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Start Over Topic computer simulation Publication Type Periodicals
13 results

1. Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection.

Author

Cox CE, Phifer JR, Ferreira da Silva L, Gonçalves Nogueira G, Ley RT, O'Loughlin EJ, Pereira Barbosa AK, Rygelski BT, and Paluch AS

Subjects
Molecular Structure, Quantum Theory, Solubility, Thermodynamics, Computer Simulation, Parabens chemistry, Solutions chemistry, Solvents chemistry
Abstract

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

Published
2017
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2. Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model.

Author

Diaz-Rodriguez S, Bozada SM, Phifer JR, and Paluch AS

Subjects
Molecular Structure, Solubility, Thermodynamics, Computer Simulation, Cyclohexanes chemistry, Models, Chemical, Pharmaceutical Preparations chemistry, Solvents chemistry, Water chemistry
Abstract

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of [Formula: see text] log units (ranking 15 out of 62 entries), the correlation coefficient (R) was [Formula: see text] (ranking 35), and [Formula: see text] of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

Published
2016
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3. Biological Testing of Organophosphorus-Inactivated Acetylcholinesterase Oxime Reactivators Identified via Virtual Screening.

Author

Berberich JA, Stouch TR, Manepalli S, Esposito EX, and Madura JD

Subjects
Databases, Chemical, Enzyme Activation drug effects, Erythrocytes enzymology, Humans, Molecular Structure, Organophosphorus Compounds pharmacology, Oximes pharmacology, Pralidoxime Compounds chemistry, Pralidoxime Compounds pharmacology, Structure-Activity Relationship, Acetylcholinesterase chemistry, Acetylcholinesterase metabolism, Computer Simulation, Organophosphorus Compounds chemistry, Oximes chemistry
Abstract

There is a pressing need for new therapeutics to reactivate covalently inactivated acetylcholinesterase (AChE) due to exposure to organophosphorus (OP) compounds. Current reactivation therapeutics (RTs) are not broad-spectrum and suffer from other liabilities, specifically the inability to cross the blood-brain-barrier. Additionally, the chemical diversity of available therapeutics is small, limiting opportunities for structure-activity relationship (SAR) studies to aid in the design of more effective compounds. In order to find new starting points for the development of oxime-containing therapeutic reactivators and to increase our base of knowledge, we have employed a combination of computational and experimental procedures to identify additional compounds with the real or potential ability to reactivate AChE while augmenting and complementing current knowledge. Computational methods were used to identify previously uninvestigated oxime-containing molecules. Experimentally, six compounds were found with reactivation capabilities comparable to, or exceeding, those of 2-pralidoxime (2-PAM) against a panel of AChE inactivated by paraoxon, diisopropylfluorophosphate (DFP), fenamiphos, and methamidophos. One compound showed enhanced reactivation ability against DFP and fenamiphos, the least tractable of these OPs to be reactivated.

Published
2016
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4. Multiscale computational model of fluid flow and matrix deformation in decellularized liver.

Author

Nishii K, Reese G, Moran EC, and Sparks JL

Subjects
Animals, Biomechanical Phenomena, Finite Element Analysis, Hemodynamics, Liver blood supply, Materials Testing, Pressure, Rats, Rats, Sprague-Dawley, Reproducibility of Results, Tissue Engineering, Computer Simulation, Hydrodynamics, Liver cytology, Mechanical Phenomena
Abstract

