Biology subjects

Volpert, V.

Publications and source records attributed to Volpert, V..

7 recordsLinked to original sources

bioRxiv2026

A Computational Framework for Understanding HCV Infection and Associated Lipid Dynamics

Hepatitis C virus (HCV) infection is strongly intertwined with host lipid metabolism and is frequently associated with hepatic steatosis, particularly in genotype-specific cases where lipid accumulation reflects direct viral effects rather than host metabolic comorbidities. Despite extensive clinical and experimental evidence, a quantitative framework capturing the bidirectional coupling between viral dynamics and lipid metabolism remains lacking. In this work, we develop a comprehensive mathematical model that integrates HCV infection dynamics with intracellular lipid regulation. The framework combines a reaction diffusion system for spatial viral spread with a coupled metabolic module describing lipid influx. Numerical simulations highlight the role of lipid feedback in shifting infection outcomes toward persistence and recurrent oscillations, demonstrating that lipid accumulation acts as a critical driver of viral amplification. The model also highlights the critical role of immune memory to study acute and chronic phase and successfully reproduces observed viral RNA trajectories. Overall, the framework provides mechanistic insights into HCV dynamics and offers a general modeling approach for studying virus metabolism interactions in liver disease.

cell biology↗

bioRxiv2025

Mathematical modelling of tissue growth control by a negative feedback

This study investigates the regulation of tissue growth through mathematical modeling of systemic and local feedback mechanisms. Employing reaction-diffusion equations, the models explore the dynamics of tissue growth, emphasizing endocrine signaling and inter-tissue communication. The analysis identifies critical factors influencing the emergence of spatial structures, bifurcation phenomena, the existence and stability of stationary pulse and wave solutions. It also elucidates mechanisms for achieving coordinated tissue growth. In particular, if negative feedback is sufficiently strong, their final finite size is provided by a stable pulse, otherwise they manifest unlimited growth in the form of a wave. These findings contribute to the theoretical insights into biological processes such as embryogenesis, regeneration, and tumor development, while highlighting the role of feedback systems in maintaining physiological homeostasis.

developmental biology↗

bioRxiv2023

Cortical Adaptation Mechanism in the Delta Band of Post-Stroke Aphasic subjects during Naming Task

AO_SCPLOWBSTRACTC_SCPLOWThis study explores differences in spatiotemporal cortical dynamics between five people with chronic post-stroke aphasia and five healthy subjects. Electroencephalography was recorded during picture naming in both groups. Frequency-specific Global Field Power (GFP) results showed that the delta band has higher power to discriminate between healthy subjects and people with aphasia (PWA) than theta and alpha bands. EEG topologies computed at the time of GFP peaks in the delta band revealed strong activation oscillating between posterior and anterior areas in PWA. On the other hand, EEG topologies from healthy subjects were variable. Then, Spatial ERP (S-ERP) were developed to add spatial resolution to classical ERP analysis. S-ERP and associated analyses confirmed the previously observed oscillatory pattern in the delta frequency band among PWA during picture naming. This oscillating pattern was alternating between occipital and prefrontal areas with almost opposite phases, a characteristic not observed in healthy subjects. In addition, all PWA performed well on the picture naming task, suggesting that this oscillating pattern may be a cortical adaptation mechanism enabling them to succeed. The observation of large-scale oscillating delta activity across the scalp in all post-stroke subjects who have substantially recovered from aphasia holds the potential to inspire innovative rehabilitation methods employing non-invasive brain stimulation techniques such as transcranial alternating current stimulation (tACS).

neuroscience↗

bioRxiv2023

Investigating Spatiotemporal Dynamics of Cortical Activity During Language Production in the Healthy and Lesioned Brain

