Work extraction in the spin-boson model

We show that work can be extracted from a two-level system (spin) coupled to a bosonic thermal bath. This is possible due to different initial temperatures of the spin and the bath, both positive (no spin population inversion) and is realized by means of a suitable sequence of sharp pulses applied to the spin. The extracted work can be of the order of the response energy of the bath, therefore much larger than the energy of the spin. Moreover, the efficiency of extraction can be very close to its maximum, given by the Carnot bound, at the same time the overall amount of the extracted work is maximal. Therefore, we get a finite power at efficiency close to the Carnot bound. The effect comes from the backreaction of the spin on the bath, and it survives for a strongly disordered (inhomogeneously broadened) ensemble of spins. It is connected with generation of coherences during the work-extraction process, and we derived it in an exactly solvable model. All the necessary general thermodynamical relations are derived from the first principles of quantum mechanics and connections are made with processes of lasing without inversion and with quantum heat engines.Comment: 30 pages, 6 figure

Stochastic deformation of a thermodynamic symplectic structure

A stochastic deformation of a thermodynamic symplectic structure is studied. The stochastic deformation procedure is analogous to the deformation of an algebra of observables like deformation quantization, but for an imaginary deformation parameter (the Planck constant). Gauge symmetries of thermodynamics and corresponding stochastic mechanics, which describes fluctuations of a thermodynamic system, are revealed and gauge fields are introduced. A physical interpretation to the gauge transformations and gauge fields is given. An application of the formalism to a description of systems with distributed parameters in a local thermodynamic equilibrium is considered.Comment: 22 pages, revtex preprint style; some notations changed and references added; some formulas and comments adde

Classical and Thermodynamic work fluctuations

We have studied the nature of classical work ($W_{c}$) and thermodynamic work ($W$) fluctuations in systems driven out of equilibrium both in transient and time periodic steady state. As the observation time of trajectory increases, we show that the number of trajectories which exhibit excursions away from the typical behaviour i.e., $W_{c}<0$, $W<\Delta F$ and dissipated heat $Q<0$ decreases as anticipated for macroscopic time scales. Analytical expressions for such trajectories are obtained. Trajectory for which $W_{c}<0$ may not correspond to $W<\Delta F$ or $Q<0$. The applicability of steady state fluctuation theorems are discussed in our linear as well as nonlinear models.Comment: Based on the talk presented by Mamata Sahoo at the Condensed Matter Days-Aug. 2008 held at Viswavarati University, Kolkata. 19 pages, 8 figure

Explanation of the Gibbs paradox within the framework of quantum thermodynamics

The issue of the Gibbs paradox is that when considering mixing of two gases within classical thermodynamics, the entropy of mixing appears to be a discontinuous function of the difference between the gases: it is finite for whatever small difference, but vanishes for identical gases. The resolution offered in the literature, with help of quantum mixing entropy, was later shown to be unsatisfactory precisely where it sought to resolve the paradox. Macroscopic thermodynamics, classical or quantum, is unsuitable for explaining the paradox, since it does not deal explicitly with the difference between the gases. The proper approach employs quantum thermodynamics, which deals with finite quantum systems coupled to a large bath and a macroscopic work source. Within quantum thermodynamics, entropy generally looses its dominant place and the target of the paradox is naturally shifted to the decrease of the maximally available work before and after mixing (mixing ergotropy). In contrast to entropy this is an unambiguous quantity. For almost identical gases the mixing ergotropy continuously goes to zero, thus resolving the paradox. In this approach the concept of ``difference between the gases'' gets a clear operational meaning related to the possibilities of controlling the involved quantum states. Difficulties which prevent resolutions of the paradox in its entropic formulation do not arise here. The mixing ergotropy has several counter-intuitive features. It can increase when less precise operations are allowed. In the quantum situation (in contrast to the classical one) the mixing ergotropy can also increase when decreasing the degree of mixing between the gases, or when decreasing their distinguishability. These points go against a direct association of physical irreversibility with lack of information.Comment: Published version. New title. 17 pages Revte

Effect of ABCB1 Gene Carriage and Drug-Drug Interactions on Apixaban and Rivaroxaban Pharmacokinetics and Clinical Outcomes in Patients with Atrial Fibrillation and Deep Vein Thrombosis

