arXiv subjects

G. Forte

Publications and source records attributed to G. Forte.

11 recordsLinked to original sources

arXiv2023

Modelling the 3D spatiotemporal organisation of chromatin replication

We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently discordant experimental evidence in favour of either scenario. Which of the two morphologies appears in our model depends on the balance between non-specific and origin-targeting interactions between chromatin and firing factors -- polymerases and other components of the replisome. Non-specific interactions are also necessary to yield clustering of factors and replication forks, creating structures akin to the replication foci observed in mammalian cells in vivo. We suggest that cluster formation provides an underappreciated but robust pathway to avoid stalled or faulty forks, which would otherwise diminish the efficiency of the replication process. Additionally, our simulations allow us to predict different modes of cluster growth during S-phase, which could be tested experimentally, and they show that the three dimensional chromatin context is important to understand replication patterns in fission yeast.

physics.bio-ph↗

arXiv2014

Structure of a low-lying isomer of BOSi$_2$, as a free-space planar cluster, using the Hartree-Fock method plus second order perturbations

The Hartree-Fock (HF) method, supplemented by low-order Moller-Plesset (MP2) perturbation theory, has been utilized to predict the nuclear geometry, assuming planarity, of a low-lying isomer of the free space cluster BOSi$_2$. The planar structure found at equilibrium geometry is shown to be stable against small amplitude molecular vibrations. Finally, some brief comments are made on the possible relevance of the above free-space cluster geometry to the known B-O defects which limit the improvement of minority carrier lifetime in a form of p-type silicon.

physics.atm-clus↗

arXiv2013

The nuclear structure and related properties of some low-lying isomers of free-space O_n clusters (n=6, 8, 12)

After some introductory comments relating to antiferromagnetism of crystalline O_2, and brief remarks on the geometry of ozone, Hartree-Fock (HF) theory plus second-order Moller-Plesset (MP2) corrections are used to predict the nuclear structure of low-lying isomers of free-space O_n clusters, for n=6, 8, and 12. The equilibrium nuclear-nuclear potential energy is also discussed in relation to the number n of oxygen atoms in the cluster.

physics.atm-clus↗

arXiv2011

Neutral and cationic free-space oxygen-silicon clusters SiOn (1 < n <= 6), and possible relevance to crystals of SiO2 under pressure

Motivated by the theoretical study of Saito and Ono (2011) on three crystalline forms of SiO2 under pressure, quantum-chemical calculations on various free-space clusters of SiOn and GeOn for 1 < n <= 6 are reported here. Both neutral and cationic clusters have been examined, for both geometry and equilibrium bond lengths. Coupled clusters and correlation-corrected MP2 calculations are presented. For the cations, we emphasize especially the structural distortions occurring in removing degeneracies.

physics.atm-clus↗

arXiv2010

A multiscale study of electronic structure and quantum transport in $C_{6n^2}H_{6n}$-based graphene quantum dots

We implement a bottom-up multiscale approach for the modeling of defect localization in $C_{6n^2}H_{6n}$ islands, i.e. graphene quantum dots with a hexagonal symmetry, by means of density functional and semiempirical approaches. Using the \textit{ab initio} calculations as a reference, we recognize the theoretical framework under which semiempirical methods describe adequately the electronic structure of the studied systems and thereon proceed to the calculation of quantum transport within the non-equilibrium Green's function formalism. The computational data reveal an impurity-like behavior of vacancies in these clusters and evidence the role of parameterization even within the same semiempirical context. In terms of conduction, failure to capture the proper chemical aspects in the presence of generic local alterations of the ideal atomic structure results in an improper description of the transport features. As an example, we show wavefunction localization phenomena induced by the presence of vacancies and discuss the importance of their modeling for the conduction characteristics of the studied structures.

cond-mat.mes-hall↗

arXiv2009

Ab initio prediction of Boron compounds arising from Borozene: Structural and electronic properties

Structure and electronic properties of two unusual boron clusters obtained by fusion of borozene rings has been studied by means of first principles calculations, based on the generalized-gradient approximation of the density functional theory, and the semiempirical tight-binding method was used for the transport calculations. The role of disorder has also been considered with single vacancies and substitutional atoms. Results show that the pure boron clusters are topologically planar and characterized by (3c-2e) bonds, which can explain, together with the aromaticity (estimated by means of NICS), the remarkable cohesive energy values obtained. Such feature makes these systems competitive with the most stable boron clusters to date. On the contrary, the introduction of impurities compromises stability and planarity in both cases. The energy gap values indicate that these clusters possess a semiconducting character, while when the larger system is considered, zero-values of the density of states are found exclusively within the HOMO-LUMO gap. Electron transport calculations within the Landauer formalism confirm these indications, showing semiconductor-like low bias differential conductance for these stuctures. Differences and similarities with Carbon clusters are highlighted in the discussion.

