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

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 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 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

Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors

International audienceC5-methylation of cytosines is strongly correlated with UV-induced mutations detected in skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of pyrimidine cyclobutane dimers (CPDs). The present study, performedfor the model DNA duplex (TCGTA)3·(TACGA)3 and the constitutive single strands, examines the factors underlying the effect of C5-methylation on pyrimidine dimerization at TCG sites. This effect is quantified for the first time by quantum yields ϕ.They were determined following irradiation at 255, 267, and 282 nm and subsequent photoproduct analysis using HPLC coupled to mass spectrometry. C5-methylation leads to an increase of the CPD quantum yield up to 80% with concomitant decrease of that of pyrimidine(6−4) pyrimidone adducts (64PPs) by at least a factor of 3. The obtained ϕ values cannot be explained only by the change of the cytosine absorption spectrum upon C5-methylation. The conformational and electronic factors that may affect the dimerization reaction are discussed in light of results obtained by fluorescence spectroscopy,molecular dynamics simulations, and quantum mechanical calculations. Thus, it appears that the presence of an extra methyl on cytosine affects the sugar puckering, thereby enhancing conformations of the TC step that are prone to CPD formation but less favorable to 64PPs. In addition, C5-methylation diminishes the amplitude of conformational motions in duplexes; in the resulting stiffer structure, ππ* excitations may be transferred from initially populated exciton states to reactive pyrimidines giving rise to CPDs

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