Finite-time adiabatic processes: derivation and speed limit

Obtaining adiabatic processes that connect equilibrium states in a given time represents a challenge for mesoscopic systems. In this paper, we explicitly show how to build these finite-time adiabatic processes for an overdamped Brownian particle in an arbitrary potential, a system that is relevant both at the conceptual and the practical level. This is achieved by jointly engineering the time evolutions of the binding potential and the fluid temperature. Moreover, we prove that the second principle imposes a speed limit for such adiabatic transformations: there appears a minimum time to connect the initial and final states. This minimum time can be explicitly calculated for a general compression/decompression situation.Comment: Main text: 5 pages; 18 pages with appendices and references; major revision with results for a general non-linear potential and study of fluctuations added; Physical Review E in pres

Structure of the Vacuum in Deformed Supersymmetric Chiral Models

We analyze the vacuum structure of N=1/2 chiral supersymmetric theories in deformed superspace. In particular we study O'Raifeartaigh models with C-deformed superpotentials and canonical and non-canonical deformed Kahler potentials. We find conditions under which the vacuum configurations are affected by the deformations.Comment: 15 pages, minor corrections. Version to appear in JHE

Role of Mo in catalysts based on noble metals in hydrodeoxygenation reactions

The use of bio-energy as a renewable alternative to fossil fuels is nowadays attracting more and more attention. The bio-fuel from biomass seems to be a potential energy substitute for fossil fuels since it is a renewable resource that could contribute to sustainable development and global environmental preservation and it appears to have significant economic potential1. The problem is its high oxygen content, which gives undesirable properties for combustion. To remove oxygen, catalytic hydrodeoxygenation (HDO) reactions are carried out. Monometallic Mo/Si, Pt/Si as well as bimetallic PtMo/Si catalysts were prepared and evaluated in the hydrodeoxygenation (HDO)reaction of dibenzofurane (DBF) as a model molecule in biomass derived bio-oil.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

The rate of the molecular clock and the cost of gratuitous protein synthesis

The nature of the protein molecular clock, the protein-specific rate of amino acid substitutions, is among the central questions of molecular evolution. Protein expression level is the dominant determinant of the clock rate in a number of organisms. It has been suggested that highly expressed proteins evolve slowly in all species mainly to maintain robustness to translation errors that generate toxic misfolded proteins. Here we investigate this hypothesis experimentally by comparing the growth rate of Escherichia coli expressing wild type and misfolding-prone variants of the LacZ protein. We show that the cost of toxic protein misfolding is small compared to other costs associated with protein synthesis. Complementary computational analyses demonstrate that there is also a relatively weaker, but statistically significant, selection for increasing solubility and polarity in highly expressed E. coli proteins. Although we cannot rule out the possibility that selection against misfolding toxicity significantly affects the protein clock in species other than E. coli, our results suggest that it is unlikely to be the dominant and universal factor determining the clock rate in all organisms. We find that in this bacterium other costs associated with protein synthesis are likely to play an important role. Interestingly, our experiments also suggest significant costs associated with volume effects, such as jamming of the cellular environment with unnecessary proteins

Development of homogeneous expression of resistance in methicillin-resistant Staphylococcus aureus clinical strains is functionally associated with a β-lactam-mediated SOS response

Objectives: One of the main characteristics of methicillin-resistant Staphylococcus aureus (MRSA) from both hospitals and community is their heterogeneous expression of resistance. Recently, we reported new heterogeneous MRSA isolates phenotypically susceptible to oxacillin despite being mecA positive. These low-level mecA-mediated resistance MRSA strains are very heterogeneous in expression (HeR) and are likely to be clinically relevant since exposure of such isolates to b-lactams can result in high-level homotypic resistance (HoR). We hypothesized that HeR to HoR selection in these clinically relevant strains may be determined by the pre-existence of a hypermutable population that favours its selection in the presence of oxacillin. Methods: Using established procedures, SA13011 HeR to HoR selection was performed by using subinhibitory concentrations of oxacillin and examined for mutability. Real-time RT-PCR and transcriptional profiling by DNA microarray were used to compare gene expression between both populations and related genetically modified SA13011 strain. Results: We found that HeR/HoR selection by oxacillin was associated with increased mutation rate and oxacillin-mediated SOS response. We determined increased expression of both mecA and SOS response lexA/recA regulators. Mutational inactivation of lexA repressor resulted in a significant decrease in both mutation rate and oxacillin resistance in the HoR cells. Complementation of the lexA mutant strain restored oxacillin resistance to the high levels observed in the corresponding HoR wild-type strain. Conclusions: The present results support the notion that SOS response is mechanistically involved in generating mutations that, in addition to mecA induction, allow the selection of a highly oxacillin-resistant population.Fil: Cuirolo, Arabela Ximena. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: Plata, Konrad. University of Virginia; Estados UnidosFil: Rosato, Adriana E.. University of Virginia; Estados Unido

Feynman diagrams with the effective action

A derivation is given of the Feynman rules to be used in the perturbative computation of the Green's functions of a generic quantum many-body theory when the action which is being perturbed is not necessarily quadratic. Some applications are discussed.Comment: Extended revised version. RevTex, 19 pages, 10 figure

Optimal work in a harmonic trap with bounded stiffness

We apply Pontryagin's principle to drive rapidly a trapped overdamped Brownian particle in contact with a thermal bath between two equilibrium states corresponding to different trap stiffness $\kappa$. We work out the optimal time dependence $\kappa(t)$ by minimising the work performed on the particle under the non-holonomic constraint $0\leq\kappa\leq\kappa_{\max}$, an experimentally relevant situation. Several important differences arise, as compared with the case of unbounded stiffness that has been analysed in the literature. First, two arbitrary equilibrium states may not always be connected. Second, depending on the operating time $t_{\text{f}}$ and the desired compression ratio $\kappa_{\text{f}}/\kappa_{\text{\i}}$, different types of solutions emerge. Finally, the differences in the minimum value of the work brought about by the bounds may become quite large, which may have a relevant impact on the optimisation of heat engines.Comment: 16 pages, 9 figures; submitted to Physical Review

Relevance of the speed and direction of pulling in simple modular proteins

A theoretical analysis of the unfolding pathway of simple modular proteins in length- controlled pulling experiments is put forward. Within this framework, we predict the first module to unfold in a chain of identical units, emphasizing the ranges of pulling speeds in which we expect our theory to hold. These theoretical predictions are checked by means of steered molecular dynamics of a simple construct, specifically a chain composed of two coiled-coils motives, where anisotropic features are revealed. These simulations also allow us to give an estimate for the range of pulling velocities in which our theoretical approach is valid.Comment: Accepted for publication in J. Chem. Theory Comput.; only one PDF file with the main text and the supporting information (generated from a docx file