arXiv subjects

Marco Sacchi

Publications and source records attributed to Marco Sacchi.

6 recordsLinked to original sources

arXiv2025

Conformational Dynamics of 8-Oxoguanine Mispairing Reveal a Mechanism of Polymerase {\lambda} Misincorporation

Experimental evidence has shown the stability of oxygen-stress-damaged guanine, known as 8-oxoguanine. This common oxygen-damaged nucleobase is often found in the presence of reactive oxygen species and can result in the mispairing between adenine and 8-oxoguanine in a Hoogsteen pair. We have computationally investigated the role of 8-oxoguanine to support experimental results and focus the investigation towards the polymerase structure, identifying how 8-oxoguanine interacts in the polymerase environment. Quantum mechanical investigations show the Hoogsteen pairing of adenine and 8-oxoguanine is the most energetically favourable state compared to a Watson-Crick state, supporting experimental evidence. Molecular Dynamical calculation of 8-oxoguanine located in B-DNA provide an average C1' backbone spacing of 1.1 nm compared to adenine-thymine spacing of 1.05 nm but remains within the error margin, however when in the polymerase environment, 8-oxoguanine and the canonical adenine - thymine spacing match at 1.11-1.12nm spacing while 8-oxoguanine is located on the template strand, but is disrupted by tyrosine 251 while situated on the triphosphate strand. We observe that 8-oxoguanine, when paired with adenine in polymerase {\lambda}, can mimic the adenine-thymine structure, as predicted in experimental results, and thus would be misincorporated, but is strongly dependent on its conformation.

physics.bio-ph↗

arXiv2025

Single-Molecule Water Motion on h-BN and Graphene: A Paradigm Shift in Understanding the Behaviour of Water on 2D Material Interfaces

Understanding water behaviour on 2D materials is crucial for sensing, microfluidics, and tribology. While water/graphene interactions are well studied, water on hexagonal boron nitride (h-BN) remains largely unexplored. Despite structural similarity to graphene, h-BN's slightly polar B-N bonds impart a large band gap, high thermal conductivity, and chemical stability, making it promising for electronics, lubricants, and coatings. Moreover, existing water studies often focus on multilayer water dynamics, overlooking single-molecular details. We bridge this gap by studying single-molecular water friction and diffusion on h-BN, comparing it with graphene using helium spin-echo experiments and ab initio calculations. Our findings show that water diffusion on h-BN/Ni follows a complex rotational-translational dynamic, unlike graphene. While conventional views treat water motion as discrete jumps between equivalent adsorption sites, we demonstrate that on h-BN, water molecules rotate freely around their centre of mass. Although the binding energies of water on h-BN and graphene are similar, the activation energy for water dynamics on h-BN is 2.5 times lower than on graphene, implying a much lower barrier for molecular mobility. The fundamentally different diffusion characteristics which classical models cannot capture, underscores the need to rethink how we model water on polar 2D materials. Moreover, our analysis reveals that the metal substrate strongly influences water friction, with h-BN/Ni showing a markedly lower friction than graphene/Ni, in stark contrast to the free-standing materials. These findings challenge assumptions about 2D material-water interactions, highlighting the crucial role of substrate effects in chemistry and material science and offer insights for designing next-generation microfluidic devices that require precise water mobility control.

cond-mat.mes-hall↗

arXiv2022

Evolution of ordered nanoporous phases during h-BN growth: Controlling the route from gas-phase precursor to 2D material by $\textit{in-situ}$ monitoring

