Showing papers by "Max Planck Society published in 2008"

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Abstract: Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

Abstract: Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.

Transparent, Conductive Graphene Electrodes for Dye-Sensitized Solar Cells

Abstract: Transparent, conductive, and ultrathin graphene films, as an alternative to the ubiquitously employed metal oxides window electrodes for solid-state dye-sensitized solar cells, are demonstrated. These graphene films are fabricated from exfoliated graphite oxide, followed by thermal reduction. The obtained films exhibit a high conductivity of 550 S/cm and a transparency of more than 70% over 1000−3000 nm. Furthermore, they show high chemical and thermal stabilities as well as an ultrasmooth surface with tunable wettability.

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation

Abstract: By removing the fastest degrees of freedom, constraints allow for an increase of the time step in molecular simulations. In the last decade parallel simulations have become commonplace. However, up till now efficient parallel constraint algorithms have not been used with domain decomposition. In this paper the parallel linear constraint solver (P-LINCS) is presented, which allows the constraining of all bonds in macromolecules. Additionally the energy conservation properties of (P-)LINCS are assessed in view of improvements in the accuracy of uncoupled angle constraints and integration in single precision.

Ceramide Triggers Budding of Exosome Vesicles into Multivesicular Endosomes

Abstract: Intraluminal vesicles of multivesicular endosomes are either sorted for cargo degradation into lysosomes or secreted as exosomes into the extracellular milieu. The mechanisms underlying the sorting of membrane into the different populations of intraluminal vesicles are unknown. Here, we find that cargo is segregated into distinct subdomains on the endosomal membrane and that the transfer of exosome-associated domains into the lumen of the endosome did not depend on the function of the ESCRT (endosomal sorting complex required for transport) machinery, but required the sphingolipid ceramide. Purified exosomes were enriched in ceramide, and the release of exosomes was reduced after the inhibition of neutral sphingomyelinases. These results establish a pathway in intraendosomal membrane transport and exosome formation.

Graphitic carbon nitride materials: variation of structure and morphology and their use as metal-free catalysts

Abstract: Graphitic carbon nitride, g-C3N4, can be made by polymerization of cyanamide, dicyandiamide or melamine. Depending on reaction conditions, different materials with different degrees of condensation, properties and reactivities are obtained. The firstly formed polymeric C3N4 structure, melon, with pendant amino groups, is a highly ordered polymer. Further reaction leads to more condensed and less defective C3N4 species, based on tri-s-triazine (C6N7) units as elementary building blocks. High resolution transmission electron microscopy proves the extended two-dimensional character of the condensation motif. Due to the polymerization-type synthesis from a liquid precursor, a variety of material nanostructures such as nanoparticles or mesoporous powders can be accessed. Those nanostructures also allow fine tuning of properties, the ability for intercalation, as well as the possibility to give surface-rich materials for heterogeneous reactions. Due to the special semiconductor properties of carbon nitrides, they show unexpected catalytic activity for a variety of reactions, such as for the activation of benzene, trimerization reactions, and also the activation of carbon dioxide. Model calculations are presented to explain this unusual case of heterogeneous, metal-free catalysis. Carbon nitride can also act as a heterogeneous reactant, and a new family of metal nitride nanostructures can be accessed from the corresponding oxides.

Origins of Human Communication

Abstract: Winner, 2009 Eleanor Maccoby Book Award in Developmental Psychology, presented by the American Psychological Association. and Honorable Mention, Literature, Language & Linguistics category, 2008 PROSE Awards presented by the Professional/Scholarly Publishing Division of the Association of American Publishers. Human communication is grounded in fundamentally cooperative, even shared, intentions. In this original and provocative account of the evolutionary origins of human communication, Michael Tomasello connects the fundamentally cooperative structure of human communication (initially discovered by Paul Grice) to the especially cooperative structure of human (as opposed to other primate) social interaction. Tomasello argues that human cooperative communication rests on a psychological infrastructure of shared intentionality (joint attention, common ground), evolved originally for collaboration and culture more generally. The basic motives of the infrastructure are helping and sharing: humans communicate to request help, inform others of things helpfully, and share attitudes as a way of bonding within the cultural group. These cooperative motives each created different functional pressures for conventionalizing grammatical constructions. Requesting help in the immediate you-and-me and here-and-now, for example, required very little grammar, but informing and sharing required increasingly complex grammatical devices. Drawing on empirical research into gestural and vocal communication by great apes and human infants (much of it conducted by his own research team), Tomasello argues further that humans' cooperative communication emerged first in the natural gestures of pointing and pantomiming. Conventional communication, first gestural and then vocal, evolved only after humans already possessed these natural gestures and their shared intentionality infrastructure along with skills of cultural learning for creating and passing along jointly understood communicative conventions. Challenging the Chomskian view that linguistic knowledge is innate, Tomasello proposes instead that the most fundamental aspects of uniquely human communication are biological adaptations for cooperative social interaction in general and that the purely linguistic dimensions of human communication are cultural conventions and constructions created by and passed along within particular cultural groups. Jean Nicod Lectures A Bradford Book

