Document Server@UHasselt
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Repository of the University of Hasselt containing publications in the fields of statistics, computer science, information strategies and material from the Institute for behavioural sciences.

1.
Current fluctuations in the weakly asymmetric exclusion process with open boundaries - GORISSEN, Mieke; VANDERZANDE, Carlo
The additivity principle allows a calculation of current fluctuations and associated density profiles in large diffusive systems. We apply this principle to the weakly asymmetric exclusion process (WASEP). We also calculate the cumulant generating function of the current and the density profiles associated with rare currents in finite systems using a numerical approach based on the density matrix renormalization group. Comparison of the two approaches allows us to verify the validity of the additivity principle and to get insight into the finite size scaling theory for current fluctuations in the WASEP. No evidence for a dynamical phase transition is found.

2.
Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond - Hadiwikarta, W. W.; Walter, J. -C.; Hooyberghs, J.; Carlon, E.
In this article, it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is...

3.
Exact Current Statistics of the Asymmetric Simple Exclusion Process with Open Boundaries - Gorissen, Mieke; Lazarescu, Alexandre; Mallick, Kirone; Vanderzande, Carlo
Nonequilibrium systems are often characterized by the transport of some quantity at a macroscopic scale, such as, for instance, a current of particles through a wire. The asymmetric simple exclusion process (ASEP) is a paradigm for nonequilibrium transport that is amenable to exact analytical solution. In the present work, we determine the full statistics of the current in the finite size open ASEP for all values of the parameters. Our exact analytical results are checked against numerical calculations using density matrix renormalization group techniques.

5.
Hybridisation thermodynamic parameters allow accurate detection of point mutations with DNA microarrays - Hooyberghs, Jef; Carlon, Enrico
We consider mixtures of two DNA sequences t and t' differing by a single nucleotide, which are analyzed by an Agilent custom DNA microarray. In particular we focus on the case in which t, the "wild type", is predominantly abundant and t' the "mutant" is at very low concentrations compared to t. We show that by using appropriately designed arrays it is possible to accurately quantify the presence of t' even at low relative concentrations (approximate to 1%). The detection method is based on thermodynamic models of DNA hybridisation and on the analysis of a large number of hybridisation intensities...

6.
Ribosome Dwell Times and the Protein Copy Number Distribution - Gorissen, Mieke; Vanderzande, Carlo
Translation is the cellular process in which ribosomes make proteins from information encoded on messenger RNA (mRNA). We model translation with an exclusion process taking into account the experimentally determined, non-exponential, waiting time between steps of a ribosome. From numerical simulations using realistic parameter values, we determine the distribution P(E) of the number of proteins E produced by one mRNA. We find that for small E this distribution is not geometric. We present a simplified and analytically solvable model that relates P(E) to the distributions of the times to produce the first E proteins.

7.
Efficiency of Isothermal Molecular Machines at Maximum Power - Van den Broeck, Christian; Kumar, Niraj; Lindenberg, Katja
We derive upper and lower bounds for the efficiency of an isothermal molecular machine operating at maximum power. The upper bound is reached when the activated state is close to the fueling or reactant state (Eyring-like), while the lower bound is reached when the activated state is close to the product state (Kramers-like).

8.
Stochastically driven single-level quantum dot: A nanoscale finite-time thermodynamic machine and its various operational modes - Esposito, Massimiliano; Kumar, Niraj; Lindenberg, Katja; Van den Broeck, Christian
We describe a single-level quantum dot in contact with two leads as a nanoscale finite-time thermodynamic machine. The dot is driven by an external stochastic force that switches its energy between two values. In the isothermal regime, it can operate as a rechargeable battery by generating an electric current against the applied bias in response to the stochastic driving and then redelivering work in the reverse cycle. This behavior is reminiscent of the Parrondo paradox. If there is a thermal gradient the device can function as a work-generating thermal engine or as a refrigerator that extracts heat from the cold...

9.
Fractional Brownian motion and the critical dynamics of zipping polymers - Walter, J. -C.; Ferrantini, A.; Carlon, E.; Vanderzande, C.
We consider two complementary polymer strands of length L attached by a common-end monomer. The two strands bind through complementary monomers and at low temperatures form a double-stranded conformation (zipping), while at high temperature they dissociate (unzipping). This is a simple model of DNA (or RNA) hairpin formation. Here we investigate the dynamics of the strands at the equilibrium critical temperature T = T-c using Monte Carlo Rouse dynamics. We find that the dynamics is anomalous, with a characteristic time scaling as tau similar to L-2.26(2), exceeding the Rouse time similar to L-2.18. We investigate the probability distribution function, velocity...

10.
Cooling by Heating: Refrigeration Powered by Photons - Cleuren, B.; Rutten, Bob; Van den Broeck, C.
We propose a new mechanism for refrigeration powered by photons. We identify the strong coupling regime for which maximum efficiency is achieved. In this case, the cooling flux is proportional to T in the low temperature limit T -> 0.

11.
Stochastic protein production and time-dependent current fluctuations - Gorissen, Mieke; Vanderzande, Carlo
Translation is the cellular process in which ribosomes make proteins from information encoded on messenger RNA. We model this process using driven lattice gases and take into account the finite lifetime of mRNA. The stochastic properties of the translation process can then be determined from the time-dependent current fluctuations of the lattice gas model. We illustrate our ideas with a totally asymmetric exclusion process with extended objects.

