News archive

2017

15.07

After finishing his master’s at the University of Cambridge, Seonghoon Choi, started a Ph.D. in our group.  Welcome, Choi!

08.05

Konstantin’s paper on “Accelerating equilibrium isotope effect calculations: I. Stochastic thermodynamic integration with respect to mass” was published in J. Chem. Phys. Congratulations!

01.05

Jiri’s paper on “Several Semiclassical Approaches to Time-resolved Spectroscopy” was published in CHIMIA. Congratulations!

01.03

Julien Roulet joined our group as a Ph.D. student. Welcome!

20.02

Tomislav Begusic joined our group as a Master student. Welcome!

20.02

Sebastien Reynaud joined our group for a semester project. Welcome!

2016

05.06

Aurélien won the Transju’trail (72km and 3200m of climb). Congratulations!

04.03

Rocco was accepted to the Ph.D. program at Oxford. Congratulations!

01.03

Thierry Tran joined our group for an internship. Welcome!

01.03

Marco started a Ph.D. program at the University of Geneva. Congratulations!

12.02

Jiri won the 2015 ERC Consolidator grant. Congratulations!

2015

20.11

Konstantin and Jiri’s paper which proposes a method that can accelerate the quantum instanton calculations of kinetic isotope effects by orders of magnitude was published in J. Chem. Phys. Congratulations to Konstantin!

20.11

Sergey Antipov joined our group as a postdoc. He is coming from Cornell where he worked with Nandini Ananth. Welcome!

01.10

Marco Sutti was awarded second prize for best poster about his Master thesis. Congratulations!

15.09

Ruben Guerrero graduated from LCPT and returned to Colombia to finish his Ph.D. Best of luck!

14.09

Rocco Meli has joined our group as a semester project student. Welcome!

01.09

Marco Sutti has started an internship at LCPT. Welcome!

06.05

Our paper “PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3’UTRs and coding sequences” was published online in Nucleic Acids Research, Web Server issue.

30.04

Our paper “On-the-fly Ab initio Semiclassical Dynamics of Floppy Molecules: Absorption and Photoelectron Spectra of Ammonia” was published online in The Journal of Physical Chemistry A.

01.04

Ruben Guerrero has started an internship at LCPT. Welcome!

2014

31.12

Solène Oberli graduated from LCPT and started a Ph.D. at Université Pierre et Marie Curie in Paris. Congratulations!

31.12

Alberto Hernando graduated from LCPT and launched a startup company SThAR. Congratulations!

01.11

Eduardo Zambrano graduated from LCPT and started a postdoctoral fellowship at the Max Planck Institute for the Physics of Complex Systems in Dresden. Congratulations!

01.10

Solène Oberli has started an internship at LCPT. Welcome!

15.09

Marco Sutti has joined our group as a semester project student. Welcome!

09.09

A short review of our research in the microRNA field was published in Chimia: “Predicting the genes regulated by microRNAs via binding sites in the 3′ untranslated and coding regions

25.07

Eduardo Zambrano received the prize for outstanding poster presentation in the American Conference on Theoretical Chemisty 2014.

26.06

Our paper “On-the-fly ab initio semiclassical dynamics: Identifying degrees of freedom essential for emission spectra of oligothiophenes” was published online in The Journal of Chemical Physics.

06.03

collaborative paper in which O’Connor and Murphy experimentally confirm our prediction that a human microRNA contributes to the latency of the human cytomegalovirus was published in the Journal of Virology.

 

