1
|
Maréchal V, Boni M, Laroche-Joubert D, Rohr O, Wallet C, Boudaud N, Raffestin S, Peyrefitte C, Bertrand I, Gantzer C, Maday Y, Moulin L. [Wastewater-based epidemiology: is the devil in the details?]. Virologie (Montrouge) 2024; 28:vir.2024.1040. [PMID: 38607294 DOI: 10.1684/vir.2024.1040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Vincent Maréchal
- Sorbonne Université, Inserm, Centre de Recherche S-Antoine, Paris, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Mickaël Boni
- Institut de recherche biomédicale des armées, Brétigny-sur-Orge, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | | | - Olivier Rohr
- Université de Strasbourg, UPR 9002 CNRS, IUT Louis Pasteur, Schiltigheim, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Clémentine Wallet
- Université de Strasbourg, UPR 9002 CNRS, IUT Louis Pasteur, Schiltigheim, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Nicolas Boudaud
- Actalia, F-50000 Saint-Lo, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Stéphanie Raffestin
- Institut Pasteur de la Guyane, 97300 Cayenne, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Christophe Peyrefitte
- Institut Pasteur de la Guyane, 97300 Cayenne, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Isabelle Bertrand
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Christophe Gantzer
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Yvon Maday
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL) et Institut universitaire de France, Paris, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Laurent Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry-sur-Seine, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| |
Collapse
|
2
|
Maréchal V, Boni M, Laroche-Joubert D, Rohr O, Wallet C, Boudaud N, Raffestin S, Peyrefitte C, Bertrand I, Gantzer C, Maday Y, Moulin L. [Épidémiologie des eaux usées : le diable se cache-t-il dans les détails ?]. Virologie (Montrouge) 2024; 28:vir.2024.1041. [PMID: 38607307 DOI: 10.1684/vir.2024.1041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Vincent Maréchal
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, Paris, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Mickaël Boni
- Institut de recherche biomédicale des armées, Brétigny-sur-Orge, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | | | - Olivier Rohr
- Université de Strasbourg, UPR 9002 CNRS, IUT Louis Pasteur, Schiltigheim, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Clémentine Wallet
- Université de Strasbourg, UPR 9002 CNRS, IUT Louis Pasteur, Schiltigheim, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Nicolas Boudaud
- Actalia, F-50000 Saint-Lo, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Stéphanie Raffestin
- Institut Pasteur de la Guyane, 97300 Cayenne, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Christophe Peyrefitte
- Institut Pasteur de la Guyane, 97300 Cayenne, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Isabelle Bertrand
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Christophe Gantzer
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Yvon Maday
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL) et Institut universitaire de France, Paris, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| | - Laurent Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry-sur-Seine, France, Groupement d'intérêt scientifique Obépine, https://www.reseau-obepine.fr
| |
Collapse
|
3
|
Zhukova A, Hecht F, Maday Y, Gascuel O. Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth-Death Epidemiological Models from Phylogenetic Trees. Syst Biol 2023; 72:1387-1402. [PMID: 37703335 PMCID: PMC10924745 DOI: 10.1093/sysbio/syad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
Multi-type birth-death (MTBD) models are phylodynamic analogies of compartmental models in classical epidemiology. They serve to infer such epidemiological parameters as the average number of secondary infections Re and the infectious time from a phylogenetic tree (a genealogy of pathogen sequences). The representatives of this model family focus on various aspects of pathogen epidemics. For instance, the birth-death exposed-infectious (BDEI) model describes the transmission of pathogens featuring an incubation period (when there is a delay between the moment of infection and becoming infectious, as for Ebola and SARS-CoV-2), and permits its estimation along with other parameters. With constantly growing sequencing data, MTBD models should be extremely useful for unravelling information on pathogen epidemics. However, existing implementations of these models in a phylodynamic framework have not yet caught up with the sequencing speed. Computing time and numerical instability issues limit their applicability to medium data sets (≤ 500 samples), while the accuracy of estimations should increase with more data. We propose a new highly parallelizable formulation of ordinary differential equations for MTBD models. We also extend them to forests to represent situations when a (sub-)epidemic started from several cases (e.g., multiple introductions to a country). We implemented it for the BDEI model in a maximum likelihood framework using a combination of numerical analysis methods for efficient equation resolution. Our implementation estimates epidemiological parameter values and their confidence intervals in two minutes on a phylogenetic tree of 10,000 samples. Comparison to the existing implementations on simulated data shows that it is not only much faster but also more accurate. An application of our tool to the 2014 Ebola epidemic in Sierra-Leone is also convincing, with very fast calculation and precise estimates. As MTBD models are closely related to Cladogenetic State Speciation and Extinction (ClaSSE)-like models, our findings could also be easily transferred to the macroevolution domain.
Collapse
Affiliation(s)
- Anna Zhukova
- Unité Bioinformatique Evolutive, Institut Pasteur, Université de Paris, 28 rue du docteur Roux, 75015 Paris, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, 28 rue du docteur Roux, 75015 Paris, France
| | - Frédéric Hecht
- Sorbonne Université, CNRS, Université Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), 4 place Jussieu, F-75005 Paris, France
| | - Yvon Maday
- Sorbonne Université, CNRS, Université Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), 4 place Jussieu, F-75005 Paris, France
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris CEDEX 05, France
| | - Olivier Gascuel
- Unité Bioinformatique Evolutive, Institut Pasteur, Université de Paris, 28 rue du docteur Roux, 75015 Paris, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB) - URM 7205 CNRS, Museum National d’Histoire Naturelle, SU, EPHE & UA, 57 rue Cuvier, CP 50 75005 Paris, France
| |
Collapse
|
4
|
Martin HA, Peruzzetto M, Viroulet S, Mangeney A, Lagrée PY, Popinet S, Maury B, Lefebvre-Lepot A, Maday Y, Bouchut F. Numerical simulations of granular dam break: Comparison between discrete element, Navier-Stokes, and thin-layer models. Phys Rev E 2023; 108:054902. [PMID: 38115420 DOI: 10.1103/physreve.108.054902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 09/20/2023] [Indexed: 12/21/2023]
Abstract
Granular flows occur in various contexts, including laboratory experiments, industrial processes, and natural geophysical flows. To investigate their dynamics, different kinds of physically based models have been developed. These models can be characterized by the length scale at which dynamic processes are described. Discrete models use a microscopic scale to individually model each grain, Navier-Stokes models use a mesoscopic scale to consider elementary volumes of grains, and thin-layer models use a macroscopic scale to model the dynamics of elementary columns of fluids. In each case, the derivation of the associated equations is well-known. However, few studies focus on the extent to which these modeling solutions yield mutually coherent results. In this article, we compare the simulations of a granular dam break on a horizontal or inclined planes for the discrete model convex optimization contact dynamics (COCD), the Navier-Stokes model Basilisk, and the thin-layer depth-averaged model SHALTOP. We show that, although all three models allow reproducing the temporal evolution of the free surface in the horizontal case (except for SHALTOP at the initiation), the modeled flow dynamics are significantly different, and, in particular, during the stopping phase. The stresses measured at the flow's bottom, reflecting the flow dynamics, are in relatively good agreement, but significant variations are obtained with the COCD model due to complex and fast-varying granular lattices. Similar conclusions are drawn using the same rheological parameters to model a granular dam break on an inclined plane. This comparison exercise is essential for assessing the limits and uncertainties of granular flow modeling.
