Principles of Soft-Matter Dynamics: Basic Theories, Non-invasive Methods, Mesoscopic Aspects

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Principles of nuclear magnetic resonance in one and two dimensions Thomas W. Magnetic Resonance Microscopy AT9. Naidich , Henri M. Mark Haacke. The basics of MRI. The basics of NMR. JP Hornak. NMR studies of translational motion. WS Price. Theory of evolution and relaxation of multi-spin systems. The protein-folding problem attracts some of the best minds in biological physics and statistical mechanics, but it will require much more effort to reach satisfactory results. The question of how a linearly synthesized protein curls up to its three-dimensional functional form continues to challenge and excite theorists.

The committee concurs with the eloquent review found in a recent National Science Foundation study. At this stage, it is clear that physicists have defined the language in which folding is being examined. Cellular chaperone proteins, which wrap a protein during its transformation from a linear chain to a three-dimensional structure, are now believed to act by reversing random errors in folding. Their action is discussed by biologists and physicists alike in terms of their kicking the protein out of snarls that might otherwise trap it on its way to correct conformation.

In this way, cellular activity is thought to facilitate what is essentially a statistical physical process. The tools to follow folding are increasingly based on physical techniques, particularly high-power, high-speed x-ray scattering and spectroscopy. Laser tweezers allow one to hold the ends of linear molecules, particularly double-helical DNA, to measure the force of extension in different solutions and.

Suddenly it is possible to think about single molecules as mechanical objects, on which physics can be performed analogous to that done on macroscopic materials. Pipette aspiration allows equivalent mechanical manipulations of membranes and bilayer vesicles see Box 5. The various moduli and deformabilities are just beginning to be codified and connected with the language of mechanics.

The actual values of these material properties still often surprise us and require new thinking. Force microscopes can be used to break bonds, stretch molecules, or observe spontaneous changes in macromolecular conformation. The breaking strengths of important bonds, such as those between an antigen and an antibody, have been observed using labeled polystyrene lattices. It has been found that the force needed to break a bond is a monotonically decreasing function of the time that the.

Many biological processes depend on associations that require no chemical bonds between molecules. Important examples are the association between antigens and antibodies that allow cells to recognize alien matter or between integrins that hold cells together. Even without being pulled apart, these molecules will spontaneously come apart with time. In a functioning cell, the precisely controlled duration of molecular association can be more important than the strength of association.

Cells create characteristic times for many processes by controlling association times. The measurements illustrated here show how times of association between a single pair of large molecules can be measured and instructively varied. The bubble is held by being gently sucked into a pipette whose suction pressure can be varied to change tension in the vesicles.

To set up the measurement, a molecule on one bubble is brought near to another bubble that contains the mating molecule; the bubbles stick at the point of molecular contact. Then, by sucking on the pipette, stretching tension can be transmitted to the two molecules. From this measured time-to-breakage, it is possible to infer the kind of contact that the molecules made and, more important, to learn how the molecules create their important times of association.

In this particular example, binding is observed between biotin and avidin. Dissociation time ranges from 0. These gentle-tug measurements show how association lifetimes can be exquisitely sensitive to small changes in applied structural forces. Physical forces can regulate cellular events. This connection between time and strength, understandable in terms of diffusion in the presence of a distance-dependent bonding potential, reveals the dynamics of molecular association in the context of biological control.

One can expect many single-molecule systems to be observed and analyzed by probe microscopies to create a nanomechanics of molecular force and assembly. There is already a small literature on the spectroscopy of single proteins trapped in small spaces and illuminated by narrowly focused laser light. Through the combined efforts of structural biologists, muscle biophysicists, and statistical physicists, force generation in muscle and in transport within cells is being seen as the combination of stochastic events and directed response. The conversion of chemical reaction to directed physical action has posed a funda-.

The puzzle is being solved through molecular tracking and stochastic models. We can now expect the design of new mechanical transduction systems. Single ionic channels show electrically detectable transitions between "open" and "closed" configurations, whose probabilities are a function of solution conditions as well as the applied transmembrane electric fields. There is now a possibility of studying the dynamics of the channel molecules, as well as the solution components that affect them, simply by watching singular molecular events over very long times see Figure 5.

With channels, as with other proteins, it has been recognized for almost 30 years that occupation of the different conductance states follows simple Boltzmann statistics that allow us to relate the probabilities of different states with the changes in energy needed to achieve them. In fact, for a channel or other responsive molecule to sense changes in condition, it is necessary that there be small differences, comparable to the thermal energy kT , in the energies of differently functioning states.

As a next step in time-resolved, small-current detection, it is possible to see changes in the "open" state when single molecules enter and exit the channel. In this way it is possible to measure the statistics and dynamics of flexible polymers as they move within the confines of a precisely defined single-molecule structure. What does it mean to watch the changes in a single molecule?

Can one use rigorous physics to describe these changes? Can this physics give us the energies and entropies that drive the system to different states? The answer seems to be yes. Statistics, statistical mechanics, and functional control present a perfect chance for physicists to bring their methods to help biologists. There can be ready extrapolation to create practical devices, such as detectors and computers, informed by biological designs, While single-molecule thinking inspires a new statistical mechanics of strongly coupled systems with enormous fluctuations.