Aim. To investigate the effect of ABCB1 gene carriage and interdrug interactions on apixaban pharmacokinetics and clinical outcomes in patients with atrial fibrillation and deep vein thrombosis.Material and methods. Patients hospitalized at Yudin State Clinical Hospital participated in the study. A total of 92 patients (50 patients received apixaban and 42 – rivaroxaban) with non-valvular atrial fibrillation and deep vein thrombosis were included. Genotyping was performed by real-time polymerase chain reaction. Direct oral anticoagulants concentrations were measured using an electrospray ionization mass spectrometer in positive ionization mode.Results. In our study we found that in patients carrying the CT+TT ABCB1 (rs4148738) C&gt;T genotype encoding the carrier protein (P-gp), the plasma concentration of rivaroxaban was statistically significantly higher p= 0.026. In addition, we found that patients taking apixaban together with a CYP3A4/P-gp inhibitor were 3.5 times more likely to have hemorrhagic complications than those without inhibitors p = 0.004.Conclusion. Our study revealed that the plasma concentration of rivaroxaban was higher in patients carrying the ABCB1 (rs4148738) C&gt;T polymorphism T allele. And patients taking apixaban together with CYP3A4/P-gp inhibitor had higher risk of hemorrhagic complications in comparison with patients not taking such drugs. Further studies are needed on the influence of pharmacogenetics and pharmacokinetics on the safety and efficacy profile of apixaban and rivaroxaban, taking into account the trend of systemic approach to optimization of anticoagulant therapy of direct oral anticoagulants based on pharmacokinetic, pharmacogenetic biomarkers

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Factors associated with diversity, quantity and zoonotic potential of ectoparasites on urban mice and voles

Wild rodents are important hosts for tick larvae but co-infestations with other mites and insects are largely neglected. Small rodents were trapped at four study sites in Berlin, Germany, to quantify their ectoparasite diversity. Host-specific, spatial and temporal occurrence of ectoparasites was determined to assess their influence on direct and indirect zoonotic risk due to mice and voles in an urban agglomeration. Rodent-associated arthropods were diverse, including 63 species observed on six host species with an overall prevalence of 99%. The tick Ixodes ricinus was the most prevalent species, found on 56% of the rodents. The trapping location clearly affected the presence of different rodent species and, therefore, the occurrence of particular host-specific parasites. In Berlin, fewer temporary and periodic parasite species as well as non-parasitic species (fleas, chiggers and nidicolous Gamasina) were detected than reported from rural areas. In addition, abundance of parasites with low host-specificity (ticks, fleas and chiggers) apparently decreased with increasing landscape fragmentation associated with a gradient of urbanisation. In contrast, stationary ectoparasites, closely adapted to the rodent host, such as the fur mites Myobiidae and Listrophoridae, were most abundant at the two urban sites. A direct zoonotic risk of infection for people may only be posed by Nosopsyllus fasciatus fleas, which were prevalent even in the city centre. More importantly, peridomestic rodents clearly supported the life cycle of ticks in the city as hosts for their subadult stages. In addition to trapping location, season, host species, body condition and host sex, infestation with fleas, gamasid Laelapidae mites and prostigmatic Myobiidae mites were associated with significantly altered abundance of I. ricinus larvae on mice and voles. Whether this is caused by predation, grooming behaviour or interaction with the host immune system is unclear. The present study constitutes a basis to identify interactions and vector function of rodent-associated arthropods and their potential impact on zoonotic diseases

Impaired innate interferon induction in severe therapy resistant atopic asthmatic children

Deficient type I interferon-β and type III interferon-λ induction by rhinoviruses has previously been reported in mild/moderate atopic asthmatic adults. No studies have yet investigated if this occurs in severe therapy resistant asthma (STRA). Here, we show that compared with non-allergic healthy control children, bronchial epithelial cells cultured ex vivo from severe therapy resistant atopic asthmatic children have profoundly impaired interferon-β and interferon-λ mRNA and protein in response to rhinovirus (RV) and polyIC stimulation. Severe treatment resistant asthmatics also exhibited increased virus load, which negatively correlated with interferon mRNA levels. Furthermore, uninfected cells from severe therapy resistant asthmatic children showed lower levels of Toll-like receptor-3 mRNA and reduced retinoic acid inducible gene and melanoma differentiation-associated gene 5 mRNA after RV stimulation. These data expand on the original work, suggesting that the innate anti-viral response to RVs is impaired in asthmatic tissues and demonstrate that this is a feature of STRA

