Browsing by Author "Aurell, Erik"

Now showing 1 - 20 of 26

Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry
(2016-06-30) Marino, Raffaele; Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
We consider coupled diffusions in n-dimensional space and on a compact manifold and the resulting effective advective-diffusive motion on large scales in space. The effective drift (advection) and effective diffusion are determined as a solvability conditions in a multiscale analysis. As an example, we consider coupled diffusions in three-dimensional space and on the group manifold SO(3) of proper rotations, generalizing results obtained by H. Brenner [J. Colloid Interface Sci. 80, 548 (1981). We show in detail how the analysis can be conveniently carried out using local charts and invariance arguments. As a further example, we consider coupled diffusions in two-dimensional complex space and on the group manifold SU(2). We show that although the local operators may be the same as for SO(3), due to the global nature of the solvability conditions the resulting diffusion will differ and generally be more isotropic.
Catch the dream Wave, Propagation of Cortical Slow Oscillation to the Striatum in anaesthetised mice
(2014-11-03) Ferreira, Tiago
Perustieteiden korkeakoulu | Master's thesis
Under anaesthesia or in deep sleep, different parts of the brain have a distinctive slow oscillatory activity, characterised by states of high membrane potential and intensive spiking activity, the Up-states; followed by hyper-polarisation and quiescence, the Down-states. This activity has been previously described in vitro and in vivo in the cortex and the striatum, across several species. Here, we look into it, during anaesthesia, in the mouse brain. Using whole-cell patch-clamp recordings of cortical cells, it was possible to compare different signal processing methods used to extract the Up-and-Down states in extracellular recordings of the cortex. Our results show that the method based on the Multi-Unit Activity (> 200Hz) have better accuracy than High-Gamma Range (20 - 100Hz) or wavelet decomposition (< 2Hz band). After establishing the most robust method, this was used to compare the intracellular recordings of striatal cells to different parts of the cortex. The results obtained here support a functional connection between the dorsolateral striatal neurons and the ipsilateral barrel field. They also support a functional connection between dorsomedial striatal cells and the primary visual cortex. The analysis of delay between recordings allowed to establish temporal relationships between the contralateral barrel field, the ipsilateral barrel field, and the dorsolateral striatum; and between the ipsilateral barrel field, the ipsilateral primary visual field and the dorsomedial striatum.
Causal analysis, Correlation-Response, and Dynamic cavity
(2016-04-06) Aurell, Erik; Ferraro, Gino Del
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
The purpose of this note is to point out analogies between causal analysis in statistics and the correlation-response theory in statistical physics. It is further shown that for some systems the dynamic cavity offers a way to compute the stationary state of a non-equilibrium process effectively, which could then be taken an alternative starting point of causal analysis.
Characteristic functions of quantum heat with baths at different temperatures
(2018-06-07) Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
This paper is about quantum heat defined as the change in energy of a bath during a process. The presentation takes into account recent developments in classical strong-coupling thermodynamics and addresses a version of quantum heat that satisfies quantum-classical correspondence. The characteristic function and the full counting statistics of quantum heat are shown to be formally similar. The paper further shows that the method can be extended to more than one bath, e.g., two baths at different temperatures, which opens up the prospect of studying correlations and heat flow. The paper extends earlier results on the expected quantum heat in the setting of one bath [E. Aurell and R. Eichhorn, New J. Phys. 17, 065007 (2015)NJOPFM1367-263010.1088/1367-2630/17/6/065007; E. Aurell, Entropy 19, 595 (2017)ENTRFG1099-430010.3390/e19110595].
Correlation-compressed direct-coupling analysis
(2018-09-11) Gao, Chen Yi; Zhou, Hai Jun; Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Learning Ising or Potts models from data has become an important topic in statistical physics and computational biology, with applications to predictions of structural contacts in proteins and other areas of biological data analysis. The corresponding inference problems are challenging since the normalization constant (partition function) of the Ising or Potts distribution cannot be computed efficiently on large instances. Different ways to address this issue have resulted in a substantial amount of methodological literature. In this paper we investigate how these methods could be used on much larger data sets than studied previously. We focus on a central aspect, that in practice these inference problems are almost always severely undersampled, and the operational result is almost always a small set of leading predictions. We therefore explore an approach where the data are prefiltered based on empirical correlations, which can be computed directly even for very large problems. Inference is only used on the much smaller instance in a subsequent step of the analysis. We show that in several relevant model classes such a combined approach gives results of almost the same quality as inference on the whole data set. It can therefore provide a potentially very large computational speedup at the price of only marginal decrease in prediction quality. We also show that the results on whole-genome epistatic couplings that were obtained in a recent computation-intensive study can be retrieved by our approach. The method of this paper hence opens up the possibility to learn parameters describing pairwise dependences among whole genomes in a computationally feasible and expedient manner.