It is known now that many biological systems, from single ionic channels to entire sensory systems, practice a kind of stochastic resonance. Physicists in the s realized that adding some noise to a weak radio signal could improve signal detection. Today's physicists and biophysicists have succeeded in generalizing those ideas, raising the hope that they might be applied to helping the heating-impaired. Protein dynamics are a subject of intense interest. Binding of small molecules see Figure 5. Timescales are especially worth recognizing here.

Nerve signals, for example, occur on timescales of milliseconds, and different nerve channel proteins act at slightly different rates. Single molecules remain "open" or "closed" for milliseconds. These millisecond-characteristic times reveal the limits of computer simulation. Considering that these simulations can cover only nanoseconds, there is still a factor of 10 6 to cover to connect molecular dynamics computations with functionally interesting molecular times.

The wit of physical theorists is the most promising way to compensate for this daunting factor in computation. There is justified pride in modem polymer synthesis, by which stretches of one or another kind of monomer allow polymers to associate in parts to multimolecular arrays of specific symmetry, packing, and material properties.

Yet this kind of packing is rough compared to that of proteins or DNA, whose every monomer has functional consequence. One mutation in one amino acid of an antibody will qualitatively weaken its antigen-antibody binding strength and specificity. One change out of six nucleic acids will spoil that sequence for recognition by a protein that controls gene expression. Strength and specificity are what count when an antigen or a hormone binds to a cell-surface receptor at. Even as x-ray diffraction reveals the intricacies of the essential contacts, we have no more than cartoon ideas of how energies are transmitted and applied.

Physical opportunities abound. Great possibilities will be realized here when physicists trained to think about molecular organization are also trained in the much easier crafts of synthesis, mutation, modification, and manipulation. For example, biosensors are being designed with biological materials for contact with the species to be detected and electrodes with integrated circuitry for amplified response.

Probably the most difficult question to speculate about is the consequence to materials physics that will result from mapping of the human genome. It is hard even to describe the magnitude of the information being collected. It will be possible to synthesize and to mutate virtually every protein in our bodies or in the body of any known organism.

There are about , identifiable human genes. The number of possible mutations is burdensome to behold. Given the 3 billion base pairs that compose our genome and the possibility of putting 4 different letter pairs at each of these 3 billion positions, the number of mutations easily exceeds anything one would try to change systematically and exhaustively.

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In the context of this chapter and this survey, it is to the learning opportunities for materials research that these numbers direct our attention. Physicists can learn to produce any protein in desired quantities and to process and package it with increasing skill. Excellent demonstration of this comes from the synthesis of polypeptides of relatively simple sequence. The lure to create new industrial and medical materials compels us to think how these gene products can be designed and manipulated. Simply knowing the amino acid sequence of a protein is yet not enough to predict its properties.

Similar to the exasperation we suffer in studying collective quantum behavior Chapter 3 , difficulties in understanding proteins come from their ability to achieve the unpredictable properties that emerge because of their physical size. As suggested at the beginning of this chapter, the nub of the matter is education. Ideally, physics students will soon be as comfortable with gene-processing procedures as they are with other ways to manipulate materials. New substances whose properties differ qualitatively from those usually considered by physicists, even in these advanced and exciting times, will also confront them.

It is probably pointless even to speculate about what we will be able to do with all these new techniques and manipulations. There is already a National Research Council study on new technology based in molecular biology. It is possible to imagine using elastin, the animal's equivalent of rubber, as an industrial product.

Talk of DNA computers and molecular motors is no longer strictly speculation or science fiction. Administration of gene therapy will come to be guided by the principles of organization learned from preparing condensed arrays of genetic material. Physicists who know how to make these materials will be in an excellent position to think about how they work and how to work with them using physical intuition. Biological materials present a large opportunity for condensed-matter and materials physics research and application.

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At the same time, they present a large uncertainty in the time needed for that opportunity to be realized. It is difficult to predict the seminal moments in an untried marriage of new physics and new biology. Despite the many different kinds of research described in this chapter, a few general themes emerge.

From these themes we can identify needs and priorities for the support of research on soft materials. Physicists have lost their pessimism about doing good physics on complex materials. Whether in physics departments or in other departments, they are studying biological materials for practical as well as fundamental research. Among many physicists there is huge optimism over the learning opportunities provided by biological systems, in spite of conflicting traditions of learning and reasoning.

Although the necessary development of physics in biology can be expected to proceed naturally, the course and pace of this merger are uncertain. The deformability and other macroscopic features of soft condensed matter are now routinely examined in terms of their microscopic structures and their large thermal fluctuations. We already think of the various forms of soft matter in terms of molecular arrangements, rather than their macroscopic properties.

1. Introduction

Biological processes are coming to be routinely discussed in atomic detail. With adequate support, structure determination and structural thinking can be expected to grow rapidly for at least another 10 years. The ability to observe, to manipulate, and to characterize single molecules and to measure forces that create functional groupings of molecules is new and exciting.

