by the CREMA collaboration, this effect is reduced to less than 0.2% of the linewidth in all possible cases, which makes it irrelevant at the present level of accuracy. © 2015 American Physical Society.
AU - Amaro, Pedro
AU - Franke, Beatrice
AU - Krauth, Julian
AU - Diepold, Marc
AU - Fratini, Filippo
AU - Safari, Laleh
AU - Machado, Jorge
AU - Antognini, Aldo
AU - Kottmann, Franz
AU - Indelicato, Paul
AU - Pohl, Randolf
AU - Santos, José
ID - 1693
IS - 2
JF - Physical Review A
TI - Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3
VL - 92
ER -
TY - JOUR
AB -
We introduce quantitative timed refinement and timed simulation (directed) metrics, incorporating zenoness checks, for timed systems. These metrics assign positive real numbers which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximal timing mismatch that can arise, (2) the “steady-state” maximal timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation distances to within any desired degree of accuracy. In order to compute the values of the quantitative simulation distances, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite-state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives in graph games, and then use these algorithms to compute the values of the timed simulation distances over timed automata.
AU - Chatterjee, Krishnendu
AU - Prabhu, Vinayak
ID - 1694
IS - 9
JF - IEEE Transactions on Automatic Control
TI - Quantitative temporal simulation and refinement distances for timed systems
VL - 60
ER -
TY - JOUR
AB - We give a comprehensive introduction into a diagrammatic method that allows for the evaluation of Gutzwiller wave functions in finite spatial dimensions. We discuss in detail some numerical schemes that turned out to be useful in the real-space evaluation of the diagrams. The method is applied to the problem of d-wave superconductivity in a two-dimensional single-band Hubbard model. Here, we discuss in particular the role of long-range contributions in our diagrammatic expansion. We further reconsider our previous analysis on the kinetic energy gain in the superconducting state.
AU - Kaczmarczyk, Jan
AU - Schickling, Tobias
AU - Bünemann, Jörg
ID - 1695
IS - 9
JF - Physica Status Solidi (B): Basic Solid State Physics
TI - Evaluation techniques for Gutzwiller wave functions in finite dimensions
VL - 252
ER -
TY - JOUR
AB - The recently proposed diagrammatic expansion (DE) technique for the full Gutzwiller wave function (GWF) is applied to the Anderson lattice model. This approach allows for a systematic evaluation of the expectation values with full Gutzwiller wave function in finite-dimensional systems. It introduces results extending in an essential manner those obtained by means of the standard Gutzwiller approximation (GA), which is variationally exact only in infinite dimensions. Within the DE-GWF approach we discuss the principal paramagnetic properties and their relevance to heavy-fermion systems. We demonstrate the formation of an effective, narrow f band originating from atomic f-electron states and subsequently interpret this behavior as a direct itineracy of f electrons; it represents a combined effect of both the hybridization and the correlations induced by the Coulomb repulsive interaction. Such a feature is absent on the level of GA, which is equivalent to the zeroth order of our expansion. Formation of the hybridization- and electron-concentration-dependent narrow f band rationalizes the common assumption of such dispersion of f levels in the phenomenological modeling of the band structure of CeCoIn5. Moreover, it is shown that the emerging f-electron direct itineracy leads in a natural manner to three physically distinct regimes within a single model that are frequently discussed for 4f- or 5f-electron compounds as separate model situations. We identify these regimes as (i) the mixed-valence regime, (ii) Kondo/almost-Kondo insulating regime, and (iii) the Kondo-lattice limit when the f-electron occupancy is very close to the f-state half filling, ⟨nˆf⟩→1. The nonstandard features of the emerging correlated quantum liquid state are stressed.
AU - Wysokiński, Marcin
AU - Kaczmarczyk, Jan
AU - Spałek, Jozef
ID - 1696
IS - 12
JF - Physical Review B
TI - Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states
VL - 92
ER -
TY - JOUR
AB - Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits.
AU - Marre, Olivier
AU - Botella Soler, Vicente
AU - Simmons, Kristina
AU - Mora, Thierry
AU - Tkacik, Gasper
AU - Berry, Michael
ID - 1697
IS - 7
JF - PLoS Computational Biology
TI - High accuracy decoding of dynamical motion from a large retinal population
VL - 11
ER -
TY - JOUR
AB - In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Multi-mean-payoff and multi-energy games replace individual weights by tuples, and the limit average (resp., running sum) of each coordinate must be (resp., remain) nonnegative. We prove finite-memory determinacy of multi-energy games and show inter-reducibility of multi-mean-payoff and multi-energy games for finite-memory strategies. We improve the computational complexity for solving both classes with finite-memory strategies: we prove coNP-completeness improving the previous known EXPSPACE bound. For memoryless strategies, we show that deciding the existence of a winning strategy for the protagonist is NP-complete. We present the first solution of multi-mean-payoff games with infinite-memory strategies: we show that mean-payoff-sup objectives can be decided in NP∩coNP, whereas mean-payoff-inf objectives are coNP-complete.
AU - Velner, Yaron
AU - Chatterjee, Krishnendu
AU - Doyen, Laurent
AU - Henzinger, Thomas A
AU - Rabinovich, Alexander
AU - Raskin, Jean
ID - 1698
IS - 4
JF - Information and Computation
TI - The complexity of multi-mean-payoff and multi-energy games
VL - 241
ER -
TY - JOUR
AB - By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.
