arXiv subjects

Prokop Hapala

Publications and source records attributed to Prokop Hapala.

17 recordsLinked to original sources

arXiv2025

GridFF: Efficient Simulation of Organic Molecules on Rigid Substrates

We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with tricubic B-spline interpolation, GridFF reduces the computational cost by orders of magnitude compared to traditional pairwise atomistic models, without compromising the accuracy of forces or trajectories. The CPU implementation of GridFF in the open-source FireCore package provides a 100-1000x speedup over all-atom simulations using LAMMPS, while the GPU implementation - running thousands of system replicas in parallel - samples millions of configurations per second, enabling an exhaustive exploration of the configuration space of small flexible molecules on surfaces within minutes. Furthermore, as demonstrated in our previous application of a similar technique to high-resolution scanning probe microscopy, GridFF can be extended beyond empirical pairwise potentials to those derived from ab initio electron densities. Altogether, this unlocks accurate high-throughput modeling of molecular self-assembly, adsorption, and scanning probe manipulation in surface science.

physics.chem-ph↗

arXiv2025

Negative differential conductance in triangular molecular assemblies

We report the creation and characterization of a molecular-scale negative differential conductance (NDC) device by assembling a triangular trimer of 4,5,9,10-tetrabromo-1,3,6,8-tetraazapyrene (TBTAP) molecules on a superconducting Pb(111) substrate. Using low-temperature scanning tunneling spectroscopy, we observe robust NDC behavior manifesting as a decrease in current with increasing voltage between 0.7-0.9 V arising from the interplay of Coulomb blockade and strong inter-molecular capacitive coupling within the molecular cluster. Gate-controlled charging and discharging processes are directly visualized via two-dimensional differential conductance mapping, which reveals the emergence of Coulomb rings and spatial regions of NDC. Theoretical modeling using a three-impurity Anderson model and master equation approach quantitatively reproduces the experimental observations and demonstrates that the NDC emerges purely from electron correlations, independent of the underlying superconductivity. By tuning the geometry to a hexamer structure, we further show that cluster topology provides versatile control over electronic properties at the molecular scale. These results establish a functional platform for implementing multifunctional molecular devices and highlight a strategy toward programmable and scalable nanoelectronics.

cond-mat.mes-hall↗

arXiv2024

Advancing Scanning Probe Microscopy Simulations: A Decade of Development in Probe-Particle Models

The Probe-Particle Model combine theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article we present the latest version of the Probe-Particle Model implemented in the open-source ppafm package, highlighting substantial advancements in accuracy, computational performance, and userfriendliness. To demonstrate this we provide a comprehensive review of approaches for simulating non-contact Atomic Force Microscopy. They vary in complexity from simple Lennard-Jones potential to the latest full density-based model. We compared those approaches with ab initio calculated references, showcasing their respective merits. All parts of the ppafm package have undergone acceleration by 1-2 orders of magnitude using OpenMP and OpenCL technologies. The updated package includes n interactive graphical user interface and seamless integration into the Python ecosystem via pip, facilitating advanced scripting and interoperability with other software. This adaptability positions ppafm as an ideal tool for high-throughput applications, including the training of machine learning models for the automatic recovery of atomic structures from nc-AFM measurements. We envision significant potential for this application in future single-molecule analysis, synthesis, and advancements in on-surface science in general. Additionally, we discuss simulations of other sub-molecular scanning-probe imaging techniques, such as bond-resolved scanning tunnelling microscopy and kelvin probe force microscopy, all built on the robust foundation of the Probe-Particle Model. Altogether this demonstrates the broad impact of the model across diverse domains of surface science and molecular chemistry.

