Optical Tweezers for Single Molecule Biology

Molecular machinery on the micro-scale, believed to be the fundamental building blocks of life, involve forces of 1-100 pN and movements of nanometers to micrometers. Micromechanical single-molecule experiments seek to understand the physics of nucleic acids, molecular motors, and other biological systems through direct measurement of forces and displacements. Optical tweezers are a popular choice among several complementary techniques for sensitive force-spectroscopy in the field of single molecule biology. The main objective of this thesis was to design and construct an optical tweezers instrument capable of investigating the physics of molecular motors and mechanisms of protein/nucleic-acid interactions on the single-molecule level. A double-trap optical tweezers instrument incorporating acousto-optic trap-steering, two independent detection channels, and a real-time digital controller was built. A numerical simulation and a theoretical study was performed to assess the signal-to-noise ratio in a constant-force molecular motor stepping experiment. Real-time feedback control of optical tweezers was explored in three studies. Position-clamping was implemented and compared to theoretical models using both proportional and predictive control. A force-clamp was implemented and tested with a DNA-tether in presence of the enzyme lambda exonuclease. The results of the study indicate that the presented models describing signal-to-noise ratio in constant-force experiments and feedback control experiments in optical tweezers agree well with experimental data. The effective trap stiffness can be increased by an order of magnitude using the presented position-clamping method. The force-clamp can be used for constant-force experiments, and the results from a proof-of-principle experiment, in which the enzyme lambda exonuclease converts double-stranded DNA to single-stranded DNA, agree with previous research. The main objective of the thesis was thus achieved. The developed instrument and presented results on feedback control serve as a stepping stone for future contributions to the growing field of single molecule biology.

Resistance fluctuations, phase randomness and noise in one-dimensional conductors with a long-range correlated potential

When the size (L) of a one-dimensional metallic conductor is less than the correlation length λ-1 of the Gaussian random potential, one expects transport properties to show ballistic behaviour. Using an invariant imbedding method, we study the exact distribution of the resistance, of the phase θ of the reflection amplitude of an incident electron of wave number k0, and of dθ/dk0, for λL ll 1. The resistance is non-self-averaging and the n-th resistance moment varies periodically as (1 - cos 2k0L)n. The charge fluctuation noise, determined by the distribution of dθ/dk0, is constant at low frequencies.

Filter design using radial basis function neural network and genetic algorithm for improved operational health monitoring

The problem of denoising damage indicator signals for improved operational health monitoring of systems is addressed by applying soft computing methods to design filters. Since measured data in operational settings is contaminated with noise and outliers, pattern recognition algorithms for fault detection and isolation can give false alarms. A direct approach to improving the fault detection and isolation is to remove noise and outliers from time series of measured data or damage indicators before performing fault detection and isolation. Many popular signal-processing approaches do not work well with damage indicator signals, which can contain sudden changes due to abrupt faults and non-Gaussian outliers. Signal-processing algorithms based on radial basis function (RBF) neural network and weighted recursive median (WRM) filters are explored for denoising simulated time series. The RBF neural network filter is developed using a K-means clustering algorithm and is much less computationally expensive to develop than feedforward neural networks trained using backpropagation. The nonlinear multimodal integer-programming problem of selecting optimal integer weights of the WRM filter is solved using genetic algorithm. Numerical results are obtained for helicopter rotor structural damage indicators based on simulated frequencies. Test signals consider low order polynomial growth of damage indicators with time to simulate gradual or incipient faults and step changes in the signal to simulate abrupt faults. Noise and outliers are added to the test signals. The WRM and RBF filters result in a noise reduction of 54 - 71 and 59 - 73% for the test signals considered in this study, respectively. Their performance is much better than the moving average FIR filter, which causes significant feature distortion and has poor outlier removal capabilities and shows the potential of soft computing methods for specific signal-processing applications. (C) 2005 Elsevier B. V. All rights reserved.

ADC Static Characterization Using Nonlinear Ramp Signal

Static characteristics of an analog-to-digital converter (ADC) can be directly determined from the histogram-based quasi-static approach by measuring the ADC output when excited by an ideal ramp/triangular signal of sufficiently low frequency. This approach requires only a fraction of time compared to the conventional dc voltage test, is straightforward, is easy to implement, and, in principle, is an accepted method as per the revised IEEE 1057. However, the only drawback is that ramp signal sources are not ideal. Thus, the nonlinearity present in the ramp signal gets superimposed on the measured ADC characteristics, which renders them, as such, unusable. In recent years, some solutions have been proposed to alleviate this problem by devising means to eliminate the contribution of signal source nonlinearity. Alternatively, a straightforward step would be to get rid of the ramp signal nonlinearity before it is applied to the ADC. Driven by this logic, this paper describes a simple method about using a nonlinear ramp signal, but yet causing little influence on the measured ADC static characteristics. Such a thing is possible because even in a nonideal ramp, there exist regions or segments that are nearly linear. Therefore, the task, essentially, is to identify these near-linear regions in a given source and employ them to test the ADC, with a suitable amplitude to match the ADC full-scale voltage range. Implementation of this method reveals that a significant reduction in the influence of source nonlinearity can be achieved. Simulation and experimental results on 8- and 10-bit ADCs are presented to demonstrate its applicability.

