Search results for " thermodynamics"
showing 8 items of 288 documents
Fast Isolation by AFLP of Sequences Containing Repeats
2013
Fast isolation by AFLP of sequences containing repeats (FIASCO) is a rapid and simple method for separating microsatellite-containing DNA fragments from genomic DNA de novo. The method takes the advantage of the amplified fragment length polymorphism (AFLP) technique that relies on effective digestion-ligation reaction. The repeat-containing fragments are selectively hybridized to biotinylated probes and harvested by streptavidin-coated magnetic beads. The enriched microsatellite-containing fragments can be cloned and sequenced to yield a variety of microsatellite loci for applications in many different fields in molecular genetics.
CH vs. HC—Promiscuous Metal Sponges in Antimicrobial Peptides and Metallophores
2023
Histidine and cysteine residues, with their imidazole and thiol moieties that deprotonate at approximately physiological pH values, are primary binding sites for Zn(II), Ni(II) and Fe(II) ions and are thus ubiquitous both in peptidic metallophores and in antimicrobial peptides that may use nutritional immunity as a way to limit pathogenicity during infection. We focus on metal complex solution equilibria of model sequences encompassing Cys–His and His–Cys motifs, showing that the position of histidine and cysteine residues in the sequence has a crucial impact on its coordination properties. CH and HC motifs occur as many as 411 times in the antimicrobial peptide database, while …
Merging Features from Green's Functions and Time Dependent Density Functional Theory: A Route to the Description of Correlated Materials out of Equil…
2016
We propose a description of nonequilibrium systems via a simple protocol that combines exchange-correlation potentials from density functional theory with self-energies of many-body perturbation theory. The approach, aimed to avoid double counting of interactions, is tested against exact results in Hubbard-type systems, with respect to interaction strength, perturbation speed and inhomogeneity, and system dimensionality and size. In many regimes, we find significant improvement over adiabatic time dependent density functional theory or second Born nonequilibrium Green's function approximations. We briefly discuss the reasons for the residual discrepancies, and directions for future work.
Exploring fast proton transfer events associated with lateral proton diffusion on the surface of membranes
2019
Proton diffusion (PD) across biological membranes is a fundamental process in many biological systems, and much experimental and theoretical effort has been employed for deciphering it. Here, we report on a spectroscopic probe, which can be tightly tethered to the membrane, for following fast (nanosecond) proton transfer events on the surface of membranes. Our probe is composed of a photoacid that serves as our light-induced proton source for the initiation of the PD process. We use our probe to follow PD, and its pH dependence, on the surface of lipid vesicles composed of a zwitterionic headgroup, a negative headgroup, a headgroup that is composed only from the negative phosphate group, or…
Understanding Structure and Stability of Monoclinic Zirconia Surfaces from First-Principles Calculations
2017
Under the water-rich pre-treatment and/or reaction conditions, structure and chemistry of the monoclinic zirconia surfaces are strongly influenced by oxygen vacancies and incorporated water. Here, we report a combined first-principles and atomistic thermodynamics study on the structure and stability of selected surfaces of the monoclinic zirconia. Our results indicate that among the studied surfaces, the most stable (111) surface is the least vulnerable towards oxygen vacancies in contrast to the less stable (011) and (101) surfaces, where formation of oxygen vacancies is energetically more favorable. Furthermore, we present a vigorous, systematic screening of water incorporation onto the s…
A Theoretical and Experimental Investigation of the Spectroscopic Properties of a DNA-Intercalator Salphen-Type ZnIIComplex
2014
The photophysical and DNA-binding properties of the cationic zinc(II) complex of 5-triethylammonium methyl salicylidene ortho-phenylenediiminato (ZnL 2 + ) were investi- gated by a combination of experimental and theoretical methods. DFT calculations were performed on both the ground and the first excited states of ZnL 2 + and on its possi- ble mono- and dioxidation products, both in vacuo and in selected solvents mimicked by the polarizable continuum model. Comparison of the calculated absorption and fluores- cence transitions with the corresponding experimental data led to the conclusion that visible light induces a two-elec- tron photooxidation process located on the phenylenediimi- nato…
New Invariant Domain Preserving Finite Volume Schemes for Compressible Flows
2021
We present new invariant domain preserving finite volume schemes for the compressible Euler and Navier–Stokes–Fourier systems. The schemes are entropy stable and preserve positivity of density and internal energy. More importantly, their convergence towards a strong solution of the limit system has been proved rigorously in [9, 11]. We will demonstrate their accuracy and robustness on a series of numerical experiments.
Thermodynamics: Classical Framework
2016
This chapter starts with a summary of the thermodynamic potentials and the relationships between them which are obtained from Legendre transformation. This is followed by an excursion to some important global properties of materials such as specific heat, expansion coefficients and others. The thermodynamic relations provide the basis for a discussion of continuous changes of state which are illustrated by the Joule-Thomson effect and the Van der Waals gas. These are models which are more realistic than the ideal gas. The discussion of Carnot cycles leads to and illustrates the second and third laws of thermodynamics. The chapter closes with a discussion of entropy as a concave function of …