Currently little is known about the biomechanical environment in decellularized tissue. The goal of this research is to quantify the mechanical microenvironment in decellularized liver, for varying organ-scale perfusion conditions, using a combined experimental/computational approach. Needle-guided ultra-miniature pressure sensors were inserted into liver tissue to measure parenchymal fluid pressure ex-situ in portal vein-perfused native (n=5) and decellularized (n=7) ferret liver, for flow rates from 3-12mL/min. Pressures were also recorded at the inlet near the portal vein cannula to estimate total vascular resistance of the specimens. Experimental results were fit to a multiscale computational model to simulate perfusion conditions inside native versus decellularized livers for four experimental flow rates. The multiscale model consists of two parts: an organ-scale electrical analog model of liver hemodynamics and a tissue-scale model that predicts pore fluid pressure, pore fluid velocity, and solid matrix stress and deformation throughout the 3D hepatic lobule. Distinct models were created for native versus decellularized liver. Results show that vascular resistance decreases by 82% as a result of decellularization. The hydraulic conductivity of the decellularized liver lobule, a measure of tissue permeability, was 5.6 times that of native liver. For the four flow rates studied, mean fluid pressures in the decellularized lobule were 0.6-2.4mmHg, mean fluid velocities were 211-767μm/s, and average solid matrix principal strains were 1.7-6.1%. In the future this modeling platform can be used to guide the optimization of perfusion seeding and conditioning strategies for decellularized scaffolds in liver bioengineering., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Published
2016
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5. Simulation of swimming of a flexible filament using the generalized lattice-spring lattice-Boltzmann method.

Author

Wu TH, Guo RS, He GW, Liu YM, and Qi D

Subjects
Flagella physiology, Reproducibility of Results, Rheology, Time Factors, Computer Simulation, Models, Theoretical, Movement, Pliability
Abstract

A generalized lattice-spring lattice-Boltzmann model (GLLM) is introduced by adding a three-body force in the traditional lattice-spring model. This method is able to deal with bending deformation of flexible biological bodies in fluids. The interactions between elastic solids and fluid are treated with the immersed boundary-lattice Boltzmann method. GLLM is validated by comparing the present results with the existing theoretical and simulation results. As an application of GLLM, swimming of flagellum in fluid is simulated and propulsive force as a function of driven frequency and fluid structures at various Reynolds numbers 0.15-5.1 are presented in this paper., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Published
2014
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6. A dynamic neural field model of multimodal merging: application to the ventriloquist effect

Author

Simon Forest, Jean-Charles Quinton, Mathieu Lefort, Statistique pour le Vivant et l’Homme (SVH), Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Systèmes Cognitifs et Systèmes Multi-Agents (SyCoSMA), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Project AMPLIFIER, funded by the French region Auvergne-Rhône-Alpes in the context of the 'Pack Ambition Recherche' initiative., Most of the computations presented in this paper were performed using the GRICAD infrastructure (https://gricad.univ-grenoble-alpes.fr), which is supported by Grenoble research communities., ANR-11-LABX-0025,PERSYVAL-lab,Systemes et Algorithmes Pervasifs au confluent des mondes physique et numérique(2011), and ANR-14-CE25-0006,GAG,Jeux et graphes(2014)

Subjects
Superior Colliculi, Arts and Humanities (miscellaneous), Cognitive Neuroscience, [SCCO.NEUR]Cognitive science/Neuroscience, Visual Perception, Humans, Bayes Theorem, Computer Simulation, [INFO.INFO-NE]Computer Science [cs]/Neural and Evolutionary Computing [cs.NE], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Photic Stimulation, Probability
Abstract

Multimodal merging encompasses the ability to localize stimuli based on imprecise information sampled through individual senses such as sight and hearing. Merging decisions are standardly described using Bayesian models that fit behaviors over many trials, encapsulated in a probability distribution. We introduce a novel computational model based on dynamic neural fields able to simulate decision dynamics and generate localization decisions, trial by trial, adapting to varying degrees of discrepancy between audio and visual stimulations. Neural fields are commonly used to model neural processes at a mesoscopic scale—for instance, neurophysiological activity in the superior colliculus. Our model is fit to human psychophysical data of the ventriloquist effect, additionally testing the influence of retinotopic projection onto the superior colliculus and providing a quantitative performance comparison to the Bayesian reference model. While models perform equally on average, a qualitative analysis of free parameters in our model allows insights into the dynamics of the decision and the individual variations in perception caused by noise. We finally show that the increase in the number of free parameters does not result in overfitting and that the parameter space may be either reduced to fit specific criteria or exploited to perform well on more demanding tasks in the future. Indeed, beyond decision or localization tasks, our model opens the door to the simulation of behavioral dynamics, as well as saccade generation driven by multimodal stimulation.