Large-area single-crystal monolayers of two-dimensional (2D) materials such as graphene and hexagonal boron nitride (h-BN) can be grown by chemical vapour deposition (CVD). However, the high temperatures and fast timescales at which the conversion from a gas-phase precursor to the 2D material appear, make it extremely challenging to simultaneously follow the atomic arrangements. We utilise helium atom scattering to discover and control the growth of novel 2D h-BN nanoporous phases during the CVD process. We find that prior to the formation of h-BN from the gas-phase precursor, a metastable $(3\times3)$ structure is formed, and that excess deposition on the resulting 2D h-BN leads to the emergence of a $(3\times4)$ structure. We illustrate that these nanoporous structures are produced by partial dehydrogenation and polymerisation of the borazine precursor upon adsorption. These steps are largely unexplored during the synthesis of 2D materials and we unveil the rich phases during CVD growth. Our results provide significant foundations for 2D materials engineering in CVD, by adjusting or carefully controlling the growth conditions and thus exploiting these intermediate structures for the synthesis of covalent self-assembled 2D networks.

cond-mat.mtrl-sci↗

arXiv2021

An Open Quantum Systems approach to proton tunnelling in DNA

One of the most important topics in molecular biology is the genetic stability of DNA. One threat to this stability is proton transfer along the hydrogen bonds of DNA that could lead to tautomerisation, hence creating point mutations. We present a theoretical analysis of the hydrogen bonds between the Guanine-Cytosine (G-C) nucleotide, which includes an accurate model of the structure of the base pairs, the quantum dynamics of the hydrogen bond proton, and the influence of the decoherent and dissipative cellular environment. We determine that the quantum tunnelling contribution to the process is several orders of magnitude larger than the contribution from classical over-the-barrier hopping. Due to this significant quantum contribution, we find that the canonical and tautomeric forms of G-C inter-convert over timescales far shorter than biological ones and hence thermal equilibrium is rapidly reached. Furthermore, we find a large tautomeric occupation probability of $1.73\times 10^{-4}$, suggesting that such proton transfer may well play a far more important role in DNA mutation than has hitherto been suggested. Our results could have far-reaching consequences for current models of genetic mutations.

physics.bio-ph↗

arXiv2021

Motion of water monomers reveals a kinetic barrier to ice nucleation on graphene

The interfacial behaviour of water remains a central question to fields as diverse as protein folding, friction and ice formation[1,2]. While the structural and dynamical properties of water at interfaces differ strongly from those in the bulk, major gaps in our knowledge at the molecular level still prevent us from understanding these ubiquitous chemical processes. Information concerning the microscopic motion of water comes mostly from computational simulation[3,4] but the dynamics of molecules, on the atomic scale, is largely unexplored by experiment. Here we present experimental results combined with ab initio calculations to provide a detailed insight into the behaviour of water monomers on a graphene surface. We show that motion occurs by activated hopping on the graphene lattice. The dynamics of water diffusion displays remarkably strong signatures of cooperative behaviour due to repulsive forces between the monomers. The repulsive forces enhance the monomer lifetime ($t_m \approx 3$ s at $T_S = 125$ K) in a $\textit{free-gas}$ phase that precedes the nucleation of ice islands and, in turn, provides the opportunity for our experiments to be performed. Our results give a unique molecular perspective of barriers to ice nucleation on material surfaces, providing new routes to understand and potentially control the more general process of ice formation.

cond-mat.mtrl-sci↗

arXiv2017

Ultrafast Molecular Transport on Carbon Surfaces: The Diffusion of Ammonia on Graphite

We present a combined experimental and theoretical study of the self-diffusion of ammonia on exfoliated graphite. Using neutron time-of-flight spectroscopy we are able to resolve the ultrafast diffusion process of adsorbed ammonia, NH$_3$, on graphite. Together with van der Waals corrected density functional theory calculations we show that the diffusion of NH$_3$ follows a hopping motion on a weakly corrugated potential energy surface with an activation energy of about 4 meV which is particularly low for this type of diffusive motion. The hopping motion includes further a significant number of long jumps and the diffusion constant of ammonia adsorbed on graphite is determined with $D=3.9 \cdot 10^{-8}~\mbox{m}^2 /\mbox{s}$ at 94 K.

cond-mat.mtrl-sci↗