A study of the spectrum of an acoustic field in shallow water due to noise sources at the surface

An expression for the spectrum and cross spectrum of an acoustic field measured at two vertically separated sensors in shallow water has been obtained for any correlated noise sources distributed over the surface. Numerical results are presented for the case where the noise sources, white noise and wind-induced colored noise, are contained within a circular disk centered over the sensors. The acoustic field is generally inhomogeneous except when the channel is deep. The coherence function becomes real for a large disk, for a radius greater than 25 times the depth of the channel, decreases with further increase of the size of the disk, and finally tapers off after certain limiting size, approximately given by 1/alpha, where alpha is the attenuation coefficient.

Analytical prediction of break-out noise from a reactive rectangular plenum with four flexible walls

This paper describes an analytical calculation of break-out noise from a rectangular plenum with four flexible walls by incorporating three-dimensional effects along with the acoustical and structural wave coupling phenomena. The breakout noise from rectangular plenums is important and the coupling between acoustic waves within the plenum and structural waves in the flexible plenum walls plays a critical role in prediction of the transverse transmission loss. The first step in breakout noise prediction is to calculate the inside plenum pressure field and the normal flexible plenum wall vibration by using an impedance-mobility approach, which results in a compact matrix formulation. In the impedance-mobility compact matrix (IMCM) approach, it is presumed that the coupled response can be described in terms of finite sets of the uncoupled acoustic subsystem and the structural subsystem. The flexible walls of the plenum are modeled as an unfolded plate to calculate natural frequencies and mode shapes of the uncoupled structural subsystem. The second step is to calculate the radiated sound power from the flexible walls using Kirchhoff-Helmholtz (KH) integral formulation. Analytical results are validated with finite element and boundary element (FEM-BEM) numerical models. (C) 2010 Acoustical Society of America. DOI: 10.1121/1.3463801]

Large low-frequency resistance noise in chemical vapor deposited graphene

We report a detailed investigation of resistance noise in single layer graphene films on Si/SiO2 substrates obtained by chemical vapor deposition (CVD) on copper foils. We find that noise in these systems to be rather large, and when expressed in the form of phenomenological Hooge equation, it corresponds to Hooge parameter as large as 0.1-0.5. We also find the variation in the noise magnitude with the gate voltage (or carrier density) and temperature to be surprisingly weak, which is also unlike the behavior of noise in other forms of graphene, in particular those from exfoliation. (C) 2010 American Institute of Physics. doi:10.1063/1.3493655]

Investigations of Noise-Related Tinnitus

Tinnitus is a frequent consequence of noise trauma. Usually, however, the main focus regarding the consequences of noise trauma is placed on hearing loss, instead of tinnitus. The objectives of the present study were to assess various aspects of noise-related tinnitus in Finland, such as to determine the main causes of conscript acute acoustic traumas (AAT) in the military, assess tinnitus prevalence after noise trauma, characterize long-term AAT-related tinnitus prevalence and characteristics, assess occupational tinnitus, and evaluate the efficacy of hearing protection regulations in preventing hearing loss and tinnitus. The study comprised several independent noise-exposed groups: conscripts performing their military duty, former conscripts who suffered an AAT over a decade earlier, bomb explosion victims, and retired army personnel. Tinnitus questionnaires were used to assess tinnitus prevalence and characteristics. For occupational tinnitus, occupational noise-induced hearing loss (NIHL) reports to the Finnish Institute of Occupational Health were reviewed. Tinnitus is a common result of AAT, blast exposure and long-term noise exposure. Despite hearing protection regulations, up to hundreds of AATs occur annually among conscripts in the Finnish Defence Forces (FDF). The most common cause is an accidental shot, accounting for approximately half of the cases. Conscript AATs are mainly due to accidental shots, while the ear is unprotected. Only seldom is an AAT due to negligence. The most common causative weapon of conscript AATs is the assault rifle, accounting for 81% of conscript AATs. After AAT, the majority of tinnitus cases resolve during military service and become asymptomatic. However, in one-fifth of the cases, tinnitus persists, causing problems such as sleeping and concentration difficulties in many. In Finland, occupational tinnitus often remains unreported in conjunction with NIHL reports. In a survey of occupational NIHL cases, tinnitus was mentioned in only four per cent. However, a subsequent inquiry revealed that almost 90% in fact had tinnitus, indicating that most cases remained undetected and unreported. The best way to prevent noise-related tinnitus is prevention of noise trauma. In the military, hearing protection guidelines have been revised several times over the years. These regulations have been effective in reducing hearing loss of professional soldiers. There has also been a reduction in cases with tinnitus, but the decrease was not significant. However, with improved hearing protection regulations, a significant reduction in the risk of more serious, disturbing tinnitus was observed.