cond-mat.mes-hall↗

arXiv2022

Evidence of trion-libron coupling in chirally adsorbed single molecules

Interplay between motion of nuclei and excited electrons in molecules plays a key role both in biological and artificial nanomachines. Here we provide a detailed analysis of coupling between quantized librational modes (librons) and charged excited states (trions) on single phthalocyanine dyes adsorbed on a surface. By means of tunnelling electron-induced electroluminescence, we identify libronic progressions on a μeV energy range in spectra of chirally adsorbed phthalocyanines, which are otherwise absent from spectra of symmetrically adsorbed species. Experimentally measured libronic spectra match very well the theoretically calculated libron eigenenergies and peak intensities (Franck-Condon factors) and reveal an unexpected depopulation channel for the zero libron of the excited state that can be effectively controlled by tuning the size of the nanocavity. Our results showcase the possibility of characterizing the dynamics of molecules by their low-energy molecular modes using μeV-resolved tip-enhanced spectroscopy.

cond-mat.mes-hall↗

arXiv2021

Real space visualization of entangled excitonic states in charged molecular assemblies

Entanglement of excitons holds great promise for the future of quantum computing, which would use individual molecular dyes as building blocks of their circuitry. Even though entangled excitonic eigenstates emerging in coupled molecular assemblies can be detected by far-field spectroscopies, access to the individual modes in real space will bring the much needed insight into the photophysics of these fascinating quantum phenomena. Here we combine tip-enhanced spectromicroscopy with atomic force microscopy to inspect delocalized single-exciton states of charged molecular assemblies engineered from individual perylenetetracarboxylic dianhydride molecules. Hyperspectral mapping of the eigenstates and comparison with calculated many-body optical transitions reveals a second low-lying excited state of the anion monomers and its role in the exciton entanglement within the assemblies. We also demonstrate control over the coupling by switching the assembly charge states. Our results reveal the possibility of tailoring excitonic properties of organic dye aggregates for advanced functionalities and establish the methodology to address them individually at the nanoscale.

physics.atm-clus↗

arXiv2019

Automated Structure Discovery in Atomic Force Microscopy

Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar aromatic molecules, due to difficulties with interpretation of highly distorted AFM images originating from non-planar molecules. Here we develop a deep learning infrastructure that matches a set of AFM images with a unique descriptor characterizing the molecular configuration, allowing us to predict the molecular structure directly. We apply this methodology to resolve several distinct adsorption configurations of 1S-camphor on Cu(111) based on low-temperature AFM measurements. This approach will open the door to apply high-resolution AFM to a large variety of systems for which routine atomic and chemical structural resolution on the level of individual objects/molecules would be a major breakthrough.

physics.comp-ph↗

arXiv2019

Computational study of radiative rate in silicon nanocrystals: Role of electronegative ligands and tensile strain

It is widely accepted that the properties of most semiconductor nanocrystals can be tuned by their core size, shape and material. In covalent semiconductor nanocrystal materials, such as silicon, germanium or carbon, certain degree of tunability of the properties can be also achieved by the surface ligands. In particular, covalently bonded ligand species on the surface of such a nanocrystal (i) contribute to the density of states of the core via orbital delocalization; (ii) might introduce strain via ligand-to-ligand steric hindrance and (iii) will cause charge transfer from/to the core. In this work we study all these effects on silicon nanocrystals (SiNCs). We analyze geometrically optimized ~ 2 nm SiNCs with electronegative organic ligands using density functional theory (DFT) simulations. We show that the radiative rate is enhanced by electronegative alkyl and fluorocarbon with respect to what is expected from quantum confinement effect, while bandgap remains unchanged. Also, we show that tensile strain caused by the ligand steric hindrance is detrimental to the rate enhancement, contrary to the positive effects of the more homogeneous tensile strain induced in pressure cell.

cond-mat.mes-hall↗

arXiv2018

Iron-based trinuclear metal-organic nanostructures on a surface with local charge accumulation

Coordination chemistry relies on harnessing active metal sites within organic matrices. Polynuclear complexes - consisting of organic ligands binding to clusters of several metal atoms are of particular interest, owing to their electronic/magnetic properties and potential for functional reactivity pathways. However, their synthesis remains challenging; only a limited number of geometries and configurations have been achieved. Here, we synthesise - via supramolecular chemistry on a noble metal surface - one-dimensional metal-organic nanostructures composed of terpyridine (tpy)-based molecules coordinated with well-defined polynuclear iron clusters. By a combination of low-temperature scanning probe microscopy techniques and density functional theory, we demonstrate that the coordination motif consists of coplanar tpy's linked via a linear tri-iron node in a mixed (positive) valence, metal-metal bond configuration. This unusual linkage is stabilized by a local accumulation of electrons at the interface between cations, ligand and surface. The latter, enabled by the bottom-up on-surface synthesis, hints at a chemically active metal centre, and opens the door to the engineering of nanomaterials with novel catalytic and magnetic functionalities.

