Publications related to A sequence-dependent rigid-base model of DNA

The stochastic heat equation: hitting probabilities and the probability density function of the supremum via Malliavin calculus

In this thesis, we study systems of linear and/or non-linear stochastic heat equations and fractional heat equations in spatial dimension

1

driven by space-time white noise. The main topic is the study of hitting probabilities for the solutions to these ...

EPFL2018

On the statistical physics of chains and rods, with application to multi-scale sequence-dependent DNA modelling

Alexandre Emmanuel Grandchamp

The complex mechanisms involved in cellular processes have been increasingly understood this past century and the central role of the DNA molecule has been recognized. The base pair sequence along a DNA fragment is observed not only to encode the genomic i ...

EPFL2016

Joint mouse-human phenome-wide association to test gene function and disease risk

Johan Auwerx, Zhi Li, Evan Graehl Williams, Xu Wang, Virginija Jovaisaite

Phenome-wide association is a novel reverse genetic strategy to analyze genome-to-phenome relations in human clinical cohorts. Here we test this approach using a large murine population segregating for similar to 5 million sequence variants, and we compare ...

Nature Publishing Group2016

Multimodel Approach to the Optical Properties of Molecular Dyes in Solution

Iurii Timrov

We introduce a multimodel approach to the simulation of the optical properties of molecular dyes in solution, whereby the effects of thermal fluctuations and of dielectric screening on the absorption spectra are accounted for by explicit and implicit solva ...

Amer Chemical Soc2016

Interactive Design of Probability Density Functions for Shape Grammars

Mark Pauly, Duygu Ceylan, Boris Neubert, Stefan Lienhard

A shape grammar defines a procedural shape space containing a variety of models of the same class, e.g. buildings, trees, furniture, airplanes, bikes, etc. We present a framework that enables a user to interactively design a probability density function (p ...

Assoc Computing Machinery2015

Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519

Matteo Dal Peraro, Hasan Pezeshgi Modarres

The physical chemical principles underlying,enzymatic thermostability are keys to understand the way evolution has shaped proteins,to adapt to a broad range of temperatures. Understanding the molecular determinants at the basis of protein thermostability i ...

Amer Chemical Soc2015

The Black cells phenotype is caused by a point mutation in the Drosophila pro-phenoloxidase 1 gene that triggers melanization and hematopoietic defects

Bruno Lemaitre, Maroun Bou Sleiman, Olivier Binggeli, Lise Bertin

Melanization contributes to arthropod-specific innate immunity through deposition of melanin at wound sites or around parasites, with concomitant release of microbicidal reactive oxygen species. Melanization requires sequential activation of proteolytic en ...

Elsevier2015

Whole Cell Target Engagement Identifies Novel Inhibitors of Mycobacterium tuberculosis Decaprenylphosphoryl-beta-D-ribose Oxidase

John McKinney, Neeraj Dhar

We have targeted the Mycobacterium tuberculosis decaprenylphosphoryl-beta-D-ribose oxidase (Mt-DprE1) for potential chemotherapeutic intervention of tuberculosis. A multicopy suppression strategy that overexpressed Mt-DprEl in M. bovis BCG was used to prof ...

Amer Chemical Soc2015

mu ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

John Maddocks, Daiva Petkeviciute, Marco Pasi, Jonathan Mitchell

We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have ex ...

Oxford Univ Press2014

The H50Q Mutation Enhances alpha-Synuclein Aggregation, Secretion, and Toxicity

Giovanni Dietler, Hilal Lashuel, Anne-Laure Mahul Mellier, Bruno Claude Daniel Fauvet, Francesco Simone Ruggeri, Abid Oueslati, Martial Mbefo Kamdem, Ossama Mohamed Salah El-Dien El-Sayed Ibrahim Khalaf, Filip Vercruysse

Over the last two decades, the identification of missense mutations in the alpha-synuclein (alpha-Syn) gene SNCA in families with inherited Parkinson disease (PD) has reinforced the central role of alpha-Syn in PD pathogenesis. Recently, a new missense mut ...

American Society for Biochemistry and Molecular Biology2014

A sequence-dependent rigid-base model of DNA

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The stochastic heat equation: hitting probabilities and the probability density function of the supremum via Malliavin calculus

On the statistical physics of chains and rods, with application to multi-scale sequence-dependent DNA modelling

Joint mouse-human phenome-wide association to test gene function and disease risk

Multimodel Approach to the Optical Properties of Molecular Dyes in Solution

Interactive Design of Probability Density Functions for Shape Grammars

Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519

The Black cells phenotype is caused by a point mutation in the Drosophila pro-phenoloxidase 1 gene that triggers melanization and hematopoietic defects

Whole Cell Target Engagement Identifies Novel Inhibitors of Mycobacterium tuberculosis Decaprenylphosphoryl-beta-D-ribose Oxidase

mu ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

The H50Q Mutation Enhances alpha-Synuclein Aggregation, Secretion, and Toxicity

Interactive Design of Probability Density Functions for Shape Grammars

Joint mouse-human phenome-wide association to test gene function and disease risk

Multimodel Approach to the Optical Properties of Molecular Dyes in Solution

Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519

On the statistical physics of chains and rods, with application to multi-scale sequence-dependent DNA modelling

The Black cells phenotype is caused by a point mutation in the Drosophila pro-phenoloxidase 1 gene that triggers melanization and hematopoietic defects

Whole Cell Target Engagement Identifies Novel Inhibitors of Mycobacterium tuberculosis Decaprenylphosphoryl-beta-D-ribose Oxidase

mu ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

The H50Q Mutation Enhances alpha-Synuclein Aggregation, Secretion, and Toxicity

The stochastic heat equation: hitting probabilities and the probability density function of the supremum via Malliavin calculus