Publications related to Coarse-grained modeling

The role of Zn in C-S-H atomic structure, nucleation and growth

The most promising solution towards cementitious materials with a lower carbon footprint is the partial substitution of the clinker by supplementary cementitious materials (SCMs) such as fly ash, blast furnace slag, limestone and calcined clays. The produc ...

EPFL2023

Thermodynamic bounds on time-reversal asymmetry

Shiling Liang

Quantifying irreversibility of a system using finite information constitutes a major challenge in stochastic thermodynamics. We introduce an observable that measures the time-reversal asymmetry between two states after a given time lag. Our central result ...

Amer Physical Soc2023

Atomistic modeling of C-S-H: bulk and surface

Ziga Casar

By replacing part of Portland cement with so-called supplementary cementitious materials (SCMs) it is possible to reduce the CO2 footprint of the cement industry. These SCMs are commonly limestone, calcined clay, slag and fly ash. While doing so the early ...

EPFL2023

Impact of dipole-dipole interactions on motility-induced phase separation

Ignacio Pagonabarraga Mora, Elena Sesé Sansa

We present a hydrodynamic theory for systems of dipolar active Brownian particles which, in the regime of weak dipolar coupling, predicts the onset of motility-induced phase separation (MIPS), consistent with Brownian dynamics (BD) simulations. The hydrody ...

ROYAL SOC CHEMISTRY2022

Adhesive wear with a coarse-grained discrete element model

Jean-François Molinari, Son-Jonathan Pham-Ba

The use of molecular dynamics (MD) simulations has led to promising results to unravel the atomistic origins of adhesive wear, and in particular for the onset of wear at nanoscale surface asperities. However, MD simulations come with a high computational c ...

ELSEVIER SCIENCE SA2022

Microscopic picture of paraelectric perovskites from structural prototypes

Nicola Marzari, Giovanni Pizzi, Michele Kotiuga, Boris Kozinsky

We highlight with first-principles molecular dynamics the persistence of intrinsic < 111 > Ti off-centerings for BaTiO3 in its cubic paraelectric phase. Intriguingly, these are inconsistent with the Pm (3) over barm space group often used to atomistically ...

AMER PHYSICAL SOC2022

Filtered data and eigenfunction estimators for statistical inference of multiscale and interacting diffusion processes

Andrea Zanoni

We study the problem of learning unknown parameters of stochastic dynamical models from data. Often, these models are high dimensional and contain several scales and complex structures. One is then interested in obtaining a reduced, coarse-grained descript ...

EPFL2022

Iterative Unbiasing of Quasi-Equilibrium Sampling

Michele Ceriotti, Bingqing Cheng, Gareth Aneurin Tribello, Federico Giberti

Atomistic modeling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an appropriately chosen s ...

AMER CHEMICAL SOC2020

Atomistic modeling of the solid-liquid interface of metals and alloys

Edoardo Baldi

Solidification is a phase transformation of utmost importance in material science, for it largely controls materials' microstructure on which a wide range of mechanical properties depends. Almost every human artifact undergoes a transformation that leads t ...

EPFL2020

Unsupervised machine learning in atomistic simulations, between predictions and understanding

Michele Ceriotti

Automated analyses of the outcome of a simulation have been an important part of atomistic modeling since the early days, addressing the need of linking the behavior of individual atoms and the collective properties that are usually the final quantity of i ...

2019

Entropy production for coarse-grained dynamics

Daniel Maria Busiello, Amos Maritan

Systems out of equilibrium exhibit a net production of entropy. We study the dynamics of a stochastic system represented by a Master equation (ME) that can be modeled by a Fokker-Planck equation in a coarse-grained, mesoscopic description. We show that the ...

2019

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

Paolo De Los Rios, Alessandro Barducci, Alberto Stefano Sassi, Salvatore Assenza

Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the struct ...

2019

Modeling the Structural and Thermal Properties of Loaded Metal–Organic Frameworks. An Interplay of Quantum and Anharmonic Fluctuations

Michele Ceriotti, Venkat Kapil

Metal–organic frameworks show both fundamental interest and great promise for applications in adsorption-based technologies, such as the separation and storage of gases. The flexibility and complexity of the molecular scaffold pose a considerable challenge ...

2019

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

Ursula Röthlisberger, Simone Meloni, Martin Peter Bircher, Viacheslav Bolnykh, Paolo Carloni

We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through th ...

AMER CHEMICAL SOC2019

Bimolecular charge transfer reactions at and through the liquid-liquid interface

Grégoire Clément Gschwend

Interfaces are ubiquitous in Nature. Among them, soft interfaces are essential constituents of biological tissues. Indeed, many electrochemical reactions and phenomena take place at these interfaces. In this respect, ITIES are an interesting model to study ...

EPFL2019

A sequence-dependent coarse-grain model of B-DNA with explicit description of bases and phosphate groups parametrised from large scale Molecular Dynamics simulations

Alessandro Samuele Patelli

We introduce a sequence-dependent coarse-grain model of double-stranded DNA with an explicit description of both the bases and the phosphate groups as interacting rigid-bodies. The model parameters are trained on extensive, state-of-the-art large scale mol ...

EPFL2019

Adhesive wear mechanisms uncovered by atomistic simulations

Jean-François Molinari, Enrico Milanese, Ramin Aghababaei, Tobias Brink, Lucas Henri Galilée Frérot

In this review, we discuss our recent advances in modeling adhesive wear mechanisms using coarse-grained atomistic simulations. In particular, we present how a model pair potential reveals the transition from ductile shearing of an asperity to the formatio ...

SPRINGEROPEN2018

Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones

Duccio Malinverni

Recent advances in DNA sequencing technologies led to the accumulation of enormous quantities of genetic information available in public databases. This rapid growth of available biological datasets calls for quantitative analysis tools and concomitantly o ...

EPFL2018

Studying membrane-protein interplay by modeling realistic conditions

Martina Audagnotto

Realistic models of cellular environments have long captured the imagination of biologists and physical scientists. More than 20 years ago, Goodshellâ s inspiring rendering of cellular environments provided the foundation for the idea of capturing the ful ...

EPFL2017

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis

Paolo De Los Rios, Alessandro Barducci, Duccio Malinverni

The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of the interaction are still elusive and contrasting models hav ...

Elife Sciences Publications Ltd2017