cond-mat.mes-hall↗

arXiv2017

Submolecular resolution by variation of IETS amplitude and its relation to AFM/STM signal

Here we show scanning tunnelling microscopy (STM), non-contact atomic force microscopy (AFM) and inelastic electron tunnelling spectroscopy (IETS) measurements on organic molecule with a CO- terminated tip at 5K. The high-resolution contrast observed simultaneously in all channels unam- biguously demonstrates the common imaging mechanism in STM/AFM/IETS, related to the lateral bending of the CO-functionalized tip. The IETS spectroscopy reveals that the submolecular con- trast at 5K consists of both renormalization of vibrational frequency and variation of the amplitude of IETS signal. This finding is also corroborated by first principles simulations. We extend accord- ingly the probe-particle AFM/STM/IETS model to include these two main ingredients necessary to reproduce the high-resolution IETS contrast. We also employ the first principles simulations to get more insight into different response of frustrated translation and rotational modes of CO-tip during imaging.

cond-mat.mtrl-sci↗

arXiv2017

Submolecular-resolution non-invasive imaging of interfacial water with atomic force microscopy

Scanning probe microscopy (SPM) has been extensively applied to probe interfacial water in many interdisciplinary fields but the disturbance of the probes on the hydrogen-bonding structure of water has remained an intractable problem. Here we report submolecular-resolution imaging of the water clusters on a NaCl(001) surface within the nearly non-invasive region by a qPlus-based noncontact atomic force microscopy. Comparison with theoretical simulations reveals that the key lies in probing the weak high-order electrostatic force between the quadrupole-like CO-terminated tip and the polar water molecules at large tip-water distances. This interaction allows the imaging and structural determination of the weakly bonded water clusters and even of their metastable states without inducing any disturbance. This work may open up new possibility of studying the intrinsic structure and electrostatics of ice or water on bulk insulating surfaces, ion hydration and biological water with atomic precision.

physics.chem-ph↗

arXiv2016

Charged-state dynamics in Kelvin probe force microscopy

We present a numerical model which allows us to study the Kelvin force probe microscopy response to the charge switching in quantum dots at various time scales. The model provides more insight into the behavior of frequency shift and dissipated energy under different scanning conditions measuring a temporarily charged quantum dot on surface. Namely, we analyze the dependence of the frequency shift, its fluctuation and of the dissipated energy, on the resonance frequency of tip and electron tunneling rates between tip - quantum dot and quantum dot - sample. We discuss two complementary approaches to simulating the charge dynamics, a stochastic and a deterministic one. In addition, we derive analytic formulas valid for small amplitudes, describing relations between the frequency shift, dissipated energy, and the characteristic rates driving the charging and discharging processes.

cond-mat.mes-hall↗

arXiv2014

The origin of high-resolution IETS-STM images of organic molecules with functionalized tips

Recently, the family of high-resolution scanning probe imaging techniques using decorated tips has been complimented by a method based on inelastic electron tunneling spectroscopy (IETS). The new technique resolves the inner structure of organic molecules by mapping the vibrational energy of a single carbonmonoxide (CO) molecule positioned at the apex of a scanning tunnelling microscope (STM) tip. Here, we explain high-resolution IETS imaging by extending the model developed earlier for STM and atomic force microscopy (AFM) imaging with decorated tips. In particular, we show that the tip decorated with CO acts as a nanoscale sensor that changes the energy of the CO frustrated translation in response to the change of the local curvature of the surface potential. In addition, we show that high resolution AFM, STM and IETS-STM images can deliver information about intramolecular charge transfer for molecules deposited on a~surface. To demonstrate this, we extended our numerical model by taking into the account the electrostatic force acting between the decorated tip and surface Hartree potential.