Collapse
Affiliation(s)
- Hugo A Martin
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, F-75005 Paris, France
- Sorbonne Université, CNRS, Université Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France
| | - Marc Peruzzetto
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, F-75005 Paris, France
- BRGM, F-45060 Orléans, France
| | - Sylvain Viroulet
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, F-75005 Paris, France
- Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS-INPT-UPS, Toulouse, France
| | - Anne Mangeney
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, F-75005 Paris, France
- Institut Universitaire de France (IUF), 75231 Paris Cedex 05, France
| | - Pierre-Yves Lagrée
- Institut Jean le Rond d'Alembert, Sorbonne Université, CNRS UMR 7190, F-75005 Paris, France
| | - Stéphane Popinet
- Institut Jean le Rond d'Alembert, Sorbonne Université, CNRS UMR 7190, F-75005 Paris, France
| | - Bertrand Maury
- Département de Mathématiques Appliquées, École Normale Supérieure, Université PSL, 75005 Paris, France
- Laboratoire de Mathématiques d'Orsay, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Aline Lefebvre-Lepot
- CMAP, CNRS, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex
| | - Yvon Maday
- Sorbonne Université, CNRS, Université Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France
- Institut Universitaire de France (IUF), 75231 Paris Cedex 05, France
| | - François Bouchut
- Laboratoire d'Analyse Mathématiques Appliquées, CNRS UMR 8050, Université Gustave Eiffel (UPEC), F-77454, Marne-la-Vallée, France
| |
Collapse
|
5
|
Maréchal V, Maday Y, Wallet C, Cluzel N, Borde C. Wastewater-based epidemiology: Retrospective, current status, and future prospects. Anaesth Crit Care Pain Med 2023; 42:101251. [PMID: 37236316 DOI: 10.1016/j.accpm.2023.101251] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023]
Affiliation(s)
- Vincent Maréchal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, F-75012 Paris, France; Groupement d'Intérêt Scientifique OBEPINE.
| | - Yvon Maday
- Sorbonne Université, CNRS, Université de Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France; Groupement d'Intérêt Scientifique OBEPINE
| | - Clémentine Wallet
- Université de Strasbourg, Unit 7292, DHPI, IUT Louis Pasteur, Schiltigheim, France; Groupement d'Intérêt Scientifique OBEPINE
| | - Nicolas Cluzel
- Sorbonne Université, Maison des Modélisations Ingénieries et Technologies (SUMMIT), 75005 Paris, France; Groupement d'Intérêt Scientifique OBEPINE
| | - Chloé Borde
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, F-75012 Paris, France; Groupement d'Intérêt Scientifique OBEPINE
| |
Collapse
|
6
|
Haidar M, Rančić MJ, Maday Y, Piquemal JP. Extension of the Trotterized Unitary Coupled Cluster to Triple Excitations. J Phys Chem A 2023; 127:3543-3550. [PMID: 37039518 DOI: 10.1021/acs.jpca.3c01753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The Trotterized Unitary Coupled Cluster Single and Double (UCCSD) ansatz has recently attracted interest due to its use in Variation Quantum Eigensolver (VQE) molecular simulations on quantum computers. However, when the size of molecules increases, UCCSD becomes less interesting as it cannot achieve sufficient accuracy. Including higher-order excitations is therefore mandatory to recover the UCC's missing correlation effects. Here, we extend the Trotterized UCC approach via the addition of (true) Triple T excitations introducing UCCSDT. We also include both spin and orbital symmetries. Indeed, in practice, the latter help to reduce unnecessary circuit excitations and thus accelerate the optimization process enabling researchers to tackle larger molecules. Our initial numerical tests (12-14 qubits) show that UCCSDT improves the overall accuracy by at least two orders of magnitude with respect to standard UCCSD. Overall, the UCCSDT ansatz is shown to reach chemical accuracy and to be competitive with the CCSD(T) gold-standard classical method of quantum chemistry.
Collapse
Affiliation(s)
- Mohammad Haidar
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
- Sorbonne Université, CNRS, Université Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), 75005 Paris, France
- TotalEnergies, 2 Place Coupole Jean Millier, 92400 Courbevoie, France
| | - Marko J Rančić
- TotalEnergies, 2 Place Coupole Jean Millier, 92400 Courbevoie, France
| | - Yvon Maday
- Sorbonne Université, CNRS, Université Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), 75005 Paris, France
- Institut Universitaire de France, 75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
| |
Collapse
|
7
|
Haidar M, Rančić MJ, Ayral T, Maday Y, Piquemal J. Open source variational quantum eigensolver extension of the quantum learning machine for quantum chemistry. WIREs Comput Mol Sci 2023. [DOI: 10.1002/wcms.1664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Mohammad Haidar
- Sorbonne Université Laboratoire de Chimie Théorique (UMR‐7616‐CNRS) Paris France
- Sorbonne Université, CNRS Université Paris Cité, Laboratoire Jacques Louis Lions (LJLL) Paris France
- TotalEnergies, Tour Coupole La Défense Paris France
| | | | - Thomas Ayral
- Atos Quantum Laboratory Les Clayes‐sous‐Bois France
| | - Yvon Maday
- Sorbonne Université, CNRS Université Paris Cité, Laboratoire Jacques Louis Lions (LJLL) Paris France
- Institut Universitaire de France Paris France
| | - Jean‐Philip Piquemal
- Sorbonne Université Laboratoire de Chimie Théorique (UMR‐7616‐CNRS) Paris France
| |
Collapse
|
8
|
Nonino M, Ballarin F, Rozza G, Maday Y. Projection Based Semi-Implicit Partitioned Reduced Basis Method for Fluid-Structure Interaction Problems. J Sci Comput 2022; 94:4. [PMID: 36437820 PMCID: PMC9684301 DOI: 10.1007/s10915-022-02049-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
In this manuscript a POD-Galerkin based Reduced Order Model for unsteady Fluid-Structure Interaction problems is presented. The model is based on a partitioned algorithm, with semi-implicit treatment of the coupling conditions. A Chorin-Temam projection scheme is applied to the incompressible Navier-Stokes problem, and a Robin coupling condition is used for the coupling between the fluid and the solid. The coupled problem is based on an Arbitrary Lagrangian Eulerian formulation, and the Proper Orthogonal Decomposition procedure is used for the generation of the reduced basis. We extend existing works on a segregated Reduced Order Model for Fluid-Structure Interaction to unsteady problems that couple an incompressible, Newtonian fluid with a linear elastic solid, in two spatial dimensions. We consider three test cases to assess the overall capabilities of the method: an unsteady, non-parametrized problem, a problem that presents a geometrical parametrization of the solid domain, and finally, a problem where a parametrization of the solid's shear modulus is taken into account.
Collapse
Affiliation(s)
- Monica Nonino
- Department of Mathematics, University of Vienna, Oskar-Morgenstern Platz, 1090 Vienna, Austria
| | - Francesco Ballarin
- Dipartimento di Matematica e Fisica, Universitá Cattolica del Sacro Cuore, Via Garzetta, 25133 Brescia, Italy
| | - Gianluigi Rozza
- MathLab, International School of Advanced Studies, Via Bonomea, 34136 Trieste, Italy
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions, Université Pierre et Marie Curie, Place Jussieu, 75005 Paris, France
| |
Collapse
|
9
|
Boni M, Gorgé O, Mullot JU, Wurtzer S, Moulin L, Maday Y, Obépine G, Canini F, Chantre M, Teyssou R, Maréchal V, Janvier F, Tournier JN. [The French Armed Forces Biomedical Research Institute (IRBA) and wastewater-based epidemiology: Applicability and relevance in armed forces]. Bull Acad Natl Med 2022; 206:1011-1021. [PMID: 36778592 PMCID: PMC9906811 DOI: 10.1016/j.banm.2022.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/29/2022] [Indexed: 11/19/2022]
Abstract
The French Armed Forces Biomedical Research Institute (IRBA) deeply involved in research on SARS-COV-2, participated in the creation of the Obépine sentinel network in charge of detecting, qualifying and quantifying the virus genome in wastewater in France. During this pandemic, wastewater-based epidemiology has proven to be a first class public health tool for assessing viral dynamics in populations and environment. Obépine has also conducted research demonstrating the low infectivity of faeces and wastewater and allowed for early detection of epidemic waves linked to new variants. The IRBA has adapted this powerful tool to the monitoring of viral infections on board the aircraft carrier Charles-de-Gaulle in order to get an operational system for anticipation after the first local outbreak in 2020. The presence of this surveillance and anticipation tool has allowed a better management of SARS-CoV-2 contingent introductions on board during stopovers or crewmembers entries. The combination of a mandatory vaccination protocol and the surveillance of viral circulation in black waters has made it possible to identify and locate cases, and thus to continue the operational mission in the COVID-19 environment while limiting the spread and preserving the health of the crew. This innovative tool can easily be redirected to the search for any other pathogens in blackwater or even, in the long term, to ensure health surveillance of any military establishment, at sea or on land, in France or on overseas bases.
