Publications related to Insights into Intrastrand Cross-Link Lesions of DNA from QM/MM Molecular Dynamics Simulations

Related publications (38)

Cooperative promotion of electroreduction of CO to n-propanol by *CO enrichment and proton regulation

The CO2/CO electroreduction reaction (CO2RR/CORR) to liquid products presents an enticing pathway to store intermittent renewable electricity. However, the selectivity for desirable high-value C3 products, such as n-propanol, remains unsatisfactory in the ...

ROYAL SOC CHEMISTRY2025

Lagnet: Better Electron Density Prediction for Lcao-based Data and Drug-like Substances

Egor Rumiantsev

The electron density is an important object in quantum chemistry that is crucial for many downstream tasks in drug design. Recent deep learning approaches predict the electron density around a molecule from atom types and atom positions. Most of these meth ...

BMC2025

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

Telomere protection against oxidative stress

Thu Trang Nguyen

Telomeres are nucleoprotein structures at the ends of linear chromosomes, being essential for the maintenance of genomic integrity. Telomeres have a unique structure which distinguishes chromosome termini from DNA damage sites. Shelterin complexes are the ...

EPFL2023

Supramolecular Polymer Brushes

Friederike Katharina Metze

Thin polymer coatings present a method to modify the surface properties of underlying substrates. Polymer-coated surfaces have been used as anticorrosive materials, surfaces with special wetting properties, antifriction materials, and as materials for biom ...

EPFL2023

Dynamics of K2Ni2(SO4)3 governed by proximity to a 3D spin liquid model

Henrik Moodysson Rønnow, Arnaud Magrez, Ivica Zivkovic, Jian Rui Soh, Aman Sharma, Virgile Yves Favre

Quantum spin liquids (QSLs) have become a key area of research in magnetism due to their remarkable properties, such as long-range entanglement, fractional excitations, and topologically protected phenomena. Recently, the search for QSLs has expanded into ...

Nature Research2024

Preomic profile of BxPC-3 cells after treatment with BRC4

Andrea Cavalli

BRCA2 and RAD51 are two proteins that play a central role in homologous recombination (HR) and DNA double strand break (DSB) repair. BRCA2 assists RAD51 fibrillation and defibrillation through binding with its eight BRC repeats, with BRC4 being one of the ...

ELSEVIER2023

Tunnel junction sensing of TATP explosive at the single-molecule level

Helena Miljkovic, Radomir Zikic

Triacetone triperoxide (TATP) is a highly potent homemade explosive commonly used in terrorist attacks. Its detection poses a significant challenge due to its volatility, and the lack of portability of current sensing techniques. To address this issue, we ...

Royal Soc Chemistry2023

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

Structural topology exploration through policy-based generation of equilibrium representations

Corentin Jean Dominique Fivet, Ioannis Mirtsopoulos

Mainstream approaches to design spatial architectural forms that are structurally relevant consist either in adapting well-known and catalogued conventional types or in searching for close-to-optimum solutions of well-defined problems. Few means exist to e ...

2023

Soft Mechanochemistry of Disulfide-Crosslinked Polymer Networks

Zhao Meng

Mechanochemistry harnesses mechanical force to facilitate chemical reactions. Traditionally, the field of polymer mechanochemistry has used methods to activate chemical bonds, which use forces that are larger than those that are required to break a covalen ...

EPFL2024

Magnetostriction-Driven Muon Localization in an Antiferromagnetic Oxide

Nicola Marzari, Iurii Timrov, Lorenzo Monacelli

Magnetostriction results from the coupling between magnetic and elastic degrees of freedom. Though it is associated with a relatively small energy, we show that it plays an important role in determining the site of an implanted muon, so that the energetica ...

Amer Physical Soc2024

Synthesis, isolation and application of a sila-ketenyl anion

Rosario Scopelliti

Ynolates or ketenyl anions, [RCCO]-, are negatively charged reactive intermediates, which can be generated in situ and used for divergent chemical transformations. Ynolates can react either at the oxygen or carbon centres or across the C-C triple bond, mak ...

Springernature2023

Chalcogen bonding catalysis

Jieping Zhu

Catalysts play a major role in chemical synthesis, and catalysis is considered to be a green and economic process. Catalysis is dominated by covalent interactions between the catalyst and substrate. The design of non-covalent catalysts came into limelight ...

Royal Society of Chemistry2024

Urtica dioica Leaf Infusion Enhances the Sensitivity of Triple-Negative Breast Cancer Cells to Cisplatin Treatment

Rita Sarkis

Urtica dioica (UD) has been widely used in traditional medicine due to its therapeutic benefits, including its anticancer effects. Natural compounds have a promising potential when used in combination with chemotherapeutic drugs. The present study explores ...

MDPI2023

The energy landscape of magnetic materials

Nicola Marzari, Louis Maurice Ponet, Enrico Di Lucente

Magnetic materials can display many solutions to the electronic-structure problem, corresponding to different local or global minima of the energy functional. In Hartree-Fock or density-functional theory different single-determinant solutions lead to diffe ...

2024

Electronic Excited States from Physically Constrained Machine Learning

Michele Ceriotti, Jigyasa Nigam, Divya Suman

Data-driven techniques are increasingly used to replace electronic-structure calculations of matter. In this context, a relevant question is whether machine learning (ML) should be applied directly to predict the desired properties or combined explicitly w ...

2024

Recycling of Polymerase Chain Reaction (PCR) Kits

Francesco Stellacci, Yong Zhu, Weina Liu

Polymerase chain reaction (PCR) kits have been used as common diagnosing tools during the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with daily worldwide usage in the millions. It is well known that at the beginn ...

AMER CHEMICAL SOC2023

Localized Ionic Reinforcement of Double Network Granular Hydrogels

Esther Amstad, Alexandra Thoma

Nature produces soft materials with fascinating combinations of mechanical properties. For example, the mussel byssus embodies a combination of stiffness and toughness, a feature that is unmatched by synthetic hydrogels. Key to enabling these excellent mec ...

Wiley-V C H Verlag Gmbh2024

Mechanistic Insight into Supramolecular Polymerization in Water Tunable by Molecular Geometry

Lukas Pfeifer

Supramolecular self-assembly in water based on non-covalent bonding is attracting major attention due to the potential of hydrogels and aqueous polymers in biomedical applications. Although supramolecular polymerization in organic solvents is well establis ...

CHINESE CHEMICAL SOC2022