The LHCb detector at the LHC

Abstract: The LHCb experiment is dedicated to precision measurements of CP violation and rare decays of B hadrons at the Large Hadron Collider (LHC) at CERN (Geneva). The initial configuration and expected performance of the detector and associated systems, as established by test beam measurements and simulation studies, is described.

Lifeact: a versatile marker to visualize F-actin

Abstract: Live imaging of the actin cytoskeleton is crucial for the study of many fundamental biological processes, but current approaches to visualize actin have several limitations. Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin (F-actin) structures in eukaryotic cells and tissues. Lifeact did not interfere with actin dynamics in vitro and in vivo and in its chemically modified peptide form allowed visualization of actin dynamics in nontransfectable cells.

The Star Formation Efficiency in Nearby Galaxies: Measuring Where Gas Forms Stars Effectively

Abstract: We measure the star formation efficiency (SFE), the star formation rate (SFR) per unit of gas, in 23 nearby galaxies and compare it with expectations from proposed star formation laws and thresholds. We use H I maps from The H I Nearby Galaxy Survey (THINGS) and derive H2 maps of CO measured by HERA CO-Line Extragalactic Survey and Berkeley-Illinois-Maryland Association Survey of Nearby Galaxies. We estimate the SFR by combining Galaxy Evolution Explorer (GALEX) far-ultraviolet maps and the Spitzer Infrared Nearby Galaxies Survey (SINGS) 24 ?m maps, infer stellar surface density profiles from SINGS 3.6 ?m data, and use kinematics from THINGS. We measure the SFE as a function of the free fall and orbital timescales, midplane gas pressure, stability of the gas disk to collapse (including the effects of stars), the ability of perturbations to grow despite shear, and the ability of a cold phase to form. In spirals, the SFE of H2 alone is nearly constant at (5.25 ? 2.5) ? 10?10 yr?1 (equivalent to an H2 depletion time of 1.9 ? 109 yr) as a function of all of these variables at our 800 pc resolution. Where the interstellar medium (ISM) is mostly H I, however, the SFE decreases with increasing radius in both spiral and dwarf galaxies, a decline reasonably described by an exponential with scale length 0.2r 25-0.25r 25. We interpret this decline as a strong dependence of giant molecular cloud (GMC) formation on environment. The ratio of molecular-to-atomic gas appears to be a smooth function of radius, stellar surface density, and pressure spanning from the H2-dominated to H I-dominated ISM. The radial decline in SFE is too steep to be reproduced only by increases in the free-fall time or orbital time. Thresholds for large-scale instability suggest that our disks are stable or marginally stable and do not show a clear link to the declining SFE. We suggest that ISM physics below the scales that we observe?phase balance in the H I, H2 formation and destruction, and stellar feedback?governs the formation of GMCs from H I.

The Aquarius Project: the subhaloes of galactic haloes

Abstract: We have performed the largest ever particle simulation of a Milky Way sized dark matter halo, and present the most comprehensive convergence study for an individual dark matter halo carried out thus far We have also simulated a sample of six ultrahighly resolved Milky Way sized haloes, allowing us to estimate the halo-to-halo scatter in substructure statistics In our largest simulation, we resolve nearly 300 000 gravitationally bound subhaloes within the virialized region of the halo Simulations of the same object differing in mass resolution by factors of up to 1800 accurately reproduce the largest subhaloes with the same mass, maximum circular velocity and position, and yield good convergence for the abundance and internal properties of dark matter substructures We detect up to four generations of subhaloes within subhaloes, but contrary to recent claims, we find less substructure in subhaloes than in the main halo when regions of equal mean overdensity are compared The overall substructure mass fraction is much lower in subhaloes than in the main halo Extrapolating the main halo's subhalo mass spectrum down to an Earth mass, we predict the mass fraction in substructure to be well below 3 per cent within 100 kpc, and to be below 01 per cent within the solar circle The inner density profiles of subhaloes show no sign of converging to a fixed asymptotic slope and are well fitted by gently curving profiles of Einasto form The mean concentrations of isolated haloes are accurately described by the fitting formula of Neto et al down to maximum circular velocities of 15 km s(-1), an extrapolation over some five orders of magnitude in mass However, at equal maximum circular velocity, subhaloes are more concentrated than field haloes, with a characteristic density that is typically similar to 26 times larger and increases with decreasing distance from halo centre

