# Soutenance de thèse – Louis Lagardère

Location:

« Calcul haute-performance et dynamique moléculaire polarisable »

Il s’agit d’une thèse à l’interface entre la chimie théorique, le calcul scientifique et les mathématiques appliquées dans laquelle on s’intéresse aux différents algorithmes utilisés pour résoudre les équations spécifiques qui apparaissent dans le cadre de la dynamique moléculaire utilisant des champs de forces polarisables dans un cadre massivement parallèle.
Cette famille de modèles nécessite en effet de résoudre des équations plus complexes que les modèles classiques usuels et rend nécessaire l’utilisation de supercalculateurs pour obtenir des résultats significatifs.
On s’intéressera plus précisément à différents cas de conditions aux limites pour rendre compte des effets de solvatation comme les conditions aux limites périodiques traitées avec la méthode du Particle Mesh Ewald et un modèle de solvatation continu discrétisé par décomposition de domaine : le ddCOSMO.

# PhD thesis offer

Location: ISCD, campus Jussieu, 33-34, 2nd floor

ISCD is actively looking for PhD candidates in computer science, or applied mathematics, or engineering for a challenging project in digital architecture.

Subject:

Design and implementation of 3D interaction techniques for exploring massive archaeological data.

Description:

The subject of the thesis is to design, implement and evaluate 3D interaction techniques for the exploration of archaeological data. The proposed techniques should allow interactive manipulation, navigation and exploration of massive data sets, as well as the visualization of intrinsic structures to facilitate the formulation of hypotheses and the scientific work of specialists. New performance criteria, exceeding those traditionally associated with this type of research (i.e., speed / reactivity, precision, versatility, etc.) should be proposed in consultation with users.

The solutions developed may be software (gestural interaction, multi-touch interaction, etc.), or hardware (haptic devices, VR helmet, etc.) or any combination of these two approaches.

This thesis is set in the working context of a multidisciplinary project-team of ISCD, gathering computer scientists, mathematicians, historians and archaeologists, around a historic building.

Skills required:

- master degree (or equivalent) in computer science (HCI, VR, etc.), applied mathematics, or engineering sciences;
- a pronounced taste for 3D interaction, human-machine interaction, virtual reality, mixed reality, haptic devices, or mathematical modeling;
- software development skills and graphics libraries (Java, C ++, QT, Android, OpenGl, etc.) and hardware (small mechanics, electronics);
- proficiency in English and good drafting skills;
- strong teamwork, exchange and communication skills.

Environment:

The thesis will be held at the University Pierre et Marie Curie (Paris) in a privileged environment for multidisciplinary work.

Contact us asap (deadline is May 20th, 2017):
contact_iscd@upmc.fr

# 6th ISCD summer school: bioinformatics and visual data analysis

Location: Marine Station, Roscoff (France), July 17 - August 11, 2017.

### Scientific trends at the interfaces:

bioinformatics and visual data analysis

This summer school program is perfect for undergraduate students (L3-M2) considering studying theoretical or computational sciences at university level. It comprises intensive courses which aim to provide attendees with an introduction to both the theoretical foundations and the practical applications of some of the modern mathematical and computational techniques currently in use. Each course has theoretical and practical classes, in which students can experiment each technique with computers.

The summer school will take place a the Marine Station in Roscoff.

Registrations are now open, until May 15, 2017. Follow this link

# Sysadmin position available

ISCD is actively looking for hiring an engineer who will be responsible for setting up and maintaining the HPC system at UPMC, and more precisely for:

- User administration (setup and maintaining account);
- Maintaining system;
- Verify that peripherals are working properly;
- Quickly arrange repair for hardware in occasion of hardware failure;
- Monitor system performance;
- Create file systems;
- Install software;
- Create a backup and recover policy;
- Monitor network communication;
- Implement the policies for the use of the computer system and network;
- Documentation in form of internal wiki;

download the description (PDF) in French.

# Postdoc available

ISCD is seeking talented candidates for a post-doctoral position, starting asap.