ВЛИЯНИЕ ПОЛИМОРФИЗМА ГЕНОВ ABCB1 И CES1 НА УРОВНИ РАВНОВЕСНЫХ КОНЦЕНТРАЦИЙ ДАБИГАТРАНА У ПАЦИЕНТОВ ПОСЛЕ ЭНДОПРОТЕЗИРОВАНИЯ КОЛЕННОГО СУСТАВА

Oral anticoagulants are widely used to prevent thromboembolic events in patients following total knee arthroplasty [1]. The genetic characteristics of patients affect the efficacy and safety of anticoagulants [2]. Dabigatran etexilate is a direct inhibitor of thrombin used as a prophylaxis of venous thromboembolic events (VTE) in Europe and Russia. [3]. This study evaluated the impact of ABCB1 and CES1 genetic polymorphisms on the peak and residual dabigatran concentration in orthopedic patients. Material and methods: A total of 30 patients aged 43 to 77 years following knee joint replacement were enrolled in the study. All patients received dabigatran etexilate at a dose of 220 mg/day for the prevention of VTEO. ABCB1 and CES1 genetic polymorphism genotyping was performed by real-time polymerase chain reaction (PCR). The peak and residual concentrations of dabigatran were determined by high-performance liquid chromatography (HPLC). Results: It was found that the ТТ genotype of the MDR1 gene С3435Т polymorphism is associated with a higher peak concentration of dabigatran than the CC genotype (p &lt;0.1). Statistically significant results for CES1 gene rs2244613 polymorphism were obtained in patients younger than 60 years (p &lt;0.05). The analysis of the haplotypes combination in two polymorphisms showed that the most common haplotype combination CC (rs1045642) ABCB1/CT (rs2244613) CES1 was significantly associated with a higher peak concentration of dabigatran compared to the rest of haplotype combinations (p = 0.002). Conclusions: The examination of a cohort of patients receiving dabigatran for the prevention of VTE during the period of large joints arthroplasty showed that SNPs C3435T ABCB1 and rs2244613 CES1 could play an important role in changing dabigatran concentrations. No data suggestive of the impact of SNP ABCB1 rs4148738 on the peak concentration of dabigatran were received.Пероральные антикоагулянты широко применяются для профилактики тромбоэмболических осложнений у пациентов после тотального эндопротезирования коленного сустава [1]. Генетические особенности пациентов влияют на эффективность и безопасность антикоагулянтов [2]. Дабигатран этексилат является прямым ингибитором тромбина, используемым в качестве профилактики венозных тромбоэмболических осложнений (ВТЭО) в Европе и России [3]. В данном исследовании оценивалось влияние полиморфизма генов ABCB1 и CES1 на пиковую и остаточную концентрацию дабигатрана у ортопедических пациентов. Материал и методы: в исследование включено 30 пациентов в возрасте от 43 до 77 лет после оперативного лечения – эндопротезирования коленного сустава. Все пациенты получали дабигатрана этексилат в дозе 220 мг/сут для профилактики ВТЭО. Генотипирование по полиморфизму генов ABCB1 и CES1 проводилось с использованием полимеразной цепной реакции (ПЦР) в режиме реального времени. Проводилось определение пиковой и остаточной концентрации дабигатрана методом высокоэффективной жидкостной хроматографии (ВЭЖХ). Результаты: обнаружено, что генотип ТТ полиморфизма С3435Т гена MDR1 ассоциируется с более высокой пиковой концентрацией дабигатрана, чем генотип CC (р &lt; 0,1). Для полиморфизма rs2244613 гена CES1 статистически значимые результаты получены у пациентов моложе 60 лет (p &lt; 0,05). При анализе комбинации гаплотипов по двум полиморфизмам выявлено, что наиболее часто встречающееся сочетание гаплотипов CC (rs1045642) ABCB1 / CT (rs2244613) CES1 достоверно связано с более высокой пиковой концентрацией дабигатрана по сравнению с совокупностью остальных комбинаций гаплотипов (p = 0,002). Выводы: при обследовании когорты пациентов, получающих дабигатран для профилактики ВТЭО в период эндопротезирования крупных суставов, подтверждено, что SNPs С3435Т ABCB1 и rs2244613 CES1 могут играть важную роль в изменении концентрации дабигатрана. Данных за влияние SNP ABCB1 rs4148738 на пиковую концентрацию дабигатрана не получено