The Star Formation Law in Nearby Galaxies on Sub-Kpc Scales

Abstract: We present a comprehensive analysis of the relationship between star formation rate surface density, ΣSFR, and gas surface density, Σgas, at sub-kpc resolution in a sample of 18 nearby galaxies. We use high-resolution H I data from The H I Nearby Galaxy Survey, CO data from HERACLES and the BIMA Survey of Nearby Galaxies, 24 μm data from the Spitzer Space Telescope, and UV data from the Galaxy Evolution Explorer. We target seven spiral galaxies and 11 late-type/dwarf galaxies and investigate how the star formation law differs between the H2 dominated centers of spiral galaxies, their H I dominated outskirts and the H I rich late-type/dwarf galaxies. We find that a Schmidt-type power law with index N = 1.0 ± 0.2 relates ΣSFR and ΣH2 across our sample of spiral galaxies, i.e., that H2 forms stars at a constant efficiency in spirals. The average molecular gas depletion time is ~2 × 109 years. The range of ΣH2 over which we measure this relation is ~3-50 M ☉ pc–2, significantly lower than in starburst environments. We find the same results when performing a pixel-by-pixel analysis, averaging in radial bins, or when varying the star formation tracer used. We interpret the linear relation and constant depletion time as evidence that stars are forming in giant molecular clouds with approximately uniform properties and that ΣH2 may be more a measure of the filling fraction of giant molecular clouds than changing conditions in the molecular gas. The relationship between total gas surface density (Σgas) and ΣSFR varies dramatically among and within spiral galaxies. Most galaxies show little or no correlation between ΣHI and ΣSFR. As a result, the star formation efficiency (SFE), ΣSFR/Σgas, varies strongly across our sample and within individual galaxies. We show that this variation is systematic and consistent with the SFE being set by local environmental factors: in spirals the SFE is a clear function of radius, while the dwarf galaxies in our sample display SFEs similar to those found in the outer optical disks of the spirals. We attribute the similarity to common environments (low density, low metallicity, H I dominated) and argue that shear (which is typically absent in dwarfs) cannot drive the SFE. In addition to a molecular Schmidt law, the other general feature of our sample is a sharp saturation of H I surface densities at ΣHI ≈ 9 M ☉ pc–2 in both the spiral and dwarf galaxies. In the case of the spirals, we observe gas in excess of this limit to be molecular.

Kernel methods in machine learning

Abstract: We review machine learning methods employing positive definite kernels. These methods formulate learning and estimation problems in a reproducing kernel Hilbert space (RKHS) of functions defined on the data domain, expanded in terms of a kernel. Working in linear spaces of function has the benefit of facilitating the construction and analysis of learning algorithms while at the same time allowing large classes of functions. The latter include nonlinear functions as well as functions defined on nonvectorial data. We cover a wide range of methods, ranging from binary classifiers to sophisticated methods for estimation with structured data.

Sun Earth Connection Coronal and Heliospheric Investigation (SECCHI)

Abstract: The Sun Earth Connection Coronal and Heliospheric Investigation (SECCHI) is a five telescope package, which has been developed for the Solar Terrestrial Relation Observatory (STEREO) mission by the Naval Research Laboratory (USA), the Lockheed Solar and Astrophysics Laboratory (USA), the Goddard Space Flight Center (USA), the University of Birmingham (UK), the Rutherford Appleton Laboratory (UK), the Max Planck Institute for Solar System Research (Germany), the Centre Spatiale de Leige (Belgium), the Institut d’Optique (France) and the Institut d’Astrophysique Spatiale (France). SECCHI comprises five telescopes, which together image the solar corona from the solar disk to beyond 1 AU. These telescopes are: an extreme ultraviolet imager (EUVI: 1–1.7 R⊙), two traditional Lyot coronagraphs (COR1: 1.5–4 R⊙ and COR2: 2.5–15 R⊙) and two new designs of heliospheric imagers (HI-1: 15–84 R⊙ and HI-2: 66–318 R⊙). All the instruments use 2048×2048 pixel CCD arrays in a backside-in mode. The EUVI backside surface has been specially processed for EUV sensitivity, while the others have an anti-reflection coating applied. A multi-tasking operating system, running on a PowerPC CPU, receives commands from the spacecraft, controls the instrument operations, acquires the images and compresses them for downlink through the main science channel (at compression factors typically up to 20×) and also through a low bandwidth channel to be used for space weather forecasting (at compression factors up to 200×). An image compression factor of about 10× enable the collection of images at the rate of about one every 2–3 minutes. Identical instruments, except for different sizes of occulters, are included on the STEREO-A and STEREO-B spacecraft.

