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Umberto Lucia, Thomas S Deisboeck
Following a thermodynamic approach, we develop a new theoretical analysis of ion transfer across cell membranes. Supported also by experimental data from the literature, we highlight that ion channels determine the typical features of cancer cells, i.e. independence from growth-regulatory signals, avoidance of apoptosis, indefinite proliferative potential, and the capability of inducing angiogenesis. Specifically, we analyse how ion transport, with particular regards to Ca2+ fluxes, modulates cancer cell proliferation, and regulates cell cycle checkpoints...
February 20, 2018: Journal of Theoretical Biology
Michael A Moxley, Kalyan C Vinnakota, Jason N Bazil, Nathan R Qi, Daniel A Beard
High capacity and low capacity running rats, HCR and LCR respectively, have been bred to represent two extremes of running endurance and have recently demonstrated disparities in fuel usage during transient aerobic exercise. HCR rats can maintain fatty acid (FA) utilization throughout the course of transient aerobic exercise whereas LCR rats rely predominantly on glucose utilization. We hypothesized that the difference between HCR and LCR fuel utilization could be explained by a difference in mitochondrial density...
February 23, 2018: PLoS Computational Biology
Sunghwan Choi, Yeonjoon Kim, Jinwoo Kim, Zeehyo Kim, Woo Youn Kim
Machine learning based on big data has emerged as a powerful solution in various chemical problems. We investigated the feasibility of machine learning models for the prediction of activation energies of gas-phase reactions. Six different models with three different types including the artificial neural network, the support vector regression, and the tree boosting methods were tested. We used the structural and thermodynamic properties of molecules and their differences as input features without resorting to specific reaction types so as to maintain the most general input form for broad applicability...
February 23, 2018: Chemistry: a European Journal
Sibin Duan, Rongming Wang, Jingyue Liu
Catalysis by supported single metal atoms has demonstrated tremendous potential for practical applications due to their unique catalytic properties. Unless they are strongly anchored to the support surfaces, supported single atoms, however, are thermodynamically unstable, which poses a major obstacle for broad applications of single-atom catalysts (SACs). In order to develop strategies to improve the stability of SACs we need to understand the intrinsic nature of the sintering processes of supported single metal atoms, especially under various gas environments that are relevant to important catalytic reactions...
February 23, 2018: Nanotechnology
Seyoung Jung, Timothy P Lodge, Theresa M Reineke
Complexation between plasmid DNA (pDNA) and a set of diblock copolymers, each with one cationic block and one hydrophilic, charge-neutral block, is examined. A range of hydrophilic block structures are explored, whereas the cationic block is fixed as poly(N-(2-aminoethyl) methacrylamide) (PAEMA) with a degree of polymerization of 60 ± 3. The hydrophilic blocks include poly(ethylene glycol) (PEG45), poly(oligo(ethylene glycol) methyl ether methacrylate) (P(OEGMA)51), and poly(2-deoxy-2-methacrylamido glucopyranose) (PMAG52)...
February 23, 2018: Journal of Physical Chemistry. B
Alex J Guseman, Shannon Leigh Speer, Gerardo M Perez Goncalves, Gary J Pielak
Protein-protein interactions are fundamental to biology, yet are rarely studied under physiologically-relevant conditions where the concentration of macromolecules can exceed 300 g/L. These high concentrations cause cosolute-complex contacts that are absent in dilute buffer. Understand-ing such interactions is important because they organize the cellular interior. We used 19F NMR, the dimer-forming A34F variant of the model protein GB1 and the cosolutes bovine serum albumin (BSA) and lysozyme to assess the effects of repulsive and attractive charge-charge dimer-cosolute interac-tions on dimer stability...
February 23, 2018: Biochemistry
Sean R German, Martin A Edwards, Hang Ren, Henry S White
Electrochemical measurements of the nucleation rate of individual H2 bubbles at the surface of Pt nanoelectrodes (radius = 7 - 41 nm) are used to determine the critical size and geometry of H2 nuclei leading to stable bubbles. Precise knowledge of the H2 concentration at the electrode surface, C_(H_2)^surf, is obtained by controlled current reduction of H+ in a H2SO4 solution. Induction times of single-bubble nucleation events are measured by stepping the current to control C_(H_2)^surf while monitoring the voltage...
