Biology subjects

Efremov, Y. M.

Publications and source records attributed to Efremov, Y. M..

4 recordsLinked to original sources

bioRxiv2025

Spheroid Assembly in Microwells of Defined Geometry for Quantitative Assessment of Visco-Capillary Velocity and Shape Control

Three-dimensional (3D) cell spheroids are widely used as in vitro tissue models, yet quantitative understanding of their morphogenesis remains limited. We present an integrated experimental-computational framework to analyze, model, and modulate the compaction of cell aggregates in agarose microwells of defined geometries. Custom 3D-printed stamps produced circular, square, and triangular microwells of equal cross-sectional area. Time-lapse imaging combined with AI-based segmentation enabled tracking of spheroid morphology, with circularity and projected area serving as quantitative descriptors of compaction. The process followed predictable exponential kinetics, with mesenchymal (HDF) spheroids compacting faster than epithelial (ARPE-19) ones. Computational fluid dynamics (CFD) simulations modeled spheroid rounding as a visco-capillary-driven process, where the extracted visco-capillary velocity unified experimental and simulated dynamics. Mechanical measurements by atomic force microscopy and compression confirmed that differences in surface tension predominantly governed the observed kinetics. Pharmacological modulation of cytoskeletal tension revealed that inhibition of contractility markedly altered spheroid formation dynamics, enabling the generation of stable, non-spherical aggregates. Using this principle as a shape-engineering strategy, we produced aggregates with distinct geometries (brick-like, prismatic, and star-shaped), characterized by an increased surface-to-volume ratio compared to conventional spheroids. Limitations of the approach include the use of pharmacological cytoskeletal modulation and constraints in geometric fidelity arising from printing resolution, agarose casting, cell filling, and intrinsic smoothing of sharp features during cell aggregation. Collectively, this work establishes a geometry-controlled platform for quantitative analysis of spheroid formation and mechanical behavior, and provides a versatile framework for designing cell aggregates with defined shapes.

biophysics↗

bioRxiv2025

Mechanical properties of adherent cell sheets analyzed by deflection of supporting membrane

Multicellular structures, including cell sheets, are actively used as model systems to study intercellular interactions and can be applied in different areas of regenerative medicine. In this paper, we present a novel approach for measuring mechanical properties of cell sheets based on a simple experimental setup and numerical simulations. The advantage of the present approach is the relative ease of the sample preparation, while previous systems for the tensile tests required specialized and sensitive equipment. With the developed approach, the cell sheet on a polymer membrane is mounted in the holder on one side, and then deflection of the free end of the membrane is measured. The deflection of this cantilever-like construction depends on the elastic modulus of the membrane (which is known) and cell sheet, and also from the traction force generated by the cell sheet. By involving an experimental step with relaxing the traction force and by conducting finite element simulations, both traction force and elastic properties of the cell sheet can be estimated. We performed such measurements on cell sheets from keratocytes from corneal explants and confirmed that the developed approach is applicable for measurement of both traction force and elastic modulus of cell sheets.

biophysics↗

bioRxiv2024

Mechanical characterization of soft biomaterials: which time and spatial scale to choose?

The mechanical properties of soft gels hold significant relevance in biomedicine and biomaterial design, including the development of tissue engineering constructs and bioequivalents. It is important to adequately characterize the gels mechanical properties since they play a role both in the overall structural properties of the construct and in cells physiological responses. The question remains which approach for mechanical characterization is most suitable for specific biomaterials. Our investigation is centered on the comparison of three types of gels and four distinct mechanical testing techniques: shear rheology, compression, microindentation, and nanoindentation by atomic force microscopy. While analyzing an elastic homogeneous synthetic hydrogel (polyacrylamide gel), we observed close mechanical results across the different testing techniques. However, our findings revealed more distinct outcomes when assessing a highly viscoelastic gel (Ecoflex) and a heterogeneous biopolymer hydrogel (enzymatically crosslinked gelatin). To ensure the precise data interpretation, we introduced correction factors to account for the boundary conditions inherent in many of the testing methods. The results of the study underscore the critical significance of considering both the temporal and spatial scales in mechanical measurements of biomaterials. Furthermore, they encourage the employment of a combination of diverse testing techniques, particularly in the characterization of heterogeneous viscoelastic materials such as biological samples. The obtained results will contribute to refining mechanical testing protocols and advance the development of soft gels for tissue engineering.

bioengineering↗

bioRxiv2020

Viscoelasticity in simple indentation-cycle experiments: a computational study

Instrumented indentation has become an indispensable tool for quantitative analysis of the mechanical properties of soft polymers and biological samples at different length scales. These types of samples are known for their prominent viscoelastic behavior, and attempts to calculate such properties from the indentation data are constantly made. The simplest indentation experiment presents a cycle of approach (deepening into the sample) and retraction of the indenter, with the output of the force and indentation depth as functions of time and a force versus indentation dependency (force curve). The linear viscoelastic theory based on the elastic-viscoelastic correspondence principle might predict the shape of force curves based on the experimental conditions and underlying relaxation function of the sample. Here, we conducted a computational analysis based on this theory and studied how the force curves were affected by the indenter geometry, type of indentation (triangular or sinusoidal ramp), and the relaxation functions. The relaxation functions of both traditional and fractional viscoelastic models were considered. The curves obtained from the analytical solutions, numerical algorithm and finite element simulations matched each other well. Common trends for the curve-related parameters (apparent Youngs modulus, normalized hysteresis area, and curve exponent) were revealed. Importantly, the apparent Youngs modulus, obtained by fitting the approach curve to the elastic model, demonstrated a direct relation to the relaxation function for all the tested cases. The study will help researchers to verify which model is more appropriate for the sample description without extensive calculations from the basic curve parameters and their dependency on the indentation rate.

biophysics↗