Collapse
Affiliation(s)
- M Boni
- Institut de recherche biomédicale des armées, 1, place Valérie-André, 91220 Brétigny-sur-Orge, France
- Groupement d'intérêt scientifique Obépine, France
| | - O Gorgé
- Institut de recherche biomédicale des armées, 1, place Valérie-André, 91220 Brétigny-sur-Orge, France
| | - J-U Mullot
- Laboratoire d'analyses de surveillance et d'expertise de la Marine, 83000 Toulon, France
- Laboratoire d'analyses de surveillance et d'expertise de la Marine, 83000 Toulon, France
| | - S Wurtzer
- Eau de Paris, département de recherche, développement et qualité de l'eau, 33, avenue Jean-Jaurès, 94200 Ivry-sur-Seine, France
- Groupement d'intérêt scientifique Obépine, France
| | - L Moulin
- Eau de Paris, département de recherche, développement et qualité de l'eau, 33, avenue Jean-Jaurès, 94200 Ivry-sur-Seine, France
- Groupement d'intérêt scientifique Obépine, France
| | - Y Maday
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), Institut universitaire de France, 75005 Paris, France
- Groupement d'intérêt scientifique Obépine, France
| | - Gis Obépine
- Groupement d'intérêt scientifique Obépine, France
| | - F Canini
- Institut de recherche biomédicale des armées, 1, place Valérie-André, 91220 Brétigny-sur-Orge, France
- École du Val-de-Grâce, 75005 Paris, France
| | - M Chantre
- Institut de recherche biomédicale des armées, 1, place Valérie-André, 91220 Brétigny-sur-Orge, France
| | - R Teyssou
- Institut de recherche biomédicale des armées, 1, place Valérie-André, 91220 Brétigny-sur-Orge, France
- École du Val-de-Grâce, 75005 Paris, France
- Groupement d'intérêt scientifique Obépine, France
| | - V Maréchal
- Sorbonne Université, Inserm, Centre de recherche Saint-Antoine, 75012 Paris, France
- Groupement d'intérêt scientifique Obépine, France
| | - F Janvier
- Hôpital d'instruction des armées Sainte-Anne, service de microbiologie et hygiène hospitalière, 83000 Toulon, France
| | - J-N Tournier
- Institut de recherche biomédicale des armées, 1, place Valérie-André, 91220 Brétigny-sur-Orge, France
- École du Val-de-Grâce, 75005 Paris, France
| |
Collapse
|
10
|
Wurtzer S, Lacote S, Murri S, Marianneau P, Monchatre-Leroy E, Boni M, Ferraris O, Maday Y, Kébé O, Dia N, Peyrefitte C, Sokol H, Moulin L, Maréchal V. Reduction in SARS-CoV-2 Virus Infectivity in Human and Hamster Feces. Viruses 2022; 14:v14081777. [PMID: 36016399 PMCID: PMC9415851 DOI: 10.3390/v14081777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Objective: There is extensive evidence that SARS-CoV-2 replicates in the gastrointestinal tract. However, the infectivity of virions in feces is poorly documented. Although the primary mode of transmission is airborne, the risk of transmission from contaminated feces remains to be assessed. Design: The persistence of SARS-CoV-2 (infectivity and RNA) in human and animal feces was evaluated by virus isolation on cell culture and RT-qPCR, respectively. The exposure of golden Syrian hamsters to experimentally contaminated feces through intranasal inoculation has also been tested to assess the fecal-oral transmission route. Results: For periods that are compatible with average intestinal transit, the SARS-CoV-2 genome was noticeably stable in human and animal feces, contrary to the virus infectivity that was reduced in a time- and temperature-dependent manner. In human stools, this reduction was variable depending on the donors. Viral RNA was excreted in the feces of infected hamsters, but exposure of naïve hamsters to feces of infected animals did not lead to any productive infection. Conversely, hamsters could be experimentally infected following exposure to spiked fresh feces. Conclusion: Infection following exposure to naturally contaminated feces has been suspected but has not been established so far. The present work demonstrates that SARS-CoV-2 rapidly lost infectivity in spiked or naturally infected feces. Although the possibility of persistent viral particles in human or animal feces cannot be fully ruled out, SARS-CoV-2 transmission after exposure to contaminated feces is unlikely.
Collapse
Affiliation(s)
- Sébastien Wurtzer
- Research and Development Department, Eau de Paris, 33 Avenue Jean Jaurès, 94200 Ivry-sur-Seine, France
- Correspondence:
| | - Sandra Lacote
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France
| | - Severine Murri
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France
| | | | | | - Mickaël Boni
- French Armed Forces Biomedical Research Institute, 91220 Brétigny-sur-Orge, France
| | - Olivier Ferraris
- French Armed Forces Biomedical Research Institute, 91220 Brétigny-sur-Orge, France
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions (LJLL), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut Universitaire de France, 75005 Paris, France
| | | | - Ndongo Dia
- Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Christophe Peyrefitte
- Institut Pasteur de Dakar, Dakar 12900, Senegal
- Institut Pasteur de la Guyane, 97300 Cayenne, France
| | - Harry Sokol
- INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Sorbonne Université, 75571 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, 75571 Paris, France
- INRAe, UMR1319 Micalis and AgroParisTech, 78350 Jouy en Josas, France
| | | | - Laurent Moulin
- Research and Development Department, Eau de Paris, 33 Avenue Jean Jaurès, 94200 Ivry-sur-Seine, France
| | - Vincent Maréchal
- INSERM U938, Centre de Recherche Saint-Antoine, Sorbonne Université, 75012 Paris, France
| |
Collapse
|
11
|
Wurtzer S, Waldman P, Levert M, Cluzel N, Almayrac JL, Charpentier C, Masnada S, Gillon-Ritz M, Mouchel JM, Maday Y, Boni M, Marechal V, Moulin L. SARS-CoV-2 genome quantification in wastewaters at regional and city scale allows precise monitoring of the whole outbreaks dynamics and variants spreading in the population. Sci Total Environ 2022; 810:152213. [PMID: 34896511 PMCID: PMC8656174 DOI: 10.1016/j.scitotenv.2021.152213] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 05/19/2023]
Abstract
SARS-CoV-2 is a coronavirus causing a globalized outbreak called COVID-19. SARS-CoV-2 transmission is associated with inhalation of contaminated respiratory droplets and could causes severe complications. Until today several "waves" of infections have been observed despite implementation of strict health policies. Decisions for such sanitary measures are based on population health monitoring. Unfortunately, for COVID-19, a significant proportion of individuals are asymptomatic but play a role in the virus transmission. To overcome these limitations, several strategies were developed including genome quantification in wastewater that could allow monitoring of the health status of population, since shedding of SARS-CoV-2 in patient stool is frequent. Wastewater-based epidemiology (WBE) was established and several countries implemented this approach to allow COVID-19 outbreak monitoring. In France, the OBEPINE project performed a quantitative analysis of SARS-CoV-2 in raw wastewater samples collected from major wastewater treatment plants (WWTP) since March 2020. In the greater Paris area 1101 samples (507 for five WWTP and 594 for sewer) were collected. This 16 months monitoring allows us to observe the outbreak dynamics. Comparison of WBE indicators with health data lead to several important observation; the good level of correlation with incidence rates, the average 3 days lead time, and the sensitivity (WBE change when incidence is > to 7/100000 inhabitants). We also compared the local monitoring (city level) with the regional monitoring, to help cluster identification. Moreover, variants of concern (VOC) emerged due to the selection pressure. We developed a specific RT-qPCR method targeting the deletion H69-V70 in the spike protein, using this deletion as a proxy of the B.1.1.7 presence in the wastewater. With this data we demonstrate the predominant role played by this strain in the third wave. All these results allow a better description and understanding of the pandemic and highlight the role of such WBE indicators.