February 23, 2018: Journal of the American Chemical Society
Kun Liang, Joo Eun Chung, Shu Jun Gao, Nunnarpas Yongvongsoontorn, Motoichi Kurisawa
Low drug loading and instability in blood circulation are two key challenges that impede the successful clinical translation of nanomedicine, as they result in only marginal therapeutic efficacy and toxic side effects associated with premature drug leakage, respectively. Herein, highly stable and ultrahigh drug loading micellar nanocomplexes (MNCs) based on the self-assembly of the anticancer drug doxorubicin (DOX) and a poly(ethylene glycol)-epigallocatechin-3-O-gallate (EGCG) conjugate are developed. The formation of these MNCs is facilitated by strong favorable intermolecular interactions between the structurally similar aromatic EGCG and DOX molecules, which impart exceptionally high drug-loading capability of up to 88% and excellent thermodynamic and kinetic stability...
February 23, 2018: Advanced Materials
Federico Fogolari, Alessandra Corazza, Gennaro Esposito
Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms...
2018: Frontiers in Molecular Biosciences
Govinder S Pawar, Asif A Tahir
Photoelectrochemical (PEC) water splitting to produce solar fuel (hydrogen) has long been considered as the Holy Grail to a carbon-free hydrogen economy. The PEC concept to produce solar fuel is to emulate the natural photosynthesis using man made materials. The bottle-neck in realising the concept practically has been the difficulty in identifying stable low-cost semiconductors that meet the thermodynamic and kinetic criteria for photoelectrolysis. We have fabricated a novel p-type LaFeO3 photoelectrode using an inexpensive and scalable spray pyrolysis method...
February 22, 2018: Scientific Reports
Lachlan P Lindoy, Gavin S Huang, Meredith J T Jordan
Quantum thermodynamic parameters can be determined using path integral Monte Carlo (PIMC) simulations. These simulations, however, become computationally demanding as the quantum nature of the system increases, although their efficiency can be improved by using higher order approximations to the thermal density matrix, specifically the action. Here we compare the standard, primitive approximation to the action (PA) and three higher order approximations, the Takahashi-Imada action (TIA), the Suzuki-Chin action (SCA) and the Chin action (CA)...
February 21, 2018: Journal of Chemical Physics
Arya Das, Sk Musharaf Ali
Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation...
February 21, 2018: Journal of Chemical Physics
Víctor M Trejos, Jacqueline Quintana-H
In this work, a molecular simulation study of confined hard-spheres particles with square-well (SW) attractive interactions with two and four associating SW sites based on the first-order perturbation form of Wertheim's theory is presented. An extended version of the Gibbs ensemble technique for inhomogeneous fluids [A. Z. Panagiotopoulos, Mol. Phys. 62, 701 (1987)] is used to predict the adsorption density profiles for associating fluids confined between opposite parallel walls. The fluid is confined in four kinds of walls: hard-wall, SW wall, Lennard-Jones (LJ) 12-6 wall potential, and LJ 10-4 wall potential...
February 21, 2018: Journal of Chemical Physics
Shavkat Mamatkulov, Nadine Schwierz
Metal cations are essential in many vital processes. In order to capture the role of different cations in all-atom molecular dynamics simulations of biological processes, an accurate parametrization is crucial. Here, we develop force field parameters for the metal cations Li+ , Na+ , K+ , Cs+ , Mg2+ , Ca2+ , Sr2+ , and Ba2+ in combination with the TIP3P water model that is frequently used in biomolecular simulations. In progressing toward improved force fields, the approach presented here is an extension of previous efforts and allows us to simultaneously reproduce thermodynamic and kinetic properties of aqueous solutions...
