The motion of DNA (in the bulk solution) and the non-Newtonian effective fluid behavior are considered separately and self-consistently with the fluid motion satisfying the no-slip boundary condition on the surface of the confining geometry in the presence of channel pressure gradients. A different approach has been developed to model DNA in the micro-channel. In this study the DNA is assumed as an elastic chain with its characteristic Young’s modulus, Poisson’s ratio and density. The force which results from the fluid dynamic pressure, viscous forces and electromotive forces is applied to the elastic chain in a coupled manner. The velocity fields in the micro-channel are influenced by the transport properties. Simulations are carried out for the DNAs attached to the micro-fluidic wall. Numerical solutions based on a coupled multiphysics finite element scheme are presented. The modeling scheme is derived based on mass conservation including biomolecular mass, momentum balance including stress due to Coulomb force field and DNA-fluid interaction, and charge transport associated to DNA and other ionic complexes in the fluid. Variation in the velocity field for the non-Newtonian flow and the deformation of the DNA strand which results from the fluid-structure interaction are first studied considering a single DNA strand. Motion of the effective center of mass is analyzed considering various straight and coil geometries. Effects of DNA statistical parameters (geometry and spatial distribution of DNAs along the channel) on the effective flow behavior are analyzed. In particular, the dynamics of different DNA physical properties such as radius of gyration, end-to-end length etc. which are obtained from various different models (Kratky-Porod, Gaussian bead-spring etc.) are correlated to the nature of interaction and physical properties under the same background fluid environment.

One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of lateral pressure. Our simulations reveal that the insertion of CTX A3 into one monolayer results in an asymmetrical change in the lateral pressure and distribution of surface tension of the individual bilayer leaflets. The relative variation in the surface tension of the two monolayers as a result of a change in the contribution of the various intermolecular forces may be expressed morphologically and lead to deformation of the lipid membrane.

The tensile properties of the cornea have been extensively studied while there are fewer studies on its compressive stiffness. The mechanical properties and structure of the cornea like many other connective tissues are derived from the function and properties of their extracellular matrix. The corneal extracellular matrix, stroma, is a polyelectrolyte gel composed of collagenous fibers embedded in an aqueous matrix. The cornea has two different functions: optical and mechanical. It is the main refractive component of the visual system and it is an effective barrier resisting the deformation caused by external and internal stresses. A necessary condition for corneal optical properties and transparency is the maintenance of a pseudo hexagonal arrangement of the collagen fibers inside the extracellular matrix. This regular arrangement is attributed to the interaction of collagen fibers with the proteoglycans. Under physiological conditions, the proteoglycans are ionized and form a hydrated gel in the empty space between the collagen fibrils by attracting the water and solutes. The interaction of the negatively fixed charges of the proteoglycans with themselves and with the free ions inside the interstitial fluid contributes to the corneal swelling pressure and subsequently to its compressive properties.

This research is intended to examine the amount of changes that can happen in material characteristics after retesting. Stress relaxation test is conducted on the same samples of the swine brain tissue for several times in small and large deformations. The mechanical properties of the substance are calculated before and after retest and the constants of the tissue, as mechanical characteristics, are determined and compared. Short- and long-term moduli, relaxation times and relaxation functions are of those data that are calculated and compared to understand how much they decay after repeating the experiments. The results show that applying different tests on one sample slightly changes the mechanical properties of the tissue and, as a result, it is partly possible to perform more than one test on the same sample resulting in less sample preparation, time and effort.

This paper studies the electrostatic contribution to the elasticity of corneal stroma using the Poisson-Boltzmann (PB) equation. Corneal stroma is a transparent connective tissue consisting of regularly organized collagen fibrils and proteoglycans (PGs) within an aqueous matrix. The cornea proteoglycan decorin is crucial for the regulation of collagen fibril diameters and their spacings. Decorin is the simplest small leucine-rich PG and is made up of a core protein and a glycosaminoglycan (GAG) side chain. Under physiological pH conditions, GAG molecules are completely ionized and become negatively charged. Their repulsive electrostatic interaction, mediated by free ions inside the bath, controls collagen interfibril spacings and contributes to corneal stiffness. In order to quantify the electrostatic contribution of GAGs to the elastic properties of the cornea, we define a unit cell in which GAGs are represented as cylindrical rods with a fixed charge density. The unit cell is deformed affinely and the electrical potential and free ion distribution inside the unit cell are obtained from the solution of the nonlinear PB equation. Having the potential and charge distribution, the changes in electrostatic free energy due to the deformation gives the electrostatic elastic moduli.

Cell behavior is mediated by variety of physiochemical properties of extracellular matrix (ECM). Material composition, surface chemistry, roughness, and distribution pattern of cell adhesive proteins are among the ECM properties which are known to modulate various cellular physiological functions. Mechanical stiffness of ECM in particular is found to be a major regulator for multiple aspects of cellular function. Experiments show that cells in general, exhibit an apparent adhesion preference for stiffer substrates with a larger projected spread area with increasing the substrate stiffness. In addition, it seems that the effect of substrates elasticity is strongly coupled with adhesivity of the substrate; on relatively stiff substrates the spread area of the cells exhibits strong biphasic dependence to the changes in ligand density, whereas on soft substrates their limited spreading is much less sensitive to the density of surface ligands. This study aims to propose a theoretical basis for the interplay between substrate elasticity and cellular adhesion, using an equilibrium thermodynamic model. Within this framework, the equilibrium contact area is assumed to ensure minimization of the free energy contributed by interfacial adhesive and repulsive interactions between the membrane and substrate as well as the deformation of cell and substrate. Hence, this thermodynamic model overlooks the contribution of intracellular signaling or actively regulated cytoskeleton and assumes that cell adhesion is solely a result of the balance between the membrane-substrate repulsive potentials, stored elastic energy, binding enthalpy, and mixing entropy of mobile receptors. The predictions of this purely mechanistic model for cell adhesion qualitatively follow the experimental results featuring the variation of cell spread area on compliant bio-adhesive substrates. This suggests that the mechanistic pathways inherent to membrane-substrate interactions may be equally important as intracellular signaling pathways to mediate the cellular adhesion.