Published
2022

7. How much does prosody help word segmentation? A simulation study on infant-directed speech

Author

Emmanuel Dupoux, Reiko Mazuka, Alejandrina Cristia, Bogdan Ludusan, RIKEN Center for Brain Science [Wako] (RIKEN CBS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Department of Psychology and Neuroscience, Duke University [Durham], Laboratoire de sciences cognitives et psycholinguistique (LSCP), Département d'Etudes Cognitives - ENS Paris (DEC), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS), Apprentissage machine et développement cognitif (CoML), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS)-Département d'Etudes Cognitives - ENS Paris (DEC), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), École des hautes études en sciences sociales (EHESS), The research reported in this paper was partly funded by JSPS Grant-in-Aid for Scientific Research (16H06319, 20H05617) and MEXT Grant-in-aid on Innovative Areas #4903 (Co-creative Language Evolution), 17H06382 to RM. It was also supported by the European Research Council (ERC-2011-AdG-295810 BOOTPHON), the Agence Nationale pour la Recherche (ANR-17-CE28-0007 LangAge, ANR-16-DATA-0004 ACLEW, ANR-14-CE30-0003 MechELex, ANR-17-EURE-0017 Frontcog, ANR-10-IDEX-0001-02 PSL*, ANR-19-P3IA-0001 PRAIRIE 3IA Institute). ED is further grateful to the CIFAR (Learning in Machines and Brain), BL to the Canon Foundation in Europe, and AC to the JS McDonnell Foundation., ANR-17-CE28-0007,LangAge,Différences dans l'apprenabilité du langage selon l'âge(2017), ANR-16-DATA-0004,ACLEW,Analyzing Child Language Experiences Around the World(2016), ANR-14-CE30-0003,MechELex,Méchanismes d'acquisition lexicale précoce(2014), ANR-17-EURE-0017,FrontCog,Frontières en cognition(2017), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), European Project: 295810,EC:FP7:ERC,ERC-2011-ADG_20110406,BOOTPHON(2012), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris)

Subjects
Linguistics and Language, Cognitive Neuroscience, Speech recognition, Experimental and Cognitive Psychology, Prosody, Infant-directed speech, 050105 experimental psychology, Language and Linguistics, Speech Acoustics, Task (project management), Infant language acquisition, Developmental and Educational Psychology, Humans, Learning, Speech, 0501 psychology and cognitive sciences, Segmentation, Computer Simulation, ComputingMilieux_MISCELLANEOUS, Computational model, 05 social sciences, Text segmentation, Infant, acquisition, [SCCO.LING]Cognitive science/Linguistics, Word segmentation, [SCCO.PSYC]Cognitive science/Psychology, Speech Perception, Infant language, Cues, Heuristics, Psychology, Word (computer architecture), 050104 developmental & child psychology
Abstract

International audience; Infants come to learn several hundreds of word forms by two years of age, and it is possible this involves carving these forms out from continuous speech. It has been proposed that the task is facilitated by the presence of prosodic boundaries. We revisit this claim by running computational models of word segmentation, with and without prosodic information, on a corpus of infant-directed speech. We use five cognitively-based algorithms, which vary in whether they employ a sub-lexical or a lexical segmentation strategy and whether they are simple heuristics or embody an ideal learner. Results show that providing expert-annotated prosodic breaks does not uniformly help all segmentation models. The sub-lexical algorithms, which perform more poorly, benefit most, while the lexical ones show a very small gain. Moreover, when prosodic information is derived automatically from the acoustic cues infants are known to be sensitive to, errors in the detection of the boundaries lead to smaller positive effects, and even negative ones for some algorithms. This shows that even though infants could potentially use prosodic breaks, it does not necessarily follow that they should incorporate prosody into their segmentation strategies, when confronted with realistic signals.

