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M.V. Bayas^1,1, K.Schulten^2,2, D. Leckb,^3,3
Molecular & Cellular Biomechanics, Vol.1, No.2, pp. 101-112, 2004, DOI:10.3970/mcb.2004.001.101
Abstract 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 Ne 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 More >

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Daxiang Cui¹, Cengiz S. Ozkan², Sathyajith Ravindran³, Yong Kong¹, Huajian Gao¹
Molecular & Cellular Biomechanics, Vol.1, No.2, pp. 113-122, 2004, DOI:10.3970/mcb.2004.001.113
Abstract 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 More >

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Kathleen Puskar¹, Leonard Apeltsin², Shlomo Ta’asan³, Russell Schwartz², Philip R. LeDuc⁴
Molecular & Cellular Biomechanics, Vol.1, No.2, pp. 123-132, 2004, DOI:10.3970/mcb.2004.001.123
Abstract 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 More >

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A. Tsourkas, R. Weissleder^1,1
Molecular & Cellular Biomechanics, Vol.1, No.2, pp. 133-146, 2004, DOI:10.3970/mcb.2004.001.133
Abstract Traditionally, fluorescent and luminescent reporter proteins have been used as indicators of gene expression and protein localization. However, insightful mutagenesis and protein engineering strategies have transformed these simple passive reporters into active biological sensors. Molecular reporters are now being designed to alter their intrinsic optical properties in response to specific biomolecular interactions. Applications for these novel biological sensors range from monitoring intracellular pH and ion fluxes to detecting protein-protein interactions and enzymatic activity. The ability to monitor the dynamics of intracellular activity in response to external stimuli can help elucidate the cascade of events involved More >

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K.Y. Volokh¹
Molecular & Cellular Biomechanics, Vol.1, No.2, pp. 147-160, 2004, DOI:10.3970/mcb.2004.001.147
Abstract 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 tosimple 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 More >

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Jun Wang¹, Wei Huang², Raghbir S. Bhullar³, Pin Tong²
Molecular & Cellular Biomechanics, Vol.1, No.2, pp. 161-168, 2004, DOI:10.3970/mcb.2004.001.161
Abstract 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… More >

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