Collapse
Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - P Waldman
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, Paris, France
| | - M Levert
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - N Cluzel
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - J L Almayrac
- SIAAP, Service process-laboratoire SIAAP site Seine Amont, Valenton, France
| | - C Charpentier
- Service de Virologie, Université de Paris, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - S Masnada
- SIAM - STV, Avenue de la courtiere, 77400 Saint Thibault des vignes, France
| | - M Gillon-Ritz
- Direction de la Propreté et de l'Eau - Service Technique de l'Eau et de l'Assainissement, rue du Commandeur, 75014 Paris, France
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, Paris, France
| | - Y Maday
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - M Boni
- Institut de Recherche Biomédicale des Armées, 1 place Valérie André, F-91220 Brétigny sur Orge, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine2, Paris, France
| | - L Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France.
| |
Collapse
|
12
|
Cluzel N, Courbariaux M, Wang S, Moulin L, Wurtzer S, Bertrand I, Laurent K, Monfort P, Gantzer C, Guyader SL, Boni M, Mouchel JM, Maréchal V, Nuel G, Maday Y. A nationwide indicator to smooth and normalize heterogeneous SARS-CoV-2 RNA data in wastewater. Environ Int 2022; 158:106998. [PMID: 34991258 PMCID: PMC8608586 DOI: 10.1016/j.envint.2021.106998] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/20/2021] [Accepted: 11/21/2021] [Indexed: 05/18/2023]
Abstract
Since many infected people experience no or few symptoms, the SARS-CoV-2 epidemic is frequently monitored through massive virus testing of the population, an approach that may be biased and may be difficult to sustain in low-income countries. Since SARS-CoV-2 RNA can be detected in stool samples, quantifying SARS-CoV-2 genome by RT-qPCR in wastewater treatment plants (WWTPs) has been carried out as a complementary tool to monitor virus circulation among human populations. However, measuring SARS-CoV-2 viral load in WWTPs can be affected by many experimental and environmental factors. To circumvent these limits, we propose here a novel indicator, the wastewater indicator (WWI), that partly reduces and corrects the noise associated with the SARS-CoV-2 genome quantification in wastewater (average noise reduction of 19%). All data processing results in an average correlation gain of 18% with the incidence rate. The WWI can take into account the censorship linked to the limit of quantification (LOQ), allows the automatic detection of outliers to be integrated into the smoothing algorithm, estimates the average measurement error committed on the samples and proposes a solution for inter-laboratory normalization in the absence of inter-laboratory assays (ILA). This method has been successfully applied in the context of Obépine, a French national network that has been quantifying SARS-CoV-2 genome in a representative sample of French WWTPs since March 5th 2020. By August 26th, 2021, 168 WWTPs were monitored in the French metropolitan and overseas territories of France. We detail the process of elaboration of this indicator, show that it is strongly correlated to the incidence rate and that the optimal time lag between these two signals is only a few days, making our indicator an efficient complement to the incidence rate. This alternative approach may be especially important to evaluate SARS-CoV-2 dynamics in human populations when the testing rate is low.
Collapse
Affiliation(s)
- Nicolas Cluzel
- Sorbonne Université, Maison des Modélisations Ingénieries et Technologies (SUMMIT), 75005 Paris, France.
| | - Marie Courbariaux
- Sorbonne Université, Maison des Modélisations Ingénieries et Technologies (SUMMIT), 75005 Paris, France
| | - Siyun Wang
- Sorbonne Université, Maison des Modélisations Ingénieries et Technologies (SUMMIT), 75005 Paris, France
| | - Laurent Moulin
- Eau de Paris, Département de Recherche, Développement et Qualité de l'Eau, 33 avenue Jean Jaurès, F-94200 Ivry sur Seine, France
| | - Sébastien Wurtzer
- Eau de Paris, Département de Recherche, Développement et Qualité de l'Eau, 33 avenue Jean Jaurès, F-94200 Ivry sur Seine, France
| | | | - Karine Laurent
- Sorbonne Université, Maison des Modélisations Ingénieries et Technologies (SUMMIT), 75005 Paris, France
| | - Patrick Monfort
- HydroSciences Montpellier, UMR 5151, Université de Montpellier, CNRS, IRD, F-34093 Montpellier, France
| | | | - Soizick Le Guyader
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, 44311 Nantes, France
| | - Mickaël Boni
- Institut de Recherche Biomédicale des Armées, 1 place Valérie André, F-91220 Brétigny-sur-Orge, France
| | - Jean-Marie Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - Vincent Maréchal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, F-75012 Paris, France
| | - Grégory Nuel
- Stochastics and Biology Group, Probability and Statistics (LPSM, CNRS 8001), Sorbonne University, Campus Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France
| | - Yvon Maday
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France; Institut Universaire de France, France.
| |
Collapse
|
13
|
Wurtzer S, Waldman P, Ferrier-Rembert A, Frenois-Veyrat G, Mouchel JM, Boni M, Maday Y, Marechal V, Moulin L. Several forms of SARS-CoV-2 RNA can be detected in wastewaters: Implication for wastewater-based epidemiology and risk assessment. Water Res 2021; 198:117183. [PMID: 33962244 DOI: 10.1101/2020.12.19.20248508] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 05/21/2023]
Abstract
The ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a public health emergency of international concern. Although SARS-CoV-2 is considered to be mainly transmitted by inhalation of contaminated droplets and aerosols, SARS-CoV-2 is also detected in human feces and to a less extent in urine, and in raw wastewaters (to date viral RNA only) suggesting that other routes of infection may exist. Monitoring SARS-CoV-2 genomes in wastewaters has been proposed as a complementary approach for tracing the dynamics of virus transmission within human population connected to wastewater network. The understanding on SARS-CoV-2 transmission through wastewater surveillance, the development of epidemic modeling and the evaluation of SARS-CoV-2 transmission from contaminated wastewater are largely limited by our knowledge on viral RNA genome persistence and virus infectivity preservation in such an environment. Using an integrity based RT-qPCR assay this study led to the discovery that SARS-CoV-2 RNA can persist under several forms in wastewaters, which provides important information on the presence of SARS-CoV-2 in raw wastewaters and associated risk assessment.
Collapse
Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D and Water quality department, 33 avenue Jean Jaurès, F-94200 Ivry sur Seine, France.
| | - P Waldman
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - A Ferrier-Rembert
- Institut de Recherche Biomédicale des Armées, Microbiology & Infectious diseases, Virology unit, 1 place Valérie André, F-91220 Brétigny-sur-Orge, France
| | - G Frenois-Veyrat
- Institut de Recherche Biomédicale des Armées, Microbiology & Infectious diseases, Virology unit, 1 place Valérie André, F-91220 Brétigny-sur-Orge, France
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - M Boni
- Institut de Recherche Biomédicale des Armées, Microbiology & Infectious diseases, Virology unit, 1 place Valérie André, F-91220 Brétigny-sur-Orge, France
| | - Y Maday
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, F-75012, Paris, France
| | - L Moulin
- Eau de Paris, R&D and Water quality department, 33 avenue Jean Jaurès, F-94200 Ivry sur Seine, France
| |
Collapse
|
14
|
Wurtzer S, Waldman P, Ferrier-Rembert A, Frenois-Veyrat G, Mouchel JM, Boni M, Maday Y, Marechal V, Moulin L. Several forms of SARS-CoV-2 RNA can be detected in wastewaters: Implication for wastewater-based epidemiology and risk assessment. Water Res 2021; 198:117183. [PMID: 33962244 PMCID: PMC8060898 DOI: 10.1016/j.watres.2021.117183] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 05/20/2023]
Abstract
The ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a public health emergency of international concern. Although SARS-CoV-2 is considered to be mainly transmitted by inhalation of contaminated droplets and aerosols, SARS-CoV-2 is also detected in human feces and to a less extent in urine, and in raw wastewaters (to date viral RNA only) suggesting that other routes of infection may exist. Monitoring SARS-CoV-2 genomes in wastewaters has been proposed as a complementary approach for tracing the dynamics of virus transmission within human population connected to wastewater network. The understanding on SARS-CoV-2 transmission through wastewater surveillance, the development of epidemic modeling and the evaluation of SARS-CoV-2 transmission from contaminated wastewater are largely limited by our knowledge on viral RNA genome persistence and virus infectivity preservation in such an environment. Using an integrity based RT-qPCR assay this study led to the discovery that SARS-CoV-2 RNA can persist under several forms in wastewaters, which provides important information on the presence of SARS-CoV-2 in raw wastewaters and associated risk assessment.
