Pascal Mayer - Academia.edu (original) (raw)
Papers by Pascal Mayer
HAL (Le Centre pour la Communication Scientifique Directe), 2015
In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICL... more In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICLEDA), which is a variant of amplification combining the advantages of rolling circle amplification (RCA) and of strand displacement amplification (SDA). Then, we formalize this process in terms of the theory of formal languages, which yields two new operations of sticking and displacement on normal and circular strings. The obtained formalism is quite expressive and we show how to implement the computation of any boolean function on DNA strands using ICLEDA. We also discuss variants of the model that could eventually bring more computational power.
L'invention concerne des procedes d'amplification et de sequencage d'au moins un acid... more L'invention concerne des procedes d'amplification et de sequencage d'au moins un acide nucleique, qui consistent a: (1) former au moins une matrice d'acide nucleique comprenant le ou les acides nucleiques a amplifier ou a sequencer, lesdits acides nucleiques contenant a l'extremite 5' une sequence oligonucleotidique Y et a l'extremite 3' une sequence oligonucleotidique Z, lesdits acides nucleiques comportant en outre, a l'extremite 5', un moyen pour se fixer a un support solide; (2) melanger cette matrice d'acide nucleique avec une ou plusieurs amorces de colonie X pouvant s'hybrider avec la sequence oligonucleotidique Z et comportant a l'extremite 5' un moyen pour fixer les amorces de colonie a un support solide, lorsque ce dernier est present, de sorte que les extremites 5' aussi bien de la matrice d'acide nucleique que des amorces de colonie se lient au support solide; (3) realiser une ou plusieurs reactions d'am...
Ce travail etudie experimentalement la dynamique des molecules d'adn dans un gel d'agaros... more Ce travail etudie experimentalement la dynamique des molecules d'adn dans un gel d'agarose lors de l'electrophorese en champ pulse. Pour cela, nous avons construit un appareil entierement automatise pour suivre la birefringence de l'adn dans un gel a l'etablissement, puis a la coupure du champ electrique. Des adn de differentes longueurs ont ete etudies en fonction du champ electrique et de la concentration d'agarose qui determine la taille des pores du gel. La relaxation de la birefringence a la coupure du champ permet de caracteriser 2 phenomenes: l'un est attribue a l'alignement du tube dans la direction du champ, l'autre au suretirement de la chaine dans son tube. La contribution la plus importante a l'orientation moleculaire est apportee par le suretirement qui relaxe suivent une loi exponentielle etiree, alors que la disparition de l'alignement, lent, fournit un temps de reptation et un facteur d'alignement du tube en accord avec...
Sequencing the three billion bases of the human genome will be a major challenge for the next dec... more Sequencing the three billion bases of the human genome will be a major challenge for the next decade. Although new analytical techniques are being suggested, gel electrophoresis of DNA sequencing fragments is likely to remain the method of choice for some time. Improving this technology will require a better understanding of the physical processes that take place during the migration of DNA in dense media
1998’s first public conference presentation at ams98 of principles, promises and experimental res... more 1998’s first public conference presentation at ams98 of principles, promises and experimental results of DNA colony (/cluster) sequencing result.
ArXiv, 2011
In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICL... more In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICLEDA), which is a new variant of amplification combining the advantages of rolling circle amplification (RCA) and of strand displacement amplification (SDA). Then, we formalize this process in terms of the theory of formal languages and show, on the basis of this formulation, how to manage OR and AND gates. We then explain how to introduce negation, which allows us to prove that, in principle, it is possible to implement the computation of any boolean function on DNA strands using ICLEDA.
Method of nucleic acid amplification (1), wherein, in a reaction volume (2), nanoparticles (8) co... more Method of nucleic acid amplification (1), wherein, in a reaction volume (2), nanoparticles (8) combined with oligonucleotides (4) transfer heat to its surroundings by excitation, characterized in that, by driving the nanoparticles (8), the environment of the nanoparticles (8) is heated locally, where the range of excitation is selected to be less than or equal to a time critical excitation t1> = (s1 * | x |) 2 / D where s1> = 100, | x | It is the average distance of nanoparticles and D is the thermal diffusivity of the medium between the particles (8).
Network pharmacology and polypharmacology are emerging as novel drug discovery paradigms. The man... more Network pharmacology and polypharmacology are emerging as novel drug discovery paradigms. The many discovery, safety and regulatory issues they raise may become tractable with polypharmacological combinations of natural compounds found in whole extracts of edible and mixes thereof. The primary goal of this work is to get general insights underlying the innocuity and the emergence of beneficial and toxic activities of combinations of many compounds in general and of edibles in particular. A simplified model of compounds’ interactions with an organism and of their desired and undesired effects is constructed by considering the departure from equilibrium of interconnected biological features. This model allows to compute the scaling of the probability of significant effects relative to nutritional diversity, organism complexity and synergy resulting from mixing compounds and edibles. It allows also to characterize massive indirect perturbation mode of action drugs as a potential novel ...
Applied and Theoretical Electrophoresis the Official Journal of the International Electrophoresis Society, Feb 1, 1994
The biased reptation model of DNA gel electrophoresis is simple enough to allow one to obtain det... more The biased reptation model of DNA gel electrophoresis is simple enough to allow one to obtain detailed analytical and numerical predictions for experimentally relevant situations. Although it is not always applicable for explaining experimental results, the biased reptation model is usually a good starting point for data analysis. Unfortunately, the model is often reported as being incapable of explaining experimental data because the users have not analyzed the data properly or because they attempted to use the model outside its expected range of applicability. This article presents a detailed practical guide to the model and its limitations, as well as a complete description of its predictions regarding the analysis of constant field mobilities.