## Background

The study addresses under-determined inverse problems also known as data assimilation aimed at estimating the state of a complex physical system based on a finite number of measurements. The measurements are obtained from a monitoring network, the link between these and the state of the system is described by some model. The study addresses in fact the case of a model describing a linear link between the measurements and the state. The inverse problem is under-determined because several states, infinitely many in fact, comply with a given set of measured values. Accordingly, the exact identification of the state of the system is not feasible and one may only propose some estimation. Most techniques considered so far rely on Tikhonov regularisation. The estimated state minimises some cost function compromising between the norm of the state and that of measurement errors. Two norms must be chosen, one for the infinite dimensional space of system states and one for the finite dimensional space of measurement vectors. The state estimated based on Tikhonov regularisation is a linear combination of adjoint functions describing the sensitivity of each measurement with respect to the various part of the environment. These functions, computed using the model, depend on the norm chosen for the state space. Thus, the choice of this norm is the most important.

Renormalisation technique may be related to Tikhonov regularisation, however it is desired that the estimated state comply exactly with the observed values of the measurements. Thus, only the norm for the state space must be chosen. Here comes the original concept of visibility. Depending on network arrangement, the various parts of the system are not seen equally well. What matters is in fact the relative arrangement of the adjoint functions. The visibility is introduced as a weight function in the definition of a norm. The regions well seen are enlarged by receiving higher weights. This may be compared with eye's view: close regions look larger. Renormalisation technique prescribes a criterion for choosing the weights: the adjoint functions allow to describe the system under consideration as a manifold and when the weights are properly chosen, this manifold becomes a submanifold of the unit sphere in the space of the measurements.

The present study is aimed at studying the geometric properties of this submanifold. For instance, one may wonder whether the submanifold obtained from renormalisation criterion displays optimal regularity properties among the submanifolds obtained from others choices of the weights. The question has been raised whether renormalisation minimises Willmore energy characterising the global curvature of a submanifold. The intiricacy of the equations makes a pureley theoretical approach very difficult and thus, numerical exploration is considered. It is however necessary to define and implement numerical schemes appropriate for computing the curvature of a manifold immersed in high dimension.

## Tasks

The study decomposes into the following three tasks:

- Task 1. The submanifold associated with renormalisation technique are weighted submanifolds of the unit sphere. Theoretical works have long been devoted to the study of weighted the concepts of Laplace-Beltrami operator and curvature was thus generalized. However, these works address submanifolds inheriting their weights from the manifold where they are immersed, and thus, this larger manifold is weighted as well. The weights of renormalised submanifolds is not inherited from a weighting of the unit sphere. To begin with, the student will list all differential geometry works addressing weighted manifolds and then, he will endeavour to propose a generalization of fundamental notions appropriate in the context or renormalisation.
- Task 2. Based on example of simple physical systems and measurements, taken from atmospheric or oceanic physics, the student will conceive and implement numerical schemes allowing to reliably compute the curvature tensor of subamnifolds, especially those associated with the renormalisation.
- Task 3. The student will utilize the implemented numerical schemes to explore the properties of the submanifolds obtained from the renormalisation. In particular, he will propose various regularity criteria to assess the eventual optimality of the renormalised submanifolds in comparison to submanifolds associated to other weights.

If interested, please contact contact_iscd@upmc.fr

December

01 *

# Sysadmin position available

ISCD is actively looking for hiring an engineer who will be responsible for setting up and maintaining the HPC system at UPMC, and more precisely for: User administration (setup and maintaining account); Maintaining system; Verify that peripherals are working properly; Quickly arrange repair for hardware in occasion of hardware failure; Monitor system performance; Create file […]

# Sysadmin position available

Location: ISCD - DSI, campus Jussieu, Paris

ISCD is actively looking for hiring an engineer who will be responsible for setting up and maintaining the HPC system at UPMC, and more precisely for:

- User administration (setup and maintaining account);
- Maintaining system;
- Verify that peripherals are working properly;
- Quickly arrange repair for hardware in occasion of hardware failure;
- Monitor system performance;
- Create file systems;
- Install software;
- Create a backup and recover policy;
- Monitor network communication;
- Implement the policies for the use of the computer system and network;
- Documentation in form of internal wiki;

download the description (PDF) in French.