12.
Thermodynamics of a stochastic twin elevator - Kumar, Niraj; Van den Broeck, Christian; Esposito, Massimiliano; Lindenberg, Katja
We study the nonequilibrium thermodynamics of a single particle with two available energy levels, in contact with a classical (Maxwell-Boltzmann) or quantum (Bose-Einstein) heat bath. The particle can undergo transitions between the levels via thermal activation or deactivation. The energy levels are alternately raised at a given rate regardless of occupation by the particle, maintaining a fixed energy gap equal to e between them. We explicitly calculate the work, heat, and entropy production rates. The efficiency in both the classical and the quantum case goes to a limit between 100 and 50% that depends on the relative rates of particle...

13.
Second law and Landauer principle far from equilibrium - Esposito, M.; VAN DEN BROECK, Christian
The amount of work that is needed to change the state of a system in contact with a heat bath between specified initial and final nonequilibrium states is at least equal to the corresponding equilibrium free energy difference plus (respectively, minus) temperature times the information of the final (respectively, the initial) state relative to the corresponding equilibrium distributions. Copyright (C) EPLA, 2011

14.
Functionality and specificity of gene markers for skin sensitization in dendritic cells - Lambrechts, Nathalie; Nelissen, Inge; Van Tendeloo, Viggo; Witters, Hilda; Van den Heuvel, Rosette; HOOYBERGHS, Jef; Schoeters, Greet
Transcriptomic analyses revealed a discriminating gene expression profile in human CD34(+) progenitor-derived dendritic cells (DC) after exposure to skin sensitizers versus non-sensitizers. Starting from the differential expression in a small set of genes, a preliminary classification model (VITOSENS (R)) has been developed to identify chemicals as (non-)sensitizing. The objective of the current study is to gain knowledge on the role of the VITOSENS (R) markers in the DC maturation process, as well as to investigate their activation by a skin sensitizer versus a non-sensitizing danger molecule. To evaluate the functional relevance of VITOSENS (R) biomarkers in DC maturation, their response...

15.
Nonequilibrium Effects in DNA Microarrays: A Multiplatform Study - Walter, J. -C.; Kroll, K. M.; HOOYBERGHS, Jef; Carlon, E.
It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15 h in standard protocols (Hooyberghs et al. Phys. Rev. E 2010, 81, 012901). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in rnicroarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and...

16.
Space-time phase transitions in the totally asymmetric simple exclusion process - GORISSEN, Mieke; VANDERZANDE, Carlo
One can drive a system away from equilibrium by bringing it in contact with reservoirs at a different temperature or chemical potential; as a result, heat or particle currents will develop. Recently, the interest in the fluctuations of these currents has increased considerably, both from a theoretical and an experimental point of view. We studied current fluctuations in the Totally Assymetric Simple Exclusion Process(TASEP), which consists of a one-dimensional lattice in which each site is either empty or occupied by at most one particle. The particles enter the lattice with rate α, and exit the lattice with rate β, provided...

17.
Surface states and photo-induced charge transfer on oxygen-terminated chemical vapor deposition diamond - DEFERME, Wim; Mackova, A.; HAENEN, Ken; NESLADEK, Milos
Time-of-Flight (ToF) experiments were carried out to study the electrical transport and charge trapping properties of oxidized freestanding single crystalline (100) CVD diamond crystals. It is shown that the diamond surface and properties of the electrical contacts are of extreme importance, influencing measured charge carrier mobility values. While sputtered Al contacts yield textbook ToF spectra and electron mobilities mu(e) exceeding 1860 cm(2)/Vs, thermally deposited contacts suffer from enhanced trapping. We propose a model in which the observed polarization effects can be explained by charge transfer to oxygen-related surface states, which interact with surface adsorbates, according to the well-known transfer-doping model....

18.
A new approach to study exhaled proteins as potential biomarkers for asthma - Bloemen, K.; Van Den Heuvel, R.; Govarts, E.; HOOYBERGHS, Jef; Nelen, V.; Witters, E.; Desager, K.; Schoeters, G.
P>Background Asthma is a complex clinical disease characterized by airway inflammation. Recently, various studies reported on the analysis of exhaled breath condensate (EBC) in the search for potential biomarkers for asthma. However, in a complex disease such as asthma, one biomarker might not be enough for early diagnosis or follow-up. Objective The use of proteome analysis may reveal disease-specific proteolytic peptide or protein patterns, and may lead to the identification of novel proteins for the detection of asthma. Methods Liquid chromatography and mass spectrometry were used to separate and detect proteins (proteolytic peptides) present in EBC samples from 30 healthy...

19.
THERMODYNAMICS OF INFORMATION: Bits for less or more for bits? - VAN DEN BROECK, Christian
Recent advances in the formulation of the second law of thermodynamics have rekindled interest in the connections between statistical mechanics and information processing. Now a 'Brownian computer' has approached the theoretical limits set by the rejuvenated second law. Or has it?

20.
Three faces of the second law. II. Fokker-Planck formulation - VAN DEN BROECK, Christian; Esposito, Massimiliano
The total entropy production is the sum of two contributions, the so-called adiabatic and nonadiabatic entropy productions, each of which is non-negative. We derive their explicit expressions for continuous Markovian processes, discuss their properties, and illustrate their behavior on two exactly solvable models.