Publications related to Structural and energetic basis for hybridization limits in high-density DNA monolayers

Related publications (33)

Revealing the Mechanism Underlying 3D-AFM Imaging of Suspended Structures by Experiments and Simulations

The invention of 3D atomic force microscopy (3D-AFM) has enabled visualizing subnanoscale 3D hydration structures. Meanwhile, its applications to imaging flexible molecular chains have started to be experimentally explored. However, the validity and princi ...

Wiley-V C H Verlag Gmbh2024

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

Nanolithography of the nanocorral structure of chemisorbed oxygen atoms on the graphitic lattice

Kumar Varoon Agrawal, Shaoxian Li

Controlled atomic patterning is an attractive tool to fine tune properties of graphitic lattice. Several O-functionalized derivatives of graphitic lattice have been widely studied, e.g., graphene oxide, reduced graphene oxide, and functionalized carbon nan ...

Pergamon-Elsevier Science Ltd2024

Scanning Tunneling Microscopy for Molecules: Effects of Electron Propagation into Vacuum

Klaus Kern, Abhishek Grewal

Using scanning tunneling microscopy (STM), we experimentally and theoretically investigate isolated platinum phthalocyanine (PtPc) molecules adsorbed on an atomically thin NaCl(100) film vapor deposited on Au(111). We obtain good agreement between theory a ...

Amer Chemical Soc2024

Plasmonically enhanced molecular junctions for investigation of atomic-scale fluctuations in self-assembled monolayers

Sakthi Priya Amirtharaj

Molecular junctions represent a fascinating frontier in the realm of nanotechnology and are one of the smallest optoelectronic devices possible, consisting of individual molecules or a group of molecules that serve as the active element sandwiched between ...

EPFL2024

Mechanistic study on the evolution of vacancies in graphene by oxidation by scanning tunneling microscopy

Shaoxian Li

Nanostructured graphitic materials, including graphene hosting Å to nanometer-sized pores, have attracted attention for various applications such as separations, sensors, and energy storage. Graphene with Å-scale pores is a promising next-generation materi ...

EPFL2023

In Situ and Time-Resolved Transmission Electron Microscopy of Nanoscale Processes

Chengcheng Yan

Observing the fast dynamics of nanoscale systems is crucial in order to understand and ultimately control their behavior. Characterizing these dynamic processes requires techniques with atomic spatial resolution and a temporal resolution that matches the t ...

EPFL2023

Self-Assembly of N-Rich Triimidazoles on Ag(111): Mixing the Pleasures and Pains of Epitaxy and Strain

Ulrich Aschauer, Christian Wäckerlin

In the present report, homochiral hydrogen-bonded assemblies of heavily N-doped (C9H6N6) heterocyclic triimidazole (TT) molecules on an Ag(111) substrate were investigated using scanning tunneling microscopy (STM) and low energy electron diffraction (LEED) ...

Amer Chemical Soc2023

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

Comparing transferability in neural network approaches and linear models for machine-learning interaction potentials

Kevin Rossi

Atomic simulations using machine learning interatomic potential (MLIP) have gained a lot of popularity owing to their accuracy in comparison to conventional empirical potentials. However, the transferability of MLIP to systems outside the training set pose ...

AMER PHYSICAL SOC2023

Nanomechanical Modeling of the Bending Response of Silicon Nanowires

Yusuf Leblebici, Zuhal Tasdemir

Understanding the mechanical behavior of silicon nanowiresis essentialfor the implementation of advanced nanoscale devices. Although bendingtests are predominantly used for this purpose, their findings shouldbe properly interpreted through modeling. Variou ...

AMER CHEMICAL SOC2023

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Kristina Makasheva

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

EPFL2023

Resonant Transducers Consisting of Graphene Ribbons with Attached Proof Masses for NEMS Sensors

Luis Guillermo Villanueva Torrijo, Daniel Moreno Garcia

The unique mechanical and electrical properties of graphene make it an exciting material for nanoelectromechanical systems (NEMS). NEMS resonators with graphene springs facilitate studies of graphene's fundamental material characteristics and thus enable i ...

Amer Chemical Soc2023

Five-Membered Rings Create Off-Zero Modes in Nanographene

Oleg Yazyev, Kristians Cernevics

The low-energy electronic structure of nanographenes can be tuned through zero-energy pi-electron states, typically referred to as zero-modes. Customizable electronic and magnetic structures have been engineered by coupling zero-modes through exchange and ...

Amer Chemical Soc2023

3D printed fiber-optic nanomechanical bioprobe

Sandor Kasas, Jiangtao Zhou

Ultrasensitive nanomechanical instruments, e.g. atomic force microscopy (AFM), can be used to perform delicate biomechanical measurements and reveal the complex mechanical environment of biological processes. However, these instruments are limited because ...

IOP Publishing Ltd2023

Advancing Computational Chemistry with Stochastic and Artificial Intelligence Approaches

Justin Villard

Computational chemistry aims to simulate reactions and molecular properties at the atomic scale, advancing the design of novel compounds and materials with economic, environmental, and societal implications. However, the field relies on approximate quantum ...

EPFL2023

Nanoscale local modification of PMMA refractive index by tip-enhanced femtosecond pulsed laser irradiation

Mihai Adrian Ionescu

Tip-enhanced optical effects have enabled a wide palette of nanoscale investigation techniques and recently they were successfully used to modify and manipulate matter with nanoscale spatial resolution. We contribute to this latter area by reporting a viab ...

ELSEVIER2023

Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

Sandrine Gerber, Mounir Driss Mensi, Perrine Agnes Edith Robin, Lucas Mayoraz, Alireza Kavand

The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be pr ...

2023

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

Time-Resolved Scanning Ion Conductance Microscopy and Single-Molecule Spectroscopy

Samuel Mendes Leitão

The evolution of the 3D morphology is at the center of many relevant biological processes ranging from cellular differentiation to cancer invasion and metastasis. Microscopy techniques, such as electron microscopy (EM), super-resolution (SR) optical micros ...

EPFL2023