December

04 *

# Postdoc available

ISCD is seeking talented candidates for a post-doctoral position, starting asap. Background The study addresses under-determined inverse problems also known as data assimilation aimed at estimating the state of a complex physical system based on a finite number of measurements. The measurements are obtained from a monitoring network, the link between these and the state […]

# Postdoc available

Location: ISCD-UPMC, campus Jussieu, Paris, France

ISCD is seeking talented candidates for a post-doctoral position, starting asap.

## Background

The study addresses under-determined inverse problems also known as data assimilation aimed at estimating the state of a complex physical system based on a finite number of measurements. The measurements are obtained from a monitoring network, the link between these and the state of the system is described by some model. The study addresses in fact the case of a model describing a linear link between the measurements and the state. The inverse problem is under-determined because several states, infinitely many in fact, comply with a given set of measured values. Accordingly, the exact identification of the state of the system is not feasible and one may only propose some estimation. Most techniques considered so far rely on Tikhonov regularisation. The estimated state minimises some cost function compromising between the norm of the state and that of measurement errors. Two norms must be chosen, one for the infinite dimensional space of system states and one for the finite dimensional space of measurement vectors. The state estimated based on Tikhonov regularisation is a linear combination of adjoint functions describing the sensitivity of each measurement with respect to the various part of the environment. These functions, computed using the model, depend on the norm chosen for the state space. Thus, the choice of this norm is the most important.

Renormalisation technique may be related to Tikhonov regularisation, however it is desired that the estimated state comply exactly with the observed values of the measurements. Thus, only the norm for the state space must be chosen. Here comes the original concept of visibility. Depending on network arrangement, the various parts of the system are not seen equally well. What matters is in fact the relative arrangement of the adjoint functions. The visibility is introduced as a weight function in the definition of a norm. The regions well seen are enlarged by receiving higher weights. This may be compared with eye's view: close regions look larger. Renormalisation technique prescribes a criterion for choosing the weights: the adjoint functions allow to describe the system under consideration as a manifold and when the weights are properly chosen, this manifold becomes a submanifold of the unit sphere in the space of the measurements.

The present study is aimed at studying the geometric properties of this submanifold. For instance, one may wonder whether the submanifold obtained from renormalisation criterion displays optimal regularity properties among the submanifolds obtained from others choices of the weights. The question has been raised whether renormalisation minimises Willmore energy characterising the global curvature of a submanifold. The intiricacy of the equations makes a pureley theoretical approach very difficult and thus, numerical exploration is considered. It is however necessary to define and implement numerical schemes appropriate for computing the curvature of a manifold immersed in high dimension.

## Tasks

The study decomposes into the following three tasks:

- Task 1. The submanifold associated with renormalisation technique are weighted submanifolds of the unit sphere. Theoretical works have long been devoted to the study of weighted the concepts of Laplace-Beltrami operator and curvature was thus generalized. However, these works address submanifolds inheriting their weights from the manifold where they are immersed, and thus, this larger manifold is weighted as well. The weights of renormalised submanifolds is not inherited from a weighting of the unit sphere. To begin with, the student will list all differential geometry works addressing weighted manifolds and then, he will endeavour to propose a generalization of fundamental notions appropriate in the context or renormalisation.
- Task 2. Based on example of simple physical systems and measurements, taken from atmospheric or oceanic physics, the student will conceive and implement numerical schemes allowing to reliably compute the curvature tensor of subamnifolds, especially those associated with the renormalisation.
- Task 3. The student will utilize the implemented numerical schemes to explore the properties of the submanifolds obtained from the renormalisation. In particular, he will propose various regularity criteria to assess the eventual optimality of the renormalised submanifolds in comparison to submanifolds associated to other weights.

If interested, please contact contact_iscd@upmc.fr

July

17 *

# 6th ISCD summer school: bioinformatics and visual data analysis

This summer school program comprises intensive courses which aim to provide attendees with an introduction to both the theoretical foundations and the practical applications of some of the modern mathematical and computational techniques currently in use.