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Mechanical properties and biological functions such as information transmission are increasingly discussed in terms of molecular structure. New tools of synthesis create new polymers and reproduce or modify natural biological polymers. These tools will become increasingly useful in the design of practical materials, medical, industrial, and domestic, and will enable systematic basic research to relate molecular cause and macroscopic effect. Because of the complexity of the materials being examined, physicists are learning to manipulate a much larger range of material properties than had been thought possible before.

Flow, deformability, microscopic patterning, strength, and durability are being evoked from substances previously not considered to have such possibilities. From better ways to design for particular properties, we may hope that industrial progress will grow less empirical and more logical.

Research on soft materials creates vast amounts of information. Whether in the possibilities built into the genetic code, the molecular details of protein structure, the many microscopic structures of liquid crystals, the nuances of medical scanning, the chemical possibilities of polymer synthesis, or the scrap heap of trial-and-error industrial innovation, the numbers that go into description are huge.

The growing size, number, and kinds of data banks are teaching us new ways to organize and use information. We may expect physicists to grow increasingly comfortable working with such ''rich" systems. When physicists work with materials that were once the province of other fields, and when scientists in those fields use what physicists have learned, they discover that there are different ways of learning, thinking, and even speaking in the different fields.

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It is easy to say that education in physics, chemistry, and biology must be broad as well as deep. It is easy to argue that tomorrow's condensed-matter physicists should not fear to synthesize polymers or handle proteins or express genes. Although such skills are easily learned, there are many obstacles to such broad learning. Even if there were time in school, subject matter changes too fast to rely only on what is learned in school.

This may be a good time for another review for physicists modeled on the landmark series in Reviews of Modern Physics. Industrial and medical results will follow naturally, as they have inevitably followed basic research in the past. Grant mechanisms can be established to encourage the necessary interdisciplinary work.

Zirkle, "Biophysical science. A study program: General features of radiobiological actions," Reviews of Modern Physics 31 , The residue from trial and error in industrial research is an abundant source of information for new physics. Biological systems are an inspiring source of solved problems for doing physics in a new place.

Basic Theories, Non-invasive Methods, Mesoscopic Aspects

We can work to create comfortable common ground for collaboration. Undersupported research areas should be identified in which results will be needed. For example, polyelectrolytes and biological polymers will be increasingly used for products to displace environmentally unfriendly organic materials. For structure determination, neutron sources in particular are urgently needed. Synchrotron x-ray, ion beam, transmission electron microscope, and surface probe facilities are high on the list.

Data processing is needed for the large amounts of information being generated and the large computations that will be undertaken. Intellectually, industrially, and medically, soft-material research has a potential that justifies funding increases like those being given to research in biology and medicine. This book identifies opportunities, priorities, and challenges for the field of condensed-matter and materials physics.

It highlights exciting recent scientific and technological developments and their societal impact and identifies outstanding questions for future research. Topics range from the science of modern technology to new materials and structures, novel quantum phenomena, nonequilibrium physics, soft condensed matter, and new experimental and computational tools.

The book also addresses structural challenges for the field, including nurturing its intellectual vitality, maintaining a healthy mixture of large and small research facilities, improving the field's integration with other disciplines, and developing new ways for scientists in academia, government laboratories, and industry to work together.

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Sign up for email notifications and we'll let you know about new publications in your areas of interest when they're released. Get This Book. Visit NAP. Looking for other ways to read this? No thanks. Page 5 Soft Condensed Matter: Complex Fluids, Macromolecular Systems, and Biological Systems The vast territory of "soft" materials extends to paints, surfactants, porous media, plastics, pharmaceuticals, coatings, ceramic precursors, minerals in suspension, foodstuffs, textiles, proteins, fats, blood, and guitar strings.

Page Share Cite. Page BOX 5. Page tively simple systems with a great deal of symmetry translation symmetry in a ferromagnet, for example. Complex Fluids As though condensed fluids were not already sufficiently complex see Box 5. Liquid Crystals and Microemulsions Most large asymmetric molecules, viruses, and lipids assemble spontaneously into ordered structures whose dimensions and macroscopic properties vary dramatically with small changes in the conditions under which they are formed.

Functional Renormalisation Group approach to the continuum limit of Group Field Theories

Page static, van der Waals, and hydration forces. Pursuing a sudden opportunity to examine the huge number of new liquid-crystal phases with natural and artificial materials in solution, theorists are BOX 5. Box continued on next page. Page Box continued from previous page The study of glasses is particularly useful here because they allow us to narrow the energy range and hence the number of configurations of the liquid that need to be considered.

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Dynamic Chemical Processes on Solid Surfaces. This property is expressed in the cohesive potential by the following equation:. Displayed are also typical scopes of different simulation methods and some typical applications pertaining to the respective scale. On the length scale of a few microns to a few hundred microns, many materials exhibit a polyhedral granular structure which is known to crucially influence their macroscopic mechanical properties. The electrostatic interaction originates the dipolar character of water which is the basic requirement for the existence of life. Joseph H.