Structure-based modeling of turnover of Bcl-2 family proteins bound to voltage-dependent anion channel 2 (VDAC2): Implications for the mechanisms of proapoptotic activation of Bak and Bax in vivo

Mitochondrial Outer Membrane (MOM) Permeabilization (MOMP) is a critical event in the mitochondrial types of apoptosis. MOMP is controled by the proteins of the Bcl-2 family and its two proapoptotic members Bak and Bax are the key effectors of MOMP. Voltage-dependent anion channel 2 (VDAC2) is an integral membrane protein that plays an important role in the regulation of Bak and Bax apoptotic function, but underlying mechanisms are not fully understood. In the present article, the mechanisms of MOMP regulation mediated by VDAC2 were explored using structure-based modeling. We show that Bak, prior to an apoptotic stimulus, possesses two low-energy conformations of high shape – and polar complementarity in respect to VDAC2, resulting in two high-affinity modes of Bak binding to VDAC2, one with Bak fully residing in the cytosol and the other with Bak α9 helix inserted into the membrane. Even higher binding affinity of VDAC2 for tBid (truncated Bid/p15) was established, suggesting the tBid-mediated displacement of Bak from the VDAC2/Bak complex resulting in the formation of the VDAC2/tBid complex. The structural analysis of the interaction of this complex with Bax revealed a very high binding affinity of this complex for Bax, suggesting the recruitment of Bax to the MOM by this complex under apoptotic conditions. Besides, we revealed one more low-energy structure of Bax of high binding affinity towards the VDAC2/tBid complex and with helix α9 inserted into the membrane.     

Modeling of biomass-based hydrogen production via catalytic sorption-enhanced reformer integrated with a gasifier

The sorption enhanced reformer concept breaks the thermodynamic limits of steam methane reforming and water-gas shift reactions with selective CO₂ removal to produce more H₂. In this paper, we propose a dynamic kinetic model for sorption-enhanced steam reformers (SERs) integrated with biomass gasifiers. An analysis of operating conditions was conducted to examine high purity hydrogen production. The kinetic model was validated with published literature results at different reactor pressures (5-20 bar), steam/carbon ratios (2-5), and reactor temperatures (673K–1023K). This study shows that biomass gasifiers can be integrated with SER reactors to produce high purity H₂.     

Engineering Heterogeneous Catalysis with Strong Metal–Support Interactions: Characterization,Theory and Manipulation

Strong metal–support interactions (SMSI) represent a classic yet fast-growing area in catalysis research. The SMSI phenomenon results in the encapsulation and stabilization of metal nanoparticles (NPs) with the support material that significantly impacts the catalytic performance through regulation of the interfacial interactions. Engineering SMSI provides a promising approach to steer catalytic performance in various chemical processes, which serves as an effective tool to tackle energy and environmental challenges. Our Minireview covers characterization, theory, catalytic activity, dependence on the catalytic structure and inducing environment of SMSI phenomena. By providing an overview and outlook on the cutting-edge techniques in this multidisciplinary research field, we not only want to provide insights into the further exploitation of SMSI in catalysis, but we also hope to inspire rational designs and characterization in the broad field of material science and physical chemistry.     

A novel quantitative model of cell cycle progression based on cyclin-dependent kinases activity and population balances

Cell cycle regulates proliferative cell capacity under normal or pathologic conditions, and in general it governs all in vivo/in vitro cell growth and proliferation processes. Mathematical simulation by means of reliable and predictive models represents an important tool to interpret experiment results, to facilitate the definition of the optimal operating conditions for in vitro cultivation, or to predict the effect of a specific drug in normal/pathologic mammalian cells. Along these lines, a novel model of cell cycle progression is proposed in this work. Specifically, it is based on a population balance (PB) approach that allows one to quantitatively describe cell cycle progression through the different phases experienced by each cell of the entire population during its own life. The transition between two consecutive cell cycle phases is simulated by taking advantage of the biochemical kinetic model developed by Gérard and Goldbeter (2009) which involves cyclin-dependent kinases (CDKs) whose regulation is achieved through a variety of mechanisms that include association with cyclins and protein inhibitors, phosphorylation–dephosphorylation, and cyclin synthesis or degradation. This biochemical model properly describes the entire cell cycle of mammalian cells by maintaining a sufficient level of detail useful to identify check point for transition and to estimate phase duration required by PB. Specific examples are discussed to illustrate the ability of the proposed model to simulate the effect of drugs for in vitro trials of interest in oncology, regenerative medicine and tissue engineering.     

