arXiv subjects

Vladik Avetisov

Publications and source records attributed to Vladik Avetisov.

5 recordsLinked to original sources

arXiv2026

DRIADA: A Python Toolkit for Cross-Scale Analysis of Single-Neuron Selectivity and Population Dynamics

Brain activity spans single-neuron, population, and network levels, and core questions in neural coding require moving between them. Yet current tools target a single paradigm and incompatible data formats, leaving cross-level questions hard to address. We present DRIADA, an open-source Python framework that unifies neural signals and time-aligned behavior in a shared data model, so selectivity testing, dimensionality reduction, and network analysis operate within a unified workflow. We evaluate it on synthetic data with known ground truth, hippocampal calcium imaging from 13~mice in an open field, and a simulated toroidal attractor network. In the hippocampal data, selectivity-based filtering restored a two-dimensional spatial embedding from a collapsed all-neuron embedding, while reverse analysis showed that ${\sim}57\%$ of neurons informative about leading manifold dimensions were not selective to any of the 11 measured behavioral features. On the toroidal benchmark, four independent modules recovered the expected topology. DRIADA makes cross-scale analysis routine across calcium imaging, spike trains, and simulated networks.

q-bio.NC↗

arXiv2026

INTENSE: Detecting and disentangling neuronal selectivity in calcium imaging data

Neurons encode information about the environment through their activity. As animals explore the environment, neurons rapidly acquire selectivity for distinct features of the external world; characterizing how these selectivity patterns emerge, reorganize, and overlap is key to linking neural activity to behavior and cognition. Calcium imaging in freely behaving animals can record large neuronal populations, but quantifying neuron-behavior selectivity directly from continuous fluorescence is challenging because both signals are temporally autocorrelated and calcium kinetics introduce time lags. Here we present INTENSE (INformation-Theoretic Evaluation of Neuronal SElectivity), an open-source framework that uses mutual information to detect neuron-behavior associations from raw calcium fluorescence data. INTENSE controls false discoveries using circular-shift permutation testing that preserves temporal structure and optimizes temporal delays to account for indicator kinetics and prospective/retrospective encoding. To separate genuine mixed selectivity from associations driven by behavioral covariance, INTENSE applies conditional mutual information-based disentanglement. We validated INTENSE on synthetic datasets, demonstrating robust detection across diverse signal-to-noise ratios and reliability conditions, whereas methods lacking temporal controls show poor performance. Applied to CA1 miniscope recordings in mice freely exploring an open field, INTENSE reveals robust selectivity to multiple variables (place, head direction, object interaction, locomotion) and refines mixed-selectivity estimates by distinguishing redundant from genuinely multi-variable encoding. Together, INTENSE enables high-throughput, information-theoretic selectivity mapping with principled control of temporal structure and behavioral covariance, bridging large-scale recordings to circuit-level hypotheses.

q-bio.NC↗

arXiv2025

Computational Design Rules for Helical Aromatic Foldamers: $π-π$ Stacking, Solvent Effects, and Conformational Stability

Molecular-scale materials with bistable behavior and tunable properties are increasingly relevant for next-generation nanoscale electronic devices. Helical foldamers are promising candidates, but their structural and mechanical properties are highly sensitive to conformational stability and environmental conditions. A systematic methodology based on quantum-chemical calculations is proposed for assessing solvent-dependent mechanical behavior, combining analysis of $π-π$ stacking interactions, conformational energetics, and environmental effects. Using this methodology we identified simple design principles for the rapid screening of new compounds, allowing evaluation of their conformational stability and effective mechanical rigidity. Applying these principles, we identify a modified helical aromatic foldamer that exhibits improved mechanical and stability characteristics compared to the initial reference compound.

cond-mat.mes-hall↗

arXiv2024

Collective bistability of pyridine-furan nanosprings coupled by a graphene plate

Nanometer-sized molecular structures exhibiting mechanical-like switching between discrete states are of great interest for their potential uses in nanotechnology and materials science. Designing such structures and understanding how they can be combined to operate synchronously is a key to creating nanoscale functional units. Notable examples recently discovered using atomistic simulations are pyridine-furan and pyridine-pyrrole nanosprings. When slightly stretched in aqueous or organic solutions, these nanosprings exhibit bistable dynamics akin to Duffing nonlinear oscillators. Based on these findings, we designed a hybrid system consisting of several pyridine furan nanosprings attached to a graphene plate in organic solvent and simulated the molecular dynamics of the construct. Our focus is on how the nanosprings coupled by a graphene plate work together, and whether such a design enables the nanosprings to respond synchronously to random perturbations and weak external stimuli. Molecular dynamics simulations of this specific construct are complemented by a theoretical model of coupled bistable systems to understand how the synchronization depends on coupling of bistable units.

cond-mat.mes-hall↗

arXiv2020

Detection of single molecules using stochastic resonance of bistable oligomers

Our computer simulations have shown that the large-scale conformational dynamics of a short oligomeric fragment of thermoresponsive polymers resemble the mechanical movement of nonlinear bistable systems. The oligomers demonstrate spontaneous vibrations and stochastic resonance activated by the thermal noise. We have observed reasonable shifts of the spontaneous vibrations and stochastic resonance modes when attaching a molecular cargo to the oligomer. All these effects indicate that bistable oligomers may work as operational units capable of detecting single molecules.

cond-mat.soft↗