Published
2022

8. Modeling Interactions among Migration, Growth and Pressure in Tumor Dynamics

Author

Juan Campos, Juan José Soler, Juan Melchor, Beatriz Blanco, [Blanco, Beatriz] Univ Granada, Dept Struct Mech, Granada 18071, Spain, [Blanco, Beatriz] Ibs GRANADA, Inst Invest Biosanitaria, Granada 18012, Spain, [Melchor, Juan] Ibs GRANADA, Inst Invest Biosanitaria, Granada 18012, Spain, [Campos, Juan] Univ Granada, Fac Ciencias, Dept Matemat Aplicada, Granada 18071, Spain, [Soler, Juan] Univ Granada, Fac Ciencias, Dept Matemat Aplicada, Granada 18071, Spain, [Campos, Juan] Univ Granada, Res Unit Modelling Nat MNat, Granada 18071, Spain, [Melchor, Juan] Univ Granada, Res Unit Modelling Nat MNat, Granada 18071, Spain, [Soler, Juan] Univ Granada, Res Unit Modelling Nat MNat, Granada 18071, Spain, [Melchor, Juan] Univ Granada, Dept Stat & Operat Res, Granada 18071, Spain, MINECO-Feder (Spain), Junta de Andalucia (Spain), Instituto de Salud Carlos III, Ministry of Science, Innovation and Universities of Spain, Consejeria de Economia, Conocimiento, Empresas y Universidad, European Regional Development Fund (ERDF), [Blanco,B] Department of Structural Mechanics, University of Granada, Granada, Spain. [Blanco,B, Melchor,J] Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Spain. [Campos,J, Soler,J] Departamento de Matemática Aplicada, Facultad de Ciencias, Universidad de Granada, Granada, Spain. [Campos,J, Melchor,J, Soler,J] Research Unit 'Modelling Nature' (MNat), Universidad de Granada, Granada, Spain., and This paper has been partially supported by the MINECO-Feder (Spain) research grant num bers RTI2018-098850-B-I00 (J.C., J.S.) & EQC2018-004508-P (B.B., J.M.), the Junta de Andalucía (Spain) Projects PY18-RT-2422 (J.C., J.S.), A-FQM-311-UGR18 (J.C., J.S.) & IE2017-5537 (B.B., J.M.), and by the Instituto de Salud Carlos III, project number DTS17/00087 (J.M., J.S.). This study was also funded by Ministry of Science, Innovation and Universities of Spain, project numbers DPI2017-85359-R (B.B., J.M.) & PID2019-106947RA-C22 (B.B., J.M.) and by Consejería de Economía, Conocimiento, Empresas y Universidad and European Regional Development Fund (ERDF), ref. SOMM17/6109/UGR (J.C., J.M., J.S.). Lastly, B.B. research was granted by Ministry of Science, Innovation and Universities of Spain, FPU2017/01415.

Subjects
Computer science, 01 natural sciences, Forces, Phenomena and Processes::Cell Physiological Phenomena::Cell Physiological Processes::Cell Movement [Medical Subject Headings], Diffusion, porous media, Qualitative behavior, Computer Science (miscellaneous), Numerical simulations, Homeostasis, Statistical physics, Diffusion (business), Solid tumor, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Data Collection::Vital Statistics::Mortality::Cause of Death [Medical Subject Headings], Cancer, 0303 health sciences, Partial differential equation, Mathematical modelling, Dynamics (mechanics), Traveling-waves, mathematical modeling, tumor dynamics, Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Signal Transduction [Medical Subject Headings], Diseases::Neoplasms [Medical Subject Headings], flux-saturated, Modelos teóricos, General Mathematics, Phenomena and Processes::Physical Phenomena::Mechanical Phenomena::Porosity [Medical Subject Headings], Context (language use), Information Science::Information Science::Communication::Cybernetics::Feedback [Medical Subject Headings], cell motility, Stress, Mechanics, 03 medical and health sciences, QA1-939, Hele-Shaw model, Movimiento celular, Phenomena and Processes::Physical Phenomena::Mechanical Phenomena::Elasticity [Medical Subject Headings], 0101 mathematics, Engineering (miscellaneous), 030304 developmental biology, Computer simulation, 010102 general mathematics, Porous-media equations, Mass, numerical simulation, Floculadores, Phenomena and Processes::Cell Physiological Phenomena::Cell Physiological Processes::Cell Transdifferentiation::Epithelial-Mesenchymal Transition [Medical Subject Headings], mechanical feedback, Phenomena and Processes::Physiological Phenomena::Physiological Processes::Homeostasis [Medical Subject Headings], Mathematics
Abstract

