arXiv subjects

Vadim Puller

Publications and source records attributed to Vadim Puller.

5 recordsLinked to original sources

arXiv2016

In-vivo mutation rates and fitness landscape of HIV-1

Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1 infection, we estimated mutation rates and fitness costs in HIV-1 from the temporal dynamics of genetic variation. At approximately neutral sites, mutations accumulate with a rate of 1.2 x 10^-5 per site per day, in agreement with the rate measured in cell cultures. The rate from G to A is largest, followed by the other transitions C to T, T to C, and A to G, while transversions are more rare. At non-neutral sites, most mutations reduce virus replication; using a model of mutation selection balance, we estimated the fitness cost of mutations at every site in the HIV-1 genome. About half of all nonsynonymous mutations have large fitness costs (greater than 10\%), while most synonymous mutations have costs below 1\%. The cost of synonymous mutations is especially low in most of gag and pol, while much higher costs are observed in important RNA structures and regulatory regions. The intrapatient fitness cost estimates are consistent across multiple patients, suggesting that the deleterious part of the fitness landscape is universal and explains a large fraction of global HIV-1 group M diversity.

q-bio.PE↗

arXiv2015

Scaling laws for the bifurcation-escape rate in a nanomechanical resonator

We report on experimental and theoretical studies of the fluctuation-induced escape time from a metastable state of a nanomechanical Duffing resonator in cryogenic environment. By tuning in situ the non-linear coefficient $γ$ we could explore a wide range of the parameter space around the bifurcation point, where the metastable state becomes unstable. We measured in a relaxation process the distribution of the escape times. We have been able to verify its exponential distribution and extract the escape rate $Γ$. We investigated the scaling of $Γ$ with respect to the distance to the bifurcation point and $γ$, finding an unprecedented quantitative agreement with the theoretical description of the stochastic problem. Simple power scaling laws turn out to hold in a large region of the parameter's space, as anticipated by recent theoretical predictions. These unique findings, implemented in a model dynamical system, are relevant to all systems experiencing under-damped saddle-node bifurcation.

cond-mat.mes-hall↗

arXiv2012

Single molecule detection of nanomechanical motion

We investigate theoretically how single-molecule spectroscopy techniques can be used to perform fast and high resolution displacement detection and manipulation of nanomechanical oscillators, such as singly clamped carbon nanotubes. We analyze the possibility of real time displacement detection by the luminescence signal and of displacement fluctuations by the degree of second order coherence. Estimates of the electro-mechanical coupling constant indicate that intriguing regimes of strong back-action between the two-level system of a molecule and the oscillator can be realized.

cond-mat.mes-hall↗

arXiv2010

How to Measure the Transmission Phase via a Quantum Dot in a Two-Terminal Interferometer

Measurement of the transmission phase through a quantum dot (QD) embedded in an arm of a two-terminal Aharonov-Bohm (AB) interferometer is inhibited by phase symmetry, i.e. the property that the linear response conductance of a two-terminal device is an even function of magnetic field. It is demonstrated that in a setup consisting of an interferometer with a QD in each of its arms, with one of the QDs capacitively coupled to a nearby quantum point contact (QPC), phase symmetry is broken when a finite voltage bias is applied to the QPC. The transmission phase via the uncoupled QD can then be deduced from the amplitude of the odd component of the AB oscillations.

cond-mat.mes-hall↗

arXiv2009

Breaking of Phase Symmetry in Non-Equilibrium Aharonov-Bohm Oscillations through a Quantum Dot

Linear response conductance of a two terminal Aharonov-Bohm (AB) interferometer is an even function of magnetic field. This "phase symmetry" is no expected to hold beyond the linear response regime. In simple AB rings the phase of the oscillations changes smoothly (almost linearly) with voltage bias. However, in an interferometer with a quantum dot in its arm, tuned to the Coulomb blockade regime, experiments indicate that phase symmetry seems to persist even in the nonlinear regime. In this letter we discuss the processes that break AB phase symmetry. In particular we show that breaking of phase symmetry in such an interferometer is possible only after the onset of inelastic cotunneling, i.e. when the voltage bias is larger than the excitation energy in the dot. The asymmetric component of AB oscillations is significant only when the contributions of different levels to the symmetric component nearly cancel out (e.g., due to different parity of these levels), which explains the sharp changes of the AB phase. We show that our theoretical results are consistent with experimental findings.

cond-mat.mes-hall↗