DCA for genome-wide epistasis analysis: The statistical genetics perspective
(2019-01-29) Gao, Chen Yi; Cecconi, Fabio; Vulpiani, Angelo; Zhou, Hai Jun; Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Direct coupling analysis (DCA) is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to sequences of homologous proteins, and also more recently to whole-genome population-wide sequencing data. We here argue that the use of DCA on the genome scale is contingent on fundamental issues of population genetics. DCA can be expected to yield meaningful results when a population is in the quasi-linkage equilibrium (QLE) phase studied by Kimura and others, but not, for instance, in a phase of clonal competition. We discuss how the exponential (Potts model) distributions emerge in QLE, and compare couplings to correlations obtained in a study of about 3000 genomes of the human pathogen Streptococcus pneumoniae.
Dynamic message-passing approach for kinetic spin models with reversible dynamics
(2015) Del Ferraro, Gino; Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
A method to approximately close the dynamic cavity equations for synchronous reversible dynamics on a locally treelike topology is presented. The method builds on (a) a graph expansion to eliminate loops from the normalizations of each step in the dynamics and (b) an assumption that a set of auxilary probability distributions on histories of pairs of spins mainly have dependencies that are local in time. The closure is then effectuated by projecting these probability distributions on n-step Markov processes. The method is shown in detail on the level of ordinary Markov processes (n=1) and outlined for higher-order approximations (n>1). Numerical validations of the technique are provided for the reconstruction of the transient and equilibrium dynamics of the kinetic Ising model on a random graph with arbitrary connectivity symmetry.
Entropy production of a Brownian ellipsoid in the overdamped limit
(2016-01-19) Marino, Raffaele; Eichhorn, Ralf; Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
We analyze the translational and rotational motion of an ellipsoidal Brownian particle from the viewpoint of stochastic thermodynamics. The particle's Brownian motion is driven by external forces and torques and takes place in an heterogeneous thermal environment where friction coefficients and (local) temperature depend on space and time. Our analysis of the particle's stochastic thermodynamics is based on the entropy production associated with single particle trajectories. It is motivated by the recent discovery that the overdamped limit of vanishing inertia effects (as compared to viscous fricion) produces a so-called "anomalous" contribution to the entropy production, which has no counterpart in the overdamped approximation, when inertia effects are simply discarded. Here we show that rotational Brownian motion in the overdamped limit generates an additional contribution to the "anomalous" entropy. We calculate its specific form by performing a systematic singular perturbation analysis for the generating function of the entropy production. As a side result, we also obtain the (well-known) equations of motion in the overdamped limit. We furthermore investigate the effects of particle shape and give explicit expressions of the "anomalous entropy" for prolate and oblate spheroids and for near-spherical Brownian particles.
Experimental Study of Magnetic Field Effects on Hairpin SNSPD Turn Designs for Single Photon Detection
(2023-08-21) Sutton, James
Sähkötekniikan korkeakoulu | Master's thesis
Superconducting Nanowire Single Photon Detectors (SNSPDs) are a promising technology for detecting single photon emissions with high efficiency and low noise. This detector class has numerous applications in quantum optics, communication, and sensing. One typical design for these devices is the hairpin structure, in which a superconducting nanowire is patterned into a meandering shape. The combination of academic research and interest from the industry is boosting the development of hairpin SNSPD devices to achieve high detection efficiency while maintaining fast response time and low jitter, requiring optimization of the device geometry, materials properties, and sophisticated readout electronics. This thesis qualitatively enquires about different device geometries, varying turn designs and features. Moreover, proposing a promising experimental setup with the potential of being scaled up to simultaneously test numerous devices with a varying magnetic field, driving the hairpin SNSPDs to their detection limit, and enabling further quantitative studies to deepen the understanding of the underlying mechanisms currently hindering the SNSPDs. Analyzing the acquired data draws results regarding the critical current and dark counts trends. Furthermore, at low magnetic field strength, the enquired devices are found to have their critical current enhanced. Moreover, comparisons are drawn among similar design structures. Furthermore, a discussion on manufacturing defects detrimental to the SNSPD performance is initiated. Finally, further studies on this topic adopting the presented method are encouraged to acquire additional quantitative results to be compared with theoretical models describing the thin superconducting structures.