Optimization of two-dimensional NMR by matched accumulation

It is well known that in the time-domain acquisition of NMR data, signal-to-noise (S/N) improves as the square root of the number of transients accumulated. However, the amplitude of the measured signal varies during the time of detection, having a functional form dependent on the coherence detected. Matching the time spent signal averaging to the expected amplitude of the signal observed should also improve the detected signal-to-noise. Following this reasoning, Barna et al. (J Magn. Reson.75, 384, 1987) demonstrated the utility of exponential sampling in one- and two-dimensional NMR, using maximum-entropy methods to analyze the data. It is proposed here that for two-dimensional experiments the exponential sampling be replaced by exponential averaging. The data thus collected can be analyzed by standard fast-Fourier-transform routines. We demonstrate the utility of exponential averaging in 2D NOESY spectra of the protein ubiquitin, in which an enhanced SIN is observed. It is also shown that the method acquires delayed double-quantum-filtered COSY without phase distortion.

Alikasvoksen mittaus ja kartoitus laserkeilauksella

Tasaikäisen metsän alle muodostuvilla alikasvoksilla on merkitystä puunkorjuun, metsänuudistamisen, näkemä-ja maisema-analyysien sekä biodiversiteetin ja hiilitaseen arvioinnin kannalta. Ilma-aluksista tehtävä laserkeilaus on osoittautunut tehokkaaksi kaukokartoitusmenetelmäksi varttuneiden puustojen mittauksessa. Laserkeilauksen käyttöönotto operatiivisessa metsäsuunnittelussa mahdollistaa aiempaa tarkemman tiedon tuottamisen alikasvoksista, mikäli alikasvoksen ominaisuuksia voidaan tulkita laseraineistoista. Tässä työssä käytettiin tarkasti mitattuja maastokoealoja ja kaikulaserkeilausaineistoja (discrete return LiDAR) usealta vuodelta (1–2 km lentokorkeus, 0,9–9,7 pulssia m-2). Laserkeilausaineistot oli hankittu Optech ALTM3100 ja Leica ALS50-II sensoreilla. Koealat edustavat suomalaisia tasaikäisiä männiköitä eri kehitysvaiheissa. Tutkimuskysymykset olivat: 1) Minkälainen on alikasvoksesta saatu lasersignaali yksittäisen pulssin tasolla ja mitkä tekijät signaaliin vaikuttavat? 2) Mikä on käytännön sovelluksissa hyödynnettävien aluepohjaisten laserpiirteiden selitysvoima alikasvospuuston ominaisuuksien ennustamisessa? Erityisesti haluttiin selvittää, miten laserpulssin energiahäviöt ylempiin latvuskerroksiin vaikuttavat saatuun signaaliin, ja voidaanko laserkaikujen intensiteetille tehdä energiahäviöiden korjaus. Puulajien väliset erot laserkaiun intensiteetissä olivat pieniä ja vaihtelivat keilauksesta toiseen. Intensiteetin käyttömahdollisuudet alikasvoksen puulajin tulkinnassa ovat siten hyvin rajoittuneet. Energiahäviöt ylempiin latvuskerroksiin aiheuttivat alikasvoksesta saatuun lasersignaaliin kohinaa. Energiahäviöiden korjaus tehtiin alikasvoksesta saaduille laserpulssin 2. ja 3. kaiuille. Korjauksen avulla pystyttiin pienentämään kohteen sisäistä intensiteetin hajontaa ja parantamaan kohteiden luokittelutarkkuutta alikasvoskerroksessa. Käytettäessä 2. kaikuja oikeinluokitusprosentti luokituksessa maan ja yleisimmän puulajin välillä oli ennen korjausta 49,2–54,9 % ja korjauksen jälkeen 57,3–62,0 %. Vastaavat kappa-arvot olivat 0,03–0,13 ja 0,10–0,22. Tärkein energiahäviöitä selittävä tekijä oli pulssista saatujen aikaisempien kaikujen intensiteetti, mutta hieman merkitystä oli myös pulssin leikkausgeometrialla ylemmän latvuskerroksen puiden kanssa. Myös 3. kaiuilla luokitustarkkuus parani. Puulajien välillä havaittiin eroja siinä, kuinka herkästi ne tuottavat kaiun laserpulssin osuessa puuhun. Kuusi tuotti kaiun suuremmalla todennäköisyydellä kuin lehtipuut. Erityisen selvä tämä ero oli pulsseilla, joissa oli energiahäviöitä. Laserkaikujen korkeusjakaumapiirteet voivat siten olla riippuvaisia puulajista. Sensorien välillä havaittiin selviä eroja intensiteettijakaumissa, mikä vaikeuttaa eri sensoreilla hankittujen aineistojen yhdistämistä. Myös kaiun todennäköisyydet erosivat jonkin verran sensorien välillä, mikä aiheutti pieniä eroavaisuuksia kaikujen korkeusjakaumiin. Aluepohjaisista laserpiirteistä löydettiin alikasvoksen runkolukua ja keskipituutta hyvin selittäviä piirteitä, kun rajoitettiin tarkastelu yli 1 m pituisiin puihin. Piirteiden selitysvoima oli parempi runkoluvulle kuin keskipituudelle. Selitysvoima ei merkittävästi alentunut pulssitiheyden pienentyessä, mikä on hyvä asia käytännön sovelluksia ajatellen. Lehtipuun osuutta ei pystytty selittämään. Tulosten perusteella kaikulaserkeilausta voi olla mahdollista hyödyntää esimerkiksi ennakkoraivaustarpeen arvioinnissa. Sen sijaan alikasvoksen tarkempi luokittelu (esim. puulajitulkinta) voi olla vaikeaa. Kaikkein pienimpiä alikasvospuita ei pystytä havaitsemaan. Lisää tutkimuksia tarvitaan tulosten yleistämiseksi erilaisiin metsiköihin.

