Biophysical Reviews and Letters

We review recent computer simulation studies of undulating lipid bilayers. Theoretical interpretations of such fluctuating membranes are most commonly based on generalized Helfrich-type elastic models, with additional contributions of local "protrusions" and/or density fluctuations. Such models provide an excellent basis for describing the fluctuations of tensionless bilayers in the fluid L_α phase at a quantitative level.

However, this description is found to fail for membranes in the gel phase and for membranes subject to high tensions. The fluctuations of tilted gel membranes (L_β′ phase) show a signature of the modulated ripple structure P_β′, which is a nearby phase observed in the pretransition regime between the L_α and L_β′ state. This complicates a quantitative analysis on mesoscopic length scales. In the case of fluid membranes under tension, the large-wavelength fluctuation modes are found to be significantly softer than predicted by theory.

In the latter context, we also address the general problem of the relation between frame tension and the fluctuation tension, which has been discussed somewhat controversially in recent years. Simulations of very simple model membranes with fixed area show that the fluctuations should be controlled by the frame tension, and not by the internal tension.

Electroporation is the formation of reversible pores in cell membranes under a brief pulse of high electric field. Dynamics of pore formation during electroporation suggests that the transmembrane potential would settle approximately at the threshold transmembrane potential and the transmembrane resistance would decrease significantly from the state of relaxation. The current electric circuit equivalent models for electroporation containing time-invariant, static and passive components are unable to capture the pore dynamics. A biophysically-inspired electric circuit equivalent model containing dynamic components for membrane pores has been derived using biological parameters. The model contains a voltage-controlled resistor driven by a two-stage cascaded integrator that is activated through a voltage-gated switch. Simulation results with the derived model showed higher accuracy compared to a commonly used model, where the transmembrane resistance decreased million-fold at the onset of electroporation and the transmembrane potential settled at 99.5% of the critical transmembrane potential, thus enabling improved dynamic behavior modeling ability of the pores in electroporation. The derived model allows fast and reliable analysis of this biophysical phenomenon and potentially aids in optimization of various parameters involved in electroporation.

The shape of the cross section of a dense fiber bundle is related to the symmetry of its molecular packing. However, this statement might be belied by type I collagen fibrils which have a rounded section of high symmetry while structural studies suggest that their molecules are assembled with a long range lateral order of lower symmetry. We examine how phyllotaxis, which is a nonconventional crystallographic solution to packing efficiency in situations of high radial symmetry, can establish a link between those two apparently conflicting points. The lateral order imposed by the algorithm of phyllotaxis, which implies an enlargement of the notion of long range lateral order beyond that used for classical crystals, provides a basis for a new analysis of the experimental data.

Nano nalidixic acid was prepared by ultrasonic method in carbon tetrachloride. Nano nalidixic acid (quinolone antibiotic) was characterized by X-ray diffraction (XRD), infrared spectroscopy (IR) and scanning electron microscope (SEM). The antibacterial activities of nano nalidixic acid were tested against microorganisms and compared with the microscale drug. The results show that nano nalidixic acid has good inhibitory properties against two Gram-positive species, Staphylococcus aureus and Bacillus subtilis. Nano nalidixic acid also showed good antifungal activity against Candida albicans. Nano nalidixic acid can be injected into the human body as a decontaminating agent to prevent the growth of harmful microorganisms more effectively than the micro-sized drug.

Cerium (III) Chloride-induced conformational changes of human serum albumin, HSA, in phosphate buffer, 10 mM at pH 7.4 was investigated, using isothermal titration calorimetry (ITC), UV and fluorescence emission spectroscopic methods. The results indicate that CeCl₃, Ce³⁺, induces irreversible denaturation of the HSA structure. The UV absorption intensity of HSA + Ce³⁺ shows a slight blueshift in the absorbance wavelength with increasing Ce³⁺ concentration. The fluorescence intensity was increased regularly and a slight redshift was observed in the emission wavelength. The HSA + Ce³⁺ complex quenches the fluorescence of HSA and changes the microenvironment of tryptophan residue. The emission intensity increases suggesting the loss of the tertiary structure of HSA. The results obtained from the ITC data are in agreement with the spectroscopic methods. The strong negative cooperativity of Ce³⁺ binding with HSA (Table 1) recovered from the extended solvation model, indicates that HSA has been denatured as a result of its interaction with Ce³⁺ ions.

The interaction between pyropheophorbide methyl ester (PPME) and Cu²⁺ was investigated using UV-vis and fluorescence spectrscopy. Study of the binding interaction between PPME and Cu²⁺ could contribute to understanding of its pharmacokinetics and pharmacodynamics. Parameters of the static and dynamic fluorescence quenching of PPME-Cu²⁺ association were calculated at different temperatures. For binding site of 1:1 at 299 K, the static binding constant (k_S), the static isosbestic concentration (), the dynamic binding constant (k_D), and the dynamic isosbestic concentration () are, respectively, 61 M^-1, 0.0164 M, 75 M^-1, and 0.0133 M. The concentrations and efficiencies of the intermediates species were modeled. Satisfactory correspondence between the experimental and calculated results was found.

Slime mould Physarum polycephalum propagates on nutrient substrates similarly to auto-waves in nonlinear media. In experimental laboratory studies we uncover that the width of geometrically constrained substrate affects the speed of Physarum propagation. We show that Physarum slows down when the width of the substrate increases. The slime mould propagates quicker from the vertex of a triangle to its base than from the base to the vertex. Physarum grows quicker in narrow channels than in wider channels. One can also slow down Physarum propagation by making a finite size expansion of the otherwise narrow channel. In computational experiments with a binary state cellular automaton model we demonstrate that a limitation on the slime mould's body mass production rate could be an underlying mechanism for the width-dependent slowdown of Physarum propagation.