Interest in electrospun polymeric nano-microfibers for tissue engineering applications has rapidly grown during the last decade. In spite of this technique’s flexibility and ability to form complex fiber assemblies, additional studies are required to elucidate how the fibrous microstructure translates into specific tissue (or meso-scale) level mechanical behavior. Deterministic structural models can quantify how key structures contribute to the mechanical response as a function of bulk deformation across multiple scales, as well as provide a better understanding of cellular mechanical response to local micro-structural deformations. Our ultimate aim is to utilize such models to assist tissue engineering scaffold design. In the current work, we present a novel approach to automatically quantify key micro-architectural descriptors (fiber overlaps, connectivity, orientation, and diameter) from SEM images of electrospun poly (ester urethane) urea (PEUU) to recreate statistically equivalent scaffold mechanical models. An appropriate representative volume element (RVE) size was determined by quantifying the point of stabilization of the architectural descriptors over image areas of increasing size. Material models were then generated specifying: fiber overlap density, fiber orientation, connectivity and fiber diameter. Macro-meso mechanical response was predicted via FEM simulations.

Erythrocyte (red blood cell, or RBC) possesses one of the simplest and best characterized molecular architectures among all cells. It contains cytosol enclosed inside a composite membrane consisting of a fluidic lipid bilayer reinforced by a single layer of protein skeleton pinned to it. In its normal state, this system demonstrates tremendous structural stability, manifested in its ability to sustain large dynamic deformations during circulation. On the other hand, it has been illustrated in experiments that triggered by mechanical loads structural remodeling may occur. A canonical example of this remodeling is vesiculation, referring to the partial separation of the lipid bilayer from the protein skeleton and the formation of vesicles that contain lipids only.

Microcantilever-based biosensors are rapidly becoming an enabling sensing technology for a variety of label-free biological applications due to their wide applicability, versatility and low cost. It is thus imperative for us to reveal the physical origin of adsorption-induced deformation, and to further analyze its implication of microscopic mechanisms on macroscopic deformation. In the paper, we study adsorption-induced surface stresses and microcantilever motion in alkanethiolate SAMs on Au surface. We develop a multiscale method that can analyze deformation of micro-cantilever beam subjected to bio-adsorption mechanisms calculated by ab-initio simulation and classical molecular dynamics. The adsorption mechanisms of different SAMs adsorbed on Au(111) surface, in the dry and liquid phase, are studied by ab-initio simulation and the adsorption-induced stresses are calculated through the multiscale method. The results give insight into the atomic forces and positions that play a key role in producing adsorption-induced surface stresses and resultant mechanical bending of microcantilevers.

The mechanical properties of DNA has very important biological implication. For example, the bending and twisting rigidities of DNA affect how it wraps around histones to form chromosomes, bends upon interactions with proteins, supercoils during replication process, and packs into the confined space within a virus. Many biologically important processes involving DNA are accompanied by the deformations of double helical structure of DNA.

Indentation, in addition to the traditional tensile testing, has been widely used for evaluating mechanical properties of hard materials such as metals and bone as well as soft materials like polymer and soft tissues. However, it is difficult to measure the contact area and surface deformation in conventional indentation tests of soft tissue which will bring large errors to the evaluation of the material properties. Also the assumption of isotropic property limited the usage of indentation test in characterizing the nonlinear, anisotropic properties of soft tissue thin film. In this project, 2D and 3D finite element analyses has been carried out to predict hyperelastic material response under indentation and punch tests. A novel indentation test system was developed, which made the direct measurement of local deformation and contact area possible. The apparatus consists of a transparent indenter, a digital microscope, and a computer based control and data acquisition system. The proposed testing system and associated finite element analysis are used to characterize the mechanical properties of multiscale (bulk and thin film) biological tissues.

Random filamentous networks and their response to the applied load can be considered as a model to study the mechanical properties of biological systems such as cytoskeleton of a cell and connective tissues. A mathematical model for the actual and complex deformation of these networks under stress is developed using a micromechanics approach. We recently studied the effect of various micro-structural parameters such as fiber length, mean segment length and fiber flexibility on the network deformation field at various length scales. The network elasticity is mapped into a two dimensional heterogeneous continuum domain in order to show that the elastic fields of dense fiber networks show long range correlations over a range of scales for which we gave the upper and lower bounds. It is concluded that the deformation of random networks is similar to that of highly heterogeneous continuum domains with stochastic distribution of moduli. We employed the stochastic finite element method to solve boundary value problems defined on the random fiber network domain. Here, we present a brief review of this methodology and report new results on scaling properties of the structure of fiber networks using box-counting method.

In this work, a microfluidics system to investigate the flow behaviour of red blood cells (RBCs) in a microcirculation-mimicking network of PDMS microchannels with thickness comparable to cell size is presented.