Concept

Molecular mechanics

Related publications (31)

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

Ursula Röthlisberger, Sophia Kathryn Johnson

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

Thermal transport of glasses via machine learning driven simulations

Federico Grasselli, Paolo Pegolo

Accessing the thermal transport properties of glasses is a major issue for the design of production strategies of glass industry, as well as for the plethora of applications and devices where glasses are employed. From the computational standpoint, the che ...

Frontiers Media Sa2024

Seebeck Coefficient of Ionic Conductors from Bayesian Regression Analysis

Paolo Pegolo

We propose a novel approach to evaluating the ionic Seebeck coefficient in electrolytes from relatively short equilibrium molecular dynamics simulations, based on the Green-Kubo theory of linear response and Bayesian regression analysis. By exploiting the ...

Amer Chemical Soc2024

Universal machine learning for the response of atomistic systems to external fields

Yaolong Zhang

Machine learned interatomic interaction potentials have enabled efficient and accurate molecular simulations of closed systems. However, external fields, which can greatly change the chemical structure and/or reactivity, have been seldom included in curren ...

Nature Portfolio2023

Atomic-level structure determination of amorphous molecular solids by NMR

David Lyndon Emsley, Arthur César Pinon, Manuel Cordova, Pinelopi Moutzouri

Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder ...

Nature Portfolio2023

Lattice Green's function method for Atomistic/Continuum coupling

Ankit Gupta

Metal plasticity is an inherently multiscale phenomenon due to the complex long-range field of atomistic dislocations that are the primary mechanism for plastic deformation in metals. Atomistic/Continuum (A/C) coupling methods are computationally efficient ...

EPFL2023

Coupled Rotary and Oscillatory Motion in a Second-Generation Molecular Motor Pd Complex

Lukas Pfeifer

Molecular machines offer many opportunities for the development of responsive materials and introduce autono-mous motion in molecular systems. While basic molecular switches and motors carry out one type of motion upon being exposed to an external stimulus ...

AMER CHEMICAL SOC2023

Computational Studies for the Design of Metalloenzyme Mimics

Guido Frisari

At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...

EPFL2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Beyond potentials: Integrated machine learning models for materials

Michele Ceriotti

Over the past decade, interatomic potentials based on machine learning (ML) techniques have become an indispensable tool in the atomic-scale modeling of materials. Trained on energies and forces obtained from electronic-structure calculations, they inherit ...

SPRINGER HEIDELBERG2022

Effects of surface rigidity and metallicity on dielectric properties and ion interactions at aqueous hydrophobic interfaces

Philip Robin Loche

Using classical molecular dynamics simulations, we investigate the dielectric properties at interfaces of water with graphene, graphite, hexane, and water vapor. For graphite, we compare metallic and nonmetallic versions. At the vapor-liquid water and hexa ...

AIP Publishing2022

Competing Effects of Hydration and Cation Complexation in Single-Chain Alginate

Zezhong Li

Alginic acid, a naturally occurring anionic polyelectrolyte, forms strong physically cross-linked hydrogels in the presence of metal cations. The latter engage in electrostatic interactions that compete with intra- and intermolecular hydrogen bonds, determ ...

American Chemical Society2022

Two-dimensional atomically bridged nanoporous silicate-based membranes for gas separation

Mostapha Dakhchoune

The synthesis of molecular-sieving two-dimensional zeolitic membranes by the assembly of crystalline building blocks without resorting to the secondary growth process is highly desirable. The precise pore size for molecular sieving, ultrathin thickness, an ...

EPFL2021

Structure and Reactivity of N-Heterocyclic Alkynyl Hypervalent Iodine Reagents

Rosario Scopelliti, Jérôme Waser, Farzaneh Fadaei Tirani, Matthew Wodrich, Eliott Hugo Joran Le Du

Ethynylbenziodoxol(on)e (EBX) cyclic hypervalent iodine reagents have become popular reagents for the alkynylation of radicals and nucleophiles, but only offer limited possibilities for further structure and reactivity fine-tuning. Herein, the synthesis of ...

2021

Revisiting Cation Complexation and Hydrogen Bonding of Single-Chain Polyguluronate Alginate

Zezhong Li

Modifying the properties of bio-based materials has garnered increasing interest in recent years. In related applications, the ability of alginates to complex with metal ions has been shown to be effective in liquid-to-gel transitions, useful in the develo ...

American Chemical Society2021

Millisecond lattice gasification for high-density CO2- and O2-sieving nanopores in single-layer graphene

Emad Oveisi, Kumar Varoon Agrawal, Mounir Driss Mensi, Luis Francisco Villalobos Vazquez de la Parra, Shiqi Huang, Mostapha Dakhchoune, Shaoxian Li, Deepu Joseph Babu, Marina Micari

Etching single-layer graphene to incorporate a high pore density with sub-angstrom precision in molecular differentiation is critical to realize the promising high-flux separation of similar-sized gas molecules, e.g., CO2 from N2. However, rapid etching ki ...

2021

Atomistic simulation and electron microscopy to characterize grain boundaries in doped beta-tricalcium phosphate ceramics

Gabrielle Anne Laguisma Sblendorio

The limitations and potential complications correlated with autogenous bone grafts have raised interest in the development of synthetic bone graft substitutes. ß-tricalcium phosphate (ß-TCP) is one of the most promising materials for synthetic bone graft s ...

EPFL2021

Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers

Luciano Andres Abriata

For years, immersive interfaces using virtual and augmented reality (AR) for molecular visualization and modeling have promised a revolution in the way how we teach, learn, communicate and work in chemistry, structural biology and related areas. However, m ...

2020

Biomolecular Simulation: a Perspective from High Performance Computing

Ursula Röthlisberger, Viacheslav Bolnykh

High-Performance Computing is impacting on all biomedical sciences, including molecular biophysics. Here, we describe general parallel computing strategies (multi-threading and distributed computing) used in all the natural sciences, including molecular bi ...

WILEY-V C H VERLAG GMBH2020

Prediction of aqueous free energies of solvation using coupled QM and MM explicit solvent simulations

Jeremy Samuel Arey, Daniel David Sadowsky

A method based on molecular dynamics simulations which employ two distinct levels of theory is proposed and tested for the prediction of Gibbs free energies of solvation for non-ionic solutes in water. The method consists of two additive contributions: (i) ...

ROYAL SOC CHEMISTRY2020