Publications related to Computational chemistry

Thermal conductivity of Li 3 PS 4 solid electrolytes with ab initio accuracy

The vast amount of computational studies on electrical conduction in solid-state electrolytes is not mirrored by comparable efforts addressing thermal conduction, which has been scarcely investigated despite its relevance to thermal management and (over)he ...

Amer Physical Soc2024

Augmenting large language models with chemistry tools

Philippe Schwaller, Oliver Tobias Schilter, Andres Camilo Marulanda Bran, Carlo Baldassari

Large language models (LLMs) have shown strong performance in tasks across domains but struggle with chemistry-related problems. These models also lack access to external knowledge sources, limiting their usefulness in scientific applications. We introduce ...

Nature Portfolio2024

Encoding quantum-chemical knowledge into machine-learning models of complex molecular properties

Ksenia Briling

Statistical (machine-learning, ML) models are more and more often used in computational chemistry as a substitute to more expensive ab initio and parametrizable methods. While the ML algorithms are capable of learning physical laws implicitly from data, ad ...

EPFL2024

Hausdorff dimension of fermions on a random lattice

Mattia Guerino Varrone

Geometric properties of lattice quantum gravity in two dimensions are studied numerically via Monte Carlo on Euclidean Dynamical Triangulations. A new computational method is proposed to simulate gravity coupled with fermions, which allows the study of int ...

Elsevier2024

A Streamline Upwind Petrov-Galerkin Reduced Order Method for Advection-Dominated Partial Differential Equations Under Optimal Control

Fabio Zoccolan, Gianluigi Rozza

In this paper we will consider distributed Linear-Quadratic Optimal Control Problems dealing with Advection-Diffusion PDEs for high values of the Peclet number. In this situation, computational instabilities occur, both for steady and unsteady cases. A Str ...

Walter De Gruyter Gmbh2024

Live-cell imaging powered by computation

Suliana Manley, Florian Jug

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preservi ...

Nature Portfolio2024

Orchestrating chromosome conformation capture analysis with Bioconductor

Cyril Matthey-Doret

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

A Combination Technique for Optimal Control Problems Constrained by Random PDEs

Fabio Nobile, Tommaso Vanzan

We present a combination technique based on mixed differences of both spatial approximations and quadrature formulae for the stochastic variables to solve efficiently a class of optimal control problems (OCPs) constrained by random partial differential equ ...

2024

Multiscale biomolecular simulations in the exascale era

Ursula Röthlisberger, Simone Meloni

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. lar dynamics (MD) simulations are crucial for capturing processes beyond the ...

Current Biology Ltd2024

FETCH: A Fast and Efficient Technique for Channel Selection in EEG Wearable Systems

David Atienza Alonso, Amir Aminifar, Alireza Amirshahi, José Angel Miranda Calero, Jonathan Dan

The rapid development of wearable biomedical systems now enables real-time monitoring of electroencephalography (EEG) signals. Acquisition of these signals relies on electrodes. These systems must meet the design challenge of selecting an optimal set of el ...

2024

Error estimates for SUPG-stabilised Dynamical Low Rank Approximations

Fabio Nobile, Thomas Simon Spencer Trigo Trindade

We perform an error analysis of a fully discretised Streamline Upwind Petrov Galerkin Dynamical Low Rank (SUPG-DLR) method for random time-dependent advection-dominated problems. The time integration scheme has a splitting-like nature, allowing for potenti ...

Springer Nature Switzerland2025

SIMPLE HIERARCHICAL PLANNING WITH DIFFUSION

Caglar Gulcehre, Chang Chen

Diffusion-based generative methods have proven effective in modeling trajectories with offline datasets. However, they often face computational challenges and can falter in generalization, especially in capturing temporal abstractions for long- horizon tas ...

2024

The role of computational methods in cardiovascular medicine: a narrative review

Alfio Quarteroni, Luca Dede', Christian Vergara, Stefano Pagani

Background and Objective: Computational models of the cardiovascular system allow for a detailed and quantitative investigation of both physiological and pathological conditions, thanks to their ability to combine clinical-possibly patient-specific-data wi ...

Ame Publishing Company2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Nonempirical semilocal density functionals for correcting the self-interaction of polaronic states

Alfredo Pasquarello, Stefano Falletta

Through the use of the piecewise-linearity condition of the total energy, we correct the self-interaction for the study of polarons by constructing nonempirical functionals at the semilocal level of theory. We consider two functionals, the gamma DFT and mu ...

Aip Publishing2024

Accurate and agile flight with winged drones

Valentin Wüest

Drones hold promise to assist in civilian tasks. To realize this application, future drones must operate within large cities, covering large distances while navigating within cluttered urban landscapes. The increased efficiency of winged drones over rotary ...

EPFL2024

EncodingActs: Modeling, Representing and Transmitting Embodied Knowledge in Traditional Martial Arts

Yumeng Hou

EncodingActs investigates how computational methods can facilitate the transmission of multifaceted knowledge within intangible cultural heritage (ICH). ICH, characterized by living, tacit, yet complex epistemic systems, is conventionally viewed as challen ...

EPFL2024

Efficient and insightful descriptors for representing molecular and material space

Alexander Jan Goscinski

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024

High-order geometric integrators for the variational Gaussian wavepacket dynamics and application to vibronic spectra at finite temperature

Roya Moghaddasi Fereidani

Molecular quantum dynamics simulations are essential for understanding many fundamental phenomena in physics and chemistry. They often require solving the time-dependent Schrödinger equation for molecular nuclei, which is challenging even for medium-sized ...

EPFL2024