AU - Uecker, Hildegard
AU - Setter, Derek
AU - Hermisson, Joachim
ID - 1699
IS - 7
JF - Journal of Mathematical Biology
TI - Adaptive gene introgression after secondary contact
VL - 70
ER -
TY - JOUR
AB - We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64×64 square lattice we demonstrate the existence of a novel phase, possessing an "ultralong-range" order. The fingerprint of this phase - the density correlation function - features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms.
AU - Van Loon, Erik
AU - Katsnelson, Mikhail
AU - Lemeshko, Mikhail
ID - 1700
IS - 8
JF - Physical Review B
TI - Ultralong-range order in the Fermi-Hubbard model with long-range interactions
VL - 92
ER -
TY - JOUR
AB - The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but, with more spikes, the number of possible patterns increases. This tradeoff between probability and numerosity is mathematically equivalent to the relationship between entropy and energy in statistical physics. We construct this relationship for populations of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination of direct and model-based analyses of experiments on the response of this network to naturalistic movies. We see signs of a thermodynamic limit, where the entropy per neuron approaches a smooth function of the energy per neuron as N increases. The form of this function corresponds to the distribution of activity being poised near an unusual kind of critical point. We suggest further tests of criticality, and give a brief discussion of its functional significance.
AU - Tkacik, Gasper
AU - Mora, Thierry
AU - Marre, Olivier
AU - Amodei, Dario
AU - Palmer, Stephanie
AU - Berry Ii, Michael
AU - Bialek, William
ID - 1701
IS - 37
JF - PNAS
TI - Thermodynamics and signatures of criticality in a network of neurons
VL - 112
ER -
TY - JOUR
AB - Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.
AU - Broadhurst, Linda
AU - Fifield, Graham
AU - Vanzella, Bindi
AU - Pickup, Melinda
ID - 1703
IS - 5
JF - Australian Journal of Botany
TI - An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas
VL - 63
ER -
TY - JOUR
AB - Given a convex function (Formula presented.) and two hermitian matrices A and B, Lewin and Sabin study in (Lett Math Phys 104:691–705, 2014) the relative entropy defined by (Formula presented.). Among other things, they prove that the so-defined quantity is monotone if and only if (Formula presented.) is operator monotone. The monotonicity is then used to properly define (Formula presented.) for bounded self-adjoint operators acting on an infinite-dimensional Hilbert space by a limiting procedure. More precisely, for an increasing sequence of finite-dimensional projections (Formula presented.) with (Formula presented.) strongly, the limit (Formula presented.) is shown to exist and to be independent of the sequence of projections (Formula presented.). The question whether this sequence converges to its "obvious" limit, namely (Formula presented.), has been left open. We answer this question in principle affirmatively and show that (Formula presented.). If the operators A and B are regular enough, that is (A − B), (Formula presented.) and (Formula presented.) are trace-class, the identity (Formula presented.) holds.
AU - Deuchert, Andreas
AU - Hainzl, Christian
AU - Seiringer, Robert
ID - 1704
IS - 10
JF - Letters in Mathematical Physics
TI - Note on a family of monotone quantum relative entropies
VL - 105
ER -
TY - CONF
AB - We consider a problem of learning kernels for use in SVM classification in the multi-task and lifelong scenarios and provide generalization bounds on the error of a large margin classifier. Our results show that, under mild conditions on the family of kernels used for learning, solving several related tasks simultaneously is beneficial over single task learning. In particular, as the number of observed tasks grows, assuming that in the considered family of kernels there exists one that yields low approximation error on all tasks, the overhead associated with learning such a kernel vanishes and the complexity converges to that of learning when this good kernel is given to the learner.
AU - Pentina, Anastasia
AU - Ben David, Shai
ID - 1706
TI - Multi-task and lifelong learning of kernels
VL - 9355
ER -
TY - JOUR
AB - The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards.
AU - Reiter, Johannes
AU - Kanodia, Ayush
AU - Gupta, Raghav
AU - Nowak, Martin
AU - Chatterjee, Krishnendu
ID - 1709
IS - 1812
JF - Proceedings of the Royal Society of London Series B Biological Sciences
TI - Biological auctions with multiple rewards
VL - 282
ER -
TY - JOUR
AB - We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞.
AU - Akopyan, Arseniy
AU - Plakhov, Alexander
ID - 1710
IS - 4
JF - Society for Industrial and Applied Mathematics
TI - Minimal resistance of curves under the single impact assumption
VL - 47
ER -
TY - JOUR
AB - The majority of immune cells in Drosophila melanogaster are plasmatocytes; they carry out similar functions to vertebrate macrophages, influencing development as well as protecting against infection and cancer. Plasmatocytes, sometimes referred to with the broader term of hemocytes, migrate widely during embryonic development and cycle in the larvae between sessile and circulating positions. Here we discuss the similarities of plasmatocyte developmental migration and its functions to that of vertebrate macrophages, considering the recent controversy regarding the functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings on the significance of adhesion for plasmatocyte migration in the embryo, as well as proliferation, trans-differentiation, and tumor responses in the larva. We spotlight parallels throughout to vertebrate immune responses.
AU - Ratheesh, Aparna
AU - Belyaeva, Vera
AU - Siekhaus, Daria E
ID - 1712
IS - 10
JF - Current Opinion in Cell Biology
TI - Drosophila immune cell migration and adhesion during embryonic development and larval immune responses
VL - 36
ER -