Search results for "kinetics"
showing 10 items of 2224 documents
Kinetics of phase separation in thin films: simulations for the diffusive case.
2005
We study the diffusion-driven kinetics of phase separation of a symmetric binary mixture (AB), confined in a thin-film geometry between two parallel walls. We consider cases where (a) both walls preferentially attract the same component (A), and (b) one wall attracts A and the other wall attracts B (with the same strength). We focus on the interplay of phase separation and wetting at the walls, which is referred to as {\it surface-directed spinodal decomposition} (SDSD). The formation of SDSD waves at the two surfaces, with wave-vectors oriented perpendicular to them, often results in a metastable layered state (also referred to as ``stratified morphology''). This state is reminiscent of th…
Thermal inactivation kinetics of Bacillus stearothermophilus spores using a linear temperature program.
1999
A systematic study of the inactivation kinetics of Bacillus stearothermophilus spores was carried out in nonisothermic heating conditions using a linear temperature increase program and analyzing the experimental data by means of a one-step nonlinear regression. The D and z values estimated are close to those obtained in isothermic conditions and estimated by using a two-step model, first D values are calculated, and then in the second step a z value is deduced (D(121 degrees C) = 3.08 and 4.38 min, respectively, and z = 7 and 7.9 degrees C, respectively). No convergence problems were observed when using the one-step nonlinear regression proposed. The results indicated that the methodology …
Pyrrolomycins as antimicrobial agents. Microwave-assisted organic synthesis and insights into their antimicrobial mechanism of action
2019
Abstract New compounds able to counteract staphylococcal biofilm formation are needed. In this study we investigate the mechanism of action of pyrrolomycins, whose potential as antimicrobial agents has been demonstrated. We performed a new efficient and easy method to use microwave organic synthesis suitable for obtaining pyrrolomycins in good yields and in suitable amount for their in vitro in-depth investigation. We evaluate the inhibitory activity towards Sortase A (SrtA), a transpeptidase responsible for covalent anchoring in Gram-positive peptidoglycan of many surface proteins involved in adhesion and in biofilm formation. All compounds show a good inhibitory activity toward SrtA, havi…
Recovery of human fibroblasts from attack by the pore-forming alpha-toxin of Staphylococcus aureus.
1994
When applied at low concentrations (10 micrograms/ml), staphylococcal alpha-toxin generates a small channel in keratinocyte and lymphocyte membranes that permits selective transmembrane flux of monovalent ions. Here we show that a moderate concentration (1-50 micrograms/ml) of alpha-toxin similarly produces a small pore in membranes of human fibroblasts. This process leads to rapid leakage of K+ and to a drop in cellular ATP to 10-20% of normal levels in 2 h. In the presence of medium supplemented with serum and at pH 7.4, the cells are able to recover from toxin attack, so that normal levels of K+ and ATP are reached after 6-8 h at 37 degrees C. The repair process is dependent on the prese…
Altered pore-forming properties of proteolytically nicked staphylococcal alpha-toxin
1993
Staphylococcal alpha-toxin is a single-chain polypeptide with a molecular weight of 34,000 that hexamerizes in lipid bilayers to form pores of 1-1.5 nm effective diameter in membranes. We demonstrate that limited proteolysis of purified alpha-toxin with proteinase K generates a hemolytically active product that yields one major protein band of 17-18 kDa in SDS-polyacrylamide gel electrophoresis. The 17-18-kDa protein band harbors two major fragments of similar size representing the N- and C-terminal halves, which remain associated with each other in non-denaturing buffers but dissociate in 6 M urea. Dissociation in urea leads to loss of hemolytic activity. In contrast, unnicked alpha-toxin …
Influence of inorganic pyrophosphate on the kinetics of muscle pyruvate kinase: a simple nonallosteric feedback model.
2002
Potassium pyrophosphate was used instead of ATP as a model ligand for magnesium cation for the study of effector influence on the kinetics of pyruvate kinase muscle isozyme M1. The pyruvate kinase activation by low concentration of pyrophosphate and inhibition by high concentration of pyrophosphate was considered to be the result of reversible reactions of magnesium cation with pyrophosphate, ADP, ATP, and PEP. The apparent Km and Vm or in some cases the pseudo-first order reaction rate constant (instead of Km and Vm) of pyruvate kinase at any given pyrophosphate concentration were analysed as a function of concentration of free magnesium cation and its complexes with all ligands present in…
Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure
2016
We study numerically the crystallization of a hard-sphere mixture with 8\% polydispersity. Although often used as a model glass former, for small system sizes we observe crystallization in molecular dynamics simulations. This opens the possibility to study the competition between crystallization and structural relaxation of the melt, which typically is out of reach due to the disparate timescales. We quantify the dependence of relaxation and crystallization times on density and system size. For one density and system size we perform a detailed committor analysis to investigate the suitability of local structures as order parameters to describe the crystallization process. We find that local…
A Hooke's law-based approach to protein folding rate
2014
Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke[U+05F3]s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons am…
Dynamics of the Selkov oscillator.
2018
A classical example of a mathematical model for oscillations in a biological system is the Selkov oscillator, which is a simple description of glycolysis. It is a system of two ordinary differential equations which, when expressed in dimensionless variables, depends on two parameters. Surprisingly it appears that no complete rigorous analysis of the dynamics of this model has ever been given. In this paper several properties of the dynamics of solutions of the model are established. With a view to studying unbounded solutions a thorough analysis of the Poincar\'e compactification of the system is given. It is proved that for any values of the parameters there are solutions which tend to inf…
A hypothetical model of the influence of inorganic phosphate on the kinetics of pyruvate kinase
2000
This paper presents a simple solution to the problem of approximating the calculated curve of reaction progress to the measured curve which is usually disturbed by initial oscillation of auxiliary lactate dehydrogenase (LDH) reaction. The experiments leading to the determination of the apparent Km for phosphoenolpyruvate (PEP) and Vm were performed. For precise estimation of kinetic parameters (Km and Vm) of the M1 isozyme of pyruvate kinase (PK), measured by coupling it to LDH reaction, the sequence of Michaelis‐Menten for pyruvate kinase and second-order kinetics for lactate dehydrogenase reaction as well as a non-zero initial concentration of lactate was assumed. The functions of apparen…