A Non Quasi-Static Small Signal Model for Long Channel Symmetric DG MOSFET

We propose a compact model for small signal non quasi static analysis of long channel symmetric double gate MOSFET The model is based on the EKV formalism and is valid in all regions of operation and thus suitable for RF circuit design Proposed model is verified with professional numerical device simulator and excellent agreement is found well beyond the cut-off frequency

Rocking response of rectangular rigid blocks under random noise base excitations

The response of a rigid rectangular block resting on a rigid foundation and acted upon simultaneously by a horizontal and a vertical random white-noise excitation is considered. In the equation of motion, the energy dissipation is modeled through a viscous damping term. Under the assumption that the body does not topple, the steady-state joint probability density function of the rotation and the rotational velocity is obtained using the Fokker-Planck equation approach. Closed form solution is obtained for a specific combination of system parameters. A more general but approximate solution to the joint probability density function based on the method of equivalent non-linearization is also presented. Further, the problem of overturning of the block is approached in the framework of the diffusion methods for first passage failure studies. The overturning of the block is deemed incipient when the response trajectories in the phase plane cross the separatrix of the conservative unforced system. Expressions for the moments of first passage time are obtained via a series solution to the governing generalized Pontriagin-Vitt equations. Numerical results illustra- tive of the theoretical solutions are presented and their validity is examined through limited amount of digital simulations.

Voluntary Energy Harvesting Relays and Selection in Cooperative Wireless Networks

The use of energy harvesting (EH) nodes as cooperative relays is a promising and emerging solution in wireless systems such as wireless sensor networks. It harnesses the spatial diversity of a multi-relay network and addresses the vexing problem of a relay's batteries getting drained in forwarding information to the destination. We consider a cooperative system in which EH nodes volunteer to serve as amplify-and-forward relays whenever they have sufficient energy for transmission. For a general class of stationary and ergodic EH processes, we introduce the notion of energy constrained and energy unconstrained relays and analytically characterize the symbol error rate of the system. Further insight is gained by an asymptotic analysis that considers the cases where the signal-to-noise-ratio or the number of relays is large. Our analysis quantifies how the energy usage at an EH relay and, consequently, its availability for relaying, depends not only on the relay's energy harvesting process, but also on its transmit power setting and the other relays in the system. The optimal static transmit power setting at the EH relays is also determined. Altogether, our results demonstrate how a system that uses EH relays differs in significant ways from one that uses conventional cooperative relays.