Modeling fluid and heat transport in the reactive, porous bed of downdraft (biomass) gasifier

A fluid flow and heat transfer model has been developed for the reactive, porous bed of the biomass gasifier to simulate pressure drop, temperature profile in the bed and flow rates. The conservation equations, momentum equation and energy equation are used to describe fluid and heat transport in porous gasifier bed. The model accounted for drag at wall, and the effect of radial as well as axial variation in bed porosity to predict pressure drop in bed. Heat transfer has been modeled using effective thermal conductivity approach. Model predictions are validated against the experiments, while effective thermal conductivity values are tested qualitatively using models available in literature. Parametric analysis has been carried out to investigate the effect of various parameters on bed temperature profile and pressure drop through the gasifier. The temperature profile is found to be very sensitive to gas flow rate, and heat generation in oxidation zone, while high bed temperature, gas flow rate and the reduction in feedstock particle size are found to cause a marked increase in pressure drop through the gasifier. The temperatures of the down stream zones are more sensitive to any change in heat generation in the bed as compared to upstream zone. Author recommends that the size of preheating zone may be extended up to pyrolysis zone in order to enhance preheating of input air, while thermal insulation should not be less than 15 cm.     

Modeling the dynamic behavior of shape memory alloys

The paper studies the single degree of freedom vibration of a rigid mass suspended by a thin-walled shape memory alloy tube under torsional loading. The behavior is analyzed for the cases of quasiplasticity (low temperatures) and pseudoelasticity (high temperatures) on the basis of an improved version of the Müller–Achenbach model. To illustrate the strong hysteresis-induced damping capacity and the non-linear vibration characteristics, both, free and forced vibrations are considered in the first part of the paper. This is done on the basis of an isothermal version of the model, while the second part of the paper focuses on the effect of non-constant temperature caused by the rate-dependent release and absorption of latent heats.     

The effect of friction reduction in the presence of in-plane vibrations

A reduction of friction by vibrations has been observed in various experiments. This effect can be applied to actively control frictional forces by modulating vibrations. Moreover, common methods of controlling friction rely on lubricants and suitable material combinations. The superimposition of vibrations can further reduce the friction force. This study presents a theoretical approach based on the Dahl friction model that describes the friction reduction observed in the presence of the tangential vibrations at an arbitrary angle. Analysis results indicated that the tangential compliance should be considered in modeling the effect of vibrations in reducing friction. At any vibration angle, the tangential compliance of the contacts reduces the friction reduction effect. The vibrations parallel to the macroscopic velocity are most effective for friction reduction.     

Non-linear Heat and Mass Transfer During Convective Drying of Kaolin Cylinder Under Non-steady Conditions

The self-consistent model of heat and mass transfer during convective drying of capillary porous media describing both the first and the second periods of drying is presented in Musielak (Wydawnictwo Politechniki Poznańskiej, seria Rozprawy, nr 386 (2004a); Chem. Process Eng. 25, 393–409 (2004b)). The results of simulations of processes in steady conditions are shown (Musielak Wydawnictwo Politechniki Poznańskiej, seria Rozprawy, nr 386 (2004a); Chem. Process Eng. 25, 393–409 (2004b)). The main aim of the present work is to compare experimental results with those from numerical simulations. Three convective drying processes have been performed experimentally. The first and the second periods of drying are considered, during which the humidity of air in the dryer changes due to evaporation. The first process is used to establish drying parameters, whereafter the two remaining processes are simulated. Good agreement between experimental and simulation results is found, both qualitative and quantitative.