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

Abstract: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

Cavity Optomechanics: Back-Action at the Mesoscale

Abstract: The coupling of optical and mechanical degrees of freedom is the underlying principle of many techniques to measure mechanical displacement, from macroscale gravitational wave detectors to microscale cantilevers used in scanning probe microscopy. Recent experiments have reached a regime where the back-action of photons caused by radiation pressure can influence the optomechanical dynamics, giving rise to a host of long-anticipated phenomena. Here we review these developments and discuss the opportunities for innovative technology as well as for fundamental science.

Flood or drought: How do aerosols affect precipitation?

Abstract: Aerosols serve as cloud condensation nuclei (CCN) and thus have a substantial effect on cloud properties and the initiation of precipitation. Large concentrations of human-made aerosols have been reported to both decrease and increase rainfall as a result of their radiative and CCN activities. At one extreme, pristine tropical clouds with low CCN concentrations rain out too quickly to mature into long-lived clouds. On the other hand, heavily polluted clouds evaporate much of their water before precipitation can occur, if they can form at all given the reduced surface heating resulting from the aerosol haze layer. We propose a conceptual model that explains this apparent dichotomy.

Methanogenic archaea: ecologically relevant differences in energy conservation.

Abstract: Most methanogenic archaea can reduce CO(2) with H(2) to methane, and it is generally assumed that the reactions and mechanisms of energy conservation that are involved are largely the same in all methanogens. However, this does not take into account the fact that methanogens with cytochromes have considerably higher growth yields and threshold concentrations for H(2) than methanogens without cytochromes. These and other differences can be explained by the proposal outlined in this Review that in methanogens with cytochromes, the first and last steps in methanogenesis from CO(2) are coupled chemiosmotically, whereas in methanogens without cytochromes, these steps are energetically coupled by a cytoplasmic enzyme complex that mediates flavin-based electron bifurcation.

The Sixth Data Release of the Sloan Digital Sky Survey

Abstract: This paper describes the Sixth Data Release of the Sloan Digital Sky Survey. With this data release, the imaging of the northern Galactic cap is now complete. The survey contains images and parameters of roughly 287 million objects over 9583 deg(2), including scans over a large range of Galactic latitudes and longitudes. The survey also includes 1.27 million spectra of stars, galaxies, quasars, and blank sky ( for sky subtraction) selected over 7425 deg2. This release includes much more stellar spectroscopy than was available in previous data releases and also includes detailed estimates of stellar temperatures, gravities, and metallicities. The results of improved photometric calibration are now available, with uncertainties of roughly 1% in g, r, i, and z, and 2% in u, substantially better than the uncertainties in previous data releases. The spectra in this data release have improved wavelength and flux calibration, especially in the extreme blue and extreme red, leading to the qualitatively better determination of stellar types and radial velocities. The spectrophotometric fluxes are now tied to point-spread function magnitudes of stars rather than fiber magnitudes. This gives more robust results in the presence of seeing variations, but also implies a change in the spectrophotometric scale, which is now brighter by roughly 0.35 mag. Systematic errors in the velocity dispersions of galaxies have been fixed, and the results of two independent codes for determining spectral classifications and red-shifts are made available. Additional spectral outputs are made available, including calibrated spectra from individual 15 minute exposures and the sky spectrum subtracted from each exposure. We also quantify a recently recognized underestimation of the brightnesses of galaxies of large angular extent due to poor sky subtraction; the bias can exceed 0.2 mag for galaxies brighter than r = 14 mag.

Degradable biomaterials based on magnesium corrosion

Abstract: Biodegradable metals are breaking the current paradigm in biomaterial science to develop only corrosion resistant metals. In particular, metals which consist of trace elements existing in the human body are promising candidates for temporary implant materials. These implants would be temporarily needed to provide mechanical support during the healing process of the injured or pathological tissue. Magnesium and its alloys have been investigated recently by many authors as a suitable biodegradable biomaterial. In this investigative review we would like to summarize the latest achievements and comment on the selection and use, test methods and the approaches to develop and produce magnesium alloys that are intended to perform clinically with an appropriate host response.

Multiple Sclerosis: An Immune or Neurodegenerative Disorder?

