arXiv subjects

Ilkka Huopaniemi

Publications and source records attributed to Ilkka Huopaniemi.

6 recordsLinked to original sources

arXiv2010

Translating biomarkers between multi-way time-series experiments

Translating potential disease biomarkers between multi-species 'omics' experiments is a new direction in biomedical research. The existing methods are limited to simple experimental setups such as basic healthy-diseased comparisons. Most of these methods also require an a priori matching of the variables (e.g., genes or metabolites) between the species. However, many experiments have a complicated multi-way experimental design often involving irregularly-sampled time-series measurements, and for instance metabolites do not always have known matchings between organisms. We introduce a Bayesian modelling framework for translating between multiple species the results from 'omics' experiments having a complex multi-way, time-series experimental design. The underlying assumption is that the unknown matching can be inferred from the response of the variables to multiple covariates including time.

stat.ML↗

arXiv2009

Multi-Way, Multi-View Learning

We extend multi-way, multivariate ANOVA-type analysis to cases where one covariate is the view, with features of each view coming from different, high-dimensional domains. The different views are assumed to be connected by having paired samples; this is a common setup in recent bioinformatics experiments, of which we analyze metabolite profiles in different conditions (disease vs. control and treatment vs. untreated) in different tissues (views). We introduce a multi-way latent variable model for this new task, by extending the generative model of Bayesian canonical correlation analysis (CCA) both to take multi-way covariate information into account as population priors, and by reducing the dimensionality by an integrated factor analysis that assumes the metabolites to come in correlated groups.

stat.ML↗

arXiv2007

Comment on ``Passage Times for Unbiased Polymer Translocation through a Narrow Pore''

One of the most fundamental quantities associated with polymer translocation through a nanopore is the translocation time $τ$ and its dependence on the chain length $N$. Our simulation results based on both the bond fluctuation Monte Carlo and Molecular Dynamics methods confirm the original prediction $τ\sim N^{2ν+1}$, which scales in the same manner as the Rouse relaxation time of the chain except for a larger prefactor, and invalidates other scaling claims.

cond-mat.soft↗

arXiv2007

Polymer translocation through a nanopore under a pulling force

We investigate polymer translocation through a nanopore under a pulling force using Langevin dynamics simulations. We concentrate on the influence of the chain length $N$ and the pulling force $F$ on the translocation time $τ$. The distribution of $τ$ is symmetric and narrow for strong $F$. We find that $τ\sim N^{2}$ and translocation velocity $v\sim N^{-1}$ for both moderate and strong $F$. For infinitely wide pores, three regimes are observed for $τ$ as a function of $F$. With increasing $F$, $τ$ is independent of $F$ for weak $F$, and then $τ\sim F^{-2+ν^{-1}}$ for moderate $F$, where $ν$ is the Flory exponent, which finally crosses over to $τ\sim F^{-1}$ for strong force. For narrow pores, even for moderate force $τ\sim F^{-1}$. Finally, the waiting time, for monomer $s$ and monomer $s+1$ to exit the pore, has a maximum for $s$ close to the end of the chain, in contrast to the case where polymer is driven by an external force within the pore.

cond-mat.soft↗

arXiv2006

Langevin Dynamics Simulations of Polymer Translocation through Nanopores

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time $τ_e$ required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that $τ_e$ scales with the chain length $N$ as $τ_e \sim N^{1+2ν}$, where $ν$ is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficient $ξ$, the driving force $E$ and the length of the chain $N$ on the translocation time $τ$, which is defind as the time duration between the first monomer entering the pore and the last monomer leaving the pore. For strong driving forces, the distribution of translocation times is symmetric and narrow without a long tail and $τ\sim E^{-1}$. The influence of $ξ$ depends on the ratio between the driving and frictional forces. For intermediate $ξ$, we find a crossover scaling for $τ$ with $N$ from $τ\sim N^{2ν}$ for relatively short chains to $τ\sim N^{1 + ν}$ for longer chains. However, for higher $ξ$, only $τ\sim N^{1 + ν}$ is observed even for short chains, and there is no crossover behavior. This result can be explained by the fact that increasing $ξ$ increases the Rouse relaxation time of the chain, in which case even relatively short chains have no time to relax during translocation. Our results are in good agreement with previous simulations based on the fluctuating bond lattice model of polymers at intermediate friction values, but reveals additional features of dependency on friction.

cond-mat.soft↗

arXiv2006

Polymer translocation through a nanopore under an applied external field

We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the 2D fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength $E$, length of the chain $N$, and length of the pore $L$ on forced translocation. As our main result, we find a crossover scaling for the translocation time $τ$ with the chain length from $τ\sim N^{2ν}$ for relatively short polymers to $τ\sim N^{1 + ν}$ for longer chains, where $ν$ is the Flory exponent. We demonstrate that this crossover is due to the change in the dependence of the translocation velocity v on the chain length. For relatively short chains $v \sim N^{- ν}$, which crosses over to $v \sim N^{- 1}$ for long polymers. The reason for this is that with increasing $N$ there is a high density of segments near the exit of the pore, which slows down the translocation process due to slow relaxation of the chain. For the case of a long nanopore for which $R_\parallel $, the radius of gyration $R_{g}$ along the pore, is smaller than the pore length, we find no clear scaling of the translocation time with the chain length. For large $N$, however, the asymptotic scaling $τ\sim N^{1 + ν}$ is recovered. In this regime, $τ$ is almost independent of $L$. We have previously found that for a polymer, which is initially placed in the middle of the pore, there is a minimum in the escape time for $R_\parallel \approx L$. We show here that this minimum persists for a weak fields $E$ such that $EL$ is less than some critical value, but vanishes for large values of $EL$.

cond-mat.soft↗