Collapse
Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D and Water quality department, 33 avenue Jean Jaurès, F-94200 Ivry sur Seine, France.
| | - P Waldman
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - A Ferrier-Rembert
- Institut de Recherche Biomédicale des Armées, Microbiology & Infectious diseases, Virology unit, 1 place Valérie André, F-91220 Brétigny-sur-Orge, France
| | - G Frenois-Veyrat
- Institut de Recherche Biomédicale des Armées, Microbiology & Infectious diseases, Virology unit, 1 place Valérie André, F-91220 Brétigny-sur-Orge, France
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - M Boni
- Institut de Recherche Biomédicale des Armées, Microbiology & Infectious diseases, Virology unit, 1 place Valérie André, F-91220 Brétigny-sur-Orge, France
| | - Y Maday
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, F-75012, Paris, France
| | - L Moulin
- Eau de Paris, R&D and Water quality department, 33 avenue Jean Jaurès, F-94200 Ivry sur Seine, France
| |
Collapse
|
15
|
Gong H, Chen Z, Maday Y, Li Q. Optimal and fast field reconstruction with reduced basis and limited observations: Application to reactor core online monitoring. Nuclear Engineering and Design 2021. [DOI: 10.1016/j.nucengdes.2021.111113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
16
|
Bakhta A, Boiveau T, Maday Y, Mula O. Epidemiological Forecasting with Model Reduction of Compartmental Models. Application to the COVID-19 Pandemic. Biology (Basel) 2020; 10:biology10010022. [PMID: 33396488 PMCID: PMC7823858 DOI: 10.3390/biology10010022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 01/04/2023]
Abstract
Simple Summary Using tools from the reduced order modeling of parametric ODEs and PDEs, including a new positivity-preserving greedy reduced basis method, we present a novel forecasting method for predicting the propagation of an epidemic. The method takes a collection of highly detailed compartmental models (with different initial conditions, initial times, epidemiological parameters and numerous compartments) and learns a model with few compartments which best fits the available health data and which is used to provide the forecasts. We illustrate the promising potential of the approach to the spread of the current COVID-19 pandemic in the case of the Paris region during the period from March to November 2020, in which two epidemic waves took place. Abstract We propose a forecasting method for predicting epidemiological health series on a two-week horizon at regional and interregional resolution. The approach is based on the model order reduction of parametric compartmental models and is designed to accommodate small amounts of sanitary data. The efficiency of the method is shown in the case of the prediction of the number of infected people and people removed from the collected data, either due to death or recovery, during the two pandemic waves of COVID-19 in France, which took place approximately between February and November 2020. Numerical results illustrate the promising potential of the approach.
Collapse
Affiliation(s)
- Athmane Bakhta
- Service de Thermo-Hydraulique et de Mécanique des Fluides, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France;
| | - Thomas Boiveau
- Institut Carnot Smiles, Sorbonne Université, 75005 Paris, France;
| | - Yvon Maday
- Sorbonne Université and Université de Paris, CNRS, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France;
- Institut Universitaire de France, 75005 Paris, France
| | - Olga Mula
- CEREMADE, CNRS, UMR 7534, Université Paris-Dauphine, PSL University, 75016 Paris, France
- Inria, Commedia Team, 75012 Paris, France
- Correspondence:
| |
Collapse
|
17
|
Wurtzer S, Marechal V, Mouchel JM, Maday Y, Teyssou R, Richard E, Almayrac JL, Moulin L. Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020. Euro Surveill 2020; 25. [PMID: 33334397 DOI: 10.2807/15607917.es.2020.25.50.2000776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations.AimTo test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers.MethodWe performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March).ResultsWe showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown.ConclusionThis work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.
Collapse
Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine2, Paris, France
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, , e-LTER Zone Atelier Seine, Paris, France
| | - Y Maday
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - R Teyssou
- Department of Virology, Institut de Recherche Biomédicale des Armées, Bretigny sur Orge, France
| | - E Richard
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - J L Almayrac
- SIAAP, Service process-laboratoire SIAAP site Seine Amont, Valenton, France
| | - L Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| |
Collapse
|
18
|
Wurtzer S, Marechal V, Mouchel JM, Maday Y, Teyssou R, Richard E, Almayrac JL, Moulin L. Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020. Euro Surveill 2020. [PMID: 33334397 DOI: 10.1101/2020.04.12.20062679%j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations.AimTo test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers.MethodWe performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March).ResultsWe showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown.ConclusionThis work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.
Collapse
Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine2, Paris, France
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, , e-LTER Zone Atelier Seine, Paris, France
| | - Y Maday
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - R Teyssou
- Department of Virology, Institut de Recherche Biomédicale des Armées, Bretigny sur Orge, France
| | - E Richard
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - J L Almayrac
- SIAAP, Service process-laboratoire SIAAP site Seine Amont, Valenton, France
| | - L Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| |
Collapse
|
19
|
Wurtzer S, Marechal V, Mouchel JM, Maday Y, Teyssou R, Richard E, Almayrac JL, Moulin L. Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020. Euro Surveill 2020. [PMID: 33334397 DOI: 10.1101/2020.04.12.2006267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations.AimTo test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers.MethodWe performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March).ResultsWe showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown.ConclusionThis work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.
Collapse
Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine2, Paris, France
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, , e-LTER Zone Atelier Seine, Paris, France
| | - Y Maday
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - R Teyssou
- Department of Virology, Institut de Recherche Biomédicale des Armées, Bretigny sur Orge, France
| | - E Richard
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - J L Almayrac
- SIAAP, Service process-laboratoire SIAAP site Seine Amont, Valenton, France
| | - L Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| |
Collapse
|
20
|
Wurtzer S, Marechal V, Mouchel JM, Maday Y, Teyssou R, Richard E, Almayrac JL, Moulin L. Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020. Euro Surveill 2020; 25:2000776. [PMID: 33334397 PMCID: PMC7812418 DOI: 10.2807/1560-7917.es.2020.25.50.2000776] [Citation(s) in RCA: 219] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/20/2020] [Indexed: 01/04/2023] Open
Abstract
IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations.AimTo test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers.MethodWe performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March).ResultsWe showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown.ConclusionThis work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.
Collapse
Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine2, Paris, France
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, , e-LTER Zone Atelier Seine, Paris, France
| | - Y Maday
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - R Teyssou
- Department of Virology, Institut de Recherche Biomédicale des Armées, Bretigny sur Orge, France
| | - E Richard
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - J L Almayrac
- SIAAP, Service process-laboratoire SIAAP site Seine Amont, Valenton, France
| | - L Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| |
Collapse
|
21
|
Wurtzer S, Marechal V, Mouchel JM, Maday Y, Teyssou R, Richard E, Almayrac JL, Moulin L. Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020. Euro Surveill 2020. [PMID: 33334397 DOI: 10.1807/1560-7917.es.2020.25.50.2000776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations.AimTo test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers.MethodWe performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March).ResultsWe showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown.ConclusionThis work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.
Collapse
Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine2, Paris, France
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, , e-LTER Zone Atelier Seine, Paris, France
| | - Y Maday
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - R Teyssou
- Department of Virology, Institut de Recherche Biomédicale des Armées, Bretigny sur Orge, France
| | - E Richard
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - J L Almayrac
- SIAAP, Service process-laboratoire SIAAP site Seine Amont, Valenton, France
| | - L Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| |
Collapse
|
22
|
Wurtzer S, Marechal V, Mouchel JM, Maday Y, Teyssou R, Richard E, Almayrac JL, Moulin L. Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020. Euro Surveill 2020. [PMID: 33334397 DOI: 10.1101/2020.04.12.20062679] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations.AimTo test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers.MethodWe performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March).ResultsWe showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown.ConclusionThis work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.
Collapse
Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine2, Paris, France
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, , e-LTER Zone Atelier Seine, Paris, France
| | - Y Maday
- These authors are co-founders of the COVID-IA/PANDEMIA initiative
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - R Teyssou
- Department of Virology, Institut de Recherche Biomédicale des Armées, Bretigny sur Orge, France
| | - E Richard
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - J L Almayrac
- SIAAP, Service process-laboratoire SIAAP site Seine Amont, Valenton, France
| | - L Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| |
Collapse
|
23
|
Abstract
In this paper, we consider the problem of accelerating the numerical simulation of time dependent problems by time domain decomposition. The available algorithms enabling such decompositions present severe efficiency limitations and are an obstacle for the solution of large scale and high dimensional problems. Our main contribution is the improvement of the parallel efficiency of the parareal in time method. The parareal method is based on combining predictions made by a numerically inexpensive solver (with coarse physics and/or coarse resolution) with corrections coming from an expensive solver (with high-fidelity physics and high resolution). At convergence, the algorithm provides a solution that has the fine solver's high-fidelity physics and high resolution. In the classical version, the fine solver has a fixed high accuracy which is the major obstacle to achieve a competitive parallel efficiency. In this paper, we develop an adaptive variant that overcomes this obstacle by dynamically increasing the accuracy of the fine solver across the parareal iterations. We theoretically show that the parallel efficiency becomes very competitive in the ideal case where the cost of the coarse solver is small, thus proving that the only remaining factors impeding full scalability become the cost of the coarse solver and communication time. The developed theory has also the merit of setting a general framework to understand the success of several extensions of parareal based on iteratively improving the quality of the fine solver and re-using information from previous parareal steps. We illustrate the actual performance of the method in stiff ODEs, which are a challenging family of problems since the only mechanism for adaptivity is time and efficiency is affected by the cost of the coarse solver.
