Direct Measurement Of Intermolecular Forces Research Articles

Structure and interactions of biological helices

Helices are essential building blocks of living organisms, be they molecular fragments of proteins ($\ensuremath{\alpha}$-helices), macromolecules (DNA and collagen), or multimolecular assemblies (microtubules and viruses). Their interactions are involved in packing of meters of genetic material within cells and phage heads, recognition of homologous genes in recombination and DNA repair, stability of tissues, and many other processes. Helical molecules form a variety of mesophases in vivo and in vitro. Recent structural studies, direct measurements of intermolecular forces, single-molecule manipulations, and other experiments have accumulated a wealth of information and revealed many puzzling physical phenomena. It is becoming increasingly clear that in many cases the physics of biological helices cannot be described by theories that treat them as simple, unstructured polyelectrolytes. The present article focuses on the most important and interesting aspects of the physics of structured macromolecules, highlighting various manifestations of the helical motif in their structure, elasticity, interactions with counterions, aggregation, and poly- and mesomorphic transitions.

Nonlinear dynamic analysis of atomic force microscopy under deterministic and random excitation

The atomic force microscope (AFM) system has evolved into a useful tool for direct measurements of intermolecular forces with atomic-resolution characterization that can be employed in a broad spectrum of applications. This paper is devoted to the analysis of nonlinear behavior of amplitude modulation (AM) and frequency modulation (FM) modes of atomic force microscopy . For this, the microcantilever (which forms the basis for the operation of AFM) is modeled as a single mode approximation and the interaction between the sample and cantilever is derived from a van der Waals potential. Using perturbation methods such as averaging, and Fourier transform nonlinear equations of motion are analytically solved and the advantageous results are extracted from this nonlinear analysis. The results of the proposed techniques for AM-AFM, clearly depict the existence of two stable and one unstable (saddle) solutions for some of exciting parameters under deterministic vibration. The basin of attraction of two stable solutions is different and dependent on the exciting frequency. From this analysis the range of the frequency which will result in a unique periodic response can be obtained and used in practical experiments. Furthermore the analytical responses determined by perturbation techniques can be used to detect the parameter region where the chaotic motion is avoided. On the other hand for FM-AFM, the relation between frequency shift and the system parameters can be extracted and used for investigation of the system nonlinear behavior. The nonlinear behavior of the oscillating tip can easily explain the observed shift of frequency as a function of tip sample distance. Also in this paper we have investigated the AM-AFM system response under a random excitation. Using two different methods we have obtained the statistical properties of the tip motion. The results show that we can use the mean square value of tip motion to image the sample when the excitation signal is random.

Acquisition of high-precision images for non-contact atomic force microscopy

The atomic force microscope (AFM) system has evolved into a useful tool for direct measurements of intermolecular forces with atomic-resolution characterization that can be employed in a broad spectrum of applications. The distance between cantilever tip and sample surface in non-contact AFM is a time-varying parameter even for a fixed sample height, and typically difficult to identify. A remedy to this problem is to directly identify the sample height in order to generate high-precision atomic-resolution images. For this, the microcantilever (which forms the basis for the operation of AFM) is modeled as a single mode approximation and the interaction between the sample and cantilever is derived from a van der Waals potential. Since in most practical applications only the microcantilever deflection is accessible, we will use merely this measurement to identify the sample height. In most non-contact AFMs, cantilevers with high-quality factors are employed essentially for acquiring high-resolution images. However, due to high-quality factor, the settling time is relatively large and the required time to achieve a periodic motion is long. As a result, identification methods based on amplitude and phase measurements cannot be efficiently utilized. The proposed method overcomes this shortfall by using a small fraction of the transient motion for parameter identification, so the scanning speed can be increased significantly. Furthermore, for acquiring atomic-scale images of atomically flat samples, the need for feedback loop to achieve setpoint amplitude is basically eliminated. On the other hand, for acquiring atomic-scale images of highly uneven samples, a simple PI controller is designed to track the desired constant sample height. Simulation results are provided to demonstrate the feasibility of the approach for both sample height identification and tracking the desired sample height.

A Fresh Insight Into the Microcantilever-Sample Interaction Problem in Non-Contact Atomic Force Microscopy

The atomic force microscope (AFM) system has evolved into a useful tool for direct measurements of intermolecular forces with atomic-resolution characterization that can be employed in a broad spectrum of applications. The non-contact AFM offers unique advantages over other contemporary scanning probe techniques such as contact AFM and scanning tunneling microscopy, especially when utilized for reliable measurements of soft samples (e.g., biological species). Current AFM imaging techniques are often based on a lumped-parameters model and ordinary differential equation (ODE) representation of the micro-cantilevers coupled with an adhoc method for atomic interaction force estimation (especially in non-contact mode). Since the magnitude of the interaction force lies within the range of nano-Newtons to pica-Newtons, precise estimation of the atomic force is crucial for accurate topographical imaging. In contrast to the previously utilized lumped modeling methods, this paper aims at improving current AFM measurement technique through developing a general distributed-parameters base modeling approach that reveals greater insight into the fundamental characteristics of the microcantilever-sample interaction. For this, the governing equations of motion are derived in the global coordinates via the Hamilton’s Extended Principle. An interaction force identification scheme is then designed based on the original infinite dimensional distributed-parameters system which, in turn, reveals the unmeasurable distance between AFM tip and sample surface. Numerical simulations are provided to support these claims.

Direct measurement of intermolecular forces between a polymer layer and mica

We report here the first direct measurement of intermolecular forces between a polymer layer and a solid surface. When solid surfaces bearing adsorbed polymer approach one another, interactions develop that may be categorized as polymer–polymer and polymer–solid (and a negligible contribution of solid–solid interactions at the large solid–solid separations imposed by adsorbed polymer). Direct measurements of the forces between polymer layers adsorbed on mica have been made recently with apparatus of the type developed by Israelachvili. Attractive forces are attributed to a combination of osmotic (polymer–polymer) and bridging (polymer–solid) interactions. Bridging occurs if macromolecules adsorbed one one surface can reach a second surface. In the work presented here, poly(α-methylstyrene) (PαMS) adsorbed on one mica sheet was brought into contact in cyclohexane with a bare mica sheet. Adhesion was measured as a function of separation and contact time and found to be more than 20 times greater than between two polymer–coated surfaces under otherwise identical conditions. This direct measurement of molecular forces between dissimilar surfaces enables estimation of the PαMS segmental sticking energy on mica in cyclohexane as (1)/(3) kT.

29] Osmotic stress for the direct measurement of intermolecular forces

This chapter focuses on the practical use of osmotic stress (OS) to measure macromolecular forces and chemical potentials. It also reviews several examples of its application. Osmotic stress is applied to a wide set of charged or electrically neutral membranes, to the arrays of muscle protein, to tobacco mosaic virus particles, to ordered arrays of DNA double helices, to sickle cell hemoglobin undergoing polymerization, to the aqueous cavities of water-in-oil liquid crystals, and to ionic channels through bilayer membranes. OS permits ascertaining the properties of boundary water under thermodynamically well-defined conditions. Three equivalent ways in which OS is consistently applied are also discussed in the chapter. The most tedious aspect of OS is getting accurate osmotic pressures of the stressing polymer solutions. The OS measurement of forces between DNA double helices demonstrates the utility of the method for examining an entire class of linear macromolecules, such as collagen triple helices and xanthan polysaccharides.