Publication
A sequence-dependent coarse-grain model of B-DNA with explicit description of bases and phosphate groups parametrised from large scale Molecular Dynamics simulations
Related publications (44)
Generalized maximum entropy estimation
We consider the problem of estimating a probability distribution that maximizes the entropy while satisfying a finite number of moment constraints, possibly corrupted by noise. Based on duality of convex programming, we present a novel approximation scheme ...
2019Towards Measuring the Amount of Discriminatory Information in Finger Vein Biometric Characteristics Using a Relative Entropy Estimator
This chapter makes the first attempt to quantify the amount of discriminatory information in finger vein biometric characteristics in terms of Relative Entropy (RE) calculated on genuine and impostor comparison scores using a Nearest Neighbour (NN) estimat ...
Springer Open2019Predicting polymorphism in molecular crystals using orientational entropy
Pablo Miguel Piaggi, Michele Parrinello
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This id ...
2018Multi-Modal Mean-Fields via Cardinality-Based Clamping
Mean Field inference is central to statistical physics. It has attracted much interest in the Computer Vision community to efficiently solve problems expressible in terms of large Conditional Random Fields. However, since it models the posterior probabilit ...
Ieee2017Multi-Modal Mean-Fields via Cardinality-Based Clamping
Mean Field inference is central to statistical physics. It has attracted much interest in the Computer Vision community to efficiently solve problems expressible in terms of large Conditional Random Fields. However, since it models the posterior probabilit ...
Ieee2017Computation and Visualization in Multiscale Modelling of DNA Mechanics
Amongst the substances found in any living organism one of the most central in the workings of each living cell is deoxyribonucleic acid (DNA). For that reason it has been the subject of research in many of its aspects. These range from DNA sequencing to a ...
EPFL2016Bayesian Calibration of Thermal-Hydraulics Model with Time-Dependent Output
Andreas Pautz, Damar Canggih Wicaksono, Omar Zerkak
The currently adopted practice for uncertainty quantification of thermal-hydraulics code predictions is done through statistical sampling where the code is evaluated multiple times using different values of input parameters that are randomly generated acco ...
2016Multi Terminal Probabilistic Compressed Sensing
In this paper, the 'Approximate Message Passing' (AMP) algorithm, initially developed for compressed sensing of signals under i.i.d. Gaussian measurement matrices, has been extended to a multi-terminal setting (MAMP algorithm). It has been shown that simil ...
Ieee2014A New Entropy Power Inequality for Integer-Valued Random Variables
Emmanuel Abbé, Saeid Haghighatshoar
The entropy power inequality (EPI) yields lower bounds on the differential entropy of the sum of two independent real-valued random variables in terms of the individual entropies. Versions of the EPI for discrete random variables have been obtained for spe ...
Institute of Electrical and Electronics Engineers2014cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA
John Maddocks, Daiva Petkeviciute, Marco Pasi
cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated fre ...
Oxford Univ Press2014