Ville V. Lehtola

Dynamics of forced biopolymer translocation

We present results from our simulations of biopolymer translocation in a solvent which explain the main experimental findings. The forced translocation can be described by simple force balance arguments for the relevant range of pore potentials in experiments and biological systems. Scaling of translocation time with polymer length varies with pore force and friction. Hydrodynamics affects this scaling and significantly reduces translocation times.

Critical evaluation of the computational methods used in the forced polymer translocation.

In forced polymer translocation, the average translocation time tau scales with respect to pore force f and polymer length N as tau approximately f;{-1}N;{beta} . We demonstrate that an artifact in the Metropolis Monte Carlo method resulting in breakage of the force scaling with large f may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent beta<or=1+nu is not universal, but depends on f . Moreover, we show that forced translocation can be described by a relatively simple force balance argument and beta to arise solely from the initial polymer configuration.

Pore-polymer interaction reveals nonuniversality in forced polymer translocation.

We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced translocation characteristics significantly in the biologically relevant range of the pore force, i.e., the driving force. Details of the model are shown to change even the obtained scaling relations, which is a strong indication of strongly out-of-equilibrium dynamics in the computational studies which have not yet succeeded in addressing the characteristics of the forced translocation for biopolymers at realistic length scale.

Comparison of the Selected State-Of-The-Art 3D Indoor Scanning and Point Cloud Generation Methods

Accurate three-dimensional (3D) data from indoor spaces are of high importance for various applications in construction, indoor navigation and real estate management. Mobile scanning techniques are offering an efficient way to produce point clouds, but with a lower accuracy than the traditional terrestrial laser scanning (TLS). In this paper, we first tackle the problem of how the quality of a point cloud should be rigorously evaluated. Previous evaluations typically operate on some point cloud subset, using a manually-given length scale, which would perhaps describe the ranging precision or the properties of the environment. Instead, the metrics that we propose perform the quality evaluation to the full point cloud and over all of the length scales, revealing the method precision along with some possible problems related to the point clouds, such as outliers, over-completeness and misregistration. The proposed methods are used to evaluate the end product point clouds of some of the latest methods. In detail, point clouds are obtained from five commercial indoor mapping systems, Matterport, NavVis, Zebedee, Stencil and Leica Pegasus: Backpack, and three research prototypes, Aalto VILMA , FGI Slammer and the Wurzburg backpack. These are compared against survey-grade TLS point clouds captured from three distinct test sites that each have different properties. Based on the presented experimental findings, we discuss the properties of the proposed metrics and the strengths and weaknesses of the above mapping systems and then suggest directions for future research.

Societal innovation at the interface of the state and civil society

The need to adapt to economic globalization and “wicked” problems such as climate change and poverty presents enormous challenges to modern developed societies. These challenges call for new solutions, not only in the form of technological or business innovations, but also through society-wide reform and renewal. In this paper, we outline a societal innovation framework to better understand the stage on which these societal challenges are being played out. Our approach builds on the classical view that considers innovation, an (radical or incremental) improvement that is both novel in its context and deployed by people. These societal innovations change the interface of the state and civil society for stakeholder benefit.

AUTOMATED IMAGE-BASED RECONSTRUCTION OF BUILDING INTERIORS - A CASE STUDY

In 3D reconstruction of indoor environments, automated methods offer possibilities for e.g. brokering, planning and decoration businesses. The application potential of these automated methods is, however, tied to the accuracy of these methods. In this paper, we perform a technical case study analysis on a state-of-the-art image-based method. For accuracy, we find that 60-70% of points in the reconstructed 3D point cloud are within 5 cm error range. Image-based 3D reconstruction thus offers potential for those various indoor-related applications that are satisfied with this level of accuracy. We also discuss other factors affecting to the applicability and robustness of this method.

Radial Distortion from Epipolar Constraint for Rectilinear Cameras

Lens distortion causes difficulties for 3D reconstruction, when uncalibrated image sets with weak geometry are used. We show that the largest part of lens distortion, known as the radial distortion, can be estimated along with the center of distortion from the epipolar constraint separately and before bundle adjustment without any calibration rig. The estimate converges as more image pairs are added. Descriptor matched scale-invariant feature (SIFT) point pairs that contain false matches can readily be given to our algorithm, EPOS (EpiPOlar-based Solver), as input. The processing is automated to the point where EPOS solves the distortion whether its type is barrel or pincushion or reports if there is no need for correction.