Collapse
Affiliation(s)
- Y. Maday
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France
- Institut Universitaire de France, France
| | - O. Mula
- CEREMADE, CNRS, UMR 7534, Université Paris-Dauphine, PSL University, 75016 Paris, France
- Inria Paris, COMMEDIA, 2 rue Simone Iff, 75012, Paris, France
| |
Collapse
|
24
|
Cluzel N, Lambert A, Maday Y, Turinici G, Danchin A. [Biochemical and statistical lessons from the evolution of the SARS-CoV-2 virus: paths for novel antiviral warfare]. C R Biol 2020; 343:177-209. [PMID: 33108121 DOI: 10.5802/crbiol.16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023]
Abstract
In the fight against the spread of COVID-19 the emphasis is on vaccination or on reactivating existing drugs used for other purposes. The tight links that necessarily exist between the virus as it multiplies and the metabolism of its host are systematically ignored. Here we show that the metabolism of all cells is coordinated by the availability of a core building block of the cell's genome, cytidine triphosphate (CTP). This metabolite is also the key to the synthesis of the viral envelope and to the translation of its genome into proteins. This unique role explains why evolution has led to the early emergence in animals of an antiviral immunity enzyme, viperin, that synthesizes a toxic analogue of CTP. The constraints arising from this dependency guide the evolution of the virus. With this in mind, we explored the real-time experiment taking place before our eyes using probabilistic modelling approaches to the molecular evolution of the virus. We have thus followed, almost on a daily basis, the evolution of the composition of the viral genome to link it to the progeny produced over time, particularly in the form of blooms that sparked a firework of viral mutations. Some of those certainly increase the propagation of the virus. This led us to make out the critical role in this evolution of several proteins of the virus, such as its nucleocapsid N, and more generally to begin to understand how the virus ties up the host metabolism to its own benefit. A way for the virus to escape CTP-dependent control in cells would be to infect cells that are not expected to grow, such as neurons. This may account for unexpected body sites of viral development in the present epidemic.
Collapse
Affiliation(s)
- Nicolas Cluzel
- Tremplin Carnot SMILES, 4 Place Jussieu, 75005 Paris, France
| | - Amaury Lambert
- Centre Interdisciplinaire de Recherche en Biologie (CIRB), Collège de France, CNRS UMR7241, INSERM U1050, PSL Research University, 11 place Marcelin Berthelot, 75005 Paris, France.,Laboratoire de Probabilités, Statistique & Modélisation (LPSM), Sorbonne Université, Université de Paris, CNRS UMR8001, 4 place Jussieu, 75005 Paris, France
| | - Yvon Maday
- Sorbonne Université and Université de Paris, CNRS, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France.,Tremplin Carnot SMILES, 4 Place Jussieu, 75005 Paris, France
| | | | - Antoine Danchin
- Kodikos Labs / Stellate Therapeutics, Institut Cochin, 24 rue du Faubourg Saint-Jacques, 75014 Paris, France.,School of Biomedical Sciences, Li KaShing Faculty of Medicine, Hong Kong University, 21 Sassoon Road, Pokfulam, SAR Hong Kong, China
| |
Collapse
|
25
|
Laplaza R, Peccati F, A. Boto R, Quan C, Carbone A, Piquemal J, Maday Y, Contreras‐García J. NCIPLOT
and the analysis of noncovalent interactions using the reduced density gradient. WIREs Comput Mol Sci 2020. [DOI: 10.1002/wcms.1497] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rubén Laplaza
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Departamento de Química Física Universidad de Zaragoza Zaragoza Spain
| | - Francesca Peccati
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université Paris France
| | - Roberto A. Boto
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Centro de Física de Materiales CFM‐MPC (CSIC‐UPV/EHU) Donostia Spain
| | - Chaoyu Quan
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université Paris France
- SUSTech International Center for Mathematics, and Department of Mathematics Southern University of Science and Technology Shenzhen China
| | - Alessandra Carbone
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB) Sorbonne Université Paris France
- Institut Universitaire de France Paris France
| | - Jean‐Philip Piquemal
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Institut Universitaire de France Paris France
| | - Yvon Maday
- SUSTech International Center for Mathematics, and Department of Mathematics Southern University of Science and Technology Shenzhen China
- Institut Universitaire de France Paris France
| | | |
Collapse
|
26
|
Boto RA, Peccati F, Laplaza R, Quan C, Carbone A, Piquemal JP, Maday Y, Contreras-Garcı A J. NCIPLOT4: Fast, Robust, and Quantitative Analysis of Noncovalent Interactions. J Chem Theory Comput 2020; 16:4150-4158. [PMID: 32470306 DOI: 10.1021/acs.jctc.0c00063] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The NonCovalent Interaction index (NCI) enables identification of attractive and repulsive noncovalent interactions from promolecular densities in a fast manner. However, the approach remained up to now qualitative, only providing visual information. We present a new version of NCIPLOT, NCIPLOT4, which allows quantifying the properties of the NCI regions (volume, charge) in small and big systems in a fast manner. Examples are provided of how this new twist enables characterization and retrieval of local information in supramolecular chemistry and biosystems at the static and dynamic levels.
Collapse
Affiliation(s)
- Roberto A Boto
- Laboratoire de Chimie Théorique (LCT), Sorbonne Université, CNRS, 75005 Paris, France.,Materials Physics Center, CSIC-UPV/EHU, 20018 Donostia-San Sebastián, Spain
| | - Francesca Peccati
- Laboratoire de Chimie Théorique (LCT), Sorbonne Université, CNRS, 75005 Paris, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique (LCT), Sorbonne Université, CNRS, 75005 Paris, France.,Departamento de Quı́mica Fı́sica, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Chaoyu Quan
- SUSTech International Center for Mathematics, and Department of Mathematics, Southern University of Science and Technology, 518055 Shenzhen, China.,Institut des Sciences du Calcul et des Données (ISCD), Sorbonne Université, 75005 Paris, France
| | - Alessandra Carbone
- Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, CNRS, IBPS, 75005 Paris, France.,Institut Universitaire de France, 75005, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique (LCT), Sorbonne Université, CNRS, 75005 Paris, France.,Institut Universitaire de France, 75005, Paris, France
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions (LJLL), Sorbonne Université, Université Paris-Diderot SPC, CNRS, F-75005 Paris, France.,Institut Universitaire de France, 75005, Paris, France
| | | |
Collapse
|
27
|
Stamm B, Lagardère L, Polack É, Maday Y, Piquemal JP. A coherent derivation of the Ewald summation for arbitrary orders of multipoles: The self-terms. J Chem Phys 2018; 149:124103. [PMID: 30278683 DOI: 10.1063/1.5044541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we provide the mathematical elements we think essential for a proper understanding of the calculus of the electrostatic energy of point-multipoles of arbitrary order under periodic boundary conditions. The emphasis is put on the expressions of the so-called self-parts of the Ewald summation where different expressions can be found in the literature. Indeed, such expressions are of prime importance in the context of new generation polarizable force field where the self-field appears in the polarization equations. We provide a general framework, where the idea of the Ewald splitting is applied to the electric potential and, subsequently, all other quantities such as the electric field, the energy, and the forces are derived consistently thereof. Mathematical well-posedness is shown for all these contributions for any order of multipolar distribution.
Collapse
Affiliation(s)
- Benjamin Stamm
- Center for Computational Engineering Science, RWTH Aachen University, Aachen, Germany
| | - Louis Lagardère
- Institut des Sciences du Calcul et des Données, Sorbonne Université, Paris, France
| | - Étienne Polack
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, Paris, France
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions, LJLL, Sorbonne Université, Université Paris-Diderot SPC, CNRS, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, Paris, France
| |
Collapse
|
28
|
Lindgren EB, Stamm B, Maday Y, Besley E, Stace AJ. Dynamic simulations of many-body electrostatic self-assembly. Philos Trans A Math Phys Eng Sci 2018; 376:20170143. [PMID: 29431686 PMCID: PMC5805913 DOI: 10.1098/rsta.2017.0143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/21/2017] [Indexed: 06/08/2023]
Abstract
Two experimental studies relating to electrostatic self-assembly have been the subject of dynamic computer simulations, where the consequences of changing the charge and the dielectric constant of the materials concerned have been explored. One series of calculations relates to experiments on the assembly of polymer particles that have been subjected to tribocharging and the simulations successfully reproduce many of the observed patterns of behaviour. A second study explores events observed following collisions between single particles and small clusters composed of charged particles derived from a metal oxide composite. As before, observations recorded during the course of the experiments are reproduced by the calculations. One study in particular reveals how particle polarizability can influence the assembly process.This article is part of the theme issue 'Modern theoretical chemistry'.
