Mechanics & chemistry of biosystems : MCB最新文献

Understanding the connection between mechanics and cell structure requires the exploration of the key molecular constituents responsible for cell shape and motility. One of these molecular bridges is the cytoskeleton, which is involved with intracellular organization and mechanotransduction. In order to examine the structure in cells, we have developed a computational technique that is able to probe the self-assembly of actin filaments through a lattice based Monte Carlo method. We have modeled the polymerization of these filaments based upon the interactions of globular actin through a probabilistic model encompassing both inert and active proteins. The results show similar response to classic ordinary differential equations at low molecular concentrations, but a bi-phasic divergence at realistic concentrations for living mammalian cells. Further, by introducing localized mobility parameters, we are able to simulate molecular gradients that are observed in nonhomogeneous protein distributions in vivo. The method and results have potential applications in cell and molecular biology as well as self-assembly for organic and inorganic systems.

A simple phenomenological framework for modeling growth of living tissues is proposed. Growth is defined as a change of mass and configuration of the tissue. Tissue is considered as an open system where mass conservation is violated and the full-scale mass balance is applied. A possible structure of constitutive equations is discussed with reference to simple growing materials. 'Thermoelastic' formulation of the simple growing material is specified. Within this framework traction free growth of cylindrical and spherical bodies is examined. It is shown that the theory accommodates the case where stresses are not generated in uniform volumetric growth. It is also found that surface growth corresponds to a boundary layer solution of the governing equations. This finding proves the ability of continuum mechanics to describe surface growth. The latter is contrary to the usual use of purely kinematical theories, which do not involve balance and constitutive equations, for treating surface growth.

Experiments on encapsulating Pt-labelled DNA molecules inside multiwalled carbon nanotubes (MWCNT) were performed under temperature and pressure conditions of 400K and 3 Bar. The DNA-CNT hybrids were purified via agarose gel electrophoresis and analyzed via high resolution transmission electron microscopy (HR-TEM) and energy dispersive X-ray spectroscopy (EDX). The results showed that the Pt-labelled DNA molecules attached to the outside walls of CNTs could be removed by electrophoresis. The HR-TEM and EDX results demonstrated that 2-3% of the Pt-labelled DNA molecules were successfully encapsulated inside the MWCNTs. The experimental study complements our previous molecular dynamics simulations on encapsulation of single stranded DNA oligonucleotides inside single wall carbon nanotubes under similar conditions in water. The van der Waals interaction between CNT and Pt-labelled DNA is believed to be the main driving force for this phenomenon. The DNA-CNT molecular complex could be further explored for potential applications in bio-nanotechnology.

The force-induced dissociation of the strand dimer interface in C-cadherin has been studied using steered molecular dynamics simulations. The dissociation occurred, without domain unraveling, after the extraction of the conserved trypthophans (Trp2) from their respective hydrophobic pockets. The simulations revealed two stable positions for the Trp2 side chain inside the pocket. The most internal stable position involved a hydrogen bond between the ring Nepsilon of Trp2 and the backbone carbonyl of Glu90. In the second stable position, the aromatic ring is located at the pocket entrance. After extracting the two tryptophans from their pockets, the complex exists in an intermediate bound state that involves a close packing of the tryptophans with residues Asp1 and Asp27 from both domains. Dissociation occurred after this residue association was broken. Simulations carried out with a complex formed between W2A mutants showed that the mutant complex dissociates more easily than the wild type complex does. These results correlate closely with the role of the conserved tryptophans suggested previously by site directed mutagenesis.

Surface-tension-driven blood flow into a capillary tube, as in some medical devices, is studied. In a previous article, we considered the early stages of the entry flow from a drop of blood into a capillary, and solved the problem analytically under the assumption that the resistance of the air is negligible. In the present note we consider a capillary tube of finite length, with the far end containing a small window which opens to the atmosphere. The dynamic reverberation of the air in the capillary tube is analyzed in conjunction with the dynamics of the blood. Existing computing programs are used to solve the Navier-Stokes equations. The interface is characterized by the surface tension between the blood and the air, and the contact angle at the triple point where the air-blood interface meets the capillary tube wall. The results tell us how good our earlier simplified analysis is. The new numerical results show that the smaller the window, the larger is the effect of aerodynamic reverberation. However, even for a window as small as 4% of the capillary cross section, and located at the end of the capillary, the difference of the time of arrival of the interface at the window is less than 5%.