cond-mat.mes-hall↗

arXiv2014

Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism

The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code Fireball, suitable for the computational study of these problems. Our methodology enables simulating photo-induced reaction mechanisms over hundreds of trajectories; therefore, large statistically significant ensembles can be calculated to accurately represent a reaction profile. As an example of the application of this approach, we report results on the [2+2] cycloaddition of ethylene with maleic anhydride and on the [2+2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

physics.comp-ph↗

arXiv2014

Silicene vs. ordered 2D silicide: the atomic and electronic structure of the Si-$(\sqrt{19}\times\sqrt{19})R23.4^{\circ}$/Pt(111) surface reconstruction

We discuss the possibility of a 2D ordered structure formed upon deposition of Si on metal surfaces. We investigate the atomic and electronic structure of the Si-$(\sqrt{19}\times\sqrt{19})R23.4^{\circ}$/Pt(111) surface reconstruction by means of a set of experimental surface-science techniques supported by theoretical calculations. The theory achieves a very good agreement with the experimental results and corroborate beyond any doubt that this phase is a surface alloy consisting of Si$_3$Pt tetramers that resembles a twisted Kagome lattice. These findings render unlikely any formation of silicene or germanene on Pt(111) and other transition metal surfaces.

cond-mat.mtrl-sci↗

arXiv2014

The mechanism of high-resolution STM/AFM imaging with functionalized tips

High resolution Atomic Force Microscopy (AFM) and Scanning Tunnelling Microscopy (STM) imaging with functionalized tips is well established, but a detailed understanding of the imaging mechanism is still missing. We present a numerical STM/AFM model, which takes into account the relaxation of the probe due to the tip-sample interaction. We demonstrate that the model is able to reproduce very well not only the experimental intra- and intermolecular contrasts, but also their evolution upon tip approach. At close distances, the simulations unveil a significant probe particle relaxation towards local minima of the interaction potential. This effect is responsible for the sharp sub-molecular resolution observed in AFM/STM experiments. In addition, we demonstrate that sharp apparent intermolecular bonds should not be interpreted as true hydrogen bonds, in the sense of representing areas of increased electron density. Instead they represent the ridge between two minima of the potential energy landscape due to neighbouring atoms.

cond-mat.mes-hall↗

arXiv2013

Combined AFM and STM measurements of a silicene sheet grown on Ag(111) surface

In this Letter, we present the first non-contact atomic force microscopy (nc-AFM) of a silicene on silver (Ag) surface, obtained by combining non-contact atomic force microscopy (nc-AFM) and scanning tunneling microscopy (STM). STM images over large areas of silicene grown on Ag(111) surface show both (sqrt13xsqrt13)R13.9° and (4x4) superstructures. For the widely observed (4x4) structure, the nc-AFM topography shows an atomic-scale contrast inversion as the tip-surface distance is decreased. At the shortest tip-surface distance, the nc-AFM topography is very similar to the STM one. The observed structure in the nc-AFM topography is compatible with only one out of two silicon atoms being visible. This indicates unambiguously a strong buckling of the silicene honeycomb layer.

cond-mat.mtrl-sci↗

arXiv2013

Theoretical analysis of electronic band structure of 2-to-3-nm Si nanocrystals

We introduce a general method which allows reconstruction of electronic band structure of nanocrystals from ordinary real-space electronic structure calculations. A comprehensive study of band structure of a realistic nanocrystal is given including full geometric and electronic relaxation with the surface passivating groups. In particular, we combine this method with large scale density functional theory calculations to obtain insight into the luminescence properties of silicon nanocrystals of up to 3 nm in size depending on the surface passivation and geometric distortion. We conclude that the band structure concept is applicable to silicon nanocrystals with diameter larger than $\approx$ 2 nm with certain limitations. We also show how perturbations due to polarized surface groups or geometric distortion can lead to considerable moderation of momentum space selection rules.

cond-mat.mes-hall↗