Collapse
Affiliation(s)
- Eric B Lindgren
- Department of Physical and Theoretical Chemistry, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Benjamin Stamm
- Centre for Computational Engineering, Mathematics Department, RWTH Aachen University, Schinkelstrasse 2, 52062 Aachen, Germany
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ Paris 06, UMR 7598, 75005 Paris, France
- Laboratoire Jacques-Louis Lions, CNRS, UMR 7598, 75005 Paris, France
- Division of Applied Mathematics, Brown University, Providence, RI, USA
| | - Elena Besley
- Department of Physical and Theoretical Chemistry, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - A J Stace
- Department of Physical and Theoretical Chemistry, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| |
Collapse
|
29
|
Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chem Sci 2018; 9:956-972. [PMID: 29732110 PMCID: PMC5909332 DOI: 10.1039/c7sc04531j] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/24/2017] [Indexed: 12/23/2022] Open
Abstract
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.
Collapse
Affiliation(s)
- Louis Lagardère
- Sorbonne Université , Institut des Sciences du Calcul et des Données , Paris , France
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Luc-Henri Jolly
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
| | - Filippo Lipparini
- Universita di Pisa , Dipartimento di Chimica e Chimica Industriale , Pisa , Italy
| | - Félix Aviat
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Benjamin Stamm
- MATHCCES , Department of Mathematics , RWTH Aachen University , Aachen , Germany
| | - Zhifeng F Jing
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Matthew Harger
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Hedieh Torabifard
- Department of Chemistry , Wayne State University , Detroit , MI 48202 , USA
| | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , TX 76202 , USA
| | - Michael J Schnieders
- The University of Iowa , Department of Biomedical Engineering , Iowa City , IA , USA
| | - Nohad Gresh
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Yvon Maday
- Sorbonne Université , Laboratoire Jacques-Louis Lions , UMR 7598 , CNRS , Paris , France
- Institut Universitaire de France , Paris , France
- Brown University , Division of Applied Maths , Providence , RI , USA
| | - Pengyu Y Ren
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Jay W Ponder
- Washington University in Saint Louis , Department of Chemistry , Saint Louis , MI , USA
| | - Jean-Philip Piquemal
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
- Institut Universitaire de France , Paris , France
| |
Collapse
|
30
|
Aviat F, Levitt A, Stamm B, Maday Y, Ren P, Ponder JW, Lagardère L, Piquemal JP. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations. J Chem Theory Comput 2016; 13:180-190. [PMID: 28068773 PMCID: PMC5228058 DOI: 10.1021/acs.jctc.6b00981] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We
introduce a new class of methods, denoted as Truncated Conjugate
Gradient(TCG), to solve the many-body polarization energy and its
associated forces in molecular simulations (i.e. molecular dynamics
(MD) and Monte Carlo). The method consists in a fixed number of Conjugate
Gradient (CG) iterations. TCG approaches provide a scalable solution
to the polarization problem at a user-chosen cost and a corresponding
optimal accuracy. The optimality of the CG-method guarantees that
the number of the required matrix-vector products are reduced to a
minimum compared to other iterative methods. This family of methods
is non-empirical, fully adaptive, and provides analytical gradients,
avoiding therefore any energy drift in MD as compared to popular iterative
solvers. Besides speed, one great advantage of this class of approximate
methods is that their accuracy is systematically improvable. Indeed,
as the CG-method is a Krylov subspace method, the associated error
is monotonically reduced at each iteration. On top of that, two improvements
can be proposed at virtually no cost: (i) the use of preconditioners
can be employed, which leads to the Truncated Preconditioned Conjugate
Gradient (TPCG); (ii) since the residual of the final step of the
CG-method is available, one additional Picard fixed point iteration
(“peek”), equivalent to one step of Jacobi Over Relaxation
(JOR) with relaxation parameter ω, can be made at almost no
cost. This method is denoted by TCG-n(ω). Black-box adaptive
methods to find good choices of ω are provided and discussed.
Results show that TPCG-3(ω) is converged to high accuracy (a
few kcal/mol) for various types of systems including proteins and
highly charged systems at the fixed cost of four matrix-vector products:
three CG iterations plus the initial CG descent direction. Alternatively,
T(P)CG-2(ω) provides robust results at a reduced cost (three
matrix-vector products) and offers new perspectives for long polarizable
MD as a production algorithm. The T(P)CG-1(ω) level provides
less accurate solutions for inhomogeneous systems, but its applicability
to well-conditioned problems such as water is remarkable, with only
two matrix-vector product evaluations.
Collapse
Affiliation(s)
- Félix Aviat
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France
| | - Antoine Levitt
- Inria Paris, F-75589 Paris Cedex 12, Université Paris-Est, CERMICS (ENPC) , Marne-la-Vallée, F-77455, France
| | - Benjamin Stamm
- MATHCCES, Department of Mathematics, RWTH Aachen University , Schinkelstraße 2, D-52062 Aachen, Germany.,Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , Jülich, 52425, Germany
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions, UPMC Université Paris 06, UMR 7598 , F-75005, Paris, France.,Institut Universitaire de France , Paris Cedex 05, 75231, France.,Division of Applied Maths, Brown University , Providence, Rhode Island 02912, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis , Campus Box 1134, One Brookings Drive, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France.,Institut du Calcul et de la Simulation, UPMC Université Paris 06 , F-75005, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France.,Institut Universitaire de France , Paris Cedex 05, 75231, France
| |
Collapse
|
31
|
Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal JP. Polarizable molecular dynamics in a polarizable continuum solvent. J Chem Theory Comput 2016; 11:623-34. [PMID: 26516318 DOI: 10.1021/ct500998q] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-term energy conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.
Collapse
Affiliation(s)
- Filippo Lipparini
- UniversitéPierre et Marie Curie−Paris 06 (UPMC), UMR 7598, Laboratoire Jacques-Louis Lions, Sorbonne Universités, F-75005, Paris, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Stamm B, Cancès E, Lipparini F, Maday Y. A new discretization for the polarizable continuum model within the domain decomposition paradigm. J Chem Phys 2016; 144:054101. [DOI: 10.1063/1.4940136] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
33
|
Lipparini F, Scalmani G, Lagardère L, Stamm B, Cancès E, Maday Y, Piquemal JP, Frisch MJ, Mennucci B. Quantum, classical, and hybrid QM/MM calculations in solution: general implementation of the ddCOSMO linear scaling strategy. J Chem Phys 2015; 141:184108. [PMID: 25399133 DOI: 10.1063/1.4901304] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We present the general theory and implementation of the Conductor-like Screening Model according to the recently developed ddCOSMO paradigm. The various quantities needed to apply ddCOSMO at different levels of theory, including quantum mechanical descriptions, are discussed in detail, with a particular focus on how to compute the integrals needed to evaluate the ddCOSMO solvation energy and its derivatives. The overall computational cost of a ddCOSMO computation is then analyzed and decomposed in the various steps: the different relative weights of such contributions are then discussed for both ddCOSMO and the fastest available alternative discretization to the COSMO equations. Finally, the scaling of the cost of the various steps with respect to the size of the solute is analyzed and discussed, showing how ddCOSMO opens significantly new possibilities when cheap or hybrid molecular mechanics/quantum mechanics methods are used to describe the solute.