What are the biomechanical implications in the dynamics and evolution of a growing solid tumor? Although the analysis of some of the biochemical aspects related to the signaling pathways involved in the spread of tumors has advanced notably in recent times, their feedback with the mechanical aspects is a crucial challenge for a global understanding of the problem. The aim of this paper is to try to illustrate the role and the interaction between some evolutionary processes (growth, pressure, homeostasis, elasticity, or dispersion by flux-saturated and porous media) that lead to collective cell dynamics and defines a propagation front that is in agreement with the experimental data. The treatment of these topics is approached mainly from the point of view of the modeling and the numerical approach of the resulting system of partial differential equations, which can be placed in the context of the Hele-Shaw-type models. This study proves that local growth terms related to homeostatic pressure give rise to retrograde diffusion phenomena, which compete against migration through flux-saturated dispersion terms., MINECO-Feder (Spain) research grant numbers RTI2018-098850-B-I00 (J.C., J.S.) & EQC2018-004508-P (B.B., J.M.), Junta de Andalucía (Spain) Projects PY18-RT-2422 (J.C., J.S.), A-FQM-311-UGR18 (J.C., J.S.) & IE2017-5537 (B.B., J.M.), Instituto de Salud Carlos III, project number DTS17/00087 (J.M., J.S.), Ministry of Science, Innovation and Universities of Spain, project numbers DPI2017-85359-R (B.B., J.M.) & PID2019-106947RA-C22 (B.B., J.M.), Consejería de Economía, Conocimiento, Empresas y Universidad and European Regional Development Fund (ERDF), ref. SOMM17/6109/UGR (J.C., J.M., J.S.), Ministry of Science, Innovation and Universities of Spain, FPU2017/01415

Published
2021

9. Some analytical solutions for validation of free surface flow computational codes

Author

Bernard Di Martino, Fabien Souillé, Jacques Sainte-Marie, Marie-Odile Bristeau, Anne Mangeney, Numerical Analysis, Geophysics and Ecology (ANGE), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), The work presented in this paper was supported in part by the ANR Mimosa (ANR-14-CE01-0012) and ERC contract ERC-CG-2013-PE10-617472 SLIDEQUAKES. The authors also acknowledge the Inria Project Lab 'Algae in Silico' for its financial support., ANR-14-CE01-0012,MIMOSA,Analyse, modélisation et utilisation du bruit sismique large bande: des microséismes aux oscillations libres de la terre(2014), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS)

Subjects
010103 numerical & computational mathematics, Analytical solutions, 01 natural sciences, law.invention, Physics::Fluid Dynamics, Free surface Euler equations, symbols.namesake, law, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], Boundary value problem, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph], 0101 mathematics, [MATH]Mathematics [math], Mathematics, Computer simulation, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Mechanics of the fluids [physics.class-ph], Mechanical Engineering, Mechanics, Euler system, Condensed Matter Physics, River dynamics, Euler equations, 010101 applied mathematics, Flow (mathematics), Mechanics of Materials, Free surface, symbols, Compressibility, Hydrostatic equilibrium
Abstract

We present several time dependent analytical solutions for the incompressible Euler system with free surface. These analytical solutions give quantitative descriptions of some physical phenomena and can be used as reference solutions when validating numerical simulation codes. They concern fluid flows governed by Euler equations with or withouthydrostatic hypothesis including wet/dry interface, variable density, wide variety of boundary conditions and possibly non-uniform bottom topographies. Some of these analytical solutions concern shallow water type models or free surface Navier-Stokes model i.e. with a viscous fluid.

