137 research outputs found
Quantum dynamics of the ππ*/nπ* decay of the epigenetic nucleobase 1,5-dimethyl-cytosine in the gas phase.
A partial ultrafast ππ* → nπ* transfer is predicted. Many vibrational modes are activated, but oscillations of bonds and angles are quickly damped
Automating the Correctness Assessment of AI-generated Code for Security Contexts
In this paper, we propose a fully automated method, named ACCA, to evaluate
the correctness of AI-generated code for security purposes. The method uses
symbolic execution to assess whether the AI-generated code behaves as a
reference implementation. We use ACCA to assess four state-of-the-art models
trained to generate security-oriented assembly code and compare the results of
the evaluation with different baseline solutions, including output similarity
metrics, widely used in the field, and the well-known ChatGPT, the AI-powered
language model developed by OpenAI. Our experiments show that our method
outperforms the baseline solutions and assesses the correctness of the
AI-generated code similar to the human-based evaluation, which is considered
the ground truth for the assessment in the field. Moreover, ACCA has a very
strong correlation with human evaluation (Pearson's correlation coefficient
r=0.84 on average). Finally, since it is a fully automated solution that does
not require any human intervention, the proposed method performs the assessment
of every code snippet in ~0.17s on average, which is definitely lower than the
average time required by human analysts to manually inspect the code, based on
our experience
Who Evaluates the Evaluators? On Automatic Metrics for Assessing AI-based Offensive Code Generators
AI-based code generators are an emerging solution for automatically writing
programs starting from descriptions in natural language, by using deep neural
networks (Neural Machine Translation, NMT). In particular, code generators have
been used for ethical hacking and offensive security testing by generating
proof-of-concept attacks. Unfortunately, the evaluation of code generators
still faces several issues. The current practice uses automatic metrics, which
compute the textual similarity of generated code with ground-truth references.
However, it is not clear what metric to use, and which metric is most suitable
for specific contexts. This practical experience report analyzes a large set of
output similarity metrics on offensive code generators. We apply the metrics on
two state-of-the-art NMT models using two datasets containing offensive
assembly and Python code with their descriptions in the English language. We
compare the estimates from the automatic metrics with human evaluation and
provide practical insights into their strengths and limitations
Enhancing Robustness of AI Offensive Code Generators via Data Augmentation
In this work, we present a method to add perturbations to the code
descriptions, i.e., new inputs in natural language (NL) from well-intentioned
developers, in the context of security-oriented code, and analyze how and to
what extent perturbations affect the performance of AI offensive code
generators. Our experiments show that the performance of the code generators is
highly affected by perturbations in the NL descriptions. To enhance the
robustness of the code generators, we use the method to perform data
augmentation, i.e., to increase the variability and diversity of the training
data, proving its effectiveness against both perturbed and non-perturbed code
descriptions
Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine-Cytosine in Chloroform
We study the ultrafast photoactivated dynamics of the hydrogen bonded dimer Guanine-Cytosine in chloroform solution, focusing on the population of the Guanine→Cytosine charge transfer state (GC-CT), an important elementary process for the photophysics and photochemistry of nucleic acids. We integrate a quantum dynamics propagation scheme, based on a linear vibronic model parameterized through time dependent density functional theory calculations, with four different solvation models, either implicit or explicit. On average, after 50 fs, 30∼40 % of the bright excited state population has been transferred to GC-CT. This process is thus fast and effective, especially when transferring from the Guanine bright excited states, in line with the available experimental studies. Independent of the adopted solvation model, the population of GC-CT is however disfavoured in solution with respect to the gas phase. We show that dynamical solvation effects are responsible for this puzzling result and assess the different chemical-physical effects modulating the population of CT states on the ultrafast time-scale. We also propose some simple analyses to predict how solvent can affect the population transfer between bright and CT states, showing that the effect of the solute/solvent electrostatic interactions on the energy of the CT state can provide a rather reliable indication of its possible population
Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine-Cytosine in Chloroform
