General no-go condition for stochastic pumping

The control of chemical dynamics requires understanding the effect of time-dependent transition rates between states of chemo-mechanical molecular configurations. Pumping refers to generating a net current, e.g. per period in the time-dependence, through a cycle of consecutive states. The working of artificial machines or synthesized molecular motors depends on it. In this paper we give short and simple proofs of no-go theorems, some of which appeared before but here with essential extensions to non-Markovian dynamics, including the study of the diffusion limit. It allows to exclude certain protocols in the working of chemical motors where only the depth of the energy well is changed in time and not the barrier height between pairs of states. We also show how pre-existing steady state currents are in general modified with a multiplicative factor when this time-dependence is turned on.Comment: 8 pages; v2: minor changes, 1 reference adde

Randomized Reference Classifier with Gaussian Distribution and Soft Confusion Matrix Applied to the Improving Weak Classifiers

In this paper, an issue of building the RRC model using probability distributions other than beta distribution is addressed. More precisely, in this paper, we propose to build the RRR model using the truncated normal distribution. Heuristic procedures for expected value and the variance of the truncated-normal distribution are also proposed. The proposed approach is tested using SCM-based model for testing the consequences of applying the truncated normal distribution in the RRC model. The experimental evaluation is performed using four different base classifiers and seven quality measures. The results showed that the proposed approach is comparable to the RRC model built using beta distribution. What is more, for some base classifiers, the truncated-normal-based SCM algorithm turned out to be better at discovering objects coming from minority classes.Comment: arXiv admin note: text overlap with arXiv:1901.0882

Geometry-controlled kinetics

It has long been appreciated that transport properties can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target -- the first-passage time (FPT). Although essential to quantify the kinetics of reactions on all time scales, determining the FPT distribution was deemed so far intractable. Here, we calculate analytically this FPT distribution and show that transport processes as various as regular diffusion, anomalous diffusion, diffusion in disordered media and in fractals fall into the same universality classes. Beyond this theoretical aspect, this result changes the views on standard reaction kinetics. More precisely, we argue that geometry can become a key parameter so far ignored in this context, and introduce the concept of "geometry-controlled kinetics". These findings could help understand the crucial role of spatial organization of genes in transcription kinetics, and more generally the impact of geometry on diffusion-limited reactions.Comment: Submitted versio

Frequency of antimicrobial resistance among invasive and colonizing Group B Streptococcal isolates

BACKGROUND: Group B Streptococcus (GBS) remains susceptible to penicillin, however, resistance to second-line antimicrobials, clindamycin and erythromycin, has increased since 1996. We describe the age-specific antibiotic susceptibility profile and capsular type distribution among invasive and colonizing GBS strains. METHODS: We tested 486 invasive GBS isolates from individuals of all ages collected by a Wisconsin surveillance system between 1998 and 2002 and 167 colonizing strains collected from nonpregnant college students during 2001 in Michigan. Antimicrobial susceptibility testing was performed by disk diffusion or Etest and capsular typing was performed using DNA dot blot hybridization RESULTS: 20.0% (97/486) of invasive and 40.7% (68/167) of colonizing isolates were resistant to clindamycin (P < .001) and 24.5% (119/486) of invasive and 41.9% (70/167) of colonizing isolates were resistant to erythromycin (P < .001). Similarly, 19.8% (96/486) of invasive and 38.3% (64/167) of colonizing isolates were resistant to both antimicrobial agents (P < .001). 29.4% (5/17) of invasive isolates from persons 18–29 years of age and 24.3% (17/70) of invasive isolates from persons 30–49 years of age were resistant to clindamycin. Similarly, 35.3% (6/17) of invasive isolates from persons 18–29 years of age and 31.4% (22/70) of invasive isolates from persons 30–49 years of age were resistant to erythromycin. 34.7% (26/75) of invasive isolates from persons < 1 year of age were capsular type Ia, whereas capsular type V predominated among isolates from adults. CONCLUSION: Clindamycin and erythromycin resistance rates were high among isolates colonizing nonpregnant college students and invasive GBS isolates, particularly among the colonizing isolates. Susceptibility profiles were similar by age although the proportion of clindamycin and erythromycin resistance among invasive isolates was highest among persons 18–49 years of age. Increasing antimicrobial resistance has implications for GBS disease treatment and intrapartum prophylaxis among penicillin intolerant patients

Weak temperature dependence of P (+) H A (-) recombination in mutant Rhodobacter sphaeroides reaction centers

International audienceIn contrast with findings on the wild-type Rhodobacter sphaeroides reaction center, biexponential P (+) H A (-) → PH A charge recombination is shown to be weakly dependent on temperature between 78 and 298 K in three variants with single amino acids exchanged in the vicinity of primary electron acceptors. These mutated reaction centers have diverse overall kinetics of charge recombination, spanning an average lifetime from ~2 to ~20 ns. Despite these differences a protein relaxation model applied previously to wild-type reaction centers was successfully used to relate the observed kinetics to the temporal evolution of the free energy level of the state P (+) H A (-) relative to P (+) B A (-) . We conclude that the observed variety in the kinetics of charge recombination, together with their weak temperature dependence, is caused by a combination of factors that are each affected to a different extent by the point mutations in a particular mutant complex. These are as follows: (1) the initial free energy gap between the states P (+) B A (-) and P (+) H A (-) , (2) the intrinsic rate of P (+) B A (-) → PB A charge recombination, and (3) the rate of protein relaxation in response to the appearance of the charge separated states. In the case of a mutant which displays rapid P (+) H A (-) recombination (ELL), most of this recombination occurs in an unrelaxed protein in which P (+) B A (-) and P (+) H A (-) are almost isoenergetic. In contrast, in a mutant in which P (+) H A (-) recombination is relatively slow (GML), most of the recombination occurs in a relaxed protein in which P (+) H A (-) is much lower in energy than P (+) H A (-) . The weak temperature dependence in the ELL reaction center and a YLH mutant was modeled in two ways: (1) by assuming that the initial P (+) B A (-) and P (+) H A (-) states in an unrelaxed protein are isoenergetic, whereas the final free energy gap between these states following the protein relaxation is large (~250 meV or more), independent of temperature and (2) by assuming that the initial and final free energy gaps between P (+) B A (-) and P (+) H A (-) are moderate and temperature dependent. In the case of the GML mutant, it was concluded that the free energy gap between P (+) B A (-) and P (+) H A (-) is large at all times