2013

03.12 Our paper “Imaginary-time nonuniform mesh method for solving the multidimensional Schordinger equation: Fermionization and melting of quantum Lennard-Jones crystals” was accepted for publication in Physical Review A.
29.10 Our paper “Kinetic isotope effect in malonaldehyde from path integral Monte Carlo simulations” written in collaboration with Markus Meuwly’s group in Basel, was published in Phys. Chem. Chem. Phys.
18.10 Marius Werhle received the prize for the most dedicated teaching assistants  in chemistry. Congratulations!
14.10 Our paper “Monte Carlo evaluation of the equilibrium isotope effects using the Takahashi-Imada factorization of the Feynman Path Integral” was published online and selected as Editor’s Choice Article in Chemical Physics Letters
15.09 Jessica Rohrbach has joined our group as a master thesis student. Welcome!
15.09 Aurelien Patoz has joined our group as a Ph.D. student. Welcome!
06.09 Aurelien Patoz was awarded the runner-up best poster prizer in Computational Chemistry at the Fall Meeting of the Swiss Chemical Society.
20.08 Aurelien Patoz succesfully defended its Master Thesis. Congratulations
05.08  Our paper “Improving the accuracy and efficiency of time-resolved electronic spectra calculations: Cellular dephasing representation with a prefactor” was published online in Journal of Chemical Physics.
18.07 Our paper “Relation of Exact Gaussian Basis Methods to the Dephasing Representation: Theory and Application to Time-Resolved Electronic Spectra” was published online in Journal of Chemical Physics.
21.06

The CECAM Workshop:

“Many-dimensional quantum dynamics with (non)classical trajectories”

organized by our group and Michele Ceotto of University of Milano took place at EPFL from June 17 to 21.

04.06 Miroslav Sulc received a 2012 Molecular Physics Young Author’s Prize for his contribution in our paper “Accelerating the calculation of time-resolved spectra with the cellular depahsing representation.
24.04 Jiri Vanicek received a 2013 OpenEye Outstanding Junior Faculty Award from the computational division of the American Chemical Society.
14.03 A collaborative paper with the Trono group was published in Science.
12.02 Our paper “Searching the coding region for microRNA targets” was published online in RNA.
10.01 Alberto Hernando has joined our group as a Postdoctoral Researcher. Welcome!

 

2012

 

25.10 Konstantin Karandashev has joined our group. Welcome!
26.08 Our paper “Analysis of the accessibility of CLIP bound sites reveals  that nucleation of the miRNA:mRNA pairing occurs  preferentially at the 3′-end of the seed match” was published online in RNA.
03.08 Ray Marín has succesfully defended its Ph.D. Thesis. Congratulations.
01.08 Our paper “Evaluation of the importance of spin-orbit couplings in the nonadiabatic quantum dynamics with quantum fidelity and with its efficient “on-the-fly” ab initio semiclassical approximation” was published online in The Journal of Chemical Physics
09.07 Our paper “Evaluation of the importance of spin-orbit couplings in the nonadiabatic quantum dynamics with quantum fidelity and with its efficient ‘on-the-fly’ ab initio semiclassical approximation has been accepted in the Journal of Chemical Physics.
20.02 Our paper “Measuring nonadiabaticity of molecular quantum dynamics with quantum fidelity and with its efficient semiclassical approximation” has been accepted in the Journal of Chemical Physics
03.07 Cesare Mollica has succesfully defended its Ph.D. Thesis. Congratulations.
03.07 Matthew Wodrich has joined our group.
25.05
Our paper “Accelerating the calculation of time-resolved electronic spectra with the cellular dephasing representation” was published online in Molecular Physics
02.04 Eduardo Zambrano has joined our group as a postdoctoral fellow.
 
06.03 PH.D. AND POSTDOCTORAL POSITIONS in theoretical chemical physics and bioinformatics are available in our group.
20.02 Our paper “Accelerating the calculation of time-resolved electronic spectra with the cellular dephasing representation” has been accepted in Molecular Physics
20.02 Our paper “Optimal Use of Conservation and Accessibility Filters in MicroRNA Target Prediction” has been accepted in PLoS ONE

 

2011

 

14.12 Our paper “Efficient sampling avoids the exponential wall in classical simulations of fidelity” was published online in Physical Review E
14.11 Our paper “Beating the efficiency of both quantum and classical simulations with a semiclassical method” was published online in Physical Review Letters
16.09 Marius Wehrle was awarded the best poster prize in Computational Chemistry at the Fall Meeting of the Swiss Chemical Society
11.03 You can now visit the website of the CUSO SUMMER SCHOOL IN COMPUTATIONAL CHEMISTRY to be held in Villars-sur-Ollon next August: “Solving the Schrödinger Equation – From Electronic Structure to Quantum Dynamics”

 

2010

 