We study the ultrafast photoactivated dynamics of the hydrogen bonded dimer Guanine-Cytosine in chloroform solution, focusing on the population of the Guanine→Cytosine charge transfer state (GC-CT), an important elementary process for the photophysics and photochemistry of nucleic acids. We integrate a quantum dynamics propagation scheme, based on a linear vibronic model parameterized through time dependent density functional theory calculations, with four different solvation models, either implicit or explicit. On average, after 50 fs, 30∼40 % of the bright excited state population has been transferred to GC-CT. This process is thus fast and effective, especially when transferring from the Guanine bright excited states, in line with the available experimental studies. Independent of the adopted solvation model, the population of GC-CT is however disfavoured in solution with respect to the gas phase. We show that dynamical solvation effects are responsible for this puzzling result and assess the different chemical-physical effects modulating the population of CT states on the ultrafast time-scale. We also propose some simple analyses to predict how solvent can affect the population transfer between bright and CT states, showing that the effect of the solute/solvent electrostatic interactions on the energy of the CT state can provide a rather reliable indication of its possible population
TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids
We present a computational study of the magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM-B3LYP functionals. Solvent effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general alter the qualitative shape of the spectra. The bands are dominated by the bright \u3c0 \u2192 \u3c0* transitions, and our calculations in solution nicely reproduce their energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n \u2192 \u3c0* excitations, but they are too weak to be observed in the experiment
Solvent Effect on the Singlet Excited-state Dynamics of 5-Fluorouracil in Acetonitrile as Compared with Water
The excited-state dynamics of 5-fluorouracil in acetonitrile has been investigated by femtosecond fluorescence upconversion spectroscopy in combination with quantum chemistry TD-DFT calculations ((PCM/TD-PBE0). Experimentally, it was found that when going from water to acetonitrile solution the fluorescence decay of 5FU becomes much faster. The calculations show that this is related to the opening of an additional decay channel in acetonitrile solution since the dark n/* excited state becomes near degenerate with the bright /* state, forming a conical intersection close to the Franck-Condon region. In both solvents, a S1-S0 conical intersection, governed by the out-of-plane motion of the fluorine atom, is active, allowing an ultrafast internal conversion to the ground state
Can NMT Understand Me? Towards Perturbation-based Evaluation of NMT Models for Code Generation
Neural Machine Translation (NMT) has reached a level of maturity to be
recognized as the premier method for the translation between different
languages and aroused interest in different research areas, including software
engineering. A key step to validate the robustness of the NMT models consists
in evaluating the performance of the models on adversarial inputs, i.e., inputs
obtained from the original ones by adding small amounts of perturbation.
However, when dealing with the specific task of the code generation (i.e., the
generation of code starting from a description in natural language), it has not
yet been defined an approach to validate the robustness of the NMT models. In
this work, we address the problem by identifying a set of perturbations and
metrics tailored for the robustness assessment of such models. We present a
preliminary experimental evaluation, showing what type of perturbations affect
the model the most and deriving useful insights for future directions.Comment: Paper accepted for publication in the proceedings of The 1st Intl.
Workshop on Natural Language-based Software Engineering (NLBSE) to be held
with ICSE 202
The resonance raman spectrum of cytosine in water: analysis of the effect of specific solute–solvent interactions and non-adiabatic couplings
In this contribution, we report a computational study of the vibrational Resonance Raman (vRR) spectra of cytosine in water, on the grounds of potential energy surfaces (PES) computed by time-dependent density functional theory (TD-DFT) and CAM-B3LYP and PBE0 functionals. Cytosine is interesting because it is characterized by several close-lying and coupled electronic states, challenging the approach commonly used to compute the vRR for systems where the excitation frequency is in quasi-resonance with a single state. We adopt two recently developed time-dependent approaches, based either on quantum dynamical numerical propagations of vibronic wavepackets on coupled PES or on analytical correlation functions for cases in which inter-state couplings were neglected. In this way, we compute the vRR spectra, considering the quasi-resonance with the eight lowest-energy excited states, disentangling the role of their inter-state couplings from the mere interference of their different contributions to the transition polarizability. We show that these effects are only moderate in the excitation energy range explored by experiments, where the spectral patterns can be rationalized from the simple analysis of displacements of the equilibrium positions along the different states. Conversely, at higher energies, interference and inter-state couplings play a major role, and the adoption of a fully non-adiabatic approach is strongly recommended. We also investigate the effect of specific solute–solvent interactions on the vRR spectra, by considering a cluster of cytosine, hydrogen-bonded by six water molecules, and embedded in a polarizable continuum. We show that their inclusion remarkably improves the agreement with the experiments, mainly altering the composition of the normal modes, in terms of internal valence coordinates. We also document cases, mostly for low-frequency modes, in which a cluster model is not sufficient, and more elaborate mixed quantum classical approaches, in explicit solvent models, need to be applie
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