February 21, 2018: Journal of Chemical Physics
Silio Lima Moura, Laura Martinez Fajardo, Leonardo Dos Anjos Cunha, Maria Del Pilar Taboada Sotomayor, Francisco Bolivar Correto Machado, Luiz Fernando Araújo Ferrão, Maria Isabel Pividori
This study addresses the rational design of a magnetic molecularly imprinted polymer (magnetic-MIP) for the selective recognition of the hormone levothyroxine. The theoretical study was carried out by the density functional theory (DFT) computations considering dispersion interaction energies, and using the D2 Grimme's correction. The B97-D/def2-SV(P)/PCM method is used not only for studying the structure of the template the and monomer-monomer interactions, but also to assess the stoichiometry, noncovalent binding energies, solvation effects and thermodynamics properties such as binding energy...
January 31, 2018: Biosensors & Bioelectronics
Edgar Herrera-Delgado, Ruben Perez-Carrasco, James Briscoe, Peter Sollich
Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and complexity of these models mean that their behaviour is not always intuitive and the underlying mechanisms can be difficult to decipher. For this reason, methods that simplify and aid exploration of complex networks are necessary. To this end we develop a broadly applicable form of the Zwanzig-Mori projection...
February 22, 2018: PLoS Computational Biology
Yuanyuan Zheng, Wenrui Zheng, Jiaoyang Wang, Huifang Chang, Danfeng Zhu
The hydrazine derivatives have been regarded as the important building blocks in organic chemistry for the synthesis of organic N-containing compounds. It is important to understand the structure-activity relationship of the thermodynamics of N-N bonds, in particular, their strength as measured by using the homolytic bond dissociation enthalpies (BDEs). We calculated the N-N BDEs of 13 organonitrogen compounds by 8 composite high-level ab initio methods including G3, G3B3, G4, G4MP2, CBS-QB3, ROCBS-QB3, CBS-Q and CBS-APNO...
February 22, 2018: Journal of Physical Chemistry. A
Eusebio Juaristi, Rafael Notario
For more than five decades now since its original conception, the α-effect has been usually advocated with arguments based on kinetic reactivity data. The present study was undertaken with the aim to gather theoretical information on thermodynamic bond energy data in systems that could in principle give rise to intramolecular α-effects. In particular, oxygen-containing six-membered rings oxa-, 1,2-dioxa-, 1,3-dioxa-, 1,2,4-trioxa- and 1,2,4,5-tetraoxacyclohexane were optimized at the B3LYP/aug-cc-PVTZ level of theory, and the magnitude of all C-H one-bond coupling constants was determined...
February 22, 2018: Journal of Organic Chemistry
Guangxing Zhang, Han Wang, Jinlong Yang, Qinghe Zhao, Luyi Yang, Hanting Tang, Chaokun Liu, Haibiao Chen, Yuan Lin, Feng Pan
Oxygen evolution reaction (OER), as the critical step in splitting water, is a thermodynamically "up-hill" process and requires highly efficient catalysts to run. Arrhenius' law suggests that the higher temperature, the faster the reaction rate, so that a larger OER current density can be achieved at a lower η. Herein, we report an abnormal temperature effect on the performance of Co-based catalysts, e.g., Co3 O4 , Li2 CoSiO4 , and Fe-doped Co(OH)x , in OER in alkaline electrolytes. The OER performance reached a maximum when the temperature increased to 65 °C, and the OER performance declined when the temperature became higher...
February 22, 2018: Inorganic Chemistry
Ying Bai, Ziwei Pei, Feng Wu, Chuan Wu
The composites of M(BH4)n-LiNH2 (1/2n molar ratio, n=1 or 2, M=Ca, Mg, Li) were synthesized by liquid ball-milling. Samples were characterized by X-ray diffraction (XRD), thermogravimetric-differential thermal analysis-mass spectroscopy (TG-DTA-MS) and kinetics models (Achar differential/Coats-Redfern integral method). The higher electronegativity metal M in M(BH4)n-4LiNH2 (M=Ca, Mg) samples not only enable [BH4]- group to release easily, so as to facilitate the interaction of [BH4]-and [NH2]- groups; but also restrain the NH3 release and slightly decrease the onset dehydrogenation temperature concluded by TG-MS...
February 22, 2018: ACS Applied Materials & Interfaces
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