cond-mat.mtrl-sci↗

arXiv2008

Modeling vacancies and hydrogen impurities in graphene: A molecular point of view

We have followed a "molecular" approach to study impurity effects in graphene. This is thought as the limiting case of an infinitely large cluster of benzene rings. Therefore, we study several carbon clusters, with increasing size, from phenalene, including three benzene rings, up to coronene 61, with 61 benzene rings. The impurities considered were a chemisorbed H atom, a vacancy, and a substitutional proton. We performed HF and UHF calculations using the STO-3G basis set. With increasing cluster size in the absence of impurities, we find a decreasing energy gap, here defined as the HOMO-LUMO difference. In the case of H chemisorption or a vacancy, the gap does not decrease appreciably, whereas it is substantially reduced in the case of a substitutional proton. The presence of an impurity invariably induces an increase of the density of states near the HOMO level. We find a zero mode only in the case of a substitutional proton. In agreement with experiments, we find that both the chemisorbed H, the substitutional proton, and the C atom near a vacancy acquire a magnetic moment. The relevance of graphene clusters for the design of novel electronic devices is also discussed.

cond-mat.str-el↗

arXiv2008

Molecules in clusters: the case of planar LiBeBCNOF built from a triangular form LiOB and a linear four-center species FBeCN

Krueger some years ago proposed a cluster LiBeBCNOF, now called periodane. His ground-state isomer proposal has recently been refined by Bera et al. using DFT. Here, we take the approach of molecules in such a cluster as starting point. We first study therefore the triangular molecule LiOB by coupled cluster theory (CCSD) and thereby specify accurately its equilibrium geometry in free space. The second fragment we consider is FBeCN, but treated now by restricted Hartree-Fock (RHF) theory. This four-center species is found to be linear, and the bond lengths are obtained from both RHF and CCSD calculations. Finally, we bring these two entities together and find that while LiOB remains largely intact, FBeCN becomes bent by the interaction with LiOB. Hartree-Fock and CCSD theories then predict precisely the same lowest isomer found by Bera et al. solely on the basis of DFT.

cond-mat.other↗

arXiv2005

Equilibrium molecular energies used to obtain molecular dissociation energies and heats of formation within the bond-order correlation approach

Ab initio calculations including electron correlation are still extremely costly except for the smallest atoms and molecules. Therefore, our purpose in the present study is to employ a bond-order correlation approach to obtain, via equilibrium molecular energies, molecular dissociation energies and heats of formation for some 20 molecules containing C, H, and O atoms, with a maximum number of electrons around 40. Finally, basis set choice is shown to be important in the proposed procedure to include electron correlation effects in determining thermodynamic properties. With the optimum choice of basis set, the average percentage error for some 20 molecules is approximately 20% for heats of formation. For molecular dissociation energies the average error is much smaller: ~0.4.

physics.chem-ph↗

arXiv2005

Electronic structure of clusters (LiBC)_n: n=1, 2, 4

A crystalline form of LiBC is known which has been predicted to be superconducting, with a Tc comparable to that of MgB_2. In both compounds, superconductivity is enhanced by the presence of two electronic bands, one of which is close to a dimensional crossover. Here, we take a quantum chemical approach, and investigate the structural and electronic properties of small clusters (LiBC)_n (n=1-4). With increasing cluster size, we find that several properties of crystalline LiBC evolve naturally from the corresponding properties of the clusters. In particular, one may recognize the origin of the solid bilayered structure, typical of magnesium diboride, and the character of the electronic sigma-band, arising from the overlap of the atomic orbitals in the in-plane BC rings. Two aspects especially emphasized are (a) the HOMO-LUMO gap as function of n and (b) the role of different spin multiplicity.

physics.atm-clus↗

arXiv2004

Bond-order correlation energies for small Si-containing molecules compared with ab initio results from low-order Moller-Plesset perturbation theory

The present study of small molecules containing silicon has been motivated by (a) the considerable interest being shown currently in the kinetics and reactivity of such molecules, and (b) the biotechnological potential of silicon-derivate surfaces as substrates in the adsorption of, for instance, amino acids and proteins. Therefore, we have studied by (i) a semi-empirical approach and (ii) an ab initio procedure employing low-order Moller-Plesset perturbation theory, the molecular correlation energies of some neutral closed and open shell silicon-containing molecules in the series SiXnYm. Procedure (i) is shown to have particular merit for the correlation of the ionic members studied in the above series, while the ab initio procedures employed come into their own for neutral species.

physics.chem-ph↗