Published
2021

10. Geometry description and mesh construction from medical imaging

Author

Silvia Bertoluzza, Minh Phan, Michela Spagnuolo, Philippe Ricka, Micol Pennacchio, Giuseppe Patanè, Michele Giuliano Carlino, Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Modeling Enablers for Multi-PHysics and InteractionS (MEMPHIS), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de Recherche Mathématique Avancée (IRMA), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de Mathématiques de Toulon - EA 2134 (IMATH), Université de Toulon (UTLN), Istituto di Matematica Applicata e Tecnologie Informatiche (IMATI), Consiglio Nazionale delle Ricerche (CNR), Istituto di Matematica Applicata e Tecnologie Informatiche (IMATI-CNR), Consiglio Nazionale delle Ricerche [Roma] (CNR), his paper has been realized in the framework of ERC Project CHANGE, which has received funding from the EuropeanResearch Council (ERC) under the European Unions Horizon 2020 research and innovation programme (grant agreement No694515., European Project: 8509436(1986), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), and National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR)

Subjects
T57-57.97, Applied mathematics. Quantitative methods, Computer simulation, Computer science, business.industry, Atlas (topology), ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, Image segmentation, Modular design, Reference image, N/A, QA1-939, Medical imaging, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, A priori and a posteriori, Computer vision, [INFO]Computer Science [cs], Artificial intelligence, business, Mathematics, ComputingMethodologies_COMPUTERGRAPHICS
Abstract

International audience; We present a new method for defining and meshing patient-specific domains from medical images. Our approach is based on an atlas image segmentation technique, and relies on the modular registration algorithm of S. Bertoluzza et al. [25]. The mesh of the patient-specific domain is generated by deforming the corresponding mesh on an a priori segmented and meshed reference image (the atlas). Our method aims at automating the process at the interface of medical imaging and numerical simulation, thus reducing the computational cost in those situations where simulations have to be managed on numerous medical images of similar patients.; Nous présentons une nouvelle méthode de reconnaissance et de maillage d’un domaine d’intérêt d’une image médicale. Notre approche se base sur une méthode de segmentation à partir d’un atlas, et dépend de la boîte à outils modulaire pour la co-registration d’images développée par S. Bertoluzza et al. [25]. Le maillage du domaine spécifique au patient est généré par déformation du maillage correspondant sur une image de référence segmentée a priori (l’atlas). Notre méthode vise à automatiser le processus à l’interface entre l’imagerie médicale et la simulation numérique, avec pour but de réduire le coût de calcul dans les situations dans lesquelles des simulations doivent être faites sur de nombreuses images similaires.

Published
2020

11. Incorporating individual historical controls and aggregate treatment effect estimates into a Bayesian survival trial: a simulation study

Author

Lisa V. Hampson, Marie-Cécile Le Deley, Caroline Brard, Nathalie Gaspar, Gwénaël Le Teuff, Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de biostatistique et d'épidémiologie (SBE), Direction de la recherche clinique [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Statistical Methodology [Bâle, Suisse], Novartis Pharma AG, Département de cancérologie de l'enfant et de l'adolescent [Gustave Roussy], Institut Gustave Roussy (IGR), Unité de Méthodologie et de Biostatistique [Lille] (UMB), Centre Régional de Lutte contre le Cancer Oscar Lambret [Lille] (UNICANCER/Lille), Université de Lille-UNICANCER-Université de Lille-UNICANCER, We acknowledge for the design, analysis, interpretation of the simulation study, and for the writing of the manuscript, funding from – PhD grant from doctoral school of public health, Paris-Sud, Paris-Saclay – Lisa Hampson’s contribution to the paper was partly funded by the UK Medical Research Council (grant MR/M013510/1) and was completed while she was an employee of Lancaster University – Ligue contre le cancer, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université Lille Nord de France (COMUE)-UNICANCER-Université Lille Nord de France (COMUE)-UNICANCER, and Bodescot, Myriam

