Biology subjects

Contera, S.

Publications and source records attributed to Contera, S..

4 recordsLinked to original sources

bioRxiv2026

Non-Equilibrium Spatial Encoding of Nanoscale Mechanical Relaxation in Growing Plant Epithelial cells

A central problem in soft and biological physics is how molecular-scale activity and remodelling coarse-grain into emergent mechanical laws at larger scales. In growing cell walls (polymeric composite materials that surround 90% of living organisms cells) irreversible deformation is not controlled by elastic stress alone. Instead, growth depends on the interplay between energy storage, dissipation, and the local timing of viscoelastic relaxation. Although dynamic atomic force microscopy (AFM) resolves storage and loss moduli (E', E'') of living walls at nanometre resolution, these observables have remained phenomenological and disconnected from constitutive field variables. Here we introduce a physics-based inversion framework that converts AFM measurements of epidermal cells of living Arabidopsis plants into spatially resolved fields of stiffness k, viscosity , and relaxation time{tau} . By analysing the spatial gradients of E' and E'', we uncover organized mechanical heterogeneities governed by cellular confinement and stress focusing. We demonstrate that the local relaxation time is encoded directly in the coupling between storage and dissipation, yielding the pointwise relation{tau} = (1/{omega}) {partial}E/{partial}E, where{omega} is the indentation frequency. This relation enables model-independent extraction of mechanical timescales and establishes a general route from nanoscale non-equilibrium rheology to continuum descriptions of growth in living and active soft materials. SignificanceHow molecular-scale activity gives rise to tissue-scale form is a central challenge in biological physics. Although growth is fundamentally a non-equilibrium mechanical process, experimental measurements at the nanoscale have not been directly connected to the constitutive parameters that govern morphogenesis. We introduce a framework that converts dynamic atomic force microscopy maps of storage and loss moduli into spatially resolved fields of stiffness, viscosity, and relaxation time in living cell walls. By revealing that mechanical relaxation is encoded in the local coupling between elastic storage and viscous dissipation, our work provides a route from nanoscale rheology to growth-relevant mechanical timing. This establishes a quantitative bridge between molecular remodeling and continuum mechanics, enabling direct experimental constraints on multiscale theories of morphogenesis.

biophysics↗

bioRxiv2023

Transcending Markov: Non-Markovian Rate Processes of Thermosensitive TRP Ion Channels

The Markov state model (MSM) is a popular theoretical tool for describing the hierarchy of time scales involved in the function of many proteins especially ion channel gating. A MSM is a particular case of the general non-Markovian model, where the rate of transition from one state to another does not depend on the history of state occupancy within the system, i.e., it only includes reversible, non-dissipative processes. However, this requires knowledge of the precise conformational state of the protein and is not predictive when those details are not known. In the case of ion channels, this simple description fails in real (non-equilibrium) situations, for example when local temperature changes, or when energy losses occur during channel gating. Here, we show it is possible to use non-Markovian equations (i.e. offer a general description that includes the MSM as a particular case) to develop a relatively simple analytical model that describes the non-equilibrium behavior of the temperature-sensitive TRP ion channels, TRPV1 and TRPM8. This model accurately predicts asymmetrical opening and closing rates, infinite processes, and the creation of new states, as well as the effect of temperature changes throughout the process. This approach therefore overcomes the limitations of the MSM and allows us to go beyond a mere phenomenological description of the dynamics of ion channel gating towards a better understanding of the physics underlying these processes. Significance StatementModeling ion channel processes has long relied on the Markovian assumption. However, Markov theory cannot translate situations in which the physical state of an ion channel changes during its gating process. By using a non-Markovian approach, we develop a simple analytical model that describes the non-equilibrium behavior of two temperature-sensitive TRP channels, TRPV1 and TRPM8. This model accurately describes and predicts their biophysical behavior as well as their temperature dependence. This approach therefore provides a better understanding of the physics underlying dynamic conformational changes such as those that occur during ion channel gating.

biophysics↗

bioRxiv2020

Mapping cellular nanoscale viscoelasticity and relaxation times relevant to growth of living Arabidopsis thaliana plants using multifrequency AFM

The shapes of living organisms are formed and maintained by precise control in time and space of growth, which is achieved by dynamically fine-tuning the mechanical (viscous and elastic) properties of their hierarchically built structures from the nanometer up. Most organisms on Earth including plants grow by yield (under pressure) of cell walls (bio-polymeric matrices equivalent to extracellular matrix in animal tissues) whose underlying nanoscale viscoelastic properties remain unknown. Multifrequency atomic force microscopy (AFM) techniques exist that are able to map properties to a small subgroup of linear viscoelastic materials (those obeying the Kelvin-Voigt model), but are not applicable to growing materials, and hence are of limited interest to most biological situations. Here, we extend existing dynamic AFM methods to image linear viscoelastic behavior in general, and relaxation times of cells of multicellular organisms in vivo with nanoscale resolution, featuring a simple method to test the validity of the mechanical model used to interpret the data. We use this technique to image cells at the surface of living Arabidopsis thaliana hypocotyls to obtain topographical maps of storage E’ = 120 − 200 MPa and loss E’’= 46 − 111 MPa moduli as well as relaxation times τ = 2.2 − 2.7 µs of their cell walls. Our results demonstrate that cell walls, despite their complex molecular composition, display a striking continuity of simple, linear, viscoelastic behavior across scales–following almost perfectly the standard linear solid model–with characteristic nanometer scale patterns of relaxation times, elasticity and viscosity, whose values correlate linearly with the speed of macroscopic growth. We show that the time-scales probed by dynamic AFM experiments (milliseconds) are key to understand macroscopic scale dynamics (e.g. growth) as predicted by physics of polymer dynamics.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2020

Lab-on-a-graphene-FET detection of key molecular events underpinning influenza virus infection and effect of antiviral drugs

Small solid-state devices are candidates for accelerating biomedical assays/drug discovery, however their potential remains unfulfilled. Here, we demonstrate that graphene-field effect transistors (FET) can be used to successfully detect the key molecular events underlying viral infections and the effect of antiviral drugs. Our device success is achieved by bio-mimicking the host-cell surface during an influenza infection at the graphene channel. In-situ AFM confirms the biological interactions at the sialic acid-functionalized graphene: viral hemagglutinin (HA) binds to sialic acid, and neuraminidase (NA) reacts with the sialic acid-HA complex. The graphene-FET detects HA binding to sialic acid, and NA cleavage of sialic acid. The inhibitory effect of the drug "zanamivir" on NA-sialic acid interactions is monitored in real-time; the reaction rate constant of NA-sialic acid reaction was successfully determined. We demonstrate that graphene-FETs are powerful platforms for measurement of biomolecular interactions and contribute to future deployment of solid-state devices in drug discovery/biosensing.

bioengineering↗