arXiv subjects

Vladik Avetisov

Publications and source records attributed to Vladik Avetisov.

5 recordsLinked to original sources

arXiv2026

DRIADA: an open-source Python toolkit for linking single-neuron selectivity and population activity to behavior

Understanding how individual neurons contribute to population activity during behavior is central to understanding brain functions across biological scales. We developed DRIADA, an open-source Python toolkit that connects analyses of individual neurons, population activity, and neuronal networks to the same behavioral parameters. We evaluated it on synthetic populations with known ground truth, calcium-imaging recordings from dorsal hippocampal CA1 in 13 mice across 39 sessions, and a simulated continuous attractor neural network (CANN) with known toroidal organization. Across most hippocampal sessions, embeddings of spatially selective neurons predicted held-out position better than equally sized random subsets and all recorded neurons. The same workflow related population dimensions back to individual neurons, including cells without detected selectivity for the measured behavioral variables. In the simulated network, complementary analyses captured features consistent with its known organization. Thus, DRIADA provides a common framework for relating neuronal selectivity, population structure, and network activity to behavioral dynamics.

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↗