Abstract: Multiple sclerosis (MS) is an inflammatory-mediated demyelinating disease of the human central nervous system. The clinical disease course is variable, usually starts with reversible episodes of neurological disability in the third or fourth decade of life, and transforms into a disease of continuous and irreversible neurological decline by the sixth or seventh decade. We review data that support neurodegeneration as the major cause of irreversible neurological disability in MS patients. We question whether inflammatory demyelination is primary or secondary in the disease process and discuss the challenges of elucidating the cause of MS and developing therapies that will delay or prevent the irreversible and progressive neurological decline that most MS patients endure.

Old-growth forests as global carbon sinks.

Abstract: Old-growth forests remove carbon dioxide from the atmosphere at rates that vary with climate and nitrogen deposition. The sequestered carbon dioxide is stored in live woody tissues and slowly decomposing organic matter in litter and soil. Old-growth forests therefore serve as a global carbon dioxide sink, but they are not protected by international treaties, because it is generally thought that ageing forests cease to accumulate carbon. Here we report a search of literature and databases for forest carbon-flux estimates. We find that in forests between 15 and 800 years of age, net ecosystem productivity (the net carbon balance of the forest including soils) is usually positive. Our results demonstrate that old-growth forests can continue to accumulate carbon, contrary to the long-standing view that they are carbon neutral. Over 30 per cent of the global forest area is unmanaged primary forest, and this area contains the remaining old-growth forests. Half of the primary forests (6 times 10 8 hectares) are located in the boreal and temperate regions of the Northern Hemisphere. On the basis of our analysis, these forests alone sequester about 1.3 plusminus 0.5 gigatonnes of carbon per year. Thus, our findings suggest that 15 per cent of the global forest area, which is currently not considered when offsetting increasing atmospheric carbon dioxide concentrations, provides at least 10 per cent of the global net ecosystem productivity. Old-growth forests accumulate carbon for centuries and contain large quantities of it. We expect, however, that much of this carbon, even soil carbon, will move back to the atmosphere if these forests are disturbed

Matrix product states, projected entangled pair states, and variational renormalization group methods for quantum spin systems

Abstract: This article reviews recent developments in the theoretical understanding and the numerical implementation of variational renormalization group methods using matrix product states and projected entangled pair states.

Vulnerability of Permafrost Carbon to Climate Change: Implications for the Global Carbon Cycle

Abstract: Thawing permafrost and the resulting microbial decomposition of previously frozen organic carbon (C) is one of the most significant potential feedbacks from terrestrial ecosystems to the atmosphere in a changing climate. In this article we present an overview of the global permafrost C pool and of the processes that might transfer this C into the atmosphere, as well as the associated ecosystem changes that occur with thawing. We show that accounting for C stored deep in the permafrost more than doubles previous high-latitude inventory estimates, with this new estimate equivalent to twice the atmospheric C pool. The thawing of permafrost with warming occurs both gradually and catastrophically, exposing organic C to microbial decomposition. Other aspects of ecosystem dynamics can be altered by climate change along with thawing permafrost, such as growing season length, plant growth rates and species composition, and ecosystem energy exchange. However, these processes do not appear to be able to com...

Computing topological parameters of biological networks

Abstract: Summary: Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. In order to gain insight into the organization and structure of the resultant large complex networks formed by the interacting molecules, we have developed the versatile Cytoscape plugin NetworkAnalyzer. It computes and displays a comprehensive set of topological parameters, which includes the number of nodes, edges, and connected components, the network diameter, radius, density, centralization, heterogeneity, and clustering coefficient, the characteristic path length, and the distributions of node degrees, neighborhood connectivities, average clustering coefficients, and shortest path lengths. NetworkAnalyzer can be applied to both directed and undirected networks and also contains extra functionality to construct the intersection or union of two networks. It is an interactive and highly customizable application that requires no expert knowledge in graph theory from the user. Availability: NetworkAnalyzer can be downloaded via the Cytoscape web site: http://www.cytoscape.org Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

Observation of electron–hole puddles in graphene using a scanning single-electron transistor

Abstract: The electronic structure of graphene causes its charge carriers to behave like relativistic particles. For a perfect graphene sheet free from impurities and disorder, the Fermi energy lies at the so-called ‘Dirac point’, where the density of electronic states vanishes. But in the inevitable presence of disorder, theory predicts that equally probable regions of electron-rich and hole-rich puddles will arise. These puddles could explain graphene’s anomalous non-zero minimal conductivity at zero average carrier density. Here, we use a scanning single-electron transistor to map the local density of states and the carrier density landscape in the vicinity of the neutrality point. Our results confirm the existence of electron–hole puddles, and rule out extrinsic substrate effects as explanations for their emergence and topology. Moreover, we find that, unlike non-relativistic particles the density of states can be quantitatively accounted for by considering non-interacting electrons and holes.