16.09 Julien Ruppen was awarded with the 2nd place for the best poster in Computational Chemistry in the SCS Fall Meeting 2010 held in Zurich.
30.08 Sergio Gonzalez joined our group as a Ph.D. student.
30.08 Our articleEfficient use of accessibility in microRNA target prediction” was published on line in Nucleic Acids Research.
13.08 Our articleEfficient use of accessibility in microRNA target prediction” is selected as a Featured Article by Nucleic Acids Research.
21.07 Our communication “Evaluation of the nondiabaticity of quantum molecular dynamics with the dephasing representation of quantum fidelity”  has been selected for the July 1, 2010 issue of Virtual Journal of Biological Physics Research.
16.07 Our communication “Evaluation of the nondiabaticity of quantum molecular dynamics with the dephasing representation of quantum fidelity” is on the list of Top 20 Most Downloaded Articles in Journal of Chemical Physics in June 2010.
28.06 Our communication “Evaluation of the nondiabaticity of quantum molecular dynamics with the dephasing representation of quantum fidelity” was published in the Journal of Chemical Physics.
14.06 Our article “Efficient evaluation of the accuracy of molecular quantum dynamics on an approximate analytical or interpolated potential energy surface” was published in the Journal of Chemical Physics.
18.05 Our article “Direct evaluation of the temperature dependence of the rate constant based on the quantum instanton approximation” was published in the Journal of Chemical Physics.
30.04 Our article “Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene” was published in the Journal of Molecular Modeling.
24.03 Submitted article: T. Zimmermann and J. Vanicek: “Evaluation of the nondiabaticity of quantum molecular dynamics with the dephasing representation of quantum fidelity.”
01.03 Marius Wehrle joined the group as a Ph.D. student.
21.01 Submitted article: M. Buchowiecki and J. Vanicek, “Direct evaluation of the temperature dependence of the rate constant based on the quantum instanton approximation.”
18.01 Submitted article: T. Zimmermann and J. Vanicek, “Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene.”

 

 2009

 

18.12 Submitted article: T. Zimmermann, J. Ruppen, B. Li, and J. Vanicek:  “Efficient evaluation of the accuracy of molecular quantum dynamics on an approximate analytical or interpolated potential energy surface.”
15.12 Submitted article: R. Marin and J. Vanicek: “Specificity of microRNA target predictions improved by RNA secondary structure calculations.”
02.11 Our article Path integral evaluation of the equilibrium isotope effect in [1,5] sigmatropic hydrogen shift reactions” is now published in the special number of Flash Informatique dedicated to the high performance computing in the EPFL.
01.09 Our article “Efficient evaluation of accuracy of molecular quantum dynamics using dephasing representation” was the most downloaded scientific paper in the Journal of Chemical Physics in August 2009! See the announcement here.
01.04 Master projects are available for the fall semester 2009.

 

2008

 

18.08 Ray Marin Florez joined our group as a Ph.D. student. Baiqing Li joined the group as a postdoctoral fellow.
02.07 Our theoretical prediction (published in PNAS in March) that microRNAs regulate viral immediate early genes in herpesviruses has a new experimental confirmation and the first citation in today’s Letter to Nature by Umbach et al.:  MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Their Letter concludes by: `Our observation that HSV-1 miRNAs are capable of downregulating key viral immediate early proteins is consistent with the recent proposal-based primarily on computational data-that herpesviruses in general may use viral miRNAs “as part of their strategy to enter and maintain latency” [28].
01.07 Marcin Buchowiecki joined the group as a postdoctoral fellow. Tomas Zimmermann joined the group for summer internship.
14.04 Version 10 of AMBER software suite has been released. Our contribution was the code for thermodynamic integration with respect to mass, and the section in the manual on isotope effects. The method is based on the AMBER implementation of Path Integral Molecular Dynamics and is useful for calculation of both equilibrium and kinetic isotope effects.
08.04 Our article “Suppression of immediate-early gene expression by herpesvirus-coded microRNAs: Implications for latency” was featured in the “In This Issue” section of the Proceedings of the National Academy of Sciences of the USA. See “Herpesvirus miRNAs control latency.”
25.03 Master projects are available for the fall semester 2008.
01.03 Cesare Mollica joined the group as a PhD student.

 

2007

 

03.10 Jiri Vanicek is now at EPFL.