Efficient language production requires rapid interactions between different brain areas. These interactions can be severely affected by brain lesions. However, the neurophysiological correlates of the spatiotemporal dynamics during language production are not well understood. The current pilot study explores differences in spatiotemporal cortical dynamics between five subjects with post-stroke aphasia and five control subjects. Electroencephalography was recorded during picture naming in both groups. Average-based analyses (event-related potential (ERP), frequency-specific Global Field Power (GFP)), reveal a strong synchronization of cortical oscillations, especially within the first 600ms post-stimulus, with a time shift between participants with aphasia and control subjects. ERPs and the corresponding brain microstates indicate coordinated brain activity alternating mainly between frontal and occipital zones. This behavior can be described as standing waves between two main sources. At the single-trial scale, traveling waves (TW) were identified from both phase and amplitude analyses. The spatiotemporal distribution of amplitude TW reveals subject-specific organization of several interconnected hubs. In patients with aphasia this spatial organization of TW reveals zones with no TW notably in the vicinity of stroke lesions. The present results provide important hints for the hypothesis that TW contribute to the synchronization and communication between different brain areas especially by interconnecting cortical hubs. Moreover, our findings show that cortical dynamics is affected by brain lesions. Contribution to the FieldO_LISpatiotemporal cortical dynamics of individual trials reveals the presence of phase and amplitude traveling waves. C_LIO_LIExploration of traveling waves on the 2D cortical surface reveals the presence of interconnected epicenters or hubs in all subjects. C_LIO_LIThe spatiotemporal distribution of traveling waves shows a higher density in the prefrontal area for people with aphasia than for healthy subjects. C_LIO_LIFor subjects with aphasia, a sparser density of traveling waves is observed in the approximated lesion area. C_LIO_LIEvent-related potential analyses reveal a consistent alternating activity between the frontal and occipital regions. C_LIO_LISubjects with aphasia present a larger and/or delayed contribution in the delta range in the GFP patterns compared to control subjects. C_LI

neuroscience↗

bioRxiv2022

Characterization of spatiotemporal dynamics in EEG data during picture naming with optical flow patterns

We present an analysis of the spatiotemporal dynamics of the oscillations in the electric potential that arises from neural activity. Depending on the frequency and phase of oscillations, these dynamics can be characterized as standing waves or as out-of-phase and modulated waves, which represent a combination of standing and moving waves. We characterize these dynamics as optical flow patterns, in terms of sources, sinks, spirals and saddles. Analytical and numerical solutions are compared with real EEG data acquired during a picture-naming task. Analytical approximation of standing waves allows us to establish some properties of pattern location and number. Namely, sources and sinks have mainly the same location, while saddles are located between them. The number of saddles correlates with the sum of all the other patterns. These properties are confirmed in both the simulated and real EEG data.

neuroscience↗

bioRxiv2021

Analysis of microvascular thrombus mechanobiology with a novel particle-based model

Platelet accumulation at the site of vascular injury is regulated by soluble platelet agonists, which induce various types of platelet responses, including integrin activation and granule secretion. The interplay between local biochemical cues, mechanical interactions between platelets and macroscopic thrombus dynamics is poorly understood. Here we describe a novel computational model of microvascular thrombus formation for detailed analysis of thrombus mechanics. Adopting a previously developed two-dimensional particle-based model focused on the thrombus shell formation, we revise it to introduce platelet agonists. Blood flow is simulated via computational fluid dynamics approach. In order to model soluble platelet activators, we apply Langevin dynamics to a large number of non-dimensional virtual particles. Taking advantage of the available data on platelet dense granule secretion kinetics, we model platelet degranulation as a stochastic agonist-dependent process. The new model qualitatively reproduces enhanced thrombus formation due to granule secretion in line with in vivo findings and provides a mechanism for thrombin confinement at the early stages of aggregate formation. Our calculations also predict that release of dense granules results in additional mechanical stabilization of the inner layers of the thrombus. Distribution of the inter-platelet forces throughout the aggregate reveals multiple weak spots in the outer regions of thrombus, which are expected to result in mechanical disruptions at the later stages of thrombus formation.

biophysics↗

bioRxiv2021

A multiscale model suggests that a moderately weak inhibition of SARS-CoV-2 replication by type I IFN could accelerate the clearance of the virus

AO_SCPLOWBSTRACTC_SCPLOWSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible RNA virus that emerged in China at the end of 2019 and caused a large global outbreak. The interaction between SARS-CoV-2 and the immune response is complex because it is regulated by various processes taking part at the intracellular, tissue, and host levels. To gain a better understanding of the pathogenesis and progression of COVID-19, we formulate a multiscale model that integrate the main mechanisms which regulate the immune response to SARS-CoV-2 across multiple scales. The model describes the effect of type I interferon on the replication of SARS-CoV-2 inside cells. At the tissue level, we simulate the interactions between infected cells and immune cells using a hybrid agent-based representation. At the same time, we model the dynamics of virus spread and adaptive immune response in the host organism. After model validation, we demonstrate that a moderately weak inhibition of virus replication by type I IFN could elicit a strong adaptive immune response which accelerates the clearance of the virus. Furthermore, numerical simulations suggest that the deficiency of lymphocytes and not dendritic cells could lead to unfavourable outcomes in the elderly population.

immunology↗