Computing Transition Rates: Models And Algorithms (Postdoctoral Funding, 12 Months Renewable)
Universities and Institutes of France
25 Aug 2023
Job InformationOrganisation/Company
École des Ponts ParisTech
Research Field
Chemistry » Computational chemistry
Mathematics » Computational mathematics
Physics » Chemical physics
Researcher Profile
Recognised Researcher (R2)
Country
France
Application Deadline
29 Sep 2023 - 18:00 (Europe/Paris)
Type of Contract
Temporary
Job Status
Full-time
Offer Starting Date
1 Jan 2024
Is the job funded through the EU Research Framework Programme?
Not funded by an EU programme
Is the Job related to staff position within a Research Infrastructure?
No
Offer DescriptionKeywords: molecular dynamics, machine learning, rare event sampling
The aim of this project is to efficiently and accurately compute reaction rates of chemical transformations, typically in the field of catalytic chemistry (for instance alcohol isomerization). A first task will be to quantitatively study the limitations of approximate formulas obtained from harmonic transition state theory (Eyring-Kramers or Eyring-Polanyi formulas), by comparing the predictions of these approximate theories to reference results obtained either by direct numerical simulations or using dedicated numerical methods such as the adaptive multilevel splitting (AMS) algorithm 1. A second task will be to improve the performance of AMS by finding a better reaction coordinate, relying on neural networks such as bottleneck autoencoders, which have proved successful for free energy computations 2,3. One novel idea to obtain this improved reaction coordinate is to minimize the transition rate of the associated effective dynamics, relying on the theoretical results of 4.
This postdoctoral fellowship is funded by the PEPR B-best, through the project MAMABIO, whose overall goal is to develop new numerical methods to study reactions of transformation of biosourced molecules.
1 T. Pigeon, G. Stoltz, M. Corral-Valero, A. Anciaux-Sedrakian, M. Moreaud, T. Lelièvre, P. Raybaud, Computing surface reaction rates by Adaptive Multilevel Splitting combined with machine learning and ab initio molecular dynamics, J. Chem. Theory Comput. 19(12), 3538–3550 (2023) https: // doi.org/10.1021/acs.jctc.3c00280"> https: // doi.org/10.1021/acs.jctc.3c00280 2 Z. Belkacemi, M. Bianciotto, H. Minoux, T. Lelièvre, G. Stoltz and P. Gkeka, Autoencoders for dimensionality reduction in molecular dynamics: collective variable dimension, biasing and transition states, J. Chem. Phys 159, 024122 (2023) https: // doi.org/10.1063/5.0151053 3 Z. Belkacemi, P. Gkeka, T. Lelièvre, G. Stoltz, Chasing collective variables using autoencoders and biased trajectories, J. Chem. Theory Comput. 18(1), 59-78 (2022) https: // doi.org/10.1021/acs.jctc.1c00415 4 W. Zhang, C. Hartmann and C. Schutte, Effective dynamics along given reaction coordinates, and reaction rate theory, Faraday Discussions, 195, 365-394 (2016) https: // doi.org/10.1039/C6FD00147E
RequirementsResearch Field
Chemistry » Computational chemistry
Education Level
PhD or equivalent
Research Field
Mathematics » Computational mathematics
Education Level
PhD or equivalent
Research Field
Physics » Chemical physics
Education Level
PhD or equivalent
Skills/Qualifications
Independent researcher with strong analytical skills, able to interact with applied mathematicians to develop new numerical methods and test the validity or limitations of certain theoretical predictions. Applications from researchers with PhDs in computational physics and/or applied mathematics, willing to turn to systems in catalytic chemistry, are welcome.
Specific Requirements
Required skills to be demonstrated/justified in the application material, e.g. through some cover letter/email: - strong expertise in the use of molecular dynamics software (VASP, LAMMPS, NAMD, ...) - experience in implementation of numerical methods, either through scripts (e.g. in python) or in the source code
Languages
ENGLISH
Level
Excellent
Selection process
The full application should contain: - a complete curriculum vitae, including a list of publications - a brief description of why the candidate believes that he/she fits the position (in particular, describe the type of numerical work which has been done in previous positions, highlighting the development of new methodologies in molecular dynamics and the type of software used)
Candidates are encouraged to discuss their application with Gabriel Stoltz ([email protected]).
Work Location(s)Number of offers available
1
Company/Institute
CERMICS
Country
France
City
Marne-la-Vallee
Postal Code
77455
Street
6-8 avenue Blaise Pascal
City
Champs sur Marne
Website
https: // cermics-lab.enpc.fr/
Street
6-8 avenue Blaise Pascal
Postal Code
77420
STATUS: EXPIRED