Subjects
Simulation study, Epidemiology, Computer science, Bayesian probability, Health Informatics, [SDV.CAN]Life Sciences [q-bio]/Cancer, Power prior, law.invention, 03 medical and health sciences, 0302 clinical medicine, Adjuvants, Immunologic, [SDV.CAN] Life Sciences [q-bio]/Cancer, Randomized controlled trial, law, Statistics, Prior probability, Humans, Computer Simulation, 030212 general & internal medicine, Set (psychology), Baseline (configuration management), Bayesian randomised survival trial, Randomized Controlled Trials as Topic, Weibull distribution, Osteosarcoma, lcsh:R5-920, Phosphatidylethanolamines, 030503 health policy & services, Aggregate (data warehouse), Bayes Theorem, Variance (accounting), Models, Theoretical, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, Control Groups, Mixture prior, 3. Good health, [SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences, Research Design, Sample Size, Individual control data, 0305 other medical science, lcsh:Medicine (General), Aggregate treatment effect, Acetylmuramyl-Alanyl-Isoglutamine, Rare disease, Algorithms, Research Article
Abstract

Background Performing well-powered randomised controlled trials (RCTs) of new treatments for rare diseases is often infeasible. However, with the increasing availability of historical data, incorporating existing information into trials with small sample sizes is appealing in order to increase the power. Bayesian approaches enable one to incorporate historical data into a trial’s analysis through a prior distribution. Methods Motivated by a RCT intended to evaluate the impact on event-free survival of mifamurtide in patients with osteosarcoma, we performed a simulation study to evaluate the impact on trial operating characteristics of incorporating historical individual control data and aggregate treatment effect estimates. We used power priors derived from historical individual control data for baseline parameters of Weibull and piecewise exponential models, while we used a mixture prior to summarise aggregate information obtained on the relative treatment effect. The impact of prior-data conflicts, both with respect to the parameters and survival models, was evaluated for a set of pre-specified weights assigned to the historical information in the prior distributions. Results The operating characteristics varied according to the weights assigned to each source of historical information, the variance of the informative and vague component of the mixture prior and the level of commensurability between the historical and new data. When historical and new controls follow different survival distributions, we did not observe any advantage of choosing a piecewise exponential model compared to a Weibull model for the new trial analysis. However, we think that it remains appealing given the uncertainty that will often surround the shape of the survival distribution of the new data. Conclusion In the setting of Sarcome-13 trial, and other similar studies in rare diseases, the gains in power and accuracy made possible by incorporating different types of historical information commensurate with the new trial data have to be balanced against the risk of biased estimates and a possible loss in power if data are not commensurate. The weights allocated to the historical data have to be carefully chosen based on this trade-off. Further simulation studies investigating methods for incorporating historical data are required to generalise the findings. Electronic supplementary material The online version of this article (10.1186/s12874-019-0714-z) contains supplementary material, which is available to authorized users.

Published
2019

12. Modeling carbon dioxide transport in PDMS-based microfluidic cell culture devices

Author

Antti-Juhana Mäki, Joose Kreutzer, Mikko Peltokangas, Pasi Kallio, S. Auvinen, Tampere University, Department of Automation Science and Engineering, Department of Materials Science, Research group: Paper Converting and Packaging, BioMediTech, and Integrated Technologies for Tissue Engineering Research (ITTE)

Subjects
Materials science, Computer simulation, Concentration Response, Applied Mathematics, General Chemical Engineering, Microfluidics, Nanotechnology, General Chemistry, 217 Medical engineering, Industrial and Manufacturing Engineering, Finite element method, chemistry.chemical_compound, Silicone, chemistry, Cell culture, Concentration gradient, Biological system, Carbon dioxide transport
Abstract

