Eindhoven University of Technology MASTER Unraveling single-bond kinetics in tethered particle motion experiments using molecular dynamics simulations Merkus, K.E. Award date: 2015 Link to publication Disclaimer This document contains a student thesis (bachelor's or master's), as authored by a student at Eindhoven University of Technology. Student theses are made available in the TU/e repository upon obtaining the required degree. The grade received is not published on the document as presented in the repository. The required complexity or quality of research of student theses may vary by program, and the required minimum study period may vary in duration. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain Eindhoven University of Technology Department of Applied Physics Theory of polymers and soft matter Unraveling single-bond kinetics in tethered particle motion experiments using molecular dynamics simulations K.E. Merkus July 2015 Under supervision of dr. C. Storm Abstract Tethered particle motion (TPM), the motion of a micro- or nanobead tethered to a substrate by a macromolecule, is widely studied to understand various properties related to the tether. However, we propose a whole new way of looking at TPM: TPM as a probe for secondary bonds. Kinetic effects in the motion pattern of a coated bead tethered to a coated substrate yield information about the bonding kinetics of the corresponding coating-molecules and/or solution. We use molecular dynamics simulations to understand the relation between the bond kinetics and the observed motion patterns. Our results show that kinetic properties of a single bond can indeed be extracted and we present experimental optimization. We provide a proof of principle that is of both fundamental and techno- logical interest. The described measurement method may be used in the fundamental study of single bond kinetics. Moreover, this principle may serve as the basis for a new kind of biosensing device. Contents 1 Introduction 1 1.1 Tethered particle motion . .2 1.2 Outline of the thesis . .4 2 Tethered particle motion system 5 2.1 Components of a tethered particle system . .5 2.2 The sandwich assay principle . .7 2.3 Model system . .9 3 Simulation methods 11 3.1 Monte Carlo . 11 3.2 Molecular dynamics . 12 3.2.1 Molecular dynamics basics . 12 3.2.2 Time integration algorithm . 12 3.2.3 Components . 13 3.2.4 Interactions . 13 3.2.5 Implicit solvent . 15 3.2.6 Timescales . 16 3.2.7 Bond creation and breaking . 17 3.3 Parameter values . 18 3.4 Hydrodynamic wall effects . 20 3.4.1 Introduction . 20 3.4.2 Correction on parallel motion . 20 3.4.3 Correction on perpendicular motion . 21 3.4.4 Implementation . 21 3.4.5 Discussion . 22 4 Bead movement 24 4.1 Motion pattern . 24 4.1.1 Experimental motion patterns . 24 4.1.2 Simulation motion patterns . 27 4.2 Analytic approach . 28 4.2.1 Geometrical framework . 28 4.2.2 Integration boundaries . 30 4.2.3 Distribution results . 32 1 CONTENTS 4.2.4 Conclusion . 34 4.3 Number of polymer beads in MD simulation . 35 4.4 Exclusion effects . 37 4.5 Influence of the engineering parameters R; L; lp ...................... 39 4.5.1 Varying the bead size . 39 4.5.2 Varying the tether length . 40 4.5.3 Varying the persistence length . 41 4.5.4 Discussion . 42 4.6 Dynamic properties . 43 4.6.1 Autocorrelation R~(t)................................. 43 4.6.2 Autocorrelation Z(t)................................. 44 4.6.3 Conclusion . 44 4.7 Hitting and return times . 45 4.7.1 Hitting times . 45 4.7.2 Return times . 45 4.7.3 Discussion . 45 4.8 Step size . 47 4.8.1 Tether length . 47 4.8.2 Bead radius . 48 5 Specific binding spots 49 5.1 Dots on the bead . 49 5.2 Spots on the substrate . 51 5.3 Single Xdot and Xsubstr .................................... 53 5.4 Kinetic regime . 54 5.4.1 Reaction process . 54 5.4.2 Quick rebinding events . 54 5.5 Analyzing bound patterns . 56 5.6 Relation to experiments . 57 5.6.1 Experimental situations . 57 5.6.2 Sources of uncertainties . 57 5.6.3 Application to experimental data . 58 6 Optimization 61 6.1 Optimize contact area . 61 6.2 Detectability . 64 6.3 Optimization in the sandwich assay . 67 7 Conclusion & outlook 69 7.1 Conclusions . 69 7.2 Outlook . 70 References 71 A Implementing anisotropic drag 75 A.1 Diffusion of a bead near a surface . 75 A.2 Implementation . 77 A.3 Control simulations . 78 A.3.1 Random forces without motion . 78 2 CONTENTS A.3.2 Movement parallel to surface . 80 A.3.3 Movement towards surface . 82 A.4 Simulation times . 83 B Tabulated values 84 3 Chapter 1 Introduction A key characteristic of modern health care is the increasing demand for point-of-care applications [1]. The measurement of glucose levels by diabetic patients is a very successful example of point-of-care immuno-biosensing that has been developed and abundantly used for decades [2]. Glucose is found in the human blood at a concentration in the order of millimolars, which is a regime in which electro- chemical detection is well-suited. One can think of many other biosensing applications that are yet to achieve such a level of commercial success. Examples are: the detection of protein markers to diagnose cardiac diseases, the detection of nucleic acid markers in case of infectious diseases, but also the screening for drugs of abuse. However, the concentration of the biomarkers that should be detected in these examples is much lower, typi- cal concentrations for these biomarkers are of the order of picomolars or even sub-picomolar [3]. A biosensing device should be able to detect these biomarkers, even if very little biomarkers are present. In other words, the biosensor should have a high sensitivity. Since such measurements are in general performed on body fluids, there are a lot of irrelevant molecules present at much higher concentrations. These other molecules should not interfere with the measure- ment, so the measurement should be highly selective. The high levels of sensitivity and selectivity that are required, are generally not achieved by enzyme-based electrochemical detection. Detections methods that are better suited for these applications exist. In particular, such a high level of selectivity and sensitivity can be achieved by using antibodies in immunoassays. Several immunoas- say sensing technologies have been developed, but one that seems particularly suited for a lab-on-chip device is the optomagnetic immunoassay technology [4]. Optomagnetic immunoassay technology involves antibody-coated nanoparticles as well as an antibody- coated substrate. The nanoparticles are magnetically actuated and optically detected in a stationary fluid. The eventual detection mechanism and resulting determination of the initial concentration of a biomarker depends on the number of beads that is bound to the substrate, ideally by an antibody- biomarker complex for which the assay was designed. Sensitivity is of vital importance in these applications, therefore it is crucial to fully understand the binding mechanism that occurs at the sub- strate and how this binding mechanism affects the observed motion pattern of the nanoparticle. 1 CHAPTER 1. INTRODUCTION Figure 1.1: A schematic representation of the system under investigation: a microsphere attached to a surface by a double-stranded DNA tether. The basic system that is described throughout this thesis consists of a bead with radius R=500 nm and a tether with length L=50 nm. This picture is not drawn to scale. The dashed line represents the projection of the bead coordinates on the surface, which is the experimentally observable value. 1.1. Tethered particle motion To study the properties of a nanoparticle adhered to a substrate bound by an antibody-biomarker complex, we resort to a model system: a nanoparticle adhered to a substrate by a double-stranded DNA (dsDNA) tether [5], as is graphically represented in figure 1.1. This brings us into the field of tethered particle motion (TPM). Several studies have already been devoted to this subject, so we can rely on literature to explore a lot of basic properties of this system. In previous research the focus was on the properties and interactions of the tether (typically.