# 6th ISCD summer school: bioinformatics and visual data analysis

Location: Marine Station, Roscoff (France), July 17 - August 11, 2017.

### Scientific trends at the interfaces:

bioinformatics and visual data analysis

This summer school program is perfect for undergraduate students (L3-M2) considering studying theoretical or computational sciences at university level. It comprises intensive courses which aim to provide attendees with an introduction to both the theoretical foundations and the practical applications of some of the modern mathematical and computational techniques currently in use. Each course has theoretical and practical classes, in which students can experiment each technique with computers.

The summer school will take place a the Marine Station in Roscoff.

Registrations are now open, until May 15, 2017. Follow this link

May

20 *

# PhD thesis offer

ISCD is actively looking for PhD candidates in computer science, or applied mathematics, or engineering for a challenging project in digital architecture. Subject: Design and implementation of 3D interaction techniques for exploring massive archaeological data. Description: The subject of the thesis is to design, implement and evaluate 3D interaction techniques for the exploration of archaeological […]

# PhD thesis offer

Location: ISCD, campus Jussieu, 33-34, 2nd floor

ISCD is actively looking for PhD candidates in computer science, or applied mathematics, or engineering for a challenging project in digital architecture.

Subject:

Design and implementation of 3D interaction techniques for exploring massive archaeological data.

Description:

The subject of the thesis is to design, implement and evaluate 3D interaction techniques for the exploration of archaeological data. The proposed techniques should allow interactive manipulation, navigation and exploration of massive data sets, as well as the visualization of intrinsic structures to facilitate the formulation of hypotheses and the scientific work of specialists. New performance criteria, exceeding those traditionally associated with this type of research (i.e., speed / reactivity, precision, versatility, etc.) should be proposed in consultation with users.

The solutions developed may be software (gestural interaction, multi-touch interaction, etc.), or hardware (haptic devices, VR helmet, etc.) or any combination of these two approaches.

This thesis is set in the working context of a multidisciplinary project-team of ISCD, gathering computer scientists, mathematicians, historians and archaeologists, around a historic building.

Skills required:

- master degree (or equivalent) in computer science (HCI, VR, etc.), applied mathematics, or engineering sciences;
- a pronounced taste for 3D interaction, human-machine interaction, virtual reality, mixed reality, haptic devices, or mathematical modeling;
- software development skills and graphics libraries (Java, C ++, QT, Android, OpenGl, etc.) and hardware (small mechanics, electronics);
- proficiency in English and good drafting skills;
- strong teamwork, exchange and communication skills.

Environment:

The thesis will be held at the University Pierre et Marie Curie (Paris) in a privileged environment for multidisciplinary work.

Contact us asap (deadline is May 20th, 2017):
contact_iscd@upmc.fr

May

15 *

# Soutenance de thèse – Louis Lagardère

« Calcul haute-performance et dynamique moléculaire polarisable » Il s’agit d’une thèse à l’interface entre la chimie théorique, le calcul scientifique et les mathématiques appliquées dans laquelle on s’intéresse aux différents algorithmes utilisés pour résoudre les équations spécifiques qui apparaissent dans le cadre de la dynamique moléculaire utilisant des champs de forces polarisables dans un […]

# Soutenance de thèse – Louis Lagardère

Location:

« Calcul haute-performance et dynamique moléculaire polarisable »

Il s’agit d’une thèse à l’interface entre la chimie théorique, le calcul scientifique et les mathématiques appliquées dans laquelle on s’intéresse aux différents algorithmes utilisés pour résoudre les équations spécifiques qui apparaissent dans le cadre de la dynamique moléculaire utilisant des champs de forces polarisables dans un cadre massivement parallèle.
Cette famille de modèles nécessite en effet de résoudre des équations plus complexes que les modèles classiques usuels et rend nécessaire l’utilisation de supercalculateurs pour obtenir des résultats significatifs.
On s’intéressera plus précisément à différents cas de conditions aux limites pour rendre compte des effets de solvatation comme les conditions aux limites périodiques traitées avec la méthode du Particle Mesh Ewald et un modèle de solvatation continu discrétisé par décomposition de domaine : le ddCOSMO.