HAL (Le Centre pour la Communication Scientifique Directe), 2015
In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICL... more In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICLEDA), which is a variant of amplification combining the advantages of rolling circle amplification (RCA) and of strand displacement amplification (SDA). Then, we formalize this process in terms of the theory of formal languages, which yields two new operations of sticking and displacement on normal and circular strings. The obtained formalism is quite expressive and we show how to implement the computation of any boolean function on DNA strands using ICLEDA. We also discuss variants of the model that could eventually bring more computational power.
L'invention concerne des procedes d'amplification et de sequencage d'au moins un acid... more L'invention concerne des procedes d'amplification et de sequencage d'au moins un acide nucleique, qui consistent a: (1) former au moins une matrice d'acide nucleique comprenant le ou les acides nucleiques a amplifier ou a sequencer, lesdits acides nucleiques contenant a l'extremite 5' une sequence oligonucleotidique Y et a l'extremite 3' une sequence oligonucleotidique Z, lesdits acides nucleiques comportant en outre, a l'extremite 5', un moyen pour se fixer a un support solide; (2) melanger cette matrice d'acide nucleique avec une ou plusieurs amorces de colonie X pouvant s'hybrider avec la sequence oligonucleotidique Z et comportant a l'extremite 5' un moyen pour fixer les amorces de colonie a un support solide, lorsque ce dernier est present, de sorte que les extremites 5' aussi bien de la matrice d'acide nucleique que des amorces de colonie se lient au support solide; (3) realiser une ou plusieurs reactions d'am...
Ce travail etudie experimentalement la dynamique des molecules d'adn dans un gel d'agaros... more Ce travail etudie experimentalement la dynamique des molecules d'adn dans un gel d'agarose lors de l'electrophorese en champ pulse. Pour cela, nous avons construit un appareil entierement automatise pour suivre la birefringence de l'adn dans un gel a l'etablissement, puis a la coupure du champ electrique. Des adn de differentes longueurs ont ete etudies en fonction du champ electrique et de la concentration d'agarose qui determine la taille des pores du gel. La relaxation de la birefringence a la coupure du champ permet de caracteriser 2 phenomenes: l'un est attribue a l'alignement du tube dans la direction du champ, l'autre au suretirement de la chaine dans son tube. La contribution la plus importante a l'orientation moleculaire est apportee par le suretirement qui relaxe suivent une loi exponentielle etiree, alors que la disparition de l'alignement, lent, fournit un temps de reptation et un facteur d'alignement du tube en accord avec...
Sequencing the three billion bases of the human genome will be a major challenge for the next dec... more Sequencing the three billion bases of the human genome will be a major challenge for the next decade. Although new analytical techniques are being suggested, gel electrophoresis of DNA sequencing fragments is likely to remain the method of choice for some time. Improving this technology will require a better understanding of the physical processes that take place during the migration of DNA in dense media
1998’s first public conference presentation at ams98 of principles, promises and experimental res... more 1998’s first public conference presentation at ams98 of principles, promises and experimental results of DNA colony (/cluster) sequencing result.
ArXiv, 2011
In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICL... more In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICLEDA), which is a new variant of amplification combining the advantages of rolling circle amplification (RCA) and of strand displacement amplification (SDA). Then, we formalize this process in terms of the theory of formal languages and show, on the basis of this formulation, how to manage OR and AND gates. We then explain how to introduce negation, which allows us to prove that, in principle, it is possible to implement the computation of any boolean function on DNA strands using ICLEDA.
Method of nucleic acid amplification (1), wherein, in a reaction volume (2), nanoparticles (8) co... more Method of nucleic acid amplification (1), wherein, in a reaction volume (2), nanoparticles (8) combined with oligonucleotides (4) transfer heat to its surroundings by excitation, characterized in that, by driving the nanoparticles (8), the environment of the nanoparticles (8) is heated locally, where the range of excitation is selected to be less than or equal to a time critical excitation t1> = (s1 * | x |) 2 / D where s1> = 100, | x | It is the average distance of nanoparticles and D is the thermal diffusivity of the medium between the particles (8).
Network pharmacology and polypharmacology are emerging as novel drug discovery paradigms. The man... more Network pharmacology and polypharmacology are emerging as novel drug discovery paradigms. The many discovery, safety and regulatory issues they raise may become tractable with polypharmacological combinations of natural compounds found in whole extracts of edible and mixes thereof. The primary goal of this work is to get general insights underlying the innocuity and the emergence of beneficial and toxic activities of combinations of many compounds in general and of edibles in particular. A simplified model of compounds’ interactions with an organism and of their desired and undesired effects is constructed by considering the departure from equilibrium of interconnected biological features. This model allows to compute the scaling of the probability of significant effects relative to nutritional diversity, organism complexity and synergy resulting from mixing compounds and edibles. It allows also to characterize massive indirect perturbation mode of action drugs as a potential novel ...
Applied and Theoretical Electrophoresis the Official Journal of the International Electrophoresis Society, Feb 1, 1994
The biased reptation model of DNA gel electrophoresis is simple enough to allow one to obtain det... more The biased reptation model of DNA gel electrophoresis is simple enough to allow one to obtain detailed analytical and numerical predictions for experimentally relevant situations. Although it is not always applicable for explaining experimental results, the biased reptation model is usually a good starting point for data analysis. Unfortunately, the model is often reported as being incapable of explaining experimental data because the users have not analyzed the data properly or because they attempted to use the model outside its expected range of applicability. This article presents a detailed practical guide to the model and its limitations, as well as a complete description of its predictions regarding the analysis of constant field mobilities.