Global Estimates of Errors in Quantum Computation by the Feynman–Vernon Formalism
(2018) Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
The operation of a quantum computer is considered as a general quantum operation on a mixed state on many qubits followed by a measurement. The general quantum operation is further represented as a Feynman–Vernon double path integral over the histories of the qubits and of an environment, and afterward tracing out the environment. The qubit histories are taken to be paths on the two-sphere (Formula presented.) as in Klauder’s coherent-state path integral of spin, and the environment is assumed to consist of harmonic oscillators initially in thermal equilibrium, and linearly coupled to to qubit operators (Formula presented.). The environment can then be integrated out to give a Feynman–Vernon influence action coupling the forward and backward histories of the qubits. This representation allows to derive in a simple way estimates that the total error of operation of a quantum computer without error correction scales linearly with the number of qubits and the time of operation. It also allows to discuss Kitaev’s toric code interacting with an environment in the same manner.
Improving Contact Prediction along Three Dimensions
(2014) Feinauer, Christoph; Skwark, Marcin J.; Pagnani, Andrea; Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members. The typical pipeline to address this task, which we in this paper refer to as the three dimensions of contact prediction, is to (i) filter and align the raw sequence data representing the evolutionarily related proteins; (ii) choose a predictive model to describe a sequence alignment; (iii) infer the model parameters and interpret them in terms of structural properties, such as an accurate contact map. We show here that all three dimensions are important for overall prediction success. In particular, we show that it is possible to improve significantly along the second dimension by going beyond the pair-wise Potts models from statistical physics, which have hitherto been the focus of the field. These (simple) extensions are motivated by multiple sequence alignments often containing long stretches of gaps which, as a data feature, would be rather untypical for independent samples drawn from a Potts model. Using a large test set of proteins we show that the combined improvements along the three dimensions are as large as any reported to date.
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis
(2017-02-01) Skwark, Marcin J.; Croucher, Nicholas J.; Puranen, Santeri; Chewapreecha, Claire; Pesonen, Maiju; Xu, Yingying; Turner, Paul; Harris, Simon R.; Beres, Stephen B.; Musser, James M.; Parkhill, Julian; Bentley, Stephen D.; Aurell, Erik; Corander, Jukka
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus). For pneumococcus we identified 5,199 putative epistatic interactions between 1,936 sites. Over three-quarters of the links were between sites within the pbp2x, pbp1a and pbp2b genes, the sequences of which are critical in determining non-susceptibility to beta-lactam antibiotics. A network-based analysis found these genes were also coupled to that encoding dihydrofolate reductase, changes to which underlie trimethoprim resistance. Distinct from these antibiotic resistance genes, a large network component of 384 protein coding sequences encompassed many genes critical in basic cellular functions, while another distinct component included genes associated with virulence. The group A Streptococcus (GAS) data set population represents a clonal population with relatively little genetic variation and a high level of linkage disequilibrium across the genome. Despite this, we were able to pinpoint two RNA pseudouridine synthases, which were each strongly linked to a separate set of loci across the chromosome, representing biologically plausible targets of co-selection. The population genomic analysis method applied here identifies statistically significantly co-evolving locus pairs, potentially arising from fitness selection interdependence reflecting underlying protein-protein interactions, or genes whose product activities contribute to the same phenotype. This discovery approach greatly enhances the future potential of epistasis analysis for systems biology, and can complement genome-wide association studies as a means of formulating hypotheses for targeted experimental work.
Landscape of RNA polyadenylation in E. coli
(2017-03-17) Maes, Alexandre; Gracia, Céline; Innocenti, Nicolas; Zhang, Kaiyang; Aurell, Erik; Hajnsdorf, Eliane
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Polyadenylation is thought to be involved in the degradation and quality control of bacterial RNAs but relatively few examples have been investigated. We used a combination of 5'-tagRACE and RNA-seq to analyze the total RNA content from a wild-type strain and froma poly(A)polymerase deletedmutant. A total of 178 transcripts were either up- or down-regulated in the mutant when compared to the wild-type strain. Poly(A)polymerase up-regulates the expression of all genes related to the FliA regulon and several previously unknown transcripts, including numerous transporters. Notable down-regulation of genes in the expression of antigen 43 and components of the type 1 fimbriae was detected. The major consequence of the absence of poly(A)polymerase was the accumulation of numerous sRNAs, antisense transcripts, REP sequences and RNA fragments resulting from the processing of entire transcripts. A new algorithm to analyze the position and composition of post-transcriptional modifications based on the sequence of unencoded 3'-ends, was developed to identify polyadenylated molecules. Overall our results shed new light on the broad spectrum of action of polyadenylation on gene expression and demonstrate the importance of poly(A) dependent degradation to remove structured RNA fragments.