Maintaining a proper pH level is crucial for successful cell culturing. Mammalian cells are commonly cultured in incubators, where the cell culture medium is saturated with a mixture of air and 5% carbon dioxide (CO2). Therefore, to keep cell culture medium pH in an acceptable level outside these incubators, a suitable CO2 concentration must be dissolved in the medium. However, it can be very difficult to control and measure precisely local concentration levels. Furthermore, possible undesired concentration gradients generated during long-term cell culturing are almost impossible to detect. Therefore, we have developed a computational model to estimate CO2 transport in silicone-based microfluidic devices. An extensive set of experiments was used to validate the finite element model. The model parameters were obtained using suitable measurement set-ups and the model was validated using a fully functional cell cultivation device. The predictions obtained by the simulations show very good responses to experiments. It is shown in this paper how the model helps to understand the dynamics of CO2 transport in silicone-based cell culturing devices possessing different geometries, thus providing cost-effective means for studying different device designs under a variety of experimental conditions without the need of actual testing. Finally, based on the results from the computational model, an alternative strategy for feeding CO2 is proposed to accelerate the system performance such that a faster and more uniform CO2 concentration response is achieved in the area of interest. acceptedVersion

Published
2015

13. Vortex cycles at the inner edges of dead zones in protoplanetary disks

Author

S. Fromang, Heloise Meheut, Julien Faure, Henrik N. Latter, Astrophysique Interprétation Modélisation (AIM (UMR7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Applied Mathematics and Theoretical Physics (DAMTP), University of Cambridge [UK] (CAM), J.F., S.F., and H.M. acknowledge funding from the European Research Council underthe European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement No. 258729. HL acknowledges support via STFC grant ST/G/002584/1. The simulations presented in this paper were granted access to the HPC resources of Cines under the allocation x2013042231 and x2014042231 made by GENCI (Grand Equipement National de Calcul Intensif)., European Project: 258729,EC:FP7:ERC,ERC-2010-StG_20091028,PETADISK(2011), Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), and Department of Applied Mathematics and Theoretical Physics / Centre for Mathematical Sciences (DAMTP/CMS)

Subjects
010504 meteorology & atmospheric sciences, FOS: Physical sciences, Context (language use), Astrophysics, Protoplanetary disk, 01 natural sciences, Instability, Physics::Fluid Dynamics, 0103 physical sciences, planets and satellites: formation, 010303 astronomy & astrophysics, 0105 earth and related environmental sciences, Physics, Earth and Planetary Astrophysics (astro-ph.EP), Computer simulation, Turbulence, protoplanetary disks, Rossby wave, Astronomy and Astrophysics, Laminar flow, Mechanics, Vortex, 13. Climate action, Space and Planetary Science, Astrophysics::Earth and Planetary Astrophysics, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Astrophysics - Earth and Planetary Astrophysics
Abstract

In protoplanetary disks, the inner boundary between the turbulent and laminar regions is a promising site for planet formation because solids may become trapped at the interface itself or in vortices generated by the Rossby wave instability. The disk thermodynamics and the turbulent dynamics at that location are entwined because of the importance of turbulent dissipation on thermal ionization and, conversely, of thermal ionisation on the turbulence. However, most previous work has neglected this dynamical coupling and have thus missed a key element of the physics in this region. In this paper, we aim to determine how the the interplay between ionization and turbulence impacts on the formation and evolution of vortices at the interface between the active and the dead zones. Using the Godunov code RAMSES, we have performed a 3D magnetohydrodynamic global numerical simulation of a cylindrical model of an MRI--turbulent protoplanetary disk, including thermodynamical effects as well as a temperature-dependant resistivity. The comparison with an analogous 2D viscous simulation has been extensively used to help identify the relevant physical processes and the disk's long-term evolution. We find that a vortex formed at the interface, due to Rossby wave instability, migrates inward and penetrates the active zone where it is destroyed by turbulent motions. Subsequently, a new vortex emerges a few tens of orbits later at the interface, and the new vortex migrates inward too. The sequence repeats itself, resulting in cycles of vortex formation, migration, and disruption. This behavior is successfully reproduced using two different codes. In this paper, we characterize this vortex life cycle and discuss its implications for planet formation at the dead/active interface. Our simulations highlight the importance of thermodynamical processes for the vortex evolution at the dead zone inner edge., Comment: 13 pages, 15 figures

Published
2015