Collapse
Affiliation(s)
- Filippo Lipparini
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac St. Bldg. 40, Wallingford, Connecticut 06492, USA
| | - Louis Lagardère
- Sorbonne Universités, UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005 Paris, France
| | - Benjamin Stamm
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
| | - Eric Cancès
- Université Paris-Est, CERMICS, Ecole des Ponts and INRIA, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée Cedex 2, France
| | - Yvon Maday
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris, France
| | - Michael J Frisch
- Gaussian, Inc., 340 Quinnipiac St. Bldg. 40, Wallingford, Connecticut 06492, USA
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| |
Collapse
|
34
|
Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald. J Chem Theory Comput 2015; 11:2589-99. [DOI: 10.1021/acs.jctc.5b00171] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Louis Lagardère
- Institut
du Calcul et de la Simulation, UPMC Univ. Paris 06, F-75005, Paris, France
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
| | - Filippo Lipparini
- Institut
du Calcul et de la Simulation, UPMC Univ. Paris 06, F-75005, Paris, France
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
| | - Étienne Polack
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
| | - Benjamin Stamm
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
- CNRS, UMR 7598 and 7616, F-75005, Paris, France
| | - Éric Cancès
- Université Paris-Est, CERMICS, Ecole des Ponts and INRIA, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée, France
| | - Michael Schnieders
- Departments
of Biomedical Engineering and Biochemistry, The University of Iowa, Iowa City, Iowa 52358, United States
| | - Pengyu Ren
- Department
of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yvon Maday
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
- Institut Universitaire de France, F-75005, Paris, France
- Division
of Applied Mathematics, Brown University, Providence, Rhode Island 02912, United States
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
| |
Collapse
|
35
|
Suárez G, Maday Y, Bustamante J. Mechanical bio-pump as a functional component of a ventricular assist system: haemodynamic-modelling study and fluid-structure solution. IJBET 2015. [DOI: 10.1504/ijbet.2015.072935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
36
|
Szopos M, Poussineau N, Maday Y, Canniffe C, Celermajer DS, Bonnet D, Ou P. Computational modeling of blood flow in the aorta—insights into eccentric dilatation of the ascending aorta after surgery for coarctation. J Thorac Cardiovasc Surg 2014; 148:1572-82. [DOI: 10.1016/j.jtcvs.2013.11.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/01/2013] [Accepted: 11/15/2013] [Indexed: 12/31/2022]
|
37
|
|
38
|
Lipparini F, Lagardère L, Scalmani G, Stamm B, Cancès E, Maday Y, Piquemal JP, Frisch MJ, Mennucci B. Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach. J Phys Chem Lett 2014; 5:953-958. [PMID: 26270973 DOI: 10.1021/jz5002506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a new implementation of continuum solvation models for semiempirical Hamiltonians that allows the description of environmental effects on very large molecular systems. In this approach based on a domain decomposition strategy of the COSMO model (ddCOSMO), the solution to the COSMO equations is no longer the computational bottleneck but becomes a negligible part of the overall computation time. In this Letter, we analyze the computational impact of COSMO on the solution of the SCF equations for large to very large molecules, using semiempirical Hamiltonians, for both the new ddCOSMO implementation and the most recent, linear scaling one, based on the fast multipole method. A further analysis is on the simulation of the UV/visible spectrum of a light-harvesting pigment-protein complex. All of the results show how the new ddCOSMO algorithm paves the way to routine computations for large molecular systems in the condensed phase.
Collapse
Affiliation(s)
- Filippo Lipparini
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- ‡Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, F-75005 Paris, France
- ¶Institut du Calcul et de la Simulation, Sorbonne Universités, UPMC Univ. Paris 06, F-75005 Paris, France
| | - Louis Lagardère
- ¶Institut du Calcul et de la Simulation, Sorbonne Universités, UPMC Univ. Paris 06, F-75005 Paris, France
| | - Giovanni Scalmani
- §Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Benjamin Stamm
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- ∥CNRS, UMR 7598 and 7616, F-75005 Paris, France
| | | | - Yvon Maday
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- #Institut Universitaire de France, France
- ∇Division of Applied Maths, Brown University, Providence, Rhode Island 02912, United States
| | - Jean-Philip Piquemal
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- ∥CNRS, UMR 7598 and 7616, F-75005 Paris, France
| | - Michael J Frisch
- §Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Benedetta Mennucci
- ◆Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| |
Collapse
|
39
|
Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald. J Chem Theory Comput 2014; 10:1638-1651. [PMID: 26512230 DOI: 10.1021/ct401096t] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this paper, we present a scalable and efficient implementation of point dipole-based polarizable force fields for molecular dynamics (MD) simulations with periodic boundary conditions (PBC). The Smooth Particle-Mesh Ewald technique is combined with two optimal iterative strategies, namely, a preconditioned conjugate gradient solver and a Jacobi solver in conjunction with the Direct Inversion in the Iterative Subspace for convergence acceleration, to solve the polarization equations. We show that both solvers exhibit very good parallel performances and overall very competitive timings in an energy-force computation needed to perform a MD step. Various tests on large systems are provided in the context of the polarizable AMOEBA force field as implemented in the newly developed Tinker-HP package which is the first implementation for a polarizable model making large scale experiments for massively parallel PBC point dipole models possible. We show that using a large number of cores offers a significant acceleration of the overall process involving the iterative methods within the context of spme and a noticeable improvement of the memory management giving access to very large systems (hundreds of thousands of atoms) as the algorithm naturally distributes the data on different cores. Coupled with advanced MD techniques, gains ranging from 2 to 3 orders of magnitude in time are now possible compared to non-optimized, sequential implementations giving new directions for polarizable molecular dynamics in periodic boundary conditions using massively parallel implementations.
Collapse
Affiliation(s)
- Louis Lagardère
- UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
| | - Filippo Lipparini
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France ; UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France
| | - Étienne Polack
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
| | - Benjamin Stamm
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; CNRS, UMR 7598 and 7616, F-75005, Paris, France
| | - Éric Cancès
- Université Paris-Est, CERMICS, Ecole des Ponts and INRIA, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée, France
| | - Michael Schnieders
- Departments of Biomedical Engineering and Biochemistry, The University of Iowa, Iowa City, Iowa 52358, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yvon Maday
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; Institut Universitaire de France ; Brown Univ, Division of Applied Maths, Providence, RI, USA
| | - Jean-Philip Piquemal
- UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
| |
Collapse
|
40
|
|
41
|
Lipparini F, Stamm B, Cancès E, Maday Y, Mennucci B. Fast Domain Decomposition Algorithm for Continuum Solvation Models: Energy and First Derivatives. J Chem Theory Comput 2013; 9:3637-48. [DOI: 10.1021/ct400280b] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Filippo Lipparini
- UPMC Université Paris
06, Institut du Calcul et de la Simulation, F-75005 Paris, France
| | - Benjamin Stamm
- UPMC Université Paris
06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France
| | - Eric Cancès
- Université Paris-Est, CERMICS, Project-team Micmac, INRIA-Ecole des Ponts, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée Cedex 2, France
| | - Yvon Maday
- UPMC Université Paris
06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France
- Institut Universitaire de France,
103 bd Saint-Michel 75005 Paris
- Brown University, Division of
Applied Maths, Providence, Rhode Island, United States
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| |
Collapse
|
42
|
|
43
|
|
44
|
Fodil R, Croce C, Louis B, Coste A, Blondeau J, Isabey D, Perchet D, Fetita C, Preteux F, Grenier P, Vial L, Caillibotte G, Till M, Maday Y, Thiriet M, de Rochefort L, Maître X, Bittoun J, Durand E, Sbirlea-Apiou G. Simulateur morphofonctionnel des voies aériennes supérieures et proximales. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.rbmret.2004.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
45
|
|
46
|
Baffico L, Bernard S, Maday Y, Turinici G, Zérah G. Parallel-in-time molecular-dynamics simulations. Phys Rev E Stat Nonlin Soft Matter Phys 2002; 66:057701. [PMID: 12513644 DOI: 10.1103/physreve.66.057701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2002] [Indexed: 05/24/2023]
Abstract
While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations.
Collapse
Affiliation(s)
- L Baffico
- Laboratoire Jacques-Louis Lions, Université Pierre et Marie Curie, Boîte Courrier 187, 75252 Paris Cedex 05, France
| | | | | | | | | |
Collapse
|
47
|
Maday Y, Patera A, Rovas D. A Blackbox Reduced-Basis Output Bound Method for Noncoercive Linear Problems. Nonlinear Partial Differential Equations and their Applications - Collège de France Seminar Volume XIV 2002. [DOI: 10.1016/s0168-2024(02)80025-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
48
|
Machiels L, Maday Y, Oliveira IB, Patera AT, Rovas DV. Output bounds for reduced-basis approximations of symmetric positive definite eigenvalue problems. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0764-4442(00)00270-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
49
|
Machiels L, Maday Y, Patera AT. A “flux-free” nodal Neumann subproblem approach to output bounds for partial differential equations. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0764-4442(00)00122-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
50
|
Maday Y, Patera AT, Peraire J. A general formulation for a posteriori bounds for output functionals of partial differential equations; application to the eigenvalue problem. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0764-4442(99)80279-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|