Local search methods based on variable focusing for random K-satisfiability
(2015) Lemoy, Rémi; Alava, Mikko J.; Aurell, Erik
School of Science | A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
We introduce variable focused local search algorithms for satisfiabiliity problems. Usual approaches focus uniformly on unsatisfied clauses. The methods described here work by focusing on random variables in unsatisfied clauses. Variants are considered where variables are selected uniformly and randomly or by introducing a bias towards picking variables participating in several unsatistified clauses. These are studied in the case of the random 3-SAT problem, together with an alternative energy definition, the number of variables in unsatisfied constraints. The variable-based focused Metropolis search (V-FMS) is found to be quite close in performance to the standard clause-based FMS at optimal noise. At infinite noise, instead, the threshold for the linearity of solution times with instance size is improved by picking preferably variables in several UNSAT clauses. Consequences for algorithmic design are discussed.
Making microarray and RNA-seq gene expression data comparable
(2012) Uziela, Karolis
Master's thesis
Measuring gene expression levels in the cell is an important tool in biomedical sciences. It can be used in new drug development, disease diagnostics and many other areas. Currently, two most popular platforms for measuring gene expression are microarrays and RNA-sequencing (RNA-seq). Making the gene expression results more comparable between these two platforms is an important topic which has not yet been investigated enough. In this thesis, we present a novel method, called PREBS, that addresses this issue. Our method adjusts RNA-seq data computational processing in a way that makes the resulting gene expression measures more similar to microarray based gene expression measures. We compare our method against two other RNA-seq processing methods, RPKM and MMSEQ, and evaluate each method's agreement with microarrays by calculating correlations between the platforms. We show that our method reaches the highest level of agreement among all of the methods in absolute expression scale and has a similar level of agreement as the other methods in differential expression scale. Additionally, this thesis provides some background on gene expression, its measurement and computational analysis of gene expression data. Moreover, it gives a brief literature review on the past microarray{RNA-seq comparisons.
The Maximum Entropy Fallacy Redux?
(2016-05-01) Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Maximum Likelihood Reconstruction for Ising Models with Asynchronous Updates
(2013) Zeng, Hong-Li; Alava, Mikko J.; Aurell, Erik; Hertz, John; Roudi, Yasser
School of Science | A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
We describe how the couplings in an asynchronous kinetic Ising model can be inferred. We consider two cases: one in which we know both the spin history and the update times and one in which we know only the spin history. For the first case, we show that one can average over all possible choices of update times to obtain a learning rule that depends only on spin correlations and can also be derived from the equations of motion for the correlations. For the second case, the same rule can be derived within a further decoupling approximation. We study all methods numerically for fully asymmetric Sherrington-Kirkpatrick models, varying the data length, system size, temperature, and external field. Good convergence is observed in accordance with the theoretical expectations.
Network inference using asynchronously updated kinetic Ising Model
(2011) Zeng, Hong-Li; Aurell, Erik; Alava, Mikko; Mahmoudi, Hamed
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Network structures are reconstructed from dynamical data by respectively naive mean field (nMF) and Thouless-Anderson-Palmer (TAP) approximations. TAP approximation adds simple corrections to the nMF approximation, taking into account the effect of the focused spin on itself via its influence on other neighboring spins. For TAP approximation, we use two methods to reconstruct the network: (a) iterative method; (b) casting the inference formula to a set of cubic equations and solving it directly. We investigate inference of the asymmetric Sherrington-Kirkpatrick (aS-K) model using asynchronous update. The solutions of the set of cubic equations depend on temperature T in the aS-K model, and a critical temperature Tc≈2.1 is found. The two methods for TAP approximation produce the same results when the iterative method is convergent. Compared to nMF, TAP is somewhat better at low temperatures, but approaches the same performance as temperature increases. Both nMF and TAP approximation reconstruct better for longer data length L, but for the degree of improvement, TAP performs better than nMF.
On the von Neumann entropy of a bath linearly coupled to a driven quantum system
(2015) Aurell, Erik; Eichhorn, Ralf
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
On work and heat in time-dependent strong coupling
(2017-11-01) Aurell, Erik
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
This paper revisits the classical problem of representing a thermal bath interacting with a system as a large collection of harmonic oscillators initially in thermal equilibrium. As is well known, the system then obeys an equation, which in the bulk and in the suitable limit tends to the Kramers-Langevin equation of physical kinetics. I consider time-dependent system-bath coupling and show that this leads to an additional harmonic force acting on the system. When the coupling is switched on and switched off rapidly, the force has delta-function support at the initial and final time. I further show that the work and heat functionals as recently defined in stochastic thermodynamics at strong coupling contain additional terms depending on the time derivative of the system-bath coupling. I discuss these terms and show that while they can be very large if the system-bath coupling changes quickly, they only give a finite contribution to the work that enters in Jarzynski's equality. I also discuss that these corrections to standard work and heat functionals provide an explanation for non-standard terms in the change of the von Neumann entropy of a quantum bath interacting